[{"oa_version":"Submitted Version","type":"conference","month":"10","pubrep_id":"644","scopus_import":"1","isi":1,"ddc":["000"],"department":[{"_id":"ToHe"}],"article_processing_charge":"No","article_number":"26","publist_id":"6223","doi":"10.1145/2968478.2968499","day":"01","_id":"1135","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"conference":{"location":"Pittsburgh, PA, USA","end_date":"2016-10-07","name":"EMSOFT: Embedded Software ","start_date":"2016-10-01"},"date_created":"2018-12-11T11:50:20Z","title":"Synthesizing time triggered schedules for switched networks with faulty links","publication":"Proceedings of the 13th International Conference on Embedded Software ","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:14:05Z","oa":1,"file":[{"file_name":"IST-2016-644-v1+1_emsoft-no-format.pdf","file_size":279240,"creator":"system","content_type":"application/pdf","relation":"main_file","date_updated":"2018-12-12T10:09:31Z","access_level":"open_access","date_created":"2018-12-12T10:09:31Z","file_id":"4755"}],"abstract":[{"text":"Time-triggered (TT) switched networks are a deterministic communication infrastructure used by real-time distributed embedded systems. These networks rely on the notion of globally discretized time (i.e. time slots) and a static TT schedule that prescribes which message is sent through which link at every time slot, such that all messages reach their destination before a global timeout. These schedules are generated offline, assuming a static network with fault-free links, and entrusting all error-handling functions to the end user. Assuming the network is static is an over-optimistic view, and indeed links tend to fail in practice. We study synthesis of TT schedules on a network in which links fail over time and we assume the switches run a very simple error-recovery protocol once they detect a crashed link. We address the problem of finding a pk; qresistant schedule; namely, one that, assuming the switches run a fixed error-recovery protocol, guarantees that the number of messages that arrive at their destination by the timeout is at least no matter what sequence of at most k links fail. Thus, we maintain the simplicity of the switches while giving a guarantee on the number of messages that meet the timeout. We show how a pk; q-resistant schedule can be obtained using a CEGAR-like approach: find a schedule, decide whether it is pk; q-resistant, and if it is not, use the witnessing fault sequence to generate a constraint that is added to the program. The newly added constraint disallows the schedule to be regenerated in a future iteration while also eliminating several other schedules that are not pk; q-resistant. We illustrate the applicability of our approach using an SMT-based implementation. © 2016 ACM.","lang":"eng"}],"ec_funded":1,"publisher":"ACM","has_accepted_license":"1","author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","last_name":"Avni"},{"last_name":"Guha","first_name":"Shibashis","full_name":"Guha, Shibashis"},{"last_name":"Rodríguez Navas","first_name":"Guillermo","full_name":"Rodríguez Navas, Guillermo"}],"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000414220100026"]},"date_published":"2016-10-01T00:00:00Z","year":"2016","publication_status":"published","status":"public","file_date_updated":"2018-12-12T10:09:31Z","citation":{"short":"G. Avni, S. Guha, G. Rodríguez Navas, in:, Proceedings of the 13th International Conference on Embedded Software , ACM, 2016.","chicago":"Avni, Guy, Shibashis Guha, and Guillermo Rodríguez Navas. “Synthesizing Time Triggered Schedules for Switched Networks with Faulty Links.” In <i>Proceedings of the 13th International Conference on Embedded Software </i>. ACM, 2016. <a href=\"https://doi.org/10.1145/2968478.2968499\">https://doi.org/10.1145/2968478.2968499</a>.","ista":"Avni G, Guha S, Rodríguez Navas G. 2016. Synthesizing time triggered schedules for switched networks with faulty links. Proceedings of the 13th International Conference on Embedded Software . EMSOFT: Embedded Software , 26.","apa":"Avni, G., Guha, S., &#38; Rodríguez Navas, G. (2016). Synthesizing time triggered schedules for switched networks with faulty links. In <i>Proceedings of the 13th International Conference on Embedded Software </i>. Pittsburgh, PA, USA: ACM. <a href=\"https://doi.org/10.1145/2968478.2968499\">https://doi.org/10.1145/2968478.2968499</a>","ieee":"G. Avni, S. Guha, and G. Rodríguez Navas, “Synthesizing time triggered schedules for switched networks with faulty links,” in <i>Proceedings of the 13th International Conference on Embedded Software </i>, Pittsburgh, PA, USA, 2016.","ama":"Avni G, Guha S, Rodríguez Navas G. Synthesizing time triggered schedules for switched networks with faulty links. In: <i>Proceedings of the 13th International Conference on Embedded Software </i>. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2968478.2968499\">10.1145/2968478.2968499</a>","mla":"Avni, Guy, et al. “Synthesizing Time Triggered Schedules for Switched Networks with Faulty Links.” <i>Proceedings of the 13th International Conference on Embedded Software </i>, 26, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2968478.2968499\">10.1145/2968478.2968499</a>."}},{"type":"conference","month":"10","oa_version":"Submitted Version","article_processing_charge":"No","department":[{"_id":"ChWo"}],"scopus_import":"1","ddc":["004"],"publist_id":"6222","article_number":"2994261","conference":{"start_date":"2016-10-10","end_date":"2016-10-12","name":"MIG: Motion in Games","location":"San Francisco, CA, USA"},"project":[{"call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"_id":"1136","day":"10","doi":"10.1145/2994258.2994261","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://hal.inria.fr/hal-01367181","open_access":"1"}],"date_updated":"2024-10-22T09:58:18Z","title":"Space-time sculpting of liquid animation","publication":"Proceedings of the 9th International Conference on Motion in Games ","date_created":"2018-12-11T11:50:20Z","acknowledgement":"This work was partly supported by the starting grant BigSplash, as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2014-StG 638176 , and ERC-2011-ADG 20110209).","publisher":"ACM","ec_funded":1,"abstract":[{"lang":"eng","text":"We propose an interactive sculpting system for seamlessly editing pre-computed animations of liquid, without the need for any resimulation. The input is a sequence of meshes without correspondences representing the liquid surface over time. Our method enables the efficient selection of consistent space-time parts of this animation, such as moving waves or droplets, which we call space-time features. Once selected, a feature can be copied, edited, or duplicated and then pasted back anywhere in space and time in the same or in another liquid animation sequence. Our method circumvents tedious user interactions by automatically computing the spatial and temporal ranges of the selected feature. We also provide space-time shape editing tools for non-uniform scaling, rotation, trajectory changes, and temporal editing to locally speed up or slow down motion. Using our tools, the user can edit and progressively refine any input simulation result, possibly using a library of precomputed space-time features extracted from other animations. In contrast to the trial-and-error loop usually required to edit animation results through the tuning of indirect simulation parameters, our method gives the user full control over the edited space-time behaviors. © 2016 Copyright held by the owner/author(s)."}],"oa":1,"author":[{"last_name":"Manteaux","first_name":"Pierre","full_name":"Manteaux, Pierre"},{"full_name":"Vimont, Ulysse","first_name":"Ulysse","last_name":"Vimont"},{"last_name":"Wojtan","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","first_name":"Christopher J"},{"first_name":"Damien","full_name":"Rohmer, Damien","last_name":"Rohmer"},{"last_name":"Cani","first_name":"Marie","full_name":"Cani, Marie"}],"has_accepted_license":"1","citation":{"mla":"Manteaux, Pierre, et al. “Space-Time Sculpting of Liquid Animation.” <i>Proceedings of the 9th International Conference on Motion in Games </i>, 2994261, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2994258.2994261\">10.1145/2994258.2994261</a>.","ista":"Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. 2016. Space-time sculpting of liquid animation. Proceedings of the 9th International Conference on Motion in Games . MIG: Motion in Games, 2994261.","ieee":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, and M. Cani, “Space-time sculpting of liquid animation,” in <i>Proceedings of the 9th International Conference on Motion in Games </i>, San Francisco, CA, USA, 2016.","ama":"Manteaux P, Vimont U, Wojtan C, Rohmer D, Cani M. Space-time sculpting of liquid animation. In: <i>Proceedings of the 9th International Conference on Motion in Games </i>. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2994258.2994261\">10.1145/2994258.2994261</a>","apa":"Manteaux, P., Vimont, U., Wojtan, C., Rohmer, D., &#38; Cani, M. (2016). Space-time sculpting of liquid animation. In <i>Proceedings of the 9th International Conference on Motion in Games </i>. San Francisco, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2994258.2994261\">https://doi.org/10.1145/2994258.2994261</a>","chicago":"Manteaux, Pierre, Ulysse Vimont, Chris Wojtan, Damien Rohmer, and Marie Cani. “Space-Time Sculpting of Liquid Animation.” In <i>Proceedings of the 9th International Conference on Motion in Games </i>. ACM, 2016. <a href=\"https://doi.org/10.1145/2994258.2994261\">https://doi.org/10.1145/2994258.2994261</a>.","short":"P. Manteaux, U. Vimont, C. Wojtan, D. Rohmer, M. Cani, in:, Proceedings of the 9th International Conference on Motion in Games , ACM, 2016."},"date_published":"2016-10-10T00:00:00Z","year":"2016","publication_status":"published","status":"public","language":[{"iso":"eng"}],"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>","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>","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.","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>.","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.","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>."},"status":"public","publication_status":"published","year":"2016","date_published":"2016-12-01T00:00:00Z","external_id":{"isi":["000388056400005"],"pmid":["27776107"]},"language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"full_name":"Salzer, Elisabeth","first_name":"Elisabeth","last_name":"Salzer"},{"last_name":"Çaǧdaş","first_name":"Deniz","full_name":"Çaǧdaş, Deniz"},{"last_name":"Hons","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6625-3348","full_name":"Hons, Miroslav","first_name":"Miroslav"},{"first_name":"Emily","full_name":"Mace, Emily","last_name":"Mace"},{"last_name":"Garncarz","full_name":"Garncarz, Wojciech","first_name":"Wojciech"},{"full_name":"Petronczki, Oezlem","first_name":"Oezlem","last_name":"Petronczki"},{"full_name":"Platzer, René","first_name":"René","last_name":"Platzer"},{"last_name":"Pfajfer","first_name":"Laurène","full_name":"Pfajfer, Laurène"},{"full_name":"Bilic, Ivan","first_name":"Ivan","last_name":"Bilic"},{"full_name":"Ban, Sol","first_name":"Sol","last_name":"Ban"},{"full_name":"Willmann, Katharina","first_name":"Katharina","last_name":"Willmann"},{"last_name":"Mukherjee","full_name":"Mukherjee, Malini","first_name":"Malini"},{"last_name":"Supper","first_name":"Verena","full_name":"Supper, Verena"},{"last_name":"Hsu","first_name":"Hsiangting","full_name":"Hsu, Hsiangting"},{"full_name":"Banerjee, Pinaki","first_name":"Pinaki","last_name":"Banerjee"},{"last_name":"Sinha","full_name":"Sinha, Papiya","first_name":"Papiya"},{"first_name":"Fabienne","full_name":"Mcclanahan, Fabienne","last_name":"Mcclanahan"},{"last_name":"Zlabinger","first_name":"Gerhard","full_name":"Zlabinger, Gerhard"},{"last_name":"Pickl","full_name":"Pickl, Winfried","first_name":"Winfried"},{"last_name":"Gribben","first_name":"John","full_name":"Gribben, John"},{"full_name":"Stockinger, Hannes","first_name":"Hannes","last_name":"Stockinger"},{"first_name":"Keiryn","full_name":"Bennett, Keiryn","last_name":"Bennett"},{"last_name":"Huppa","full_name":"Huppa, Johannes","first_name":"Johannes"},{"last_name":"Dupré","full_name":"Dupré, Loï̈C","first_name":"Loï̈C"},{"last_name":"Sanal","full_name":"Sanal, Özden","first_name":"Özden"},{"first_name":"Ulrich","full_name":"Jäger, Ulrich","last_name":"Jäger"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","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","full_name":"Boztug, Kaan","last_name":"Boztug"}],"issue":"12","intvolume":"        17","publisher":"Nature Publishing Group","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."}],"oa":1,"date_updated":"2025-09-22T14:13:22Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6400263","open_access":"1"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"publication":"Nature Immunology","title":"RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics","date_created":"2018-12-11T11:50:21Z","volume":17,"_id":"1137","doi":"10.1038/ni.3575","day":"01","publist_id":"6221","article_type":"original","article_processing_charge":"No","page":"1352 - 1360","department":[{"_id":"MiSi"}],"isi":1,"scopus_import":"1","month":"12","type":"journal_article","oa_version":"Submitted Version"},{"oa_version":"Preprint","type":"conference","month":"07","scopus_import":"1","isi":1,"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"page":"76 - 85","article_processing_charge":"No","publist_id":"6220","day":"05","doi":"10.1145/2933575.2933588","_id":"1138","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"conference":{"end_date":"2016-07-08","name":"LICS: Logic in Computer Science","location":"New York, NY, USA","start_date":"2016-07-05"},"date_created":"2018-12-11T11:50:21Z","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","title":"Quantitative automata under probabilistic semantics","publication":"Proceedings of the 31st Annual ACM/IEEE Symposium","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","main_file_link":[{"url":"https://arxiv.org/abs/1604.06764","open_access":"1"}],"date_updated":"2025-09-22T14:12:47Z","arxiv":1,"oa":1,"abstract":[{"lang":"eng","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."}],"ec_funded":1,"publisher":"IEEE","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"}],"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000387609200008"],"arxiv":["1604.06764"]},"date_published":"2016-07-05T00:00:00Z","year":"2016","publication_status":"published","status":"public","citation":{"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>.","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.","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>","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.","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>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings of the 31st Annual ACM/IEEE Symposium, IEEE, 2016, pp. 76–85."}},{"publisher":"Oxford University Press","article_processing_charge":"No","page":"3563 - 3573","abstract":[{"text":"Microtubules switch stochastically between phases of growth and shrinkage. The molecular mechanism responsible for the end of a growth phase, an event called catastrophe, is still not understood. The probability for a catastrophe to occur increases with microtubule age, putting constraints on the possible molecular mechanism of catastrophe induction. Here we used microfluidics-Assisted fast tubulin washout experiments to induce microtubule depolymerization in a controlled manner at different times after the start of growth. We found that aging can also be observed in this assay, providing valuable new constraints against which theoretical models of catastrophe induction can be tested. We found that the data can be quantitatively well explained by a simple kinetic threshold model that assumes an age-dependent broadening of the protective cap at the microtubule end as a result of an evolving tapered end structure; this leads to a decrease of the cap density and its stability. This analysis suggests an intuitive picture of the role of morphological changes of the protective cap for the age dependence of microtubule stability.","lang":"eng"}],"date_updated":"2021-01-12T06:48:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","publication":"Molecular Biology and Evolution","title":"Microtubule aging probed by microfluidics assisted tubulin washout","type":"journal_article","oa_version":"None","date_created":"2018-12-11T11:50:21Z","citation":{"chicago":"Düllberg, Christian F, Nicholas Cade, and Thomas Surrey. “Microtubule Aging Probed by Microfluidics Assisted Tubulin Washout.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1091/mbc.E16-07-0548\">https://doi.org/10.1091/mbc.E16-07-0548</a>.","short":"C.F. Düllberg, N. Cade, T. Surrey, Molecular Biology and Evolution 27 (2016) 3563–3573.","mla":"Düllberg, Christian F., et al. “Microtubule Aging Probed by Microfluidics Assisted Tubulin Washout.” <i>Molecular Biology and Evolution</i>, vol. 27, no. 22, Oxford University Press, 2016, pp. 3563–73, doi:<a href=\"https://doi.org/10.1091/mbc.E16-07-0548\">10.1091/mbc.E16-07-0548</a>.","apa":"Düllberg, C. F., Cade, N., &#38; Surrey, T. (2016). Microtubule aging probed by microfluidics assisted tubulin washout. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1091/mbc.E16-07-0548\">https://doi.org/10.1091/mbc.E16-07-0548</a>","ieee":"C. F. Düllberg, N. Cade, and T. Surrey, “Microtubule aging probed by microfluidics assisted tubulin washout,” <i>Molecular Biology and Evolution</i>, vol. 27, no. 22. Oxford University Press, pp. 3563–3573, 2016.","ama":"Düllberg CF, Cade N, Surrey T. Microtubule aging probed by microfluidics assisted tubulin washout. <i>Molecular Biology and Evolution</i>. 2016;27(22):3563-3573. doi:<a href=\"https://doi.org/10.1091/mbc.E16-07-0548\">10.1091/mbc.E16-07-0548</a>","ista":"Düllberg CF, Cade N, Surrey T. 2016. Microtubule aging probed by microfluidics assisted tubulin washout. Molecular Biology and Evolution. 27(22), 3563–3573."},"volume":27,"status":"public","extern":"1","publication_status":"published","_id":"1139","date_published":"2016-11-07T00:00:00Z","year":"2016","language":[{"iso":"eng"}],"doi":"10.1091/mbc.E16-07-0548","day":"07","publist_id":"6218","author":[{"last_name":"Düllberg","first_name":"Christian F","full_name":"Düllberg, Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6335-9748"},{"last_name":"Cade","first_name":"Nicholas","full_name":"Cade, Nicholas"},{"last_name":"Surrey","full_name":"Surrey, Thomas","first_name":"Thomas"}],"issue":"22","intvolume":"        27"},{"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.","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>.","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.","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.","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>","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>."},"alternative_title":["Proceedings Symposium on Logic in Computer Science"],"status":"public","publication_status":"published","year":"2016","date_published":"2016-07-05T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"isi":["000387609200020"],"arxiv":["1602.02670"]},"quality_controlled":"1","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"first_name":"Wolfgang","full_name":"Dvoák, Wolfgang","last_name":"Dvoák"},{"last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Veronika","full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer"}],"publisher":"IEEE","abstract":[{"lang":"eng","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."}],"oa":1,"date_updated":"2025-09-22T14:12:05Z","main_file_link":[{"url":"https://arxiv.org/abs/1602.02670","open_access":"1"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"publication":"Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science","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.","date_created":"2018-12-11T11:50:22Z","conference":{"start_date":"2016-07-05","name":"LICS: Logic in Computer Science","end_date":"2016-07-08","location":"New York, NY, USA"},"_id":"1140","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"day":"05","doi":"10.1145/2933575.2935304","publist_id":"6219","article_processing_charge":"No","page":"197 - 206","department":[{"_id":"KrCh"}],"isi":1,"scopus_import":"1","month":"07","type":"conference","oa_version":"Preprint"},{"title":"Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization","publication":"Journal of Computational Science","date_created":"2018-12-11T11:50:22Z","acknowledgement":"The work presented in this paper was partially supported by Polish National Science Centre grant nos. DEC-2012/05/N/ST6/03433 and DEC-2011/03/B/ST6/01393. Radosław Łazarz was supported by Polish National Science Centre grant no. DEC-2013/10/M/ST6/00531.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:11:23Z","abstract":[{"text":"In this paper we introduce the Multiobjective Optimization Hierarchic Genetic Strategy with maturing (MO-mHGS), a meta-algorithm that performs evolutionary optimization in a hierarchy of populations. The maturing mechanism improves growth and reduces redundancy. The performance of MO-mHGS with selected state-of-the-art multiobjective evolutionary algorithms as internal algorithms is analysed on benchmark problems and their modifications for which single fitness evaluation time depends on the solution accuracy. We compare the proposed algorithm with the Island Model Genetic Algorithm as well as with single-deme methods, and discuss the impact of internal algorithms on the MO-mHGS meta-algorithm. © 2016 Elsevier B.V.","lang":"eng"}],"publisher":"Elsevier","author":[{"last_name":"Łazarz","full_name":"Łazarz, Radosław","first_name":"Radosław"},{"last_name":"Idzik","full_name":"Idzik, Michał","first_name":"Michał"},{"last_name":"Gądek","first_name":"Konrad","full_name":"Gądek, Konrad"},{"last_name":"Gajda-Zagorska","first_name":"Ewa P","full_name":"Gajda-Zagorska, Ewa P","id":"47794CF0-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        17","issue":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000390625600021"]},"quality_controlled":"1","citation":{"short":"R. Łazarz, M. Idzik, K. Gądek, E.P. Gajda-Zagorska, Journal of Computational Science 17 (2016) 249–260.","chicago":"Łazarz, Radosław, Michał Idzik, Konrad Gądek, and Ewa P Gajda-Zagorska. “Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective Optimization.” <i>Journal of Computational Science</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">https://doi.org/10.1016/j.jocs.2016.03.004</a>.","ista":"Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. 2016. Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. Journal of Computational Science. 17(1), 249–260.","ama":"Łazarz R, Idzik M, Gądek K, Gajda-Zagorska EP. Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. <i>Journal of Computational Science</i>. 2016;17(1):249-260. doi:<a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">10.1016/j.jocs.2016.03.004</a>","apa":"Łazarz, R., Idzik, M., Gądek, K., &#38; Gajda-Zagorska, E. P. (2016). Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization. <i>Journal of Computational Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">https://doi.org/10.1016/j.jocs.2016.03.004</a>","ieee":"R. Łazarz, M. Idzik, K. Gądek, and E. P. Gajda-Zagorska, “Hierarchic genetic strategy with maturing as a generic tool for multiobjective optimization,” <i>Journal of Computational Science</i>, vol. 17, no. 1. Elsevier, pp. 249–260, 2016.","mla":"Łazarz, Radosław, et al. “Hierarchic Genetic Strategy with Maturing as a Generic Tool for Multiobjective Optimization.” <i>Journal of Computational Science</i>, vol. 17, no. 1, Elsevier, 2016, pp. 249–60, doi:<a href=\"https://doi.org/10.1016/j.jocs.2016.03.004\">10.1016/j.jocs.2016.03.004</a>."},"year":"2016","date_published":"2016-11-01T00:00:00Z","status":"public","publication_status":"published","type":"journal_article","month":"11","oa_version":"None","department":[{"_id":"ChWo"}],"page":"249 - 260","scopus_import":"1","isi":1,"article_processing_charge":"No","publist_id":"6217","doi":"10.1016/j.jocs.2016.03.004","day":"01","_id":"1141","volume":17},{"intvolume":"        17","issue":"12","author":[{"last_name":"Martins","full_name":"Martins, Rui","first_name":"Rui"},{"last_name":"Maier","full_name":"Maier, Julia","first_name":"Julia"},{"full_name":"Gorki, Anna","first_name":"Anna","last_name":"Gorki"},{"last_name":"Huber","full_name":"Huber, Kilian","first_name":"Kilian"},{"full_name":"Sharif, Omar","first_name":"Omar","last_name":"Sharif"},{"full_name":"Starkl, Philipp","first_name":"Philipp","last_name":"Starkl"},{"full_name":"Saluzzo, Simona","first_name":"Simona","last_name":"Saluzzo"},{"full_name":"Quattrone, Federica","first_name":"Federica","last_name":"Quattrone"},{"full_name":"Gawish, Riem","first_name":"Riem","last_name":"Gawish"},{"last_name":"Lakovits","first_name":"Karin","full_name":"Lakovits, Karin"},{"last_name":"Aichinger","full_name":"Aichinger, Michael","first_name":"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","first_name":"Anastasiya","last_name":"Hladik"},{"last_name":"Korosec","full_name":"Korosec, Ana","first_name":"Ana"},{"last_name":"Brown","first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus"},{"last_name":"Vaahtomeri","id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari","first_name":"Kari"},{"last_name":"Duggan","full_name":"Duggan, Michelle","id":"2EDEA62C-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle"},{"full_name":"Kerjaschki, Dontscho","first_name":"Dontscho","last_name":"Kerjaschki"},{"last_name":"Esterbauer","full_name":"Esterbauer, Harald","first_name":"Harald"},{"full_name":"Colinge, Jacques","first_name":"Jacques","last_name":"Colinge"},{"last_name":"Eisenbarth","full_name":"Eisenbarth, Stephanie","first_name":"Stephanie"},{"full_name":"Decker, Thomas","first_name":"Thomas","last_name":"Decker"},{"first_name":"Keiryn","full_name":"Bennett, Keiryn","last_name":"Bennett"},{"full_name":"Kubicek, Stefan","first_name":"Stefan","last_name":"Kubicek"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt"},{"first_name":"Giulio","full_name":"Superti Furga, Giulio","last_name":"Superti Furga"},{"last_name":"Knapp","full_name":"Knapp, Sylvia","first_name":"Sylvia"}],"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000388056400006"]},"year":"2016","date_published":"2016-12-01T00:00:00Z","status":"public","publication_status":"published","citation":{"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>.","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.","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>.","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.","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>","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>"},"date_created":"2018-12-11T11:50:22Z","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":"Nature Immunology","main_file_link":[{"url":"https://ora.ox.ac.uk/objects/uuid:f53a464e-1e5b-4f08-a7d8-b6749b852b9d","open_access":"1"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:10:50Z","oa":1,"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."}],"publisher":"Nature Publishing Group","publist_id":"6216","day":"01","doi":"10.1038/ni.3590","_id":"1142","volume":17,"oa_version":"Submitted Version","type":"journal_article","month":"12","scopus_import":"1","isi":1,"department":[{"_id":"MiSi"},{"_id":"PeJo"}],"page":"1361 - 1372","article_processing_charge":"No"},{"author":[{"first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","full_name":"Nam, Phan","last_name":"Nam"},{"last_name":"Rougerie","full_name":"Rougerie, Nicolas","first_name":"Nicolas"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert"}],"intvolume":"         9","issue":"2","citation":{"short":"P. Nam, N. Rougerie, R. Seiringer, Analysis and PDE 9 (2016) 459–485.","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>.","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.","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.","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>","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>","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>."},"year":"2016","date_published":"2016-03-24T00:00:00Z","publication_status":"published","status":"public","external_id":{"arxiv":["1503.07061"],"isi":["000378287000006"]},"language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1503.07061","open_access":"1"}],"date_updated":"2025-09-22T14:10:16Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Ground states of large bosonic systems: The gross Pitaevskii limit revisited","publication":"Analysis and PDE","date_created":"2018-12-11T11:50:23Z","publisher":"Mathematical Sciences Publishers","ec_funded":1,"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"}],"oa":1,"publist_id":"6215","_id":"1143","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"volume":9,"day":"24","doi":"10.2140/apde.2016.9.459","type":"journal_article","month":"03","oa_version":"Preprint","article_processing_charge":"No","department":[{"_id":"RoSe"}],"page":"459 - 485","scopus_import":"1","isi":1},{"ddc":["530"],"month":"08","type":"journal_article","oa_version":"Published Version","volume":6,"_id":"100","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1103/PhysRevX.6.031016","day":"03","publist_id":"7954","article_number":"031016","publisher":"American Physical Society","file":[{"content_type":"application/pdf","relation":"main_file","creator":"kschuh","file_size":2142676,"file_name":"2016_PhysRevX_Aasen.pdf","date_created":"2019-05-15T14:12:31Z","success":1,"file_id":"6458","access_level":"open_access","date_updated":"2019-05-15T14:12:31Z"}],"abstract":[{"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.","lang":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:47:33Z","publication":"Physical Review X","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.).","date_created":"2018-12-11T11:44:37Z","citation":{"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>.","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).","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>.","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.","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>","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.","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>"},"file_date_updated":"2019-05-15T14:12:31Z","status":"public","publication_status":"published","extern":"1","date_published":"2016-08-03T00:00:00Z","year":"2016","language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"first_name":"David","full_name":"Aasen, David","last_name":"Aasen"},{"last_name":"Hell","full_name":"Hell, Michael","first_name":"Michael"},{"full_name":"Mishmash, Ryan","first_name":"Ryan","last_name":"Mishmash"},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","last_name":"Higginbotham"},{"last_name":"Danon","first_name":"Jeroen","full_name":"Danon, Jeroen"},{"last_name":"Leijnse","first_name":"Martin","full_name":"Leijnse, Martin"},{"first_name":"Thomas","full_name":"Jespersen, Thomas","last_name":"Jespersen"},{"full_name":"Folk, Joshua","first_name":"Joshua","last_name":"Folk"},{"full_name":"Marcs, Charles","first_name":"Charles","last_name":"Marcs"},{"last_name":"Flensberg","full_name":"Flensberg, Karsten","first_name":"Karsten"},{"last_name":"Alicea","full_name":"Alicea, Jason","first_name":"Jason"}],"issue":"3","intvolume":"         6","has_accepted_license":"1"},{"author":[{"last_name":"Gnügge","first_name":"Robert","full_name":"Gnügge, Robert"},{"full_name":"Dharmarajan, Lekshmi","first_name":"Lekshmi","last_name":"Dharmarajan"},{"last_name":"Lang","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz"},{"first_name":"Jörg","full_name":"Stelling, Jörg","last_name":"Stelling"}],"issue":"10","intvolume":"         5","citation":{"chicago":"Gnügge, Robert, Lekshmi Dharmarajan, Moritz Lang, and Jörg Stelling. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” <i>ACS Synthetic Biology</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acssynbio.6b00013\">https://doi.org/10.1021/acssynbio.6b00013</a>.","short":"R. Gnügge, L. Dharmarajan, M. Lang, J. Stelling, ACS Synthetic Biology 5 (2016) 1098–1107.","mla":"Gnügge, Robert, et al. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” <i>ACS Synthetic Biology</i>, vol. 5, no. 10, American Chemical Society, 2016, pp. 1098–107, doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00013\">10.1021/acssynbio.6b00013</a>.","ama":"Gnügge R, Dharmarajan L, Lang M, Stelling J. An orthogonal permease–inducer–repressor feedback loop shows bistability. <i>ACS Synthetic Biology</i>. 2016;5(10):1098-1107. doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00013\">10.1021/acssynbio.6b00013</a>","apa":"Gnügge, R., Dharmarajan, L., Lang, M., &#38; Stelling, J. (2016). An orthogonal permease–inducer–repressor feedback loop shows bistability. <i>ACS Synthetic Biology</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssynbio.6b00013\">https://doi.org/10.1021/acssynbio.6b00013</a>","ieee":"R. Gnügge, L. Dharmarajan, M. Lang, and J. Stelling, “An orthogonal permease–inducer–repressor feedback loop shows bistability,” <i>ACS Synthetic Biology</i>, vol. 5, no. 10. American Chemical Society, pp. 1098–1107, 2016.","ista":"Gnügge R, Dharmarajan L, Lang M, Stelling J. 2016. An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. 5(10), 1098–1107."},"publication_status":"published","status":"public","year":"2016","date_published":"2016-05-05T00:00:00Z","external_id":{"isi":["000386196100008"]},"language":[{"iso":"eng"}],"quality_controlled":"1","date_updated":"2025-09-22T14:20:45Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"ACS Synthetic Biology","title":"An orthogonal permease–inducer–repressor feedback loop shows bistability","acknowledgement":"We thank Julio Polaina (Instituto de Agroqu ı ́ mica y Tecnolog ı ́ a de Alimentos, C.S.I.C., Paterna, Spain) for the gift of plasmid pMR4, Gregor W. Schmidt for provision of and support with the micro fl uidic device, Markus Du ̈ rr for the cell tracking R script, and Lukas Widmer for the script for MEIGO using “ parfor ” in MATLAB. We acknowledge the members of the Stelling group for discussions, comments, and support.","date_created":"2018-12-11T11:49:40Z","publisher":"American Chemical Society","abstract":[{"lang":"eng","text":"Feedback loops in biological networks, among others, enable differentiation and cell cycle progression, and increase robustness in signal transduction. In natural networks, feedback loops are often complex and intertwined, making it challenging to identify which loops are mainly responsible for an observed behavior. However, minimal synthetic replicas could allow for such identification. Here, we engineered a synthetic permease-inducer-repressor system in Saccharomyces cerevisiae to analyze if a transport-mediated positive feedback loop could be a core mechanism for the switch-like behavior in the regulation of metabolic gene networks such as the S. cerevisiae GAL system or the Escherichia coli lac operon. We characterized the synthetic circuit using deterministic and stochastic mathematical models. Similar to its natural counterparts, our synthetic system shows bistable and hysteretic behavior, and the inducer concentration range for bistability as well as the switching rates between the two stable states depend on the repressor concentration. Our results indicate that a generic permease–inducer–repressor circuit with a single feedback loop is sufficient to explain the experimentally observed bistable behavior of the natural systems. We anticipate that the approach of reimplementing natural systems with orthogonal parts to identify crucial network components is applicable to other natural systems such as signaling pathways."}],"publist_id":"6390","volume":5,"_id":"1008","doi":"10.1021/acssynbio.6b00013","day":"05","month":"05","type":"journal_article","oa_version":"None","article_processing_charge":"No","page":"1098 - 1107","department":[{"_id":"CaGu"}],"isi":1},{"intvolume":"       531","issue":"7593","author":[{"last_name":"Albrecht","first_name":"S M","full_name":"Albrecht, S M"},{"last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P"},{"last_name":"Jespersen","first_name":"Thomas","full_name":"Jespersen, Thomas"},{"first_name":"Morten","full_name":"Madsen, Morten","last_name":"Madsen"},{"full_name":"Kuemmeth, Ferdinand","first_name":"Ferdinand","last_name":"Kuemmeth"},{"last_name":"Nygård","first_name":"Jesper","full_name":"Nygård, Jesper"},{"first_name":"Peter","full_name":"Krogstrup, Peter","last_name":"Krogstrup"},{"last_name":"Marcus","first_name":"Charles","full_name":"Marcus, Charles"}],"date_published":"2016-03-10T00:00:00Z","year":"2016","extern":"1","publication_status":"published","status":"public","citation":{"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>.","short":"S.M. Albrecht, A.P. Higginbotham, T. Jespersen, M. Madsen, F. Kuemmeth, J. Nygård, P. Krogstrup, C. Marcus, Nature 531 (2016) 206–209.","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>.","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.","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.","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>","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>"},"quality_controlled":"1","external_id":{"arxiv":["1603.03217"]},"language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:47:37Z","arxiv":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://arxiv.org/abs/1603.03217","open_access":"1"}],"date_created":"2018-12-11T11:44:38Z","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.","title":"Exponential protection of zero modes in Majorana islands","publication":"Nature","publisher":"Nature Publishing Group","oa":1,"abstract":[{"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.","lang":"eng"}],"publist_id":"7953","_id":"101","volume":531,"doi":"10.1038/nature17162","day":"10","oa_version":"Submitted Version","type":"journal_article","month":"03","page":"206 - 209"},{"issue":"24","intvolume":"        93","author":[{"first_name":"Ryan","full_name":"Mishmash, Ryan","last_name":"Mishmash"},{"last_name":"Aasen","first_name":"David","full_name":"Aasen, David"},{"last_name":"Higginbotham","first_name":"Andrew P","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jason","full_name":"Alicea, Jason","last_name":"Alicea"}],"quality_controlled":"1","external_id":{"arxiv":["1601.07908"]},"language":[{"iso":"eng"}],"status":"public","extern":"1","publication_status":"published","year":"2016","date_published":"2016-06-08T00:00:00Z","citation":{"ista":"Mishmash R, Aasen D, Higginbotham AP, Alicea J. 2016. Approaching a topological phase transition in Majorana nanowires. Physical Review B. 93(24), 245404.","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.","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>","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>","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>.","short":"R. Mishmash, D. Aasen, A.P. Higginbotham, J. Alicea, Physical Review B 93 (2016).","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>."},"date_created":"2018-12-11T11:44:38Z","publication":"Physical Review B","title":"Approaching a topological phase transition in Majorana nanowires","main_file_link":[{"url":"https://arxiv.org/abs/1601.07908","open_access":"1"}],"date_updated":"2021-01-12T06:47:42Z","arxiv":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"abstract":[{"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.","lang":"eng"}],"publisher":"American Physical Society","article_number":"245404","publist_id":"7952","day":"08","doi":"10.1103/PhysRevB.93.245404","volume":93,"_id":"102","oa_version":"Preprint","month":"06","type":"journal_article"},{"author":[{"first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić"},{"last_name":"Michaels","full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T."},{"last_name":"Zaccone","first_name":"Alessio","full_name":"Zaccone, Alessio"},{"full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J.","last_name":"Knowles"},{"first_name":"Daan","full_name":"Frenkel, Daan","last_name":"Frenkel"}],"intvolume":"       145","issue":"21","citation":{"short":"A. Šarić, T.C.T. Michaels, A. Zaccone, T.P.J. Knowles, D. Frenkel, The Journal of Chemical Physics 145 (2016).","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>.","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>","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.","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>."},"year":"2016","date_published":"2016-12-01T00:00:00Z","status":"public","extern":"1","publication_status":"published","language":[{"iso":"eng"}],"external_id":{"arxiv":["1610.02320"],"pmid":["28799382"]},"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1610.02320","open_access":"1"}],"date_updated":"2021-11-29T10:33:11Z","pmid":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","arxiv":1,"title":"Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation","keyword":["physical and theoretical chemistry","general physics and astronomy"],"publication":"The Journal of Chemical Physics","date_created":"2021-11-29T10:01:57Z","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.).","publisher":"American Institute of Physics","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."}],"oa":1,"article_number":"211926","article_type":"original","_id":"10376","volume":145,"day":"01","doi":"10.1063/1.4965040","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"type":"journal_article","month":"12","oa_version":"Preprint","article_processing_charge":"No","scopus_import":"1"},{"intvolume":"         6","issue":"1","author":[{"last_name":"van der Wel","full_name":"van der Wel, Casper","first_name":"Casper"},{"last_name":"Vahid","first_name":"Afshin","full_name":"Vahid, Afshin"},{"last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"},{"last_name":"Idema","first_name":"Timon","full_name":"Idema, Timon"},{"first_name":"Doris","full_name":"Heinrich, Doris","last_name":"Heinrich"},{"first_name":"Daniela J.","full_name":"Kraft, Daniela J.","last_name":"Kraft"}],"has_accepted_license":"1","date_published":"2016-09-13T00:00:00Z","year":"2016","status":"public","publication_status":"published","extern":"1","file_date_updated":"2021-11-29T10:50:00Z","citation":{"short":"C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, D.J. Kraft, Scientific Reports 6 (2016).","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>.","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.","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>","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>","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.","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>."},"quality_controlled":"1","external_id":{"arxiv":["1603.04644"],"pmid":["27618764"]},"language":[{"iso":"eng"}],"pmid":1,"main_file_link":[{"url":"https://www.nature.com/articles/srep32825","open_access":"1"}],"arxiv":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-11-29T11:08:15Z","date_created":"2021-11-29T10:34:08Z","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.","title":"Lipid membrane-mediated attraction between curvature inducing objects","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/srep37382"}]},"publication":"Scientific Reports","keyword":["multidisciplinary"],"publisher":"Springer Nature","oa":1,"abstract":[{"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.","lang":"eng"}],"file":[{"file_size":1598289,"file_name":"2016_SciRep_vanderWel.pdf","creator":"cchlebak","checksum":"d6cf16dd511e15726b001e7cc287cf1d","content_type":"application/pdf","relation":"main_file","date_updated":"2021-11-29T10:50:00Z","access_level":"open_access","date_created":"2021-11-29T10:50:00Z","success":1,"file_id":"10379"}],"article_number":"32825","article_type":"original","_id":"10377","volume":6,"publication_identifier":{"issn":["2045-2322"]},"day":"13","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1038/srep32825","oa_version":"Published Version","type":"journal_article","month":"09","article_processing_charge":"No","scopus_import":"1","ddc":["540"]},{"publisher":"Springer Nature","oa":1,"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"}],"date_updated":"2021-11-29T11:07:25Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"url":"https://discovery.ucl.ac.uk/id/eprint/1517406/","open_access":"1"}],"pmid":1,"date_created":"2021-11-29T10:36:11Z","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","publication":"Nature Physics","keyword":["general physics and astronomy"],"date_published":"2016-07-18T00:00:00Z","year":"2016","extern":"1","publication_status":"published","status":"public","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.","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>.","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>","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.","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>."},"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["31031819"]},"intvolume":"        12","issue":"9","author":[{"last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"last_name":"Buell","full_name":"Buell, Alexander K.","first_name":"Alexander K."},{"full_name":"Meisl, Georg","first_name":"Georg","last_name":"Meisl"},{"full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T.","last_name":"Michaels"},{"last_name":"Dobson","full_name":"Dobson, Christopher M.","first_name":"Christopher M."},{"first_name":"Sara","full_name":"Linse, Sara","last_name":"Linse"},{"first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J.","last_name":"Knowles"},{"first_name":"Daan","full_name":"Frenkel, Daan","last_name":"Frenkel"}],"article_processing_charge":"No","scopus_import":"1","page":"874-880","oa_version":"Preprint","type":"journal_article","month":"07","_id":"10378","volume":12,"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"doi":"10.1038/nphys3828","day":"18","article_type":"original"},{"oa_version":"Preprint","type":"journal_article","month":"06","article_processing_charge":"No","scopus_import":"1","article_number":"224102","article_type":"original","_id":"10380","volume":144,"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"day":"10","doi":"10.1063/1.4953036","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"url":"https://arxiv.org/abs/1602.02734","open_access":"1"}],"pmid":1,"date_updated":"2021-11-29T13:09:08Z","arxiv":1,"date_created":"2021-11-29T11:08:52Z","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","publication":"The Journal of Chemical Physics","keyword":["physical and theoretical chemistry","general physics and astronomy"],"publisher":"American Institute of Physics","oa":1,"abstract":[{"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.","lang":"eng"}],"intvolume":"       144","issue":"22","author":[{"last_name":"Wirnsberger","first_name":"P.","full_name":"Wirnsberger, P."},{"last_name":"Fijan","full_name":"Fijan, D.","first_name":"D."},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"last_name":"Neumann","first_name":"M.","full_name":"Neumann, M."},{"full_name":"Dellago, C.","first_name":"C.","last_name":"Dellago"},{"last_name":"Frenkel","first_name":"D.","full_name":"Frenkel, D."}],"date_published":"2016-06-10T00:00:00Z","year":"2016","extern":"1","publication_status":"published","status":"public","citation":{"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.","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>","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.","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>","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>.","short":"P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, D. Frenkel, The Journal of Chemical Physics 144 (2016).","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>."},"quality_controlled":"1","external_id":{"arxiv":["1602.02734"],"pmid":["27305991"]},"language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"external_id":{"pmid":["27722701"],"arxiv":["1608.05788"]},"quality_controlled":"1","citation":{"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>.","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.","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>","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.","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>","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>.","short":"S.J. Bachmann, J. Kotar, L. Parolini, A. Šarić, P. Cicuta, L. Di Michele, B.M. Mognetti, Soft Matter 12 (2016) 7804–7817."},"date_published":"2016-08-19T00:00:00Z","year":"2016","publication_status":"published","extern":"1","status":"public","author":[{"last_name":"Bachmann","first_name":"Stephan Jan","full_name":"Bachmann, Stephan Jan"},{"first_name":"Jurij","full_name":"Kotar, Jurij","last_name":"Kotar"},{"first_name":"Lucia","full_name":"Parolini, Lucia","last_name":"Parolini"},{"first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić"},{"full_name":"Cicuta, Pietro","first_name":"Pietro","last_name":"Cicuta"},{"first_name":"Lorenzo","full_name":"Di Michele, Lorenzo","last_name":"Di Michele"},{"first_name":"Bortolo Matteo","full_name":"Mognetti, Bortolo Matteo","last_name":"Mognetti"}],"intvolume":"        12","issue":"37","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."}],"oa":1,"publisher":"Royal Society of Chemistry","title":"Melting transition in lipid vesicles functionalised by mobile DNA linkers","keyword":["condensed matter physics","general chemistry"],"publication":"Soft Matter","date_created":"2021-11-29T11:09:55Z","main_file_link":[{"url":"https://arxiv.org/abs/1608.05788","open_access":"1"}],"arxiv":1,"date_updated":"2021-11-29T13:09:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","pmid":1,"day":"19","doi":"10.1039/c6sm01515h","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"_id":"10381","volume":12,"article_type":"original","page":"7804-7817","scopus_import":"1","article_processing_charge":"No","type":"journal_article","month":"08","oa_version":"Preprint"},{"page":"1911-1914","article_processing_charge":"No","oa_version":"None","month":"10","type":"journal_article","publication_identifier":{"eissn":["1439-7633"],"issn":["1439-4227"]},"day":"17","doi":"10.1002/cbic.201600281","volume":17,"_id":"21099","article_type":"original","abstract":[{"lang":"eng","text":"Quinoline‐based oligoamide foldamers have been identified as a potent class of ligands for G‐quadruplex DNA. Their helical structure is thought to target G‐quadruplex loops or grooves and not G‐tetrads. We report a co‐crystal structure of the antiparallel hairpin dimeric DNA G‐quadruplex (G4T4G4)2 with tetramer 1a helically folded oligo‐quinolinecarboxamide bearing cationic side chains—that is consistent with this hypothesis. Multivalent foldamer-DNA interactions that modify the packing of (G4T4G4)2 in the solid state are observed."}],"publisher":"Wiley","date_created":"2026-01-29T21:36:22Z","publication":"ChemBioChem","title":"Multivalent interactions between an aromatic helical foldamer and a DNA G‐quadruplex in the solid state","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-02-23T09:21:50Z","quality_controlled":"1","language":[{"iso":"eng"}],"publication_status":"published","status":"public","extern":"1","date_published":"2016-10-17T00:00:00Z","year":"2016","OA_type":"closed access","citation":{"ieee":"P. K. Mandal, B. Baptiste, B. Langlois d’Estaintot, B. Kauffmann, and I. Huc, “Multivalent interactions between an aromatic helical foldamer and a DNA G‐quadruplex in the solid state,” <i>ChemBioChem</i>, vol. 17, no. 20. Wiley, pp. 1911–1914, 2016.","apa":"Mandal, P. K., Baptiste, B., Langlois d’Estaintot, B., Kauffmann, B., &#38; Huc, I. (2016). Multivalent interactions between an aromatic helical foldamer and a DNA G‐quadruplex in the solid state. <i>ChemBioChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cbic.201600281\">https://doi.org/10.1002/cbic.201600281</a>","ama":"Mandal PK, Baptiste B, Langlois d’Estaintot B, Kauffmann B, Huc I. Multivalent interactions between an aromatic helical foldamer and a DNA G‐quadruplex in the solid state. <i>ChemBioChem</i>. 2016;17(20):1911-1914. doi:<a href=\"https://doi.org/10.1002/cbic.201600281\">10.1002/cbic.201600281</a>","ista":"Mandal PK, Baptiste B, Langlois d’Estaintot B, Kauffmann B, Huc I. 2016. Multivalent interactions between an aromatic helical foldamer and a DNA G‐quadruplex in the solid state. ChemBioChem. 17(20), 1911–1914.","mla":"Mandal, Pradeep K., et al. “Multivalent Interactions between an Aromatic Helical Foldamer and a DNA G‐quadruplex in the Solid State.” <i>ChemBioChem</i>, vol. 17, no. 20, Wiley, 2016, pp. 1911–14, doi:<a href=\"https://doi.org/10.1002/cbic.201600281\">10.1002/cbic.201600281</a>.","short":"P.K. Mandal, B. Baptiste, B. Langlois d’Estaintot, B. Kauffmann, I. Huc, ChemBioChem 17 (2016) 1911–1914.","chicago":"Mandal, Pradeep K, Benoît Baptiste, Béatrice Langlois d’Estaintot, Brice Kauffmann, and Ivan Huc. “Multivalent Interactions between an Aromatic Helical Foldamer and a DNA G‐quadruplex in the Solid State.” <i>ChemBioChem</i>. Wiley, 2016. <a href=\"https://doi.org/10.1002/cbic.201600281\">https://doi.org/10.1002/cbic.201600281</a>."},"has_accepted_license":"1","issue":"20","intvolume":"        17","author":[{"orcid":"0000-0001-5996-956X","full_name":"Mandal, Pradeep K","id":"6a3def15-d4b4-11ef-9fa9-a24c1f545ec3","first_name":"Pradeep K","last_name":"Mandal"},{"first_name":"Benoît","full_name":"Baptiste, Benoît","last_name":"Baptiste"},{"full_name":"Langlois d'Estaintot, Béatrice","first_name":"Béatrice","last_name":"Langlois d'Estaintot"},{"last_name":"Kauffmann","full_name":"Kauffmann, Brice","first_name":"Brice"},{"last_name":"Huc","full_name":"Huc, Ivan","first_name":"Ivan"}]},{"oa_version":"None","month":"06","type":"journal_article","article_processing_charge":"No","page":"9355-9358","article_type":"original","volume":52,"_id":"21100","publication_identifier":{"eissn":["1364-548X"],"issn":["1359-7345"]},"doi":"10.1039/c6cc04466b","day":"28","date_updated":"2026-02-23T09:18:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2026-01-29T21:42:03Z","publication":"Chemical Communications","title":"Crystal structure of a complex between β-glucopyranose and a macrocyclic receptor with dendritic multicharged water solubilizing chains","publisher":"Royal Society of Chemistry","abstract":[{"lang":"eng","text":"Using commercial screens for crystallization of biomolecules and taking advantage of the use of racemic crystallography allowed the production of X-ray quality single crystals and the elucidation at 1.08 Å resolution of the solid state structure of a difficult target: the complex between glucopyranose and a water soluble macrocyclic receptor equipped with dendritic multianionic solubilizing chains."}],"issue":"60","intvolume":"        52","author":[{"first_name":"Pradeep K","full_name":"Mandal, Pradeep K","id":"6a3def15-d4b4-11ef-9fa9-a24c1f545ec3","orcid":"0000-0001-5996-956X","last_name":"Mandal"},{"last_name":"Kauffmann","first_name":"Brice","full_name":"Kauffmann, Brice"},{"last_name":"Destecroix","full_name":"Destecroix, Harry","first_name":"Harry"},{"first_name":"Yann","full_name":"Ferrand, Yann","last_name":"Ferrand"},{"first_name":"Anthony P.","full_name":"Davis, Anthony P.","last_name":"Davis"},{"last_name":"Huc","full_name":"Huc, Ivan","first_name":"Ivan"}],"has_accepted_license":"1","status":"public","extern":"1","publication_status":"published","year":"2016","date_published":"2016-06-28T00:00:00Z","citation":{"short":"P.K. Mandal, B. Kauffmann, H. Destecroix, Y. Ferrand, A.P. Davis, I. Huc, Chemical Communications 52 (2016) 9355–9358.","chicago":"Mandal, Pradeep K, Brice Kauffmann, Harry Destecroix, Yann Ferrand, Anthony P. Davis, and Ivan Huc. “Crystal Structure of a Complex between β-Glucopyranose and a Macrocyclic Receptor with Dendritic Multicharged Water Solubilizing Chains.” <i>Chemical Communications</i>. Royal Society of Chemistry, 2016. <a href=\"https://doi.org/10.1039/c6cc04466b\">https://doi.org/10.1039/c6cc04466b</a>.","ama":"Mandal PK, Kauffmann B, Destecroix H, Ferrand Y, Davis AP, Huc I. Crystal structure of a complex between β-glucopyranose and a macrocyclic receptor with dendritic multicharged water solubilizing chains. <i>Chemical Communications</i>. 2016;52(60):9355-9358. doi:<a href=\"https://doi.org/10.1039/c6cc04466b\">10.1039/c6cc04466b</a>","apa":"Mandal, P. K., Kauffmann, B., Destecroix, H., Ferrand, Y., Davis, A. P., &#38; Huc, I. (2016). Crystal structure of a complex between β-glucopyranose and a macrocyclic receptor with dendritic multicharged water solubilizing chains. <i>Chemical Communications</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c6cc04466b\">https://doi.org/10.1039/c6cc04466b</a>","ieee":"P. K. Mandal, B. Kauffmann, H. Destecroix, Y. Ferrand, A. P. Davis, and I. Huc, “Crystal structure of a complex between β-glucopyranose and a macrocyclic receptor with dendritic multicharged water solubilizing chains,” <i>Chemical Communications</i>, vol. 52, no. 60. Royal Society of Chemistry, pp. 9355–9358, 2016.","ista":"Mandal PK, Kauffmann B, Destecroix H, Ferrand Y, Davis AP, Huc I. 2016. Crystal structure of a complex between β-glucopyranose and a macrocyclic receptor with dendritic multicharged water solubilizing chains. Chemical Communications. 52(60), 9355–9358.","mla":"Mandal, Pradeep K., et al. “Crystal Structure of a Complex between β-Glucopyranose and a Macrocyclic Receptor with Dendritic Multicharged Water Solubilizing Chains.” <i>Chemical Communications</i>, vol. 52, no. 60, Royal Society of Chemistry, 2016, pp. 9355–58, doi:<a href=\"https://doi.org/10.1039/c6cc04466b\">10.1039/c6cc04466b</a>."},"OA_type":"closed access","quality_controlled":"1","language":[{"iso":"eng"}]}]