[{"publist_id":"7953","oa":1,"language":[{"iso":"eng"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Majorana zero modes are quasiparticle excitations in condensed matter systems that have been proposed as building blocks of fault-tolerant quantum computers. They are expected to exhibit non-Abelian particle statistics, in contrast to the usual statistics of fermions and bosons, enabling quantum operations to be performed by braiding isolated modes around one another. Quantum braiding operations are topologically protected insofar as these modes are pinned near zero energy, with the departure from zero expected to be exponentially small as the modes become spatially separated. Following theoretical proposals, several experiments have identified signatures of Majorana modes in nanowires with proximity-induced superconductivity and atomic chains, with small amounts of mode splitting potentially explained by hybridization of Majorana modes. Here, we use Coulomb-blockade spectroscopy in an InAs nanowire segment with epitaxial aluminium, which forms a proximity-induced superconducting Coulomb island (a â ∼ Majorana islandâ (tm)) that is isolated from normal-metal leads by tunnel barriers, to measure the splitting of near-zero-energy Majorana modes. We observe exponential suppression of energy splitting with increasing wire length. For short devices of a few hundred nanometres, sub-gap state energies oscillate as the magnetic field is varied, as is expected for hybridized Majorana modes. Splitting decreases by a factor of about ten for each half a micrometre of increased wire length. For devices longer than about one micrometre, transport in strong magnetic fields occurs through a zero-energy state that is energetically isolated from a continuum, yielding uniformly spaced Coulomb-blockade conductance peaks, consistent with teleportation via Majorana modes. Our results help to explain the trivial-to-topological transition in finite systems and to quantify the scaling of topological protection with end-mode separation."}],"publication_status":"published","publisher":"Nature Publishing Group","citation":{"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.","short":"S.M. Albrecht, A.P. Higginbotham, T. Jespersen, M. Madsen, F. Kuemmeth, J. Nygård, P. Krogstrup, C. Marcus, Nature 531 (2016) 206–209.","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>","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>","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.","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>.","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>."},"intvolume":"       531","_id":"101","date_published":"2016-03-10T00:00:00Z","status":"public","year":"2016","volume":531,"quality_controlled":"1","doi":"10.1038/nature17162","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.","page":"206 - 209","day":"10","author":[{"first_name":"S M","last_name":"Albrecht","full_name":"Albrecht, S M"},{"orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P"},{"full_name":"Jespersen, Thomas","last_name":"Jespersen","first_name":"Thomas"},{"full_name":"Madsen, Morten","first_name":"Morten","last_name":"Madsen"},{"last_name":"Kuemmeth","first_name":"Ferdinand","full_name":"Kuemmeth, Ferdinand"},{"first_name":"Jesper","last_name":"Nygård","full_name":"Nygård, Jesper"},{"full_name":"Krogstrup, Peter","first_name":"Peter","last_name":"Krogstrup"},{"first_name":"Charles","last_name":"Marcus","full_name":"Marcus, Charles"}],"arxiv":1,"type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1603.03217"]},"main_file_link":[{"url":"https://arxiv.org/abs/1603.03217","open_access":"1"}],"title":"Exponential protection of zero modes in Majorana islands","date_created":"2018-12-11T11:44:38Z","publication":"Nature","date_updated":"2021-01-12T06:47:37Z","fulldoi":"https://doi.org/10.1038/nature17162","extern":"1","month":"03","issue":"7593"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","arxiv":1,"day":"08","author":[{"last_name":"Mishmash","first_name":"Ryan","full_name":"Mishmash, Ryan"},{"full_name":"Aasen, David","first_name":"David","last_name":"Aasen"},{"last_name":"Higginbotham","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P"},{"first_name":"Jason","last_name":"Alicea","full_name":"Alicea, Jason"}],"external_id":{"arxiv":["1601.07908"]},"date_created":"2018-12-11T11:44:38Z","publication":"Physical Review B","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.07908"}],"title":"Approaching a topological phase transition in Majorana nanowires","month":"06","issue":"24","extern":"1","fulldoi":"https://doi.org/10.1103/PhysRevB.93.245404","date_updated":"2021-01-12T06:47:42Z","publist_id":"7952","language":[{"iso":"eng"}],"oa":1,"article_number":"245404","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.","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>.","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.","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>.","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>","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>"},"intvolume":"        93","publication_status":"published","publisher":"American Physical Society","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"}],"oa_version":"Preprint","doi":"10.1103/PhysRevB.93.245404","volume":93,"quality_controlled":"1","status":"public","year":"2016","_id":"102","date_published":"2016-06-08T00:00:00Z"},{"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"publication_status":"published","publisher":"American Institute of Physics","intvolume":"       145","citation":{"short":"A. Šarić, T.C.T. Michaels, A. Zaccone, T.P.J. Knowles, D. Frenkel, The Journal of Chemical Physics 145 (2016).","ista":"Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. 2016. Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation. The Journal of Chemical Physics. 145(21), 211926.","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>.","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>.","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>","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>"},"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"volume":145,"quality_controlled":"1","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.).","doi":"10.1063/1.4965040","date_published":"2016-12-01T00:00:00Z","_id":"10376","year":"2016","status":"public","language":[{"iso":"eng"}],"pmid":1,"article_processing_charge":"No","scopus_import":"1","article_number":"211926","oa":1,"publication":"The Journal of Chemical Physics","date_created":"2021-11-29T10:01:57Z","title":"Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation","main_file_link":[{"url":"https://arxiv.org/abs/1610.02320","open_access":"1"}],"issue":"21","month":"12","date_updated":"2021-11-29T10:33:11Z","fulldoi":"https://doi.org/10.1063/1.4965040","extern":"1","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"first_name":"Thomas C. T.","last_name":"Michaels","full_name":"Michaels, Thomas C. T."},{"full_name":"Zaccone, Alessio","first_name":"Alessio","last_name":"Zaccone"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."},{"last_name":"Frenkel","first_name":"Daan","full_name":"Frenkel, Daan"}],"day":"01","arxiv":1,"keyword":["physical and theoretical chemistry","general physics and astronomy"],"article_type":"original","external_id":{"arxiv":["1610.02320"],"pmid":["28799382"]}},{"date_created":"2021-11-29T10:34:08Z","publication":"Scientific Reports","title":"Lipid membrane-mediated attraction between curvature inducing objects","main_file_link":[{"url":"https://www.nature.com/articles/srep32825","open_access":"1"}],"has_accepted_license":"1","month":"09","issue":"1","date_updated":"2021-11-29T11:08:15Z","fulldoi":"https://doi.org/10.1038/srep32825","extern":"1","file_date_updated":"2021-11-29T10:50:00Z","type":"journal_article","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/srep37382"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"13","author":[{"full_name":"van der Wel, Casper","first_name":"Casper","last_name":"van der Wel"},{"last_name":"Vahid","first_name":"Afshin","full_name":"Vahid, Afshin"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"full_name":"Idema, Timon","last_name":"Idema","first_name":"Timon"},{"full_name":"Heinrich, Doris","last_name":"Heinrich","first_name":"Doris"},{"first_name":"Daniela J.","last_name":"Kraft","full_name":"Kraft, Daniela J."}],"arxiv":1,"article_type":"original","file":[{"date_updated":"2021-11-29T10:50:00Z","file_size":1598289,"file_name":"2016_SciRep_vanderWel.pdf","relation":"main_file","access_level":"open_access","success":1,"creator":"cchlebak","file_id":"10379","checksum":"d6cf16dd511e15726b001e7cc287cf1d","content_type":"application/pdf","date_created":"2021-11-29T10:50:00Z"}],"keyword":["multidisciplinary"],"external_id":{"arxiv":["1603.04644"],"pmid":["27618764"]},"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"issn":["2045-2322"]},"citation":{"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>","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.","mla":"van der Wel, Casper, et al. “Lipid Membrane-Mediated Attraction between Curvature Inducing Objects.” <i>Scientific Reports</i>, vol. 6, no. 1, 32825, Springer Nature, 2016, doi:<a href=\"https://doi.org/10.1038/srep32825\">10.1038/srep32825</a>.","chicago":"Wel, Casper van der, Afshin Vahid, Anđela Šarić, Timon Idema, Doris Heinrich, and Daniela J. Kraft. “Lipid Membrane-Mediated Attraction between Curvature Inducing Objects.” <i>Scientific Reports</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/srep32825\">https://doi.org/10.1038/srep32825</a>.","short":"C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, D.J. Kraft, Scientific Reports 6 (2016).","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."},"intvolume":"         6","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","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"}],"quality_controlled":"1","volume":6,"doi":"10.1038/srep32825","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.","_id":"10377","date_published":"2016-09-13T00:00:00Z","status":"public","year":"2016","ddc":["540"],"language":[{"iso":"eng"}],"pmid":1,"article_processing_charge":"No","oa":1,"article_number":"32825","scopus_import":"1"},{"language":[{"iso":"eng"}],"pmid":1,"article_processing_charge":"No","scopus_import":"1","oa":1,"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"publication_status":"published","publisher":"Springer Nature","intvolume":"        12","citation":{"short":"A. Šarić, A.K. Buell, G. Meisl, T.C.T. Michaels, C.M. Dobson, S. Linse, T.P.J. Knowles, D. Frenkel, Nature Physics 12 (2016) 874–880.","ista":"Šarić A, Buell AK, Meisl G, Michaels TCT, Dobson CM, Linse S, Knowles TPJ, Frenkel D. 2016. Physical determinants of the self-replication of protein fibrils. Nature Physics. 12(9), 874–880.","chicago":"Šarić, Anđela, Alexander K. Buell, Georg Meisl, Thomas C. T. Michaels, Christopher M. Dobson, Sara Linse, Tuomas P. J. Knowles, and Daan Frenkel. “Physical Determinants of the Self-Replication of Protein Fibrils.” <i>Nature Physics</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/nphys3828\">https://doi.org/10.1038/nphys3828</a>.","mla":"Šarić, Anđela, et al. “Physical Determinants of the Self-Replication of Protein Fibrils.” <i>Nature Physics</i>, vol. 12, no. 9, Springer Nature, 2016, pp. 874–80, doi:<a href=\"https://doi.org/10.1038/nphys3828\">10.1038/nphys3828</a>.","ieee":"A. Šarić <i>et al.</i>, “Physical determinants of the self-replication of protein fibrils,” <i>Nature Physics</i>, vol. 12, no. 9. Springer Nature, pp. 874–880, 2016.","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>"},"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"volume":12,"quality_controlled":"1","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.).","doi":"10.1038/nphys3828","date_published":"2016-07-18T00:00:00Z","_id":"10378","year":"2016","status":"public","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"first_name":"Alexander K.","last_name":"Buell","full_name":"Buell, Alexander K."},{"last_name":"Meisl","first_name":"Georg","full_name":"Meisl, Georg"},{"full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T.","last_name":"Michaels"},{"full_name":"Dobson, Christopher M.","first_name":"Christopher M.","last_name":"Dobson"},{"full_name":"Linse, Sara","first_name":"Sara","last_name":"Linse"},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."},{"full_name":"Frenkel, Daan","first_name":"Daan","last_name":"Frenkel"}],"day":"18","page":"874-880","keyword":["general physics and astronomy"],"article_type":"original","external_id":{"pmid":["31031819"]},"publication":"Nature Physics","date_created":"2021-11-29T10:36:11Z","title":"Physical determinants of the self-replication of protein fibrils","main_file_link":[{"open_access":"1","url":"https://discovery.ucl.ac.uk/id/eprint/1517406/"}],"issue":"9","month":"07","date_updated":"2021-11-29T11:07:25Z","fulldoi":"https://doi.org/10.1038/nphys3828","extern":"1"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","arxiv":1,"author":[{"full_name":"Wirnsberger, P.","first_name":"P.","last_name":"Wirnsberger"},{"full_name":"Fijan, D.","last_name":"Fijan","first_name":"D."},{"last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Neumann, M.","first_name":"M.","last_name":"Neumann"},{"last_name":"Dellago","first_name":"C.","full_name":"Dellago, C."},{"first_name":"D.","last_name":"Frenkel","full_name":"Frenkel, D."}],"day":"10","keyword":["physical and theoretical chemistry","general physics and astronomy"],"article_type":"original","external_id":{"arxiv":["1602.02734"],"pmid":["27305991"]},"date_created":"2021-11-29T11:08:52Z","publication":"The Journal of Chemical Physics","title":"Non-equilibrium simulations of thermally induced electric fields in water","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.02734"}],"issue":"22","month":"06","extern":"1","fulldoi":"https://doi.org/10.1063/1.4953036","date_updated":"2021-11-29T13:09:08Z","pmid":1,"language":[{"iso":"eng"}],"scopus_import":"1","oa":1,"article_number":"224102","article_processing_charge":"No","intvolume":"       144","citation":{"short":"P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, D. Frenkel, The Journal of Chemical Physics 144 (2016).","ista":"Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. 2016. Non-equilibrium simulations of thermally induced electric fields in water. The Journal of Chemical Physics. 144(22), 224102.","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>","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.","chicago":"Wirnsberger, P., D. Fijan, Anđela Šarić, M. Neumann, C. Dellago, and D. Frenkel. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in Water.” <i>The Journal of Chemical Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1063/1.4953036\">https://doi.org/10.1063/1.4953036</a>.","mla":"Wirnsberger, P., et al. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in Water.” <i>The Journal of Chemical Physics</i>, vol. 144, no. 22, 224102, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1063/1.4953036\">10.1063/1.4953036</a>."},"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"publication_status":"published","publisher":"American Institute of Physics","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"}],"oa_version":"Preprint","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).","doi":"10.1063/1.4953036","volume":144,"quality_controlled":"1","year":"2016","status":"public","date_published":"2016-06-10T00:00:00Z","_id":"10380"},{"citation":{"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>","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>.","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>.","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.","short":"S.J. Bachmann, J. Kotar, L. Parolini, A. Šarić, P. Cicuta, L. Di Michele, B.M. Mognetti, Soft Matter 12 (2016) 7804–7817.","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."},"intvolume":"        12","publisher":"Royal Society of Chemistry","publication_status":"published","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"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_version":"Preprint","doi":"10.1039/c6sm01515h","quality_controlled":"1","volume":12,"status":"public","year":"2016","_id":"10381","date_published":"2016-08-19T00:00:00Z","pmid":1,"language":[{"iso":"eng"}],"oa":1,"scopus_import":"1","article_processing_charge":"No","date_created":"2021-11-29T11:09:55Z","publication":"Soft Matter","title":"Melting transition in lipid vesicles functionalised by mobile DNA linkers","main_file_link":[{"url":"https://arxiv.org/abs/1608.05788","open_access":"1"}],"month":"08","issue":"37","extern":"1","date_updated":"2021-11-29T13:09:00Z","fulldoi":"https://doi.org/10.1039/c6sm01515h","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","arxiv":1,"page":"7804-7817","day":"19","author":[{"last_name":"Bachmann","first_name":"Stephan Jan","full_name":"Bachmann, Stephan Jan"},{"full_name":"Kotar, Jurij","first_name":"Jurij","last_name":"Kotar"},{"first_name":"Lucia","last_name":"Parolini","full_name":"Parolini, Lucia"},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Cicuta","first_name":"Pietro","full_name":"Cicuta, Pietro"},{"full_name":"Di Michele, Lorenzo","first_name":"Lorenzo","last_name":"Di Michele"},{"last_name":"Mognetti","first_name":"Bortolo Matteo","full_name":"Mognetti, Bortolo Matteo"}],"article_type":"original","keyword":["condensed matter physics","general chemistry"],"external_id":{"pmid":["27722701"],"arxiv":["1608.05788"]}},{"oa_version":"None","abstract":[{"lang":"eng","text":"Far-field super-resolution fluorescence microscopy discerns fluorophores residing closer than the diffraction barrier by briefly transferring them in different (typically ON and OFF) states before detection. In coordinate-targeted super-resolution variants, such as stimulated emission depletion (STED) microscopy, this state difference is created by the intensity minima and maxima of an optical pattern, causing all fluorophores to assume the off state, for instance, except at the minima. Although strong spatial confinement of the on state enables high resolution, it also subjects the fluorophores to excess intensities and state cycles at the maxima. Here, we address these issues by driving the fluorophores into a second off state that is inert to the excess light. By using reversibly switchable fluorescent proteins as labels, our approach reduces bleaching and enhances resolution and contrast in live-cell STED microscopy. Using two or more transitions to off states is a useful strategy for augmenting the power of coordinate-targeted super-resolution microscopy."}],"publication_identifier":{"eissn":["1749-4893"],"issn":["1749-4885"]},"publisher":"Springer Nature","publication_status":"published","intvolume":"        10","citation":{"ista":"Danzl JG, Sidenstein S, Gregor C, Urban N, Ilgen P, Jakobs S, Hell S. 2016. Coordinate-targeted fluorescence nanoscopy with multiple off states. Nature Photonics. 10, 122–128.","short":"J.G. Danzl, S. Sidenstein, C. Gregor, N. Urban, P. Ilgen, S. Jakobs, S. Hell, Nature Photonics 10 (2016) 122–128.","ama":"Danzl JG, Sidenstein S, Gregor C, et al. Coordinate-targeted fluorescence nanoscopy with multiple off states. <i>Nature Photonics</i>. 2016;10:122-128. doi:<a href=\"https://doi.org/10.1038/nphoton.2015.266\">10.1038/nphoton.2015.266</a>","apa":"Danzl, J. G., Sidenstein, S., Gregor, C., Urban, N., Ilgen, P., Jakobs, S., &#38; Hell, S. (2016). Coordinate-targeted fluorescence nanoscopy with multiple off states. <i>Nature Photonics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nphoton.2015.266\">https://doi.org/10.1038/nphoton.2015.266</a>","chicago":"Danzl, Johann G, Sven Sidenstein, Carola Gregor, Nicolai Urban, Peter Ilgen, Stefan Jakobs, and Stefan Hell. “Coordinate-Targeted Fluorescence Nanoscopy with Multiple off States.” <i>Nature Photonics</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/nphoton.2015.266\">https://doi.org/10.1038/nphoton.2015.266</a>.","ieee":"J. G. Danzl <i>et al.</i>, “Coordinate-targeted fluorescence nanoscopy with multiple off states,” <i>Nature Photonics</i>, vol. 10. Springer Nature, pp. 122–128, 2016.","mla":"Danzl, Johann G., et al. “Coordinate-Targeted Fluorescence Nanoscopy with Multiple off States.” <i>Nature Photonics</i>, vol. 10, Springer Nature, 2016, pp. 122–28, doi:<a href=\"https://doi.org/10.1038/nphoton.2015.266\">10.1038/nphoton.2015.266</a>."},"date_published":"2016-02-01T00:00:00Z","_id":"1057","year":"2016","status":"public","quality_controlled":"1","volume":10,"acknowledgement":"We thank T. Gilat and E. Rothermel (both MPI) for help with preparing samples, and J. Keller for discussion. J.G.D. acknowledges support by the European Union through a Marie Curie fellowship PIEF-GA-2011-299283. S.W.H. acknowledges support by the Körber Foundation.","doi":"10.1038/nphoton.2015.266","publist_id":"6331","article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"title":"Coordinate-targeted fluorescence nanoscopy with multiple off states","publication":"Nature Photonics","date_created":"2018-12-11T11:49:55Z","fulldoi":"https://doi.org/10.1038/nphoton.2015.266","date_updated":"2026-05-20T14:02:20Z","extern":"1","month":"02","author":[{"last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"full_name":"Sidenstein, Sven","first_name":"Sven","last_name":"Sidenstein"},{"full_name":"Gregor, Carola","first_name":"Carola","last_name":"Gregor"},{"first_name":"Nicolai","last_name":"Urban","full_name":"Urban, Nicolai"},{"last_name":"Ilgen","first_name":"Peter","full_name":"Ilgen, Peter"},{"full_name":"Jakobs, Stefan","first_name":"Stefan","last_name":"Jakobs"},{"last_name":"Hell","first_name":"Stefan","full_name":"Hell, Stefan"}],"day":"01","page":"122 - 128","type":"journal_article","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_type":"closed access","article_type":"original"},{"extern":"1","fulldoi":"https://doi.org/10.1002/anie.201511018","date_updated":"2021-01-12T06:47:59Z","month":"03","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"10","title":"Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells","date_created":"2018-12-11T11:49:55Z","publication":"Angewandte Chemie - International Edition","page":"3290 - 3294","author":[{"first_name":"Alexey","last_name":"Butkevich","full_name":"Butkevich, Alexey"},{"first_name":"Gyuzel","last_name":"Mitronova","full_name":"Mitronova, Gyuzel"},{"full_name":"Sidenstein, Sven","last_name":"Sidenstein","first_name":"Sven"},{"first_name":"Jessica","last_name":"Klocke","full_name":"Klocke, Jessica"},{"last_name":"Kamin","first_name":"Dirk","full_name":"Kamin, Dirk"},{"first_name":"Dirk","last_name":"Meineke","full_name":"Meineke, Dirk"},{"first_name":"Elisa","last_name":"D'Este","full_name":"D'Este, Elisa"},{"full_name":"Kraemer, Philip","first_name":"Philip","last_name":"Kraemer"},{"last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"},{"first_name":"Vladimir","last_name":"Belov","full_name":"Belov, Vladimir"},{"full_name":"Hell, Stefan","last_name":"Hell","first_name":"Stefan"}],"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","year":"2016","_id":"1059","date_published":"2016-03-01T00:00:00Z","doi":"10.1002/anie.201511018","acknowledgement":"We thank Prof. Y. Okada (RIKEN Quantitative Biology Center, Osaka, Japan) for the gift of β-tubulin-Halo plasmid, T. Gilat and Dr. E. Rothermel (MPIBPC, Göttingen, Germany) for cell culture and transfection, M. Pulst, J. Bienert (MPIBPC), Dr. M. John, Dr. H. Frauendorf, and co-workers (Institut für Organische und Biomolekulare Chemie, Georg-August-Universität, Göttingen, Germany) for UV/Vis, NMR, and ESI-MS spectra, Prof. M. L. Bossi (University of Buenos-Aires, Argentina) for measuring fluorescence lifetimes, and Dr. S. Vos and Prof. P. Cramer (MPIBPC) for access to a Tecan microplate reader. S.W.H. acknowledges a grant from the Bundesministerium für Bildung und Forschung (BMBF 513) within the program “Optische Technologien für Biowissenschaften und Gesundheit” (FKZ 13N11066). J.G.D. was supported by funds from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013; REA grant agreement PIEF-GA-2011-299283).","volume":55,"abstract":[{"lang":"eng","text":"A range of bright and photostable rhodamines and carbopyronines with absorption maxima in the range of λ=500-630 nm were prepared, and enabled the specific labeling of cytoskeletal filaments using HaloTag technology followed by staining with 1 μm solutions of the dye-ligand conjugates. The synthesis, photophysical parameters, fluorogenic behavior, and structure-property relationships of the new dyes are discussed. Light microscopy with stimulated emission depletion (STED) provided one- and two-color images of living cells with an optical resolution of 40-60 nm."}],"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"oa_version":"None","citation":{"short":"A. Butkevich, G. Mitronova, S. Sidenstein, J. Klocke, D. Kamin, D. Meineke, E. D’Este, P. Kraemer, J.G. Danzl, V. Belov, S. Hell, Angewandte Chemie - International Edition 55 (2016) 3290–3294.","ista":"Butkevich A, Mitronova G, Sidenstein S, Klocke J, Kamin D, Meineke D, D’Este E, Kraemer P, Danzl JG, Belov V, Hell S. 2016. Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells. Angewandte Chemie - International Edition. 55(10), 3290–3294.","ama":"Butkevich A, Mitronova G, Sidenstein S, et al. Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells. <i>Angewandte Chemie - International Edition</i>. 2016;55(10):3290-3294. doi:<a href=\"https://doi.org/10.1002/anie.201511018\">10.1002/anie.201511018</a>","apa":"Butkevich, A., Mitronova, G., Sidenstein, S., Klocke, J., Kamin, D., Meineke, D., … Hell, S. (2016). Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells. <i>Angewandte Chemie - International Edition</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/anie.201511018\">https://doi.org/10.1002/anie.201511018</a>","chicago":"Butkevich, Alexey, Gyuzel Mitronova, Sven Sidenstein, Jessica Klocke, Dirk Kamin, Dirk Meineke, Elisa D’Este, et al. “Fluorescent Rhodamines and Fluorogenic Carbopyronines for Super-Resolution STED Microscopy in Living Cells.” <i>Angewandte Chemie - International Edition</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1002/anie.201511018\">https://doi.org/10.1002/anie.201511018</a>.","ieee":"A. Butkevich <i>et al.</i>, “Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells,” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 10. Wiley-Blackwell, pp. 3290–3294, 2016.","mla":"Butkevich, Alexey, et al. “Fluorescent Rhodamines and Fluorogenic Carbopyronines for Super-Resolution STED Microscopy in Living Cells.” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 10, Wiley-Blackwell, 2016, pp. 3290–94, doi:<a href=\"https://doi.org/10.1002/anie.201511018\">10.1002/anie.201511018</a>."},"intvolume":"        55","publication_status":"published","publisher":"Wiley-Blackwell","article_processing_charge":"No","language":[{"iso":"eng"}],"publist_id":"6330"},{"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"25","author":[{"last_name":"Sidenstein","first_name":"Sven","full_name":"Sidenstein, Sven"},{"first_name":"Elisa","last_name":"D'Este","full_name":"D'Este, Elisa"},{"first_name":"Marvin","last_name":"Böhm","full_name":"Böhm, Marvin"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G"},{"last_name":"Belov","first_name":"Vladimir","full_name":"Belov, Vladimir"},{"last_name":"Hell","first_name":"Stefan","full_name":"Hell, Stefan"}],"publist_id":"6329","page":"1 - 8","language":[{"iso":"eng"}],"article_processing_charge":"No","publication":"Scientific Reports","date_created":"2018-12-11T11:49:56Z","publisher":"Nature Publishing Group","publication_status":"published","intvolume":"         6","citation":{"chicago":"Sidenstein, Sven, Elisa D’Este, Marvin Böhm, Johann G Danzl, Vladimir Belov, and Stefan Hell. “Multicolour Multilevel STED Nanoscopy of Actin/Spectrin Organization at Synapses.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep26725\">https://doi.org/10.1038/srep26725</a>.","ieee":"S. Sidenstein, E. D’Este, M. Böhm, J. G. Danzl, V. Belov, and S. Hell, “Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, pp. 1–8, 2016.","mla":"Sidenstein, Sven, et al. “Multicolour Multilevel STED Nanoscopy of Actin/Spectrin Organization at Synapses.” <i>Scientific Reports</i>, vol. 6, Nature Publishing Group, 2016, pp. 1–8, doi:<a href=\"https://doi.org/10.1038/srep26725\">10.1038/srep26725</a>.","apa":"Sidenstein, S., D’Este, E., Böhm, M., Danzl, J. G., Belov, V., &#38; Hell, S. (2016). Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep26725\">https://doi.org/10.1038/srep26725</a>","ama":"Sidenstein S, D’Este E, Böhm M, Danzl JG, Belov V, Hell S. Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses. <i>Scientific Reports</i>. 2016;6:1-8. doi:<a href=\"https://doi.org/10.1038/srep26725\">10.1038/srep26725</a>","short":"S. Sidenstein, E. D’Este, M. Böhm, J.G. Danzl, V. Belov, S. Hell, Scientific Reports 6 (2016) 1–8.","ista":"Sidenstein S, D’Este E, Böhm M, Danzl JG, Belov V, Hell S. 2016. Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses. Scientific Reports. 6, 1–8."},"oa_version":"None","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"title":"Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses","abstract":[{"lang":"eng","text":"Superresolution fluorescence microscopy of multiple fluorophores still requires development. Here we present simultaneous three-colour stimulated emission depletion (STED) nanoscopy relying on a single STED beam at 620 nm. Toggling the STED beam between two or more power levels (&quot;multilevelSTEDv) optimizes resolution and contrast in all colour channels, which are intrinsically co-aligned and well separated. Three-colour recording is demonstrated by imaging the nanoscale cytoskeletal organization in cultured hippocampal neurons. The down to ∼35 nm resolution identified periodic actin/betaII spectrin lattices along dendrites and spines; however, at presynaptic and postsynaptic sites, these patterns were found to be absent. Both our multicolour scheme and the 620 nm STED line should be attractive for routine STED microscopy applications."}],"volume":6,"month":"05","acknowledgement":"We acknowledge the assistance of I. Herfort with neuron preparation, and of J. Bienert and K. Müller with analyses of the dye 540R derivatives. We thank T. Gilat and E. Rothermel for sample preparation as well as J. Keller, F. Winter (all MPI-BPC) and C.A. Wurm (Abberior Instruments) for helpful discussion, and S.J. Sahl (MPI-BPC) for a critical reading of the manuscript.","doi":"10.1038/srep26725","fulldoi":"https://doi.org/10.1038/srep26725","date_updated":"2021-01-12T06:47:59Z","date_published":"2016-05-25T00:00:00Z","_id":"1060","year":"2016","status":"public","extern":"1"},{"publist_id":"6317","ddc":["000","004","006"],"language":[{"iso":"eng"}],"pubrep_id":"779","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","scopus_import":"1","department":[{"_id":"KrCh"}],"oa":1,"article_number":"25","ec_funded":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","intvolume":"        58","conference":{"end_date":"2016-08-26","location":"Krakow, Poland","name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2016-08-22"},"citation":{"ista":"Chatterjee K, Dvorák W, Henzinger M, Loitzenbauer V. 2016. Conditionally optimal algorithms for generalized Büchi Games. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 58, 25.","short":"K. Chatterjee, W. Dvorák, M. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M., &#38; Loitzenbauer, V. (2016). Conditionally optimal algorithms for generalized Büchi Games (Vol. 58). Presented at the MFCS: Mathematical Foundations of Computer Science, Krakow, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">https://doi.org/10.4230/LIPIcs.MFCS.2016.25</a>","ama":"Chatterjee K, Dvorák W, Henzinger M, Loitzenbauer V. Conditionally optimal algorithms for generalized Büchi Games. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">10.4230/LIPIcs.MFCS.2016.25</a>","ieee":"K. Chatterjee, W. Dvorák, M. Henzinger, and V. Loitzenbauer, “Conditionally optimal algorithms for generalized Büchi Games,” presented at the MFCS: Mathematical Foundations of Computer Science, Krakow, Poland, 2016, vol. 58.","mla":"Chatterjee, Krishnendu, et al. <i>Conditionally Optimal Algorithms for Generalized Büchi Games</i>. Vol. 58, 25, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">10.4230/LIPIcs.MFCS.2016.25</a>.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika Henzinger, and Veronika Loitzenbauer. “Conditionally Optimal Algorithms for Generalized Büchi Games,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">https://doi.org/10.4230/LIPIcs.MFCS.2016.25</a>."},"oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"abstract":[{"text":"Games on graphs provide the appropriate framework to study several central problems in computer science, such as verification and synthesis of reactive systems. One of the most basic objectives for games on graphs is the liveness (or Büchi) objective that given a target set of vertices requires that some vertex in the target set is visited infinitely often. We study generalized Büchi objectives (i.e., conjunction of liveness objectives), and implications between two generalized Büchi objectives (known as GR(1) objectives), that arise in numerous applications in computer-aided verification. We present improved algorithms and conditional super-linear lower bounds based on widely believed assumptions about the complexity of (A1) combinatorial Boolean matrix multiplication and (A2) CNF-SAT. We consider graph games with n vertices, m edges, and generalized Büchi objectives with k conjunctions. First, we present an algorithm with running time O(k*n^2), improving the previously known O(k*n*m) and O(k^2*n^2) worst-case bounds. Our algorithm is optimal for dense graphs under (A1). Second, we show that the basic algorithm for the problem is optimal for sparse graphs when the target sets have constant size under (A2). Finally, we consider GR(1) objectives, with k_1 conjunctions in the antecedent and k_2 conjunctions in the consequent, and present an O(k_1 k_2 n^{2.5})-time algorithm, improving the previously known O(k_1*k_2*n*m)-time algorithm for m &gt; n^{1.5}. ","lang":"eng"}],"volume":58,"quality_controlled":"1","acknowledgement":"K. C., M. H., and W. D. are partially supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Start grant (279307","doi":"10.4230/LIPIcs.MFCS.2016.25","date_published":"2016-08-01T00:00:00Z","alternative_title":["LIPIcs"],"_id":"1068","year":"2016","status":"public","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Dvorák, Wolfgang","first_name":"Wolfgang","last_name":"Dvorák"},{"first_name":"Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Loitzenbauer, Veronika","first_name":"Veronika","last_name":"Loitzenbauer"}],"file":[{"file_name":"IST-2017-779-v1+1_LIPIcs-MFCS-2016-25.pdf","date_updated":"2018-12-12T10:16:02Z","file_size":632786,"relation":"main_file","access_level":"open_access","creator":"system","file_id":"5187","content_type":"application/pdf","date_created":"2018-12-12T10:16:02Z"}],"date_created":"2018-12-11T11:49:58Z","has_accepted_license":"1","title":"Conditionally optimal algorithms for generalized Büchi Games","license":"https://creativecommons.org/licenses/by/3.0/","month":"08","fulldoi":"https://doi.org/10.4230/LIPIcs.MFCS.2016.25","date_updated":"2025-07-10T11:49:55Z","file_date_updated":"2018-12-12T10:16:02Z"},{"file":[{"access_level":"open_access","relation":"main_file","creator":"system","file_name":"IST-2017-778-v1+1_LIPIcs-ICALP-2016-100.pdf","date_updated":"2018-12-12T10:16:26Z","file_size":521415,"date_created":"2018-12-12T10:16:26Z","content_type":"application/pdf","file_id":"5213"}],"author":[{"id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Chonev, Ventsislav K","first_name":"Ventsislav K","last_name":"Chonev"},{"full_name":"Ouaknine, Joël","last_name":"Ouaknine","first_name":"Joël"},{"full_name":"Worrell, James","last_name":"Worrell","first_name":"James"}],"day":"01","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-03T11:32:08Z","fulldoi":"https://doi.org/10.4230/LIPIcs.ICALP.2016.100","file_date_updated":"2018-12-12T10:16:26Z","month":"08","has_accepted_license":"1","title":"On the skolem problem for continuous linear dynamical systems","date_created":"2018-12-11T11:49:59Z","article_processing_charge":"No","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"KrCh"}],"scopus_import":"1","article_number":"100","oa":1,"pubrep_id":"778","language":[{"iso":"eng"}],"ddc":["004","006"],"publist_id":"6314","date_published":"2016-08-01T00:00:00Z","alternative_title":["LIPIcs"],"_id":"1069","year":"2016","status":"public","volume":55,"quality_controlled":"1","acknowledgement":"Ventsislav Chonev is supported by Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307:  Graph Games), and ERC Advanced Grant (267989: QUAREM).","doi":"10.4230/LIPIcs.ICALP.2016.100","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"abstract":[{"text":"The Continuous Skolem Problem asks whether a real-valued function satisfying a linear differen-\r\ntial equation has a zero in a given interval of real numbers. This is a fundamental reachability\r\nproblem for continuous linear dynamical systems, such as linear hybrid automata and continuous-\r\ntime Markov chains. Decidability of the problem is currently open – indeed decidability is open\r\neven for the sub-problem in which a zero is sought in a bounded interval. In this paper we show\r\ndecidability of the bounded problem subject to Schanuel’s Conjecture, a unifying conjecture in\r\ntranscendental number theory. We furthermore analyse the unbounded problem in terms of the\r\nfrequencies of the differential equation, that is, the imaginary parts of the characteristic roots.\r\nWe show that the unbounded problem can be reduced to the bounded problem if there is at most\r\none rationally linearly independent frequency, or if there are two rationally linearly independent\r\nfrequencies and all characteristic roots are simple. We complete the picture by showing that de-\r\ncidability of the unbounded problem in the case of two (or more) rationally linearly independent\r\nfrequencies would entail a major new effectiveness result in Diophantine approximation, namely\r\ncomputability of the Diophantine-approximation types of all real algebraic numbers.","lang":"eng"}],"publication_status":"published","ec_funded":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"        55","citation":{"ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On the skolem problem for continuous linear dynamical systems. ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 100.","short":"V.K. Chonev, J. Ouaknine, J. Worrell, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ama":"Chonev VK, Ouaknine J, Worrell J. On the skolem problem for continuous linear dynamical systems. In: Vol 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">10.4230/LIPIcs.ICALP.2016.100</a>","apa":"Chonev, V. K., Ouaknine, J., &#38; Worrell, J. (2016). On the skolem problem for continuous linear dynamical systems (Vol. 55). Presented at the ICALP: Automata, Languages and Programming, Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">https://doi.org/10.4230/LIPIcs.ICALP.2016.100</a>","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Skolem Problem for Continuous Linear Dynamical Systems,” Vol. 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">https://doi.org/10.4230/LIPIcs.ICALP.2016.100</a>.","mla":"Chonev, Ventsislav K., et al. <i>On the Skolem Problem for Continuous Linear Dynamical Systems</i>. Vol. 55, 100, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">10.4230/LIPIcs.ICALP.2016.100</a>.","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On the skolem problem for continuous linear dynamical systems,” presented at the ICALP: Automata, Languages and Programming, Rome, Italy, 2016, vol. 55."},"conference":{"end_date":"2016-07-15","location":"Rome, Italy","name":"ICALP: Automata, Languages and Programming","start_date":"2016-07-12"}},{"date_created":"2018-12-11T11:49:59Z","has_accepted_license":"1","title":"Computation tree logic for synchronization properties","month":"01","fulldoi":"https://doi.org/10.4230/LIPIcs.ICALP.2016.98","date_updated":"2025-06-03T11:18:54Z","file_date_updated":"2018-12-12T10:08:52Z","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"}],"file":[{"creator":"system","access_level":"open_access","relation":"main_file","file_name":"IST-2017-812-v1+1_LIPIcs-ICALP-2016-98.pdf","date_updated":"2018-12-12T10:08:52Z","file_size":546133,"date_created":"2018-12-12T10:08:52Z","content_type":"application/pdf","file_id":"4714"}],"publication_status":"published","ec_funded":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"        55","citation":{"mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Computation Tree Logic for Synchronization Properties</i>. Vol. 55, 98, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">10.4230/LIPIcs.ICALP.2016.98</a>.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Computation Tree Logic for Synchronization Properties,” Vol. 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">https://doi.org/10.4230/LIPIcs.ICALP.2016.98</a>.","ieee":"K. Chatterjee and L. Doyen, “Computation tree logic for synchronization properties,” presented at the ICALP: Automata, Languages and Programming, Rome, Italy, 2016, vol. 55.","ama":"Chatterjee K, Doyen L. Computation tree logic for synchronization properties. In: Vol 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">10.4230/LIPIcs.ICALP.2016.98</a>","apa":"Chatterjee, K., &#38; Doyen, L. (2016). Computation tree logic for synchronization properties (Vol. 55). Presented at the ICALP: Automata, Languages and Programming, Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">https://doi.org/10.4230/LIPIcs.ICALP.2016.98</a>","ista":"Chatterjee K, Doyen L. 2016. Computation tree logic for synchronization properties. ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 98.","short":"K. Chatterjee, L. Doyen, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016."},"conference":{"end_date":"2016-07-15","location":"Rome, Italy","name":"ICALP: Automata, Languages and Programming","start_date":"2016-07-12"},"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"abstract":[{"lang":"eng","text":"We present a logic that extends CTL (Computation Tree Logic) with operators that express synchronization properties. A property is synchronized in a system if it holds in all paths of a certain length. The new logic is obtained by using the same path quantifiers and temporal operators as in CTL, but allowing a different order of the quantifiers. This small syntactic variation induces a logic that can express non-regular properties for which known extensions of MSO with equality of path length are undecidable. We show that our variant of CTL is decidable and that the model-checking problem is in Delta_3^P = P^{NP^NP}, and is DP-hard. We analogously consider quantifier exchange in extensions of CTL, and we present operators defined using basic operators of CTL* that express the occurrence of infinitely many synchronization points. We show that the model-checking problem remains in Delta_3^P. The distinguishing power of CTL and of our new logic coincide if the Next operator is allowed in the logics, thus the classical bisimulation quotient can be used for state-space reduction before model checking. "}],"quality_controlled":"1","volume":55,"acknowledgement":"This research was partially supported by Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003, and European project Cassting (FP7-601148).\r\n\r\nWe thank Stefan Göller and anonymous reviewers for their insightful\r\ncomments and suggestions.\r\n","doi":"10.4230/LIPIcs.ICALP.2016.98","date_published":"2016-01-01T00:00:00Z","alternative_title":["LIPIcs"],"_id":"1070","year":"2016","status":"public","publist_id":"6313","ddc":["005"],"language":[{"iso":"eng"}],"pubrep_id":"812","article_processing_charge":"No","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"scopus_import":"1","department":[{"_id":"KrCh"}],"article_number":"98","oa":1},{"date_created":"2018-12-11T11:49:59Z","has_accepted_license":"1","title":"Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs","month":"08","date_updated":"2026-04-08T14:22:16Z","fulldoi":"https://doi.org/10.4230/LIPIcs.ESA.2016.28","file_date_updated":"2018-12-12T10:14:31Z","type":"conference","related_material":{"record":[{"status":"public","id":"821","relation":"dissertation_contains"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus"},{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"day":"01","file":[{"file_name":"IST-2017-777-v1+1_LIPIcs-ESA-2016-28.pdf","date_updated":"2018-12-12T10:14:31Z","file_size":579225,"creator":"system","access_level":"open_access","relation":"main_file","file_id":"5084","content_type":"application/pdf","date_created":"2018-12-12T10:14:31Z"}],"ec_funded":1,"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"        57","citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2016. Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs. ESA: European Symposium on Algorithms, LIPIcs, vol. 57, 28.","mla":"Chatterjee, Krishnendu, et al. <i>Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant Treewidth Graphs</i>. Vol. 57, 28, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">10.4230/LIPIcs.ESA.2016.28</a>.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant Treewidth Graphs,” Vol. 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">https://doi.org/10.4230/LIPIcs.ESA.2016.28</a>.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs,” presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark, 2016, vol. 57.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs. In: Vol 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">10.4230/LIPIcs.ESA.2016.28</a>","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2016). Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs (Vol. 57). Presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">https://doi.org/10.4230/LIPIcs.ESA.2016.28</a>"},"conference":{"location":"Aarhus, Denmark","end_date":"2016-08-24","start_date":"2016-08-22","name":"ESA: European Symposium on Algorithms"},"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"abstract":[{"text":"We consider data-structures for answering reachability and distance queries on constant-treewidth graphs with n nodes, on the standard RAM computational model with wordsize W=Theta(log n). Our first contribution is a data-structure that after O(n) preprocessing time, allows (1) pair reachability queries in O(1) time; and (2) single-source reachability queries in O(n/log n) time. This is (asymptotically) optimal and is faster than DFS/BFS when answering more than a constant number of single-source queries. The data-structure uses at all times O(n) space. Our second contribution is a space-time tradeoff data-structure for distance queries. For any epsilon in [1/2,1], we provide a data-structure with polynomial preprocessing time that allows pair queries in O(n^{1-\\epsilon} alpha(n)) time, where alpha is the inverse of the Ackermann function, and at all times uses O(n^epsilon) space. The input graph G is not considered in the space complexity. ","lang":"eng"}],"quality_controlled":"1","volume":57,"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE) and ERC Start grant (279307: Graph Games).","doi":"10.4230/LIPIcs.ESA.2016.28","date_published":"2016-08-01T00:00:00Z","alternative_title":["LIPIcs"],"_id":"1071","year":"2016","status":"public","ddc":["004","006"],"publist_id":"6312","pubrep_id":"777","language":[{"iso":"eng"}],"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"}],"article_processing_charge":"No","scopus_import":"1","department":[{"_id":"KrCh"}],"article_number":"28","oa":1},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Vortex states in superconducting (SC) structures, their dynamics and ways to manipulate them are topics of great interest. We report a new method of magnetic force microscopy (MFM) that allows the study of vortex states in mesoscopic SC samples. For the case of a SC ring, which is biased to a half-integer flux quantum, the flux modulation through the ring caused by the motion of the magnetic tip drives the ring between two consecutive fluxoid states. The corresponding current switching in the ring produces strong position-dependent forces on the cantilever. In the regime where the frequency of the thermally activated jumps between fluxoid states is close to the frequency of the cantilever, large changes in the cantilever frequency and dissipation are observed. This effect may be understood as a stochastic resonance (SR) process. These changes in the cantilever’s mechanical properties are used to “image” the barrier energies between fluxoid states. Additionally, SR imaging of the barrier energies are used to study the effect of the locally applied magnetic field from the MFM tip on the barrier heights. We report the results of measurements for Al rings. Further, the same imaging technique can be applied to more sophisticated SC structures such as arrays of Josephson junctions."}],"publisher":"American Physical Society","publication_status":"published","publication_identifier":{"issn":["0003-0503"]},"citation":{"ieee":"H. Polshyn, T. Naibert, V. Chua, and R. Budakian, “Study of vortex states and dynamics in mesoscopic superconducting samples with MFM,” in <i>APS March Meeting 2016</i>, Baltimore, MD, United States, 2016, vol. 61, no. 2.","mla":"Polshyn, Hryhoriy, et al. “Study of Vortex States and Dynamics in Mesoscopic Superconducting Samples with MFM.” <i>APS March Meeting 2016</i>, vol. 61, no. 2, E25.00007, American Physical Society, 2016.","chicago":"Polshyn, Hryhoriy, Tyler Naibert, Victor Chua, and Raffi Budakian. “Study of Vortex States and Dynamics in Mesoscopic Superconducting Samples with MFM.” In <i>APS March Meeting 2016</i>, Vol. 61. American Physical Society, 2016.","ama":"Polshyn H, Naibert T, Chua V, Budakian R. Study of vortex states and dynamics in mesoscopic superconducting samples with MFM. In: <i>APS March Meeting 2016</i>. Vol 61. American Physical Society; 2016.","apa":"Polshyn, H., Naibert, T., Chua, V., &#38; Budakian, R. (2016). Study of vortex states and dynamics in mesoscopic superconducting samples with MFM. In <i>APS March Meeting 2016</i> (Vol. 61). Baltimore, MD, United States: American Physical Society.","ista":"Polshyn H, Naibert T, Chua V, Budakian R. 2016. Study of vortex states and dynamics in mesoscopic superconducting samples with MFM. APS March Meeting 2016. APS: American Physical Society, Bulletin of the American Physical Society, vol. 61, E25.00007.","short":"H. Polshyn, T. Naibert, V. Chua, R. Budakian, in:, APS March Meeting 2016, American Physical Society, 2016."},"conference":{"start_date":"2016-03-14","name":"APS: American Physical Society","location":"Baltimore, MD, United States","end_date":"2016-03-18"},"intvolume":"        61","alternative_title":["Bulletin of the American Physical Society"],"_id":"10746","date_published":"2016-03-01T00:00:00Z","status":"public","year":"2016","quality_controlled":"1","volume":61,"article_processing_charge":"No","article_number":"E25.00007","oa":1,"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR16/Session/E25.7","open_access":"1"}],"title":"Study of vortex states and dynamics in mesoscopic superconducting samples with MFM","date_created":"2022-02-08T09:55:09Z","publication":"APS March Meeting 2016","date_updated":"2022-02-08T10:44:06Z","extern":"1","month":"03","issue":"2","author":[{"first_name":"Hryhoriy","last_name":"Polshyn","full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"first_name":"Tyler","last_name":"Naibert","full_name":"Naibert, Tyler"},{"first_name":"Victor","last_name":"Chua","full_name":"Chua, Victor"},{"full_name":"Budakian, Raffi","last_name":"Budakian","first_name":"Raffi"}],"day":"01","type":"conference","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"language":[{"iso":"eng"}],"article_processing_charge":"No","oa":1,"article_number":"H25.00006","volume":61,"quality_controlled":"1","alternative_title":["Bulletin of the American Physical Society"],"_id":"10747","date_published":"2016-03-01T00:00:00Z","status":"public","year":"2016","publisher":"American Physical Society","publication_status":"published","publication_identifier":{"issn":["0003-0503"]},"citation":{"ista":"Naibert T, Polshyn H, Wolin B, Durkin M, Garrido Menacho R, Shem IM, Chua V, Hughes T, Mason N, Budakian R. 2016. Stochastic resonance magnetic force microscopy imaging of Josephson arrays. APS March Meeting 2016. APS: American Physical Society, Bulletin of the American Physical Society, vol. 61, H25.00006.","short":"T. Naibert, H. Polshyn, B. Wolin, M. Durkin, R. Garrido Menacho, I.M. Shem, V. Chua, T. Hughes, N. Mason, R. Budakian, in:, APS March Meeting 2016, American Physical Society, 2016.","ieee":"T. Naibert <i>et al.</i>, “Stochastic resonance magnetic force microscopy imaging of Josephson arrays,” in <i>APS March Meeting 2016</i>, Baltimore, MD, United States, 2016, vol. 61, no. 2.","mla":"Naibert, Tyler, et al. “Stochastic Resonance Magnetic Force Microscopy Imaging of Josephson Arrays.” <i>APS March Meeting 2016</i>, vol. 61, no. 2, H25.00006, American Physical Society, 2016.","chicago":"Naibert, Tyler, Hryhoriy Polshyn, Brian Wolin, Malcolm Durkin, Rita Garrido Menacho, Ian Mondragon Shem, Victor Chua, Taylor Hughes, Nadya Mason, and Raffi Budakian. “Stochastic Resonance Magnetic Force Microscopy Imaging of Josephson Arrays.” In <i>APS March Meeting 2016</i>, Vol. 61. American Physical Society, 2016.","apa":"Naibert, T., Polshyn, H., Wolin, B., Durkin, M., Garrido Menacho, R., Shem, I. M., … Budakian, R. (2016). Stochastic resonance magnetic force microscopy imaging of Josephson arrays. In <i>APS March Meeting 2016</i> (Vol. 61). Baltimore, MD, United States: American Physical Society.","ama":"Naibert T, Polshyn H, Wolin B, et al. Stochastic resonance magnetic force microscopy imaging of Josephson arrays. In: <i>APS March Meeting 2016</i>. Vol 61. American Physical Society; 2016."},"conference":{"name":"APS: American Physical Society","start_date":"2016-03-14","end_date":"2016-03-18","location":"Baltimore, MD, United States"},"intvolume":"        61","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Vortex interactions are key to explaining the behavior of many two dimensional superconducting systems. We report on the development of a technique to locally probe vortex interactions in a 2D array of Josephson junctions. Scanning a magnetic tip attached to an ultra-soft cantilever over the array produces changes in the frequency of the cantilever along certain lines, forming geometric patterns in the scans. Different tip-surface separations and external magnetic fields produce a number of different patterns. These patterns correspond to tip locations in which two configurations of vortices in the lattice have degenerate energies. By imaging the locations of these degeneracies, information on the local vortex interactions may be obtained."}],"type":"conference","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","author":[{"first_name":"Tyler","last_name":"Naibert","full_name":"Naibert, Tyler"},{"last_name":"Polshyn","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"full_name":"Wolin, Brian","first_name":"Brian","last_name":"Wolin"},{"last_name":"Durkin","first_name":"Malcolm","full_name":"Durkin, Malcolm"},{"first_name":"Rita","last_name":"Garrido Menacho","full_name":"Garrido Menacho, Rita"},{"full_name":"Shem, Ian Mondragon","last_name":"Shem","first_name":"Ian Mondragon"},{"first_name":"Victor","last_name":"Chua","full_name":"Chua, Victor"},{"last_name":"Hughes","first_name":"Taylor","full_name":"Hughes, Taylor"},{"last_name":"Mason","first_name":"Nadya","full_name":"Mason, Nadya"},{"first_name":"Raffi","last_name":"Budakian","full_name":"Budakian, Raffi"}],"month":"03","issue":"2","date_updated":"2022-02-08T10:43:33Z","extern":"1","date_created":"2022-02-08T10:10:39Z","publication":"APS March Meeting 2016","title":"Stochastic resonance magnetic force microscopy imaging of Josephson arrays","main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR16/Session/H25.6","open_access":"1"}]},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","author":[{"last_name":"Łangowski","first_name":"Łukasz","full_name":"Łangowski, Łukasz"},{"last_name":"Wabnik","first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560"},{"id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Hongjiang","orcid":"0000-0001-5039-9660","last_name":"Li","first_name":"Hongjiang"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"full_name":"Tanaka, Hirokazu","first_name":"Hirokazu","last_name":"Tanaka"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml"}],"day":"19","file":[{"file_name":"IST-2017-757-v1+1_celldisc201618.pdf","file_size":5261671,"date_updated":"2018-12-12T10:13:33Z","relation":"main_file","access_level":"open_access","creator":"system","file_id":"5017","content_type":"application/pdf","date_created":"2018-12-12T10:13:33Z"}],"external_id":{"isi":["000414797400001"]},"date_created":"2018-12-11T11:50:02Z","publication":"Cell Discovery","title":"Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells","has_accepted_license":"1","month":"07","file_date_updated":"2018-12-12T10:13:33Z","fulldoi":"https://doi.org/10.1038/celldisc.2016.18","date_updated":"2025-09-22T14:19:46Z","isi":1,"ddc":["580"],"publist_id":"6299","language":[{"iso":"eng"}],"pubrep_id":"757","oa":1,"article_number":"16018","scopus_import":"1","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300"}],"article_processing_charge":"No","citation":{"ama":"Łangowski Ł, Wabnik KT, Li H, et al. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. <i>Cell Discovery</i>. 2016;2. doi:<a href=\"https://doi.org/10.1038/celldisc.2016.18\">10.1038/celldisc.2016.18</a>","apa":"Łangowski, Ł., Wabnik, K. T., Li, H., Vanneste, S., Naramoto, S., Tanaka, H., &#38; Friml, J. (2016). Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. <i>Cell Discovery</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/celldisc.2016.18\">https://doi.org/10.1038/celldisc.2016.18</a>","ieee":"Ł. Łangowski <i>et al.</i>, “Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells,” <i>Cell Discovery</i>, vol. 2. Nature Publishing Group, 2016.","chicago":"Łangowski, Łukasz, Krzysztof T Wabnik, Hongjiang Li, Steffen Vanneste, Satoshi Naramoto, Hirokazu Tanaka, and Jiří Friml. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” <i>Cell Discovery</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/celldisc.2016.18\">https://doi.org/10.1038/celldisc.2016.18</a>.","mla":"Łangowski, Łukasz, et al. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” <i>Cell Discovery</i>, vol. 2, 16018, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/celldisc.2016.18\">10.1038/celldisc.2016.18</a>.","ista":"Łangowski Ł, Wabnik KT, Li H, Vanneste S, Naramoto S, Tanaka H, Friml J. 2016. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. 2, 16018.","short":"Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J. Friml, Cell Discovery 2 (2016)."},"intvolume":"         2","publication_status":"published","publisher":"Nature Publishing Group","ec_funded":1,"abstract":[{"lang":"eng","text":"The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","doi":"10.1038/celldisc.2016.18","acknowledgement":"We thank Bonnie Bartel, Jenny Russinova and Niko Geldner\r\nfor sharing published material, Martine de Cock and Annick\r\nBleys for help in preparing the manuscript. This work was\r\nsupported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP); Czech Science Foundation\r\nGAČR (GA13-40637S); project CEITEC—Central European\r\nInstitute of Technology (CZ.1.05/1.1.00/02.0068). SV is a\r\npostdoctoral fellow of the Research Foundation-Flanders.\r\nSN is a Project Assistant Professor supported by the Japanese\r\nSociety for the Promotion of Science (JSPS; 30612022 to SN),\r\nthe NC-CARP project of the Ministry of Education, Culture,\r\nSports, Science and Technology in Japan to SN.","volume":2,"quality_controlled":"1","status":"public","year":"2016","_id":"1081","date_published":"2016-07-19T00:00:00Z"},{"main_file_link":[{"url":"https://doi.org/10.22489/cinc.2016.090-500","open_access":"1"}],"title":"SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography","date_created":"2022-03-03T10:43:10Z","publication":"2016 Computing in Cardiology Conference","fulldoi":"https://doi.org/10.22489/cinc.2016.090-500","date_updated":"2026-06-18T08:48:07Z","month":"03","author":[{"full_name":"Rubel, Paul","last_name":"Rubel","first_name":"Paul"},{"full_name":"Pani, Danilo","first_name":"Danilo","last_name":"Pani"},{"first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100"},{"full_name":"Fayn, Jocelyne","first_name":"Jocelyne","last_name":"Fayn"},{"full_name":"Badilini, Fabio","last_name":"Badilini","first_name":"Fabio"},{"last_name":"Macfarlane","first_name":"Peter","full_name":"Macfarlane, Peter"},{"full_name":"Varri, Alpo","last_name":"Varri","first_name":"Alpo"}],"day":"01","page":"309-312","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","abstract":[{"text":"The main goal of the SCP-ECG standard is to address ECG data and related metadata structuring, semantics and syntax, with the objective of facilitating interoperability and thus supporting and promoting the exchange of the relevant information for unary and serial ECG diagnosis. Starting with version V3.0, the standard now also provides support for the storage of continuous, long-term ECG recordings and affords a repository for selected ECG sequences and the related metadata to accommodate stress tests, drug trials and protocol-based ECG recordings. The global and per-lead measurements sections have been extended and three new sections have been introduced for storing beat-by-beat and/or spike-by-spike measurements\r\nand annotations. The used terminology and the provided measurements and annotations have been harmonized with the ISO/IEEE 11073-10102 Annotated ECG standard. Emphasis has also been put on harmonizing the Universal Statement Codes with the CDISC and the categorized AHA statement codes and similarly the drug and implanted devices codes with the ATC and NASPE/BPEG codes. ","lang":"eng"}],"oa_version":"Published Version","intvolume":"        43","conference":{"location":"Vancouver, Canada","end_date":"2016-09-14","start_date":"2016-09-11","name":"CinC: Computing in Cardiology"},"citation":{"short":"P. Rubel, D. Pani, A. Schlögl, J. Fayn, F. Badilini, P. Macfarlane, A. Varri, in:, 2016 Computing in Cardiology Conference, Computing in Cardiology, 2016, pp. 309–312.","ista":"Rubel P, Pani D, Schlögl A, Fayn J, Badilini F, Macfarlane P, Varri A. 2016. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. 2016 Computing in Cardiology Conference. CinC: Computing in Cardiology vol. 43, 309–312.","apa":"Rubel, P., Pani, D., Schlögl, A., Fayn, J., Badilini, F., Macfarlane, P., &#38; Varri, A. (2016). SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In <i>2016 Computing in Cardiology Conference</i> (Vol. 43, pp. 309–312). Vancouver, Canada: Computing in Cardiology. <a href=\"https://doi.org/10.22489/cinc.2016.090-500\">https://doi.org/10.22489/cinc.2016.090-500</a>","ama":"Rubel P, Pani D, Schlögl A, et al. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In: <i>2016 Computing in Cardiology Conference</i>. Vol 43. Computing in Cardiology; 2016:309-312. doi:<a href=\"https://doi.org/10.22489/cinc.2016.090-500\">10.22489/cinc.2016.090-500</a>","chicago":"Rubel, Paul, Danilo Pani, Alois Schlögl, Jocelyne Fayn, Fabio Badilini, Peter Macfarlane, and Alpo Varri. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” In <i>2016 Computing in Cardiology Conference</i>, 43:309–12. Computing in Cardiology, 2016. <a href=\"https://doi.org/10.22489/cinc.2016.090-500\">https://doi.org/10.22489/cinc.2016.090-500</a>.","ieee":"P. Rubel <i>et al.</i>, “SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography,” in <i>2016 Computing in Cardiology Conference</i>, Vancouver, Canada, 2016, vol. 43, pp. 309–312.","mla":"Rubel, Paul, et al. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” <i>2016 Computing in Cardiology Conference</i>, vol. 43, Computing in Cardiology, 2016, pp. 309–12, doi:<a href=\"https://doi.org/10.22489/cinc.2016.090-500\">10.22489/cinc.2016.090-500</a>."},"publication_identifier":{"issn":["2325-887X"]},"publisher":"Computing in Cardiology","publication_status":"published","year":"2016","status":"public","date_published":"2016-03-01T00:00:00Z","_id":"10810","acknowledgement":"The authors are thankful to Drs. Roger Abaecherli, Nikus Kjell, Paul Kligfield, Jay Mason, Patrice Nony, Vito Starc, Anders Thurin and the late Galen Wagner for their in depth review and constructive comments.","doi":"10.22489/cinc.2016.090-500","quality_controlled":"1","volume":43,"ddc":["000"],"scopus_import":"1","department":[{"_id":"CampIT"}],"oa":1,"article_processing_charge":"No","language":[{"iso":"eng"}]},{"file":[{"date_updated":"2020-07-14T12:48:01Z","file_name":"2016_PlosGenetics_Tang.PDF","file_size":3266119,"relation":"main_file","access_level":"open_access","creator":"dernst","file_id":"7612","content_type":"application/pdf","checksum":"ff0ab9a6bed11cda800a6e59820866a0","date_created":"2020-03-23T12:15:31Z"}],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","day":"16","author":[{"full_name":"Tang, Yong","first_name":"Yong","last_name":"Tang"},{"last_name":"Zhao","first_name":"Chun-Yan","full_name":"Zhao, Chun-Yan"},{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","first_name":"Shutang"},{"full_name":"Xue, Hong-Wei","last_name":"Xue","first_name":"Hong-Wei"}],"month":"08","issue":"8","extern":"1","file_date_updated":"2020-07-14T12:48:01Z","fulldoi":"https://doi.org/10.1371/journal.pgen.1006252","date_updated":"2021-01-12T08:14:25Z","date_created":"2020-03-21T16:08:33Z","publication":"PLOS Genetics","title":"Arabidopsis type II phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through interacting with membrane-bound transcription factor ANAC078","has_accepted_license":"1","language":[{"iso":"eng"}],"article_number":"e1006252","oa":1,"article_processing_charge":"No","ddc":["580"],"doi":"10.1371/journal.pgen.1006252","volume":12,"quality_controlled":"1","status":"public","year":"2016","_id":"7599","date_published":"2016-08-16T00:00:00Z","citation":{"apa":"Tang, Y., Zhao, C.-Y., Tan, S., &#38; Xue, H.-W. (2016). Arabidopsis type II phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through interacting with membrane-bound transcription factor ANAC078. <i>PLOS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1006252\">https://doi.org/10.1371/journal.pgen.1006252</a>","ama":"Tang Y, Zhao C-Y, Tan S, Xue H-W. Arabidopsis type II phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through interacting with membrane-bound transcription factor ANAC078. <i>PLOS Genetics</i>. 2016;12(8). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1006252\">10.1371/journal.pgen.1006252</a>","ieee":"Y. Tang, C.-Y. Zhao, S. Tan, and H.-W. Xue, “Arabidopsis type II phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through interacting with membrane-bound transcription factor ANAC078,” <i>PLOS Genetics</i>, vol. 12, no. 8. Public Library of Science, 2016.","chicago":"Tang, Yong, Chun-Yan Zhao, Shutang Tan, and Hong-Wei Xue. “Arabidopsis Type II Phosphatidylinositol 4-Kinase PI4Kγ5 Regulates Auxin Biosynthesis and Leaf Margin Development through Interacting with Membrane-Bound Transcription Factor ANAC078.” <i>PLOS Genetics</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pgen.1006252\">https://doi.org/10.1371/journal.pgen.1006252</a>.","mla":"Tang, Yong, et al. “Arabidopsis Type II Phosphatidylinositol 4-Kinase PI4Kγ5 Regulates Auxin Biosynthesis and Leaf Margin Development through Interacting with Membrane-Bound Transcription Factor ANAC078.” <i>PLOS Genetics</i>, vol. 12, no. 8, e1006252, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1006252\">10.1371/journal.pgen.1006252</a>.","ista":"Tang Y, Zhao C-Y, Tan S, Xue H-W. 2016. Arabidopsis type II phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through interacting with membrane-bound transcription factor ANAC078. PLOS Genetics. 12(8), e1006252.","short":"Y. Tang, C.-Y. Zhao, S. Tan, H.-W. Xue, PLOS Genetics 12 (2016)."},"intvolume":"        12","publication_status":"published","publisher":"Public Library of Science","publication_identifier":{"issn":["1553-7404"]},"abstract":[{"lang":"eng","text":"Normal leaf margin development is important for leaf morphogenesis and contributes to diverse leaf shapes in higher plants. We here show the crucial roles of an atypical type II phosphatidylinositol 4-kinase, PI4Kγ5, in Arabidopsis leaf margin development. PI4Kγ5 presents a dynamics expression pattern along with leaf development and a T-DNA mutant lacking PI4Kγ5, pi4kγ5–1, presents serrated leaves, which is resulted from the accelerated cell division and increased auxin concentration at serration tips. Studies revealed that PI4Kγ5 interacts with and phosphorylates a membrane-bound NAC transcription factor, ANAC078. Previous studies demonstrated that membrane-bound transcription factors regulate gene transcription by undergoing proteolytic process to translocate into nucleus, and ANAC078 undergoes proteolysis by cleaving off the transmembrane region and carboxyl terminal. Western blot analysis indeed showed that ANAC078 deleting of carboxyl terminal is significantly reduced in pi4kγ5–1, indicating that PI4Kγ5 is important for the cleavage of ANAC078. This is consistent with the subcellular localization observation showing that fluorescence by GFP-ANAC078 is detected at plasma membrane but not nucleus in pi4kγ5–1 mutant and that expression of ANAC078 deleting of carboxyl terminal, driven by PI4Kγ5 promoter, could rescue the leaf serration defects of pi4kγ5–1. Further analysis showed that ANAC078 suppresses the auxin synthesis by directly binding and regulating the expression of auxin synthesis-related genes. These results indicate that PI4Kγ5 interacts with ANAC078 to negatively regulate auxin synthesis and hence influences cell proliferation and leaf development, providing informative clues for the regulation of in situ auxin synthesis and cell division, as well as the cleavage and functional mechanism of membrane-bound transcription factors."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version"},{"issue":"11","volume":73,"quality_controlled":"1","month":"11","doi":"10.1001/jamapsychiatry.2016.2566","date_published":"2016-11-01T00:00:00Z","fulldoi":"https://doi.org/10.1001/jamapsychiatry.2016.2566","date_updated":"2021-01-12T08:15:11Z","_id":"7734","year":"2016","status":"public","extern":"1","publication_identifier":{"issn":["2168-622X"]},"date_created":"2020-04-30T10:48:41Z","publication":"JAMA Psychiatry","publication_status":"published","publisher":"American Medical Association","intvolume":"        73","citation":{"ista":"Peyrot WJ, Robinson MR, Penninx BWJH, Wray NR. 2016. Exploring boundaries for the genetic consequences of assortative mating for psychiatric traits. JAMA Psychiatry. 73(11), 1189–1195.","short":"W.J. Peyrot, M.R. Robinson, B.W.J.H. Penninx, N.R. Wray, JAMA Psychiatry 73 (2016) 1189–1195.","apa":"Peyrot, W. J., Robinson, M. R., Penninx, B. W. J. H., &#38; Wray, N. R. (2016). Exploring boundaries for the genetic consequences of assortative mating for psychiatric traits. <i>JAMA Psychiatry</i>. American Medical Association. <a href=\"https://doi.org/10.1001/jamapsychiatry.2016.2566\">https://doi.org/10.1001/jamapsychiatry.2016.2566</a>","ama":"Peyrot WJ, Robinson MR, Penninx BWJH, Wray NR. Exploring boundaries for the genetic consequences of assortative mating for psychiatric traits. <i>JAMA Psychiatry</i>. 2016;73(11):1189-1195. doi:<a href=\"https://doi.org/10.1001/jamapsychiatry.2016.2566\">10.1001/jamapsychiatry.2016.2566</a>","chicago":"Peyrot, Wouter J., Matthew Richard Robinson, Brenda W. J. H. Penninx, and Naomi R. Wray. “Exploring Boundaries for the Genetic Consequences of Assortative Mating for Psychiatric Traits.” <i>JAMA Psychiatry</i>. American Medical Association, 2016. <a href=\"https://doi.org/10.1001/jamapsychiatry.2016.2566\">https://doi.org/10.1001/jamapsychiatry.2016.2566</a>.","mla":"Peyrot, Wouter J., et al. “Exploring Boundaries for the Genetic Consequences of Assortative Mating for Psychiatric Traits.” <i>JAMA Psychiatry</i>, vol. 73, no. 11, American Medical Association, 2016, pp. 1189–95, doi:<a href=\"https://doi.org/10.1001/jamapsychiatry.2016.2566\">10.1001/jamapsychiatry.2016.2566</a>.","ieee":"W. J. Peyrot, M. R. Robinson, B. W. J. H. Penninx, and N. R. Wray, “Exploring boundaries for the genetic consequences of assortative mating for psychiatric traits,” <i>JAMA Psychiatry</i>, vol. 73, no. 11. American Medical Association, pp. 1189–1195, 2016."},"oa_version":"None","abstract":[{"text":"Importance: Considerable partner resemblances have been found for a wide range of psychiatric disorders, meaning that partners of affected individuals have an increased risk of being affected compared with partners of unaffected individuals. If this resemblance is reflected in genetic similarity between partners, genetic risk is anticipated to accumulate in offspring, but these potential consequences have not been quantified and have been left implicit.\r\n\r\nObservations: The anticipated consequences of partner resemblance on prevalence and heritability of psychiatric traits in the offspring generation were modeled for disorders with varying heritabilities, population prevalence (lifetime risk), and magnitudes of partner resemblance. These models facilitate interpretation for a wide range of psychiatric disorders, such as autism, schizophrenia, and depression. The genetic consequences of partner resemblance are most pronounced when attributable to phenotypic assortment (driven by the psychiatric trait). Phenotypic assortment results in increased genetic variance in the offspring generation, which may result in increased heritability and population prevalence. These consequences add generation after generation to a limit, but assortative mating is unlikely to balance the impact of reduced fecundity of patients with psychiatric disorders in the long term. This modeling suggests that the heritabilities of psychiatric disorders are unlikely to increase by more than 5% from 1 generation of assortative mating (maximally 13% across multiple generations). The population prevalence will increase most for less common disorders with high heritability; for example, the prevalence of autism might increase by 1.5-fold after 1 generation of assortative mating (≥2.4-fold in the long term) depending on several assumptions.\r\n\r\nConclusions and Relevance: The considerable partner resemblances found for psychiatric disorders deserve more detailed interpretation than has been provided thus far. Although the limitations of modeling are emphasized, the anticipated consequences are at most modest for the heritability but may be considerable for the population prevalence of rare disorders with a high heritability.","lang":"eng"}],"title":"Exploring boundaries for the genetic consequences of assortative mating for psychiatric traits","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Peyrot, Wouter J.","last_name":"Peyrot","first_name":"Wouter J."},{"first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"},{"full_name":"Penninx, Brenda W. J. H.","first_name":"Brenda W. J. H.","last_name":"Penninx"},{"full_name":"Wray, Naomi R.","last_name":"Wray","first_name":"Naomi R."}],"day":"01","page":"1189-1195"}]