[{"author":[{"first_name":"Shrinivas","full_name":"Kudekar, Shrinivas","last_name":"Kudekar"},{"last_name":"Kumar","full_name":"Kumar, Santhosh","first_name":"Santhosh"},{"last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","first_name":"Marco"},{"last_name":"Pfister","full_name":"Pfister, Henry D.","first_name":"Henry D."},{"full_name":"Urbankez, Rudiger","first_name":"Rudiger","last_name":"Urbankez"}],"month":"08","citation":{"apa":"Kudekar, S., Kumar, S., Mondelli, M., Pfister, H. D., &#38; Urbankez, R. (2016). Comparing the bit-MAP and block-MAP decoding thresholds of Reed-Muller codes on BMS channels. In <i>2016 IEEE International Symposium on Information Theory </i> (pp. 1755–1759). Barcelona, Spain: IEEE. <a href=\"https://doi.org/10.1109/isit.2016.7541600\">https://doi.org/10.1109/isit.2016.7541600</a>","ama":"Kudekar S, Kumar S, Mondelli M, Pfister HD, Urbankez R. Comparing the bit-MAP and block-MAP decoding thresholds of Reed-Muller codes on BMS channels. In: <i>2016 IEEE International Symposium on Information Theory </i>. IEEE; 2016:1755-1759. doi:<a href=\"https://doi.org/10.1109/isit.2016.7541600\">10.1109/isit.2016.7541600</a>","short":"S. Kudekar, S. Kumar, M. Mondelli, H.D. Pfister, R. Urbankez, in:, 2016 IEEE International Symposium on Information Theory , IEEE, 2016, pp. 1755–1759.","mla":"Kudekar, Shrinivas, et al. “Comparing the Bit-MAP and Block-MAP Decoding Thresholds of Reed-Muller Codes on BMS Channels.” <i>2016 IEEE International Symposium on Information Theory </i>, IEEE, 2016, pp. 1755–59, doi:<a href=\"https://doi.org/10.1109/isit.2016.7541600\">10.1109/isit.2016.7541600</a>.","chicago":"Kudekar, Shrinivas, Santhosh Kumar, Marco Mondelli, Henry D. Pfister, and Rudiger Urbankez. “Comparing the Bit-MAP and Block-MAP Decoding Thresholds of Reed-Muller Codes on BMS Channels.” In <i>2016 IEEE International Symposium on Information Theory </i>, 1755–59. IEEE, 2016. <a href=\"https://doi.org/10.1109/isit.2016.7541600\">https://doi.org/10.1109/isit.2016.7541600</a>.","ista":"Kudekar S, Kumar S, Mondelli M, Pfister HD, Urbankez R. 2016. Comparing the bit-MAP and block-MAP decoding thresholds of Reed-Muller codes on BMS channels. 2016 IEEE International Symposium on Information Theory . ISIT: International Symposium on Information Theory, 1755–1759.","ieee":"S. Kudekar, S. Kumar, M. Mondelli, H. D. Pfister, and R. Urbankez, “Comparing the bit-MAP and block-MAP decoding thresholds of Reed-Muller codes on BMS channels,” in <i>2016 IEEE International Symposium on Information Theory </i>, Barcelona, Spain, 2016, pp. 1755–1759."},"day":"11","extern":"1","_id":"6733","publisher":"IEEE","quality_controlled":"1","language":[{"iso":"eng"}],"abstract":[{"text":"The question whether RM codes are capacity-achieving is a long-standing open problem in coding theory that was recently answered in the affirmative for transmission over erasure channels [1], [2]. Remarkably, the proof does not rely on specific properties of RM codes, apart from their symmetry. Indeed, the main technical result consists in showing that any sequence of linear codes, with doubly-transitive permutation groups, achieves capacity on the memoryless erasure channel under bit-MAP decoding. Thus, a natural question is what happens under block-MAP decoding. In [1], [2], by exploiting further symmetries of the code, the bit-MAP threshold was shown to be sharp enough so that the block erasure probability also converges to 0. However, this technique relies heavily on the fact that the transmission is over an erasure channel. We present an alternative approach to strengthen results regarding the bit-MAP threshold to block-MAP thresholds. This approach is based on a careful analysis of the weight distribution of RM codes. In particular, the flavor of the main result is the following: assume that the bit-MAP error probability decays as N -δ , for some δ > 0. Then, the block-MAP error probability also converges to 0. This technique applies to transmission over any binary memoryless symmetric channel. Thus, it can be thought of as a first step in extending the proof that RM codes are capacity-achieving to the general case.","lang":"eng"}],"arxiv":1,"date_created":"2019-07-31T06:36:16Z","publication":"2016 IEEE International Symposium on Information Theory ","external_id":{"arxiv":["1601.06048"]},"main_file_link":[{"url":"https://arxiv.org/abs/1601.06048","open_access":"1"}],"date_updated":"2021-01-12T08:08:44Z","conference":{"name":"ISIT: International Symposium on Information Theory","location":"Barcelona, Spain","end_date":"2016-07-15","start_date":"2016-07-10"},"oa":1,"date_published":"2016-08-11T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa_version":"Preprint","type":"conference","doi":"10.1109/isit.2016.7541600","year":"2016","title":"Comparing the bit-MAP and block-MAP decoding thresholds of Reed-Muller codes on BMS channels","status":"public","page":"1755-1759"},{"citation":{"ieee":"D. Aasen <i>et al.</i>, “Milestones toward Majorana-based quantum computing,” <i>Physical Review X</i>, vol. 6, no. 3. American Physical Society, 2016.","mla":"Aasen, David, et al. “Milestones toward Majorana-Based Quantum Computing.” <i>Physical Review X</i>, vol. 6, no. 3, 031016, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">10.1103/PhysRevX.6.031016</a>.","chicago":"Aasen, David, Michael Hell, Ryan Mishmash, Andrew P Higginbotham, Jeroen Danon, Martin Leijnse, Thomas Jespersen, et al. “Milestones toward Majorana-Based Quantum Computing.” <i>Physical Review X</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">https://doi.org/10.1103/PhysRevX.6.031016</a>.","ista":"Aasen D, Hell M, Mishmash R, Higginbotham AP, Danon J, Leijnse M, Jespersen T, Folk J, Marcs C, Flensberg K, Alicea J. 2016. Milestones toward Majorana-based quantum computing. Physical Review X. 6(3), 031016.","short":"D. Aasen, M. Hell, R. Mishmash, A.P. Higginbotham, J. Danon, M. Leijnse, T. Jespersen, J. Folk, C. Marcs, K. Flensberg, J. Alicea, Physical Review X 6 (2016).","ama":"Aasen D, Hell M, Mishmash R, et al. Milestones toward Majorana-based quantum computing. <i>Physical Review X</i>. 2016;6(3). doi:<a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">10.1103/PhysRevX.6.031016</a>","apa":"Aasen, D., Hell, M., Mishmash, R., Higginbotham, A. P., Danon, J., Leijnse, M., … Alicea, J. (2016). Milestones toward Majorana-based quantum computing. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.6.031016\">https://doi.org/10.1103/PhysRevX.6.031016</a>"},"day":"03","publisher":"American Physical Society","_id":"100","date_updated":"2021-01-12T06:47:33Z","oa":1,"language":[{"iso":"eng"}],"volume":6,"date_created":"2018-12-11T11:44:37Z","abstract":[{"text":"We introduce a scheme for preparation, manipulation, and read out of Majorana zero modes in semiconducting wires with mesoscopic superconducting islands. Our approach synthesizes recent advances in materials growth with tools commonly used in quantum-dot experiments, including gate control of tunnel barriers and Coulomb effects, charge sensing, and charge pumping. We outline a sequence of milestones interpolating between zero-mode detection and quantum computing that includes (1) detection of fusion rules for non-Abelian anyons using either proximal charge sensors or pumped current, (2) validation of a prototype topological qubit, and (3) demonstration of non-Abelian statistics by braiding in a branched geometry. The first two milestones require only a single wire with two islands, and additionally enable sensitive measurements of the system\\'s excitation gap, quasiparticle poisoning rates, residual Majorana zero-mode splittings, and topological-qubit coherence times. These pre-braiding experiments can be adapted to other manipulation and read out schemes as well.","lang":"eng"}],"issue":"3","file_date_updated":"2019-05-15T14:12:31Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7954","type":"journal_article","status":"public","title":"Milestones toward Majorana-based quantum computing","quality_controlled":"1","article_number":"031016","month":"08","intvolume":"         6","author":[{"last_name":"Aasen","first_name":"David","full_name":"Aasen, David"},{"full_name":"Hell, Michael","first_name":"Michael","last_name":"Hell"},{"last_name":"Mishmash","first_name":"Ryan","full_name":"Mishmash, Ryan"},{"full_name":"Higginbotham, Andrew P","first_name":"Andrew P","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Danon","full_name":"Danon, Jeroen","first_name":"Jeroen"},{"full_name":"Leijnse, Martin","first_name":"Martin","last_name":"Leijnse"},{"last_name":"Jespersen","full_name":"Jespersen, Thomas","first_name":"Thomas"},{"last_name":"Folk","full_name":"Folk, Joshua","first_name":"Joshua"},{"first_name":"Charles","full_name":"Marcs, Charles","last_name":"Marcs"},{"last_name":"Flensberg","first_name":"Karsten","full_name":"Flensberg, Karsten"},{"full_name":"Alicea, Jason","first_name":"Jason","last_name":"Alicea"}],"extern":"1","publication":"Physical Review X","date_published":"2016-08-03T00:00:00Z","acknowledgement":"We acknowledge support from Microsoft Research, the National Science Foundation through Grant No. DMR-1341822 (J. A.); the Alfred P. Sloan Foundation (J. A.); the Caltech Institute for Quantum Information and Matter, an NSF Physics Frontiers Center with support of the Gordon and Betty Moore Foundation through Grant No. GBMF1250; the Walter Burke Institute for Theoretical Physics at Caltech; the NSERC PGSD program (D. A.); the Crafoord Foundation (M. L. and M. H.) and the Swedish Research Council (M. L.); The Danish National Research Foundation, and the Villum Foundation (C. M.); The Danish Council for Independent Research/Natural Sciences, and Danmarks Nationalbank (J. F.). Part of this work was performed at the Aspen Center for Physics, which is supported by National Science Foundation Grant No. PHY-1066293 (R. V. M.).","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","has_accepted_license":"1","file":[{"content_type":"application/pdf","date_updated":"2019-05-15T14:12:31Z","file_id":"6458","relation":"main_file","success":1,"access_level":"open_access","file_name":"2016_PhysRevX_Aasen.pdf","date_created":"2019-05-15T14:12:31Z","creator":"kschuh","file_size":2142676}],"doi":"10.1103/PhysRevX.6.031016","year":"2016","ddc":["530"]},{"_id":"101","publisher":"Nature Publishing Group","day":"10","citation":{"short":"S.M. Albrecht, A.P. Higginbotham, T. Jespersen, M. Madsen, F. Kuemmeth, J. Nygård, P. Krogstrup, C. Marcus, Nature 531 (2016) 206–209.","apa":"Albrecht, S. M., Higginbotham, A. P., Jespersen, T., Madsen, M., Kuemmeth, F., Nygård, J., … Marcus, C. (2016). Exponential protection of zero modes in Majorana islands. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature17162\">https://doi.org/10.1038/nature17162</a>","ama":"Albrecht SM, Higginbotham AP, Jespersen T, et al. Exponential protection of zero modes in Majorana islands. <i>Nature</i>. 2016;531(7593):206-209. doi:<a href=\"https://doi.org/10.1038/nature17162\">10.1038/nature17162</a>","mla":"Albrecht, S. M., et al. “Exponential Protection of Zero Modes in Majorana Islands.” <i>Nature</i>, vol. 531, no. 7593, Nature Publishing Group, 2016, pp. 206–09, doi:<a href=\"https://doi.org/10.1038/nature17162\">10.1038/nature17162</a>.","chicago":"Albrecht, S M, Andrew P Higginbotham, Thomas Jespersen, Morten Madsen, Ferdinand Kuemmeth, Jesper Nygård, Peter Krogstrup, and Charles Marcus. “Exponential Protection of Zero Modes in Majorana Islands.” <i>Nature</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nature17162\">https://doi.org/10.1038/nature17162</a>.","ista":"Albrecht SM, Higginbotham AP, Jespersen T, Madsen M, Kuemmeth F, Nygård J, Krogstrup P, Marcus C. 2016. Exponential protection of zero modes in Majorana islands. Nature. 531(7593), 206–209.","ieee":"S. M. Albrecht <i>et al.</i>, “Exponential protection of zero modes in Majorana islands,” <i>Nature</i>, vol. 531, no. 7593. Nature Publishing Group, pp. 206–209, 2016."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.03217"}],"date_updated":"2021-01-12T06:47:37Z","volume":531,"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."}],"date_created":"2018-12-11T11:44:38Z","language":[{"iso":"eng"}],"issue":"7593","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"206 - 209","title":"Exponential protection of zero modes in Majorana islands","status":"public","type":"journal_article","publist_id":"7953","quality_controlled":"1","extern":"1","month":"03","intvolume":"       531","author":[{"first_name":"S M","full_name":"Albrecht, S M","last_name":"Albrecht"},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","first_name":"Andrew P","full_name":"Higginbotham, Andrew P"},{"last_name":"Jespersen","full_name":"Jespersen, Thomas","first_name":"Thomas"},{"full_name":"Madsen, Morten","first_name":"Morten","last_name":"Madsen"},{"last_name":"Kuemmeth","full_name":"Kuemmeth, Ferdinand","first_name":"Ferdinand"},{"last_name":"Nygård","first_name":"Jesper","full_name":"Nygård, Jesper"},{"last_name":"Krogstrup","full_name":"Krogstrup, Peter","first_name":"Peter"},{"last_name":"Marcus","full_name":"Marcus, Charles","first_name":"Charles"}],"date_published":"2016-03-10T00:00:00Z","external_id":{"arxiv":["1603.03217"]},"publication":"Nature","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.","arxiv":1,"oa_version":"Submitted Version","publication_status":"published","year":"2016","doi":"10.1038/nature17162"},{"external_id":{"arxiv":["1601.07908"]},"publication":"Physical Review B","date_published":"2016-06-08T00:00:00Z","arxiv":1,"quality_controlled":"1","article_number":"245404","month":"06","intvolume":"        93","author":[{"full_name":"Mishmash, Ryan","first_name":"Ryan","last_name":"Mishmash"},{"last_name":"Aasen","full_name":"Aasen, David","first_name":"David"},{"last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P"},{"full_name":"Alicea, Jason","first_name":"Jason","last_name":"Alicea"}],"extern":"1","doi":"10.1103/PhysRevB.93.245404","year":"2016","oa_version":"Preprint","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.07908"}],"date_updated":"2021-01-12T06:47:42Z","oa":1,"language":[{"iso":"eng"}],"volume":93,"date_created":"2018-12-11T11:44:38Z","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"}],"citation":{"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.","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>.","ista":"Mishmash R, Aasen D, Higginbotham AP, Alicea J. 2016. Approaching a topological phase transition in Majorana nanowires. Physical Review B. 93(24), 245404.","mla":"Mishmash, Ryan, et al. “Approaching a Topological Phase Transition in Majorana Nanowires.” <i>Physical Review B</i>, vol. 93, no. 24, 245404, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevB.93.245404\">10.1103/PhysRevB.93.245404</a>.","short":"R. Mishmash, D. Aasen, A.P. Higginbotham, J. Alicea, Physical Review B 93 (2016).","ama":"Mishmash R, Aasen D, Higginbotham AP, Alicea J. Approaching a topological phase transition in Majorana nanowires. <i>Physical Review B</i>. 2016;93(24). doi:<a href=\"https://doi.org/10.1103/PhysRevB.93.245404\">10.1103/PhysRevB.93.245404</a>","apa":"Mishmash, R., Aasen, D., Higginbotham, A. P., &#38; Alicea, J. (2016). Approaching a topological phase transition in Majorana nanowires. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.93.245404\">https://doi.org/10.1103/PhysRevB.93.245404</a>"},"day":"08","_id":"102","publisher":"American Physical Society","type":"journal_article","publist_id":"7952","status":"public","title":"Approaching a topological phase transition in Majorana nanowires","issue":"24","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","title":"Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation","status":"public","scopus_import":"1","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"issue":"21","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_type":"original","date_updated":"2021-11-29T10:33:11Z","main_file_link":[{"url":"https://arxiv.org/abs/1610.02320","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"date_created":"2021-11-29T10:01:57Z","volume":145,"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"}],"keyword":["physical and theoretical chemistry","general physics and astronomy"],"citation":{"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.","mla":"Šarić, Anđela, et al. “Kinetics of Spontaneous Filament Nucleation via Oligomers: Insights from Theory and Simulation.” <i>The Journal of Chemical Physics</i>, vol. 145, no. 21, 211926, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1063/1.4965040\">10.1063/1.4965040</a>.","chicago":"Šarić, Anđela, Thomas C. T. Michaels, Alessio Zaccone, Tuomas P. J. Knowles, and Daan Frenkel. “Kinetics of Spontaneous Filament Nucleation via Oligomers: Insights from Theory and Simulation.” <i>The Journal of Chemical Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1063/1.4965040\">https://doi.org/10.1063/1.4965040</a>.","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.","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>","short":"A. Šarić, T.C.T. Michaels, A. Zaccone, T.P.J. Knowles, D. Frenkel, The Journal of Chemical Physics 145 (2016)."},"day":"01","_id":"10376","publisher":"American Institute of Physics","doi":"10.1063/1.4965040","year":"2016","oa_version":"Preprint","article_processing_charge":"No","publication_status":"published","publication":"The Journal of Chemical Physics","external_id":{"pmid":["28799382"],"arxiv":["1610.02320"]},"date_published":"2016-12-01T00:00:00Z","pmid":1,"arxiv":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.).","quality_controlled":"1","article_number":"211926","month":"12","author":[{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"last_name":"Michaels","full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T."},{"last_name":"Zaccone","first_name":"Alessio","full_name":"Zaccone, Alessio"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."},{"full_name":"Frenkel, Daan","first_name":"Daan","last_name":"Frenkel"}],"intvolume":"       145","extern":"1"},{"citation":{"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>.","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.","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>","short":"C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, D.J. Kraft, Scientific Reports 6 (2016)."},"day":"13","publisher":"Springer Nature","_id":"10377","keyword":["multidisciplinary"],"language":[{"iso":"eng"}],"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"}],"volume":6,"date_created":"2021-11-29T10:34:08Z","date_updated":"2021-11-29T11:08:15Z","main_file_link":[{"url":"https://www.nature.com/articles/srep32825","open_access":"1"}],"article_type":"original","oa":1,"file_date_updated":"2021-11-29T10:50:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"1","type":"journal_article","publication_identifier":{"issn":["2045-2322"]},"status":"public","title":"Lipid membrane-mediated attraction between curvature inducing objects","scopus_import":"1","month":"09","author":[{"last_name":"van der Wel","first_name":"Casper","full_name":"van der Wel, Casper"},{"last_name":"Vahid","first_name":"Afshin","full_name":"Vahid, Afshin"},{"full_name":"Šarić, Anđela","first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Timon","full_name":"Idema, Timon","last_name":"Idema"},{"last_name":"Heinrich","full_name":"Heinrich, Doris","first_name":"Doris"},{"last_name":"Kraft","full_name":"Kraft, Daniela J.","first_name":"Daniela J."}],"intvolume":"         6","extern":"1","quality_controlled":"1","article_number":"32825","pmid":1,"arxiv":1,"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.","external_id":{"pmid":["27618764"],"arxiv":["1603.04644"]},"publication":"Scientific Reports","date_published":"2016-09-13T00:00:00Z","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","oa_version":"Published Version","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/srep37382"}]},"ddc":["540"],"file":[{"checksum":"d6cf16dd511e15726b001e7cc287cf1d","file_size":1598289,"access_level":"open_access","creator":"cchlebak","file_name":"2016_SciRep_vanderWel.pdf","date_created":"2021-11-29T10:50:00Z","file_id":"10379","date_updated":"2021-11-29T10:50:00Z","content_type":"application/pdf","success":1,"relation":"main_file"}],"has_accepted_license":"1","doi":"10.1038/srep32825","year":"2016"},{"type":"journal_article","page":"874-880","status":"public","title":"Physical determinants of the self-replication of protein fibrils","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"scopus_import":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"9","language":[{"iso":"eng"}],"abstract":[{"text":"The ability of biological molecules to replicate themselves is the foundation of life, requiring a complex cellular machinery. However, a range of aberrant processes involve the self-replication of pathological protein structures without any additional assistance. One example is the autocatalytic generation of pathological protein aggregates, including amyloid fibrils, involved in neurodegenerative disorders. Here, we use computer simulations to identify the necessary requirements for the self-replication of fibrillar assemblies of proteins. We establish that a key physical determinant for this process is the affinity of proteins for the surfaces of fibrils. We find that self-replication can take place only in a very narrow regime of inter-protein interactions, implying a high level of sensitivity to system parameters and experimental conditions. We then compare our theoretical predictions with kinetic and biosensor measurements of fibrils formed from the Aβ peptide associated with Alzheimer’s disease. Our results show a quantitative connection between the kinetics of self-replication and the surface coverage of fibrils by monomeric proteins. These findings reveal the fundamental physical requirements for the formation of supra-molecular structures able to replicate themselves, and shed light on mechanisms in play in the proliferation of protein aggregates in nature.","lang":"eng"}],"volume":12,"date_created":"2021-11-29T10:36:11Z","main_file_link":[{"url":"https://discovery.ucl.ac.uk/id/eprint/1517406/","open_access":"1"}],"article_type":"original","date_updated":"2021-11-29T11:07:25Z","oa":1,"citation":{"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>","short":"A. Šarić, A.K. Buell, G. Meisl, T.C.T. Michaels, C.M. Dobson, S. Linse, T.P.J. Knowles, D. Frenkel, Nature Physics 12 (2016) 874–880.","chicago":"Šarić, Anđela, Alexander K. Buell, Georg Meisl, Thomas C. T. Michaels, Christopher M. Dobson, Sara Linse, Tuomas P. J. Knowles, and Daan Frenkel. “Physical Determinants of the Self-Replication of Protein Fibrils.” <i>Nature Physics</i>. Springer Nature, 2016. <a href=\"https://doi.org/10.1038/nphys3828\">https://doi.org/10.1038/nphys3828</a>.","ista":"Šarić A, Buell AK, Meisl G, Michaels TCT, Dobson CM, Linse S, Knowles TPJ, Frenkel D. 2016. Physical determinants of the self-replication of protein fibrils. Nature Physics. 12(9), 874–880.","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."},"publisher":"Springer Nature","_id":"10378","day":"18","keyword":["general physics and astronomy"],"doi":"10.1038/nphys3828","year":"2016","article_processing_charge":"No","publication_status":"published","oa_version":"Preprint","pmid":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.).","external_id":{"pmid":["31031819"]},"publication":"Nature Physics","date_published":"2016-07-18T00:00:00Z","author":[{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić"},{"last_name":"Buell","full_name":"Buell, Alexander K.","first_name":"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"},{"last_name":"Dobson","first_name":"Christopher M.","full_name":"Dobson, Christopher M."},{"last_name":"Linse","full_name":"Linse, Sara","first_name":"Sara"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."},{"first_name":"Daan","full_name":"Frenkel, Daan","last_name":"Frenkel"}],"intvolume":"        12","month":"07","extern":"1","quality_controlled":"1"},{"language":[{"iso":"eng"}],"volume":144,"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"}],"date_created":"2021-11-29T11:08:52Z","date_updated":"2021-11-29T13:09:08Z","main_file_link":[{"url":"https://arxiv.org/abs/1602.02734","open_access":"1"}],"article_type":"original","oa":1,"citation":{"short":"P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, D. Frenkel, The Journal of Chemical Physics 144 (2016).","apa":"Wirnsberger, P., Fijan, D., Šarić, A., Neumann, M., Dellago, C., &#38; Frenkel, D. (2016). Non-equilibrium simulations of thermally induced electric fields in water. <i>The Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4953036\">https://doi.org/10.1063/1.4953036</a>","ama":"Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. Non-equilibrium simulations of thermally induced electric fields in water. <i>The Journal of Chemical Physics</i>. 2016;144(22). doi:<a href=\"https://doi.org/10.1063/1.4953036\">10.1063/1.4953036</a>","mla":"Wirnsberger, P., et al. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in Water.” <i>The Journal of Chemical Physics</i>, vol. 144, no. 22, 224102, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1063/1.4953036\">10.1063/1.4953036</a>.","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.","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>.","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."},"publisher":"American Institute of Physics","_id":"10380","day":"10","keyword":["physical and theoretical chemistry","general physics and astronomy"],"type":"journal_article","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"scopus_import":"1","title":"Non-equilibrium simulations of thermally induced electric fields in water","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"22","pmid":1,"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).","arxiv":1,"publication":"The Journal of Chemical Physics","external_id":{"pmid":["27305991"],"arxiv":["1602.02734"]},"date_published":"2016-06-10T00:00:00Z","intvolume":"       144","author":[{"last_name":"Wirnsberger","full_name":"Wirnsberger, P.","first_name":"P."},{"full_name":"Fijan, D.","first_name":"D.","last_name":"Fijan"},{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","orcid":"0000-0002-7854-2139"},{"first_name":"M.","full_name":"Neumann, M.","last_name":"Neumann"},{"last_name":"Dellago","first_name":"C.","full_name":"Dellago, C."},{"full_name":"Frenkel, D.","first_name":"D.","last_name":"Frenkel"}],"month":"06","extern":"1","quality_controlled":"1","article_number":"224102","doi":"10.1063/1.4953036","year":"2016","article_processing_charge":"No","publication_status":"published","oa_version":"Preprint"},{"intvolume":"        12","author":[{"last_name":"Bachmann","first_name":"Stephan Jan","full_name":"Bachmann, Stephan Jan"},{"last_name":"Kotar","first_name":"Jurij","full_name":"Kotar, Jurij"},{"last_name":"Parolini","first_name":"Lucia","full_name":"Parolini, Lucia"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela","orcid":"0000-0002-7854-2139"},{"last_name":"Cicuta","full_name":"Cicuta, Pietro","first_name":"Pietro"},{"first_name":"Lorenzo","full_name":"Di Michele, Lorenzo","last_name":"Di Michele"},{"first_name":"Bortolo Matteo","full_name":"Mognetti, Bortolo Matteo","last_name":"Mognetti"}],"month":"08","extern":"1","quality_controlled":"1","pmid":1,"arxiv":1,"external_id":{"pmid":["27722701"],"arxiv":["1608.05788"]},"publication":"Soft Matter","date_published":"2016-08-19T00:00:00Z","article_processing_charge":"No","publication_status":"published","oa_version":"Preprint","doi":"10.1039/c6sm01515h","year":"2016","citation":{"apa":"Bachmann, S. J., Kotar, J., Parolini, L., Šarić, A., Cicuta, P., Di Michele, L., &#38; Mognetti, B. M. (2016). Melting transition in lipid vesicles functionalised by mobile DNA linkers. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c6sm01515h\">https://doi.org/10.1039/c6sm01515h</a>","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>","short":"S.J. Bachmann, J. Kotar, L. Parolini, A. Šarić, P. Cicuta, L. Di Michele, B.M. Mognetti, Soft Matter 12 (2016) 7804–7817.","mla":"Bachmann, Stephan Jan, et al. “Melting Transition in Lipid Vesicles Functionalised by Mobile DNA Linkers.” <i>Soft Matter</i>, vol. 12, no. 37, Royal Society of Chemistry, 2016, pp. 7804–17, doi:<a href=\"https://doi.org/10.1039/c6sm01515h\">10.1039/c6sm01515h</a>.","ista":"Bachmann SJ, Kotar J, Parolini L, Šarić A, Cicuta P, Di Michele L, Mognetti BM. 2016. Melting transition in lipid vesicles functionalised by mobile DNA linkers. Soft Matter. 12(37), 7804–7817.","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>.","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."},"day":"19","_id":"10381","publisher":"Royal Society of Chemistry","keyword":["condensed matter physics","general chemistry"],"language":[{"iso":"eng"}],"date_created":"2021-11-29T11:09:55Z","volume":12,"abstract":[{"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.","lang":"eng"}],"date_updated":"2021-11-29T13:09:00Z","article_type":"original","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.05788"}],"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"37","type":"journal_article","title":"Melting transition in lipid vesicles functionalised by mobile DNA linkers","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"scopus_import":"1","status":"public","page":"7804-7817"},{"citation":{"ama":"Chatterjee K, Dvorák W, Henzinger MH, 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>","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., &#38; Loitzenbauer, V. (2016). Conditionally optimal algorithms for generalized Büchi Games (Vol. 58). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), 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>","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Conditionally optimal algorithms for generalized Büchi Games,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Krakow, Poland, 2016, vol. 58.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2016. Conditionally optimal algorithms for generalized Büchi Games. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 58, 25.","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 H 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>."},"day":"01","_id":"1068","pubrep_id":"779","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"alternative_title":["LIPIcs"],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:49:58Z","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,"date_updated":"2025-06-02T08:53:50Z","oa":1,"ec_funded":1,"file_date_updated":"2018-12-12T10:16:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by/3.0/","publist_id":"6317","type":"conference","scopus_import":"1","title":"Conditionally optimal algorithms for generalized Büchi Games","status":"public","intvolume":"        58","month":"08","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Dvorák","first_name":"Wolfgang","full_name":"Dvorák, Wolfgang"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"first_name":"Veronika","full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer"}],"quality_controlled":"1","article_number":"25","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","conference":{"start_date":"2016-08-22","end_date":"2016-08-26","location":"Krakow, Poland","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"date_published":"2016-08-01T00:00:00Z","article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"publication_status":"published","oa_version":"Published Version","project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"ddc":["000","004","006"],"has_accepted_license":"1","file":[{"file_size":632786,"date_updated":"2018-12-12T10:16:02Z","file_id":"5187","content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"system","file_name":"IST-2017-779-v1+1_LIPIcs-MFCS-2016-25.pdf","date_created":"2018-12-12T10:16:02Z"}],"doi":"10.4230/LIPIcs.MFCS.2016.25","year":"2016"},{"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"}],"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","has_accepted_license":"1","file":[{"file_size":521415,"access_level":"open_access","creator":"system","date_created":"2018-12-12T10:16:26Z","file_name":"IST-2017-778-v1+1_LIPIcs-ICALP-2016-100.pdf","date_updated":"2018-12-12T10:16:26Z","file_id":"5213","content_type":"application/pdf","relation":"main_file"}],"doi":"10.4230/LIPIcs.ICALP.2016.100","year":"2016","ddc":["004","006"],"quality_controlled":"1","article_number":"100","author":[{"full_name":"Chonev, Ventsislav K","first_name":"Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Chonev"},{"full_name":"Ouaknine, Joël","first_name":"Joël","last_name":"Ouaknine"},{"last_name":"Worrell","first_name":"James","full_name":"Worrell, James"}],"intvolume":"        55","month":"08","conference":{"location":"Rome, Italy","name":"ICALP: Automata, Languages and Programming","end_date":"2016-07-15","start_date":"2016-07-12"},"date_published":"2016-08-01T00:00:00Z","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).","ec_funded":1,"file_date_updated":"2018-12-12T10:16:26Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6314","type":"conference","status":"public","title":"On the skolem problem for continuous linear dynamical systems","scopus_import":1,"department":[{"_id":"KrCh"}],"alternative_title":["LIPIcs"],"citation":{"short":"V.K. Chonev, J. Ouaknine, J. Worrell, in:, Schloss Dagstuhl- Leibniz-Zentrum fur 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 fur 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 fur Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">https://doi.org/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.","mla":"Chonev, Ventsislav K., et al. <i>On the Skolem Problem for Continuous Linear Dynamical Systems</i>. Vol. 55, 100, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">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 fur Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">https://doi.org/10.4230/LIPIcs.ICALP.2016.100</a>.","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."},"day":"01","_id":"1069","publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik","pubrep_id":"778","date_updated":"2021-01-12T06:48:03Z","oa":1,"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:49:59Z","volume":55,"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","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"oa_version":"Published Version","ddc":["005"],"doi":"10.4230/LIPIcs.ICALP.2016.98","file":[{"file_size":546133,"relation":"main_file","content_type":"application/pdf","date_updated":"2018-12-12T10:08:52Z","file_id":"4714","creator":"system","date_created":"2018-12-12T10:08:52Z","file_name":"IST-2017-812-v1+1_LIPIcs-ICALP-2016-98.pdf","access_level":"open_access"}],"has_accepted_license":"1","year":"2016","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"}],"month":"01","intvolume":"        55","quality_controlled":"1","article_number":"98","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","date_published":"2016-01-01T00:00:00Z","conference":{"name":"ICALP: Automata, Languages and Programming","location":"Rome, Italy","start_date":"2016-07-12","end_date":"2016-07-15"},"file_date_updated":"2018-12-12T10:08:52Z","ec_funded":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6313","type":"conference","status":"public","title":"Computation tree logic for synchronization properties","scopus_import":1,"citation":{"mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Computation Tree Logic for Synchronization Properties</i>. Vol. 55, 98, Schloss Dagstuhl- Leibniz-Zentrum fur 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 fur Informatik, 2016. <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.","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.","short":"K. Chatterjee, L. Doyen, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016.","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 fur Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">https://doi.org/10.4230/LIPIcs.ICALP.2016.98</a>","ama":"Chatterjee K, Doyen L. Computation tree logic for synchronization properties. In: Vol 55. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">10.4230/LIPIcs.ICALP.2016.98</a>"},"publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik","_id":"1070","pubrep_id":"812","day":"01","department":[{"_id":"KrCh"}],"alternative_title":["LIPIcs"],"language":[{"iso":"eng"}],"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. "}],"date_created":"2018-12-11T11:49:59Z","volume":55,"date_updated":"2021-01-12T06:48:03Z","oa":1},{"year":"2016","doi":"10.4230/LIPIcs.ESA.2016.28","file":[{"file_size":579225,"relation":"main_file","content_type":"application/pdf","file_id":"5084","date_updated":"2018-12-12T10:14:31Z","creator":"system","file_name":"IST-2017-777-v1+1_LIPIcs-ESA-2016-28.pdf","date_created":"2018-12-12T10:14:31Z","access_level":"open_access"}],"has_accepted_license":"1","ddc":["004","006"],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"821"}]},"oa_version":"Published Version","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2016-08-01T00:00:00Z","conference":{"start_date":"2016-08-22","end_date":"2016-08-24","location":"Aarhus, Denmark","name":"ESA: European Symposium on Algorithms"},"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).","article_number":"28","quality_controlled":"1","month":"08","intvolume":"        57","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"title":"Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs","scopus_import":1,"status":"public","publist_id":"6312","type":"conference","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2018-12-12T10:14:31Z","ec_funded":1,"oa":1,"date_updated":"2023-09-07T12:01:58Z","volume":57,"abstract":[{"lang":"eng","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. "}],"date_created":"2018-12-11T11:49:59Z","language":[{"iso":"eng"}],"alternative_title":["LIPIcs"],"department":[{"_id":"KrCh"}],"pubrep_id":"777","_id":"1071","publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik","day":"01","citation":{"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 fur Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">https://doi.org/10.4230/LIPIcs.ESA.2016.28</a>","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 fur Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">10.4230/LIPIcs.ESA.2016.28</a>","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Schloss Dagstuhl- Leibniz-Zentrum fur 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.","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 fur Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">https://doi.org/10.4230/LIPIcs.ESA.2016.28</a>.","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 fur Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">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."}},{"oa_version":"Published Version","publication_status":"published","article_processing_charge":"No","year":"2016","article_number":"E25.00007","quality_controlled":"1","extern":"1","month":"03","intvolume":"        61","author":[{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy"},{"last_name":"Naibert","full_name":"Naibert, Tyler","first_name":"Tyler"},{"last_name":"Chua","full_name":"Chua, Victor","first_name":"Victor"},{"first_name":"Raffi","full_name":"Budakian, Raffi","last_name":"Budakian"}],"conference":{"end_date":"2016-03-18","start_date":"2016-03-14","name":"APS: American Physical Society","location":"Baltimore, MD, United States"},"date_published":"2016-03-01T00:00:00Z","publication":"APS March Meeting 2016","issue":"2","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Study of vortex states and dynamics in mesoscopic superconducting samples with MFM","publication_identifier":{"issn":["0003-0503"]},"status":"public","type":"conference","alternative_title":["Bulletin of the American Physical Society"],"day":"01","_id":"10746","publisher":"American Physical Society","citation":{"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.","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.","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.","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.","short":"H. Polshyn, T. Naibert, V. Chua, R. Budakian, in:, APS March Meeting 2016, 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.","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."},"oa":1,"date_updated":"2022-02-08T10:44:06Z","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR16/Session/E25.7"}],"date_created":"2022-02-08T09:55:09Z","volume":61,"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."}],"language":[{"iso":"eng"}]},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"2","publication_identifier":{"issn":["0003-0503"]},"status":"public","title":"Stochastic resonance magnetic force microscopy imaging of Josephson arrays","type":"conference","day":"01","_id":"10747","publisher":"American Physical Society","citation":{"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.","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.","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.","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."},"alternative_title":["Bulletin of the American Physical Society"],"date_created":"2022-02-08T10:10:39Z","volume":61,"abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"oa":1,"date_updated":"2022-02-08T10:43:33Z","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR16/Session/H25.6"}],"publication_status":"published","article_processing_charge":"No","oa_version":"Published Version","year":"2016","extern":"1","intvolume":"        61","author":[{"last_name":"Naibert","first_name":"Tyler","full_name":"Naibert, Tyler"},{"full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn"},{"last_name":"Wolin","first_name":"Brian","full_name":"Wolin, Brian"},{"last_name":"Durkin","full_name":"Durkin, Malcolm","first_name":"Malcolm"},{"last_name":"Garrido Menacho","first_name":"Rita","full_name":"Garrido Menacho, Rita"},{"last_name":"Shem","full_name":"Shem, Ian Mondragon","first_name":"Ian Mondragon"},{"full_name":"Chua, Victor","first_name":"Victor","last_name":"Chua"},{"full_name":"Hughes, Taylor","first_name":"Taylor","last_name":"Hughes"},{"full_name":"Mason, Nadya","first_name":"Nadya","last_name":"Mason"},{"full_name":"Budakian, Raffi","first_name":"Raffi","last_name":"Budakian"}],"month":"03","article_number":"H25.00006","quality_controlled":"1","conference":{"location":"Baltimore, MD, United States","name":"APS: American Physical Society","start_date":"2016-03-14","end_date":"2016-03-18"},"date_published":"2016-03-01T00:00:00Z","publication":"APS March Meeting 2016"},{"date_published":"2016-07-19T00:00:00Z","publication":"Cell Discovery","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.","article_number":"16018","quality_controlled":"1","intvolume":"         2","month":"07","author":[{"first_name":"Łukasz","full_name":"Łangowski, Łukasz","last_name":"Łangowski"},{"orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T","last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang","first_name":"Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"last_name":"Naramoto","full_name":"Naramoto, Satoshi","first_name":"Satoshi"},{"last_name":"Tanaka","first_name":"Hirokazu","full_name":"Tanaka, Hirokazu"},{"first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"year":"2016","doi":"10.1038/celldisc.2016.18","has_accepted_license":"1","file":[{"relation":"main_file","content_type":"application/pdf","file_id":"5017","date_updated":"2018-12-12T10:13:33Z","creator":"system","date_created":"2018-12-12T10:13:33Z","file_name":"IST-2017-757-v1+1_celldisc201618.pdf","access_level":"open_access","file_size":5261671}],"ddc":["580"],"oa_version":"Published Version","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"date_updated":"2021-01-12T06:48:08Z","date_created":"2018-12-11T11:50:02Z","volume":2,"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."}],"language":[{"iso":"eng"}],"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publisher":"Nature Publishing Group","_id":"1081","pubrep_id":"757","day":"19","citation":{"short":"Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J. Friml, Cell Discovery 2 (2016).","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.","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.","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>."},"title":"Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells","status":"public","scopus_import":1,"publist_id":"6299","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2018-12-12T10:13:33Z","ec_funded":1},{"quality_controlled":"1","intvolume":"        43","month":"03","author":[{"last_name":"Rubel","full_name":"Rubel, Paul","first_name":"Paul"},{"first_name":"Danilo","full_name":"Pani, Danilo","last_name":"Pani"},{"first_name":"Alois","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl"},{"full_name":"Fayn, Jocelyne","first_name":"Jocelyne","last_name":"Fayn"},{"first_name":"Fabio","full_name":"Badilini, Fabio","last_name":"Badilini"},{"last_name":"Macfarlane","full_name":"Macfarlane, Peter","first_name":"Peter"},{"last_name":"Varri","full_name":"Varri, Alpo","first_name":"Alpo"}],"conference":{"end_date":"2016-09-14","start_date":"2016-09-11","name":"CinC: Computing in Cardiology","location":"Vancouver, Canada"},"date_published":"2016-03-01T00:00:00Z","publication":"2016 Computing in Cardiology Conference","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.","oa_version":"Published Version","publication_status":"published","article_processing_charge":"No","year":"2016","doi":"10.22489/cinc.2016.090-500","department":[{"_id":"CampIT"}],"day":"01","publisher":"Computing in Cardiology","_id":"10810","citation":{"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>.","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.","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>.","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.","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>","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."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.22489/cinc.2016.090-500","open_access":"1"}],"date_updated":"2022-03-04T07:34:45Z","volume":43,"abstract":[{"lang":"eng","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. "}],"date_created":"2022-03-03T10:43:10Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography","publication_identifier":{"issn":["2325-887X"]},"scopus_import":"1","status":"public","page":"309-312","type":"conference"},{"type":"journal_article","scopus_import":"1","status":"public","title":"Mechanism for DNA transposons to generate introns on genomic scales","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"page":"533-536","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"7626","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The discovery of introns four decades ago was one of the most unexpected findings in molecular biology. Introns are sequences interrupting genes that must be removed as part of messenger RNA production. Genome sequencing projects have shown that most eukaryotic genes contain at least one intron, and frequently many. Comparison of these genomes reveals a history of long evolutionary periods during which few introns were gained, punctuated by episodes of rapid, extensive gain. However, although several detailed mechanisms for such episodic intron generation have been proposed, none has been empirically supported on a genomic scale. Here we show how short, non-autonomous DNA transposons independently generated hundreds to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte Aureococcus anophagefferens. Each transposon carries one splice site. The other splice site is co-opted from the gene sequence that is duplicated upon transposon insertion, allowing perfect splicing out of the RNA. The distributions of sequences that can be co-opted are biased with respect to codons, and phasing of transposon-generated introns is similarly biased. These transposons insert between pre-existing nucleosomes, so that multiple nearby insertions generate nucleosome-sized intervening segments. Thus, transposon insertion and sequence co-option may explain the intron phase biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall, the two independent examples of proliferating elements illustrate a general DNA transposon mechanism that can plausibly account for episodes of rapid, extensive intron gain during eukaryotic evolution."}],"volume":538,"date_created":"2021-06-04T11:34:55Z","date_updated":"2021-12-14T07:55:30Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/","open_access":"1"}],"article_type":"letter_note","oa":1,"citation":{"short":"J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.","apa":"Huff, J. T., Zilberman, D., &#38; Roy, S. W. (2016). Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. Springer Nature . <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>","ama":"Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. 2016;538(7626):533-536. doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>","mla":"Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>, vol. 538, no. 7626, Springer Nature , 2016, pp. 533–36, doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>.","ista":"Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate introns on genomic scales. Nature. 538(7626), 533–536.","chicago":"Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>. Springer Nature , 2016. <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>.","ieee":"J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to generate introns on genomic scales,” <i>Nature</i>, vol. 538, no. 7626. Springer Nature , pp. 533–536, 2016."},"day":"27","_id":"9456","publisher":"Springer Nature ","department":[{"_id":"DaZi"}],"doi":"10.1038/nature20110","year":"2016","article_processing_charge":"No","publication_status":"published","oa_version":"Submitted Version","pmid":1,"publication":"Nature","external_id":{"pmid":["27760113"]},"date_published":"2016-10-27T00:00:00Z","month":"10","author":[{"full_name":"Huff, Jason T.","first_name":"Jason T.","last_name":"Huff"},{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","full_name":"Zilberman, Daniel"},{"full_name":"Roy, Scott W.","first_name":"Scott W.","last_name":"Roy"}],"intvolume":"       538","extern":"1","quality_controlled":"1"},{"publication_status":"published","article_processing_charge":"No","oa_version":"Published Version","year":"2016","doi":"10.1073/pnas.1619074114","extern":"1","month":"12","intvolume":"       113","author":[{"last_name":"Hsieh","full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung"},{"full_name":"He, Shengbo","first_name":"Shengbo","last_name":"He"},{"first_name":"Toby","full_name":"Buttress, Toby","last_name":"Buttress"},{"last_name":"Gao","first_name":"Hongbo","full_name":"Gao, Hongbo"},{"last_name":"Couchman","full_name":"Couchman, Matthew","first_name":"Matthew"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi"}],"quality_controlled":"1","pmid":1,"date_published":"2016-12-27T00:00:00Z","external_id":{"pmid":["27956643"]},"publication":"Proceedings of the National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"52","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"status":"public","title":"Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues","scopus_import":"1","page":"15132-15137","type":"journal_article","day":"27","_id":"9473","publisher":"National Academy of Sciences","citation":{"short":"P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman, X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.","apa":"Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L., … Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>","ama":"Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15132-15137. doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>","ista":"Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 113(52), 15132–15137.","mla":"Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15132–37, doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>.","chicago":"Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman, Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>.","ieee":"P.-H. Hsieh <i>et al.</i>, “Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15132–15137, 2016."},"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"abstract":[{"text":"Cytosine DNA methylation regulates the expression of eukaryotic genes and transposons. Methylation is copied by methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Transgenerational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of transgenerational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases. We find that DNA methylation dependency on these enzymes is similar in sperm, vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin in vegetative cells, likely reflecting transcription of heterochromatic transposons in this cell type. We also show that lack of histone H1, which elevates heterochromatic DNA methylation in somatic tissues, does not have this effect in pollen. Instead, levels of CG methylation in wild-type sperm and vegetative cells, as well as in wild-type microspores from which both pollen cell types originate, are substantially higher than in wild-type somatic tissues and similar to those of H1-depleted roots. Our results demonstrate that the mechanisms of methylation maintenance are similar between pollen and somatic cells, but the efficiency of CG methylation is higher in pollen, allowing methylation patterns to be accurately inherited across generations.","lang":"eng"}],"date_created":"2021-06-07T06:21:39Z","volume":113,"language":[{"iso":"eng"}],"oa":1,"date_updated":"2023-05-08T11:00:40Z","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1619074114"}]},{"citation":{"ieee":"K. Park <i>et al.</i>, “DNA demethylation is initiated in the central cells of Arabidopsis and rice,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.","ista":"Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 113(52), 15138–15143.","mla":"Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>.","chicago":"Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun, Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>.","short":"K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman, R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy of Sciences 113 (2016) 15138–15143.","ama":"Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15138-15143. doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>","apa":"Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten, S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>"},"day":"27","publisher":"National Academy of Sciences","_id":"9477","keyword":["Multidisciplinary"],"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Cytosine methylation is a DNA modification with important regulatory functions in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive DNA demethylation, which is required for proper gene expression in the endosperm, a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm cell carried in the pollen and a female central cell. Endosperm DNA demethylation is observed specifically on the chromosomes inherited from the central cell in Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase in Arabidopsis. DEMETER is expressed in the central cell before fertilization, suggesting that endosperm demethylation patterns are inherited from the central cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed to contribute to central cell demethylation. However, with the exception of three maize genes, central cell DNA methylation has not been directly measured, leaving the origin and mechanism of endosperm demethylation uncertain. Here, we report genome-wide analysis of DNA methylation in the central cells of Arabidopsis and rice—species that diverged 150 million years ago—as well as in rice egg cells. We find that DNA demethylation in both species is initiated in central cells, which requires DEMETER in Arabidopsis. However, we do not observe a global reduction of CG methylation that would be indicative of lowered MET1 activity; on the contrary, CG methylation efficiency is elevated in female gametes compared with nonsexual tissues. Our results demonstrate that locus-specific, active DNA demethylation in the central cell is the origin of maternal chromosome hypomethylation in the endosperm."}],"volume":113,"date_created":"2021-06-07T07:10:59Z","date_updated":"2023-05-08T11:00:07Z","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1619047114","open_access":"1"}],"article_type":"original","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"52","type":"journal_article","title":"DNA demethylation is initiated in the central cells of Arabidopsis and rice","scopus_import":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"status":"public","page":"15138-15143","author":[{"last_name":"Park","full_name":"Park, Kyunghyuk","first_name":"Kyunghyuk"},{"last_name":"Kim","full_name":"Kim, M. Yvonne","first_name":"M. Yvonne"},{"full_name":"Vickers, Martin","first_name":"Martin","last_name":"Vickers"},{"last_name":"Park","first_name":"Jin-Sup","full_name":"Park, Jin-Sup"},{"last_name":"Hyun","first_name":"Youbong","full_name":"Hyun, Youbong"},{"full_name":"Okamoto, Takashi","first_name":"Takashi","last_name":"Okamoto"},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234"},{"first_name":"Yeonhee","full_name":"Choi, Yeonhee","last_name":"Choi"},{"last_name":"Scholten","full_name":"Scholten, Stefan","first_name":"Stefan"}],"intvolume":"       113","month":"12","extern":"1","quality_controlled":"1","pmid":1,"publication":"Proceedings of the National Academy of Sciences","external_id":{"pmid":["27956642"]},"date_published":"2016-12-27T00:00:00Z","article_processing_charge":"No","publication_status":"published","oa_version":"Published Version","doi":"10.1073/pnas.1619047114","year":"2016"}]