[{"arxiv":1,"author":[{"first_name":"Shrinivas","full_name":"Kudekar, Shrinivas","last_name":"Kudekar"},{"last_name":"Kumar","full_name":"Kumar, Santhosh","first_name":"Santhosh"},{"full_name":"Mondelli, Marco","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","orcid":"0000-0002-3242-7020"},{"last_name":"Pfister","full_name":"Pfister, Henry D.","first_name":"Henry D."},{"last_name":"Urbankez","first_name":"Rudiger","full_name":"Urbankez, Rudiger"}],"publication_status":"published","month":"08","conference":{"end_date":"2016-07-15","location":"Barcelona, Spain","start_date":"2016-07-10","name":"ISIT: International Symposium on Information Theory"},"abstract":[{"lang":"eng","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"11","oa_version":"Preprint","external_id":{"arxiv":["1601.06048"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.06048"}],"type":"conference","date_published":"2016-08-11T00:00:00Z","status":"public","publisher":"IEEE","quality_controlled":"1","extern":"1","page":"1755-1759","year":"2016","date_updated":"2021-01-12T08:08:44Z","oa":1,"title":"Comparing the bit-MAP and block-MAP decoding thresholds of Reed-Muller codes on BMS channels","citation":{"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.","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>.","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>.","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.","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.","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>"},"date_created":"2019-07-31T06:36:16Z","_id":"6733","language":[{"iso":"eng"}],"publication":"2016 IEEE International Symposium on Information Theory ","doi":"10.1109/isit.2016.7541600"},{"month":"03","conference":{"location":"Zurich, Switzerland","end_date":"2016-03-04","name":"IZS: International Zurich Seminar on Communications","start_date":"2016-03-02"},"abstract":[{"text":"We describe a new method to compare the bit-MAP and block-MAP decoding thresholds of Reed-Muller (RM) codes for transmission over a binary memoryless symmetric channel. The question whether RM codes are capacity-achieving is a long-standing open problem in coding theory and it has recently been answered in the affirmative for transmission over\r\nerasure channels. 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. A natural question is what happens under block-MAP decoding. If the minimum distance of the code family is close to linear (e.g., of order N/ log(N)), then one can combine an upper bound on the bit-MAP error probability with a lower bound on the minimum distance to show that the code family is also capacity-achieving under block-MAP decoding. This strategy is successful for BCH codes. Unfortunately, the minimum distance of RM codes scales only as √N, which does not suffice to obtain the desired result. Then, one can exploit further symmetries of RM codes to show that the bit-MAP threshold is sharp enough so that the block erasure probability also tends to 0. However, this technique relies heavily on the fact that the transmission is over an erasure channel.\r\nWe 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\r\nerror probability also converges to 0. This technique applies to the 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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"None","author":[{"full_name":"Mondelli, Marco","first_name":"Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"last_name":"Kudekar","full_name":"Kudekar, Shrinivas","first_name":"Shrinivas"},{"full_name":"Kumar, Santosh","first_name":"Santosh","last_name":"Kumar"},{"full_name":"Pfister, Henry D.","first_name":"Henry D.","last_name":"Pfister"},{"first_name":"Eren","full_name":"Şaşoğlu, Eren","last_name":"Şaşoğlu"},{"last_name":"Urbanke","first_name":"Rüdiger","full_name":"Urbanke, Rüdiger"}],"publication_status":"published","status":"public","type":"conference","date_published":"2016-03-01T00:00:00Z","publisher":"ETH Zürich","quality_controlled":"1","page":"50","extern":"1","year":"2016","date_updated":"2021-01-12T08:08:57Z","date_created":"2019-08-05T12:43:48Z","citation":{"chicago":"Mondelli, Marco, Shrinivas Kudekar, Santosh Kumar, Henry D. Pfister, Eren Şaşoğlu, and Rüdiger Urbanke. “Reed-Muller Codes: Thresholds and Weight Distribution.” In <i>24th International Zurich Seminar on Communications</i>, 50. ETH Zürich, 2016. <a href=\"https://doi.org/10.3929/ETHZ-A-010646484\">https://doi.org/10.3929/ETHZ-A-010646484</a>.","mla":"Mondelli, Marco, et al. “Reed-Muller Codes: Thresholds and Weight Distribution.” <i>24th International Zurich Seminar on Communications</i>, ETH Zürich, 2016, p. 50, doi:<a href=\"https://doi.org/10.3929/ETHZ-A-010646484\">10.3929/ETHZ-A-010646484</a>.","ista":"Mondelli M, Kudekar S, Kumar S, Pfister HD, Şaşoğlu E, Urbanke R. 2016. Reed-Muller codes: Thresholds and weight distribution. 24th International Zurich Seminar on Communications. IZS: International Zurich Seminar on Communications, 50.","ieee":"M. Mondelli, S. Kudekar, S. Kumar, H. D. Pfister, E. Şaşoğlu, and R. Urbanke, “Reed-Muller codes: Thresholds and weight distribution,” in <i>24th International Zurich Seminar on Communications</i>, Zurich, Switzerland, 2016, p. 50.","ama":"Mondelli M, Kudekar S, Kumar S, Pfister HD, Şaşoğlu E, Urbanke R. Reed-Muller codes: Thresholds and weight distribution. In: <i>24th International Zurich Seminar on Communications</i>. ETH Zürich; 2016:50. doi:<a href=\"https://doi.org/10.3929/ETHZ-A-010646484\">10.3929/ETHZ-A-010646484</a>","short":"M. Mondelli, S. Kudekar, S. Kumar, H.D. Pfister, E. Şaşoğlu, R. Urbanke, in:, 24th International Zurich Seminar on Communications, ETH Zürich, 2016, p. 50.","apa":"Mondelli, M., Kudekar, S., Kumar, S., Pfister, H. D., Şaşoğlu, E., &#38; Urbanke, R. (2016). Reed-Muller codes: Thresholds and weight distribution. In <i>24th International Zurich Seminar on Communications</i> (p. 50). Zurich, Switzerland: ETH Zürich. <a href=\"https://doi.org/10.3929/ETHZ-A-010646484\">https://doi.org/10.3929/ETHZ-A-010646484</a>"},"title":"Reed-Muller codes: Thresholds and weight distribution","publication":"24th International Zurich Seminar on Communications","doi":"10.3929/ETHZ-A-010646484","_id":"6770","language":[{"iso":"eng"}]},{"oa":1,"date_updated":"2021-01-12T06:47:33Z","issue":"3","title":"Milestones toward Majorana-based quantum computing","intvolume":"         6","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Physical Review X","author":[{"last_name":"Aasen","full_name":"Aasen, David","first_name":"David"},{"last_name":"Hell","full_name":"Hell, Michael","first_name":"Michael"},{"first_name":"Ryan","full_name":"Mishmash, Ryan","last_name":"Mishmash"},{"orcid":"0000-0003-2607-2363","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","first_name":"Andrew P"},{"first_name":"Jeroen","full_name":"Danon, Jeroen","last_name":"Danon"},{"last_name":"Leijnse","full_name":"Leijnse, Martin","first_name":"Martin"},{"full_name":"Jespersen, Thomas","first_name":"Thomas","last_name":"Jespersen"},{"last_name":"Folk","first_name":"Joshua","full_name":"Folk, Joshua"},{"last_name":"Marcs","first_name":"Charles","full_name":"Marcs, Charles"},{"full_name":"Flensberg, Karsten","first_name":"Karsten","last_name":"Flensberg"},{"first_name":"Jason","full_name":"Alicea, Jason","last_name":"Alicea"}],"month":"08","oa_version":"Published Version","day":"03","file":[{"success":1,"file_id":"6458","file_name":"2016_PhysRevX_Aasen.pdf","date_created":"2019-05-15T14:12:31Z","date_updated":"2019-05-15T14:12:31Z","creator":"kschuh","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":2142676}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","type":"journal_article","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.).","year":"2016","publist_id":"7954","citation":{"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>","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>","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>.","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.","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>."},"date_created":"2018-12-11T11:44:37Z","article_number":"031016","file_date_updated":"2019-05-15T14:12:31Z","_id":"100","doi":"10.1103/PhysRevX.6.031016","publication_status":"published","ddc":["530"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","text":"We introduce a scheme for preparation, manipulation, and read out of Majorana zero modes in semiconducting wires with mesoscopic superconducting islands. Our approach synthesizes recent advances in materials growth with tools commonly used in quantum-dot experiments, including gate control of tunnel barriers and Coulomb effects, charge sensing, and charge pumping. We outline a sequence of milestones interpolating between zero-mode detection and quantum computing that includes (1) detection of fusion rules for non-Abelian anyons using either proximal charge sensors or pumped current, (2) validation of a prototype topological qubit, and (3) demonstration of non-Abelian statistics by braiding in a branched geometry. The first two milestones require only a single wire with two islands, and additionally enable sensitive measurements of the system\\'s excitation gap, quasiparticle poisoning rates, residual Majorana zero-mode splittings, and topological-qubit coherence times. These pre-braiding experiments can be adapted to other manipulation and read out schemes as well."}],"publisher":"American Physical Society","date_published":"2016-08-03T00:00:00Z","extern":"1","quality_controlled":"1","volume":6},{"publist_id":"6390","date_created":"2018-12-11T11:49:40Z","title":"An orthogonal permease–inducer–repressor feedback loop shows bistability","citation":{"chicago":"Gnügge, Robert, Lekshmi Dharmarajan, Moritz Lang, and Jörg Stelling. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” <i>ACS Synthetic Biology</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acssynbio.6b00013\">https://doi.org/10.1021/acssynbio.6b00013</a>.","mla":"Gnügge, Robert, et al. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” <i>ACS Synthetic Biology</i>, vol. 5, no. 10, American Chemical Society, 2016, pp. 1098–107, doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00013\">10.1021/acssynbio.6b00013</a>.","ista":"Gnügge R, Dharmarajan L, Lang M, Stelling J. 2016. An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. 5(10), 1098–1107.","ama":"Gnügge R, Dharmarajan L, Lang M, Stelling J. An orthogonal permease–inducer–repressor feedback loop shows bistability. <i>ACS Synthetic Biology</i>. 2016;5(10):1098-1107. doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00013\">10.1021/acssynbio.6b00013</a>","ieee":"R. Gnügge, L. Dharmarajan, M. Lang, and J. Stelling, “An orthogonal permease–inducer–repressor feedback loop shows bistability,” <i>ACS Synthetic Biology</i>, vol. 5, no. 10. American Chemical Society, pp. 1098–1107, 2016.","short":"R. Gnügge, L. Dharmarajan, M. Lang, J. Stelling, ACS Synthetic Biology 5 (2016) 1098–1107.","apa":"Gnügge, R., Dharmarajan, L., Lang, M., &#38; Stelling, J. (2016). An orthogonal permease–inducer–repressor feedback loop shows bistability. <i>ACS Synthetic Biology</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssynbio.6b00013\">https://doi.org/10.1021/acssynbio.6b00013</a>"},"issue":"10","year":"2016","date_updated":"2021-01-12T06:47:37Z","acknowledgement":"We thank Julio Polaina (Instituto de Agroqu ı ́ mica y Tecnolog ı ́ a de Alimentos, C.S.I.C., Paterna, Spain) for the gift of plasmid pMR4, Gregor W. Schmidt for provision of and support with the micro fl uidic device, Markus Du ̈ rr for the cell tracking R script, and Lukas Widmer for the script for MEIGO using “ parfor ” in MATLAB. We acknowledge the members of the Stelling group for discussions, comments, and support.","intvolume":"         5","language":[{"iso":"eng"}],"_id":"1008","doi":"10.1021/acssynbio.6b00013","publication":"ACS Synthetic Biology","publication_status":"published","author":[{"last_name":"Gnügge","full_name":"Gnügge, Robert","first_name":"Robert"},{"full_name":"Dharmarajan, Lekshmi","first_name":"Lekshmi","last_name":"Dharmarajan"},{"last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz","first_name":"Moritz"},{"last_name":"Stelling","full_name":"Stelling, Jörg","first_name":"Jörg"}],"abstract":[{"lang":"eng","text":"Feedback loops in biological networks, among others, enable differentiation and cell cycle progression, and increase robustness in signal transduction. In natural networks, feedback loops are often complex and intertwined, making it challenging to identify which loops are mainly responsible for an observed behavior. However, minimal synthetic replicas could allow for such identification. Here, we engineered a synthetic permease-inducer-repressor system in Saccharomyces cerevisiae to analyze if a transport-mediated positive feedback loop could be a core mechanism for the switch-like behavior in the regulation of metabolic gene networks such as the S. cerevisiae GAL system or the Escherichia coli lac operon. We characterized the synthetic circuit using deterministic and stochastic mathematical models. Similar to its natural counterparts, our synthetic system shows bistable and hysteretic behavior, and the inducer concentration range for bistability as well as the switching rates between the two stable states depend on the repressor concentration. Our results indicate that a generic permease–inducer–repressor circuit with a single feedback loop is sufficient to explain the experimentally observed bistable behavior of the natural systems. We anticipate that the approach of reimplementing natural systems with orthogonal parts to identify crucial network components is applicable to other natural systems such as signaling pathways."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","day":"05","month":"05","quality_controlled":"1","volume":5,"page":"1098 - 1107","department":[{"_id":"CaGu"}],"date_published":"2016-05-05T00:00:00Z","status":"public","type":"journal_article","publisher":"American Chemical Society"},{"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.","year":"2016","citation":{"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>","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.","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>.","short":"S.M. Albrecht, A.P. Higginbotham, T. Jespersen, M. Madsen, F. Kuemmeth, J. Nygård, P. Krogstrup, C. Marcus, Nature 531 (2016) 206–209.","ama":"Albrecht SM, Higginbotham AP, Jespersen T, et al. Exponential protection of zero modes in Majorana islands. <i>Nature</i>. 2016;531(7593):206-209. doi:<a href=\"https://doi.org/10.1038/nature17162\">10.1038/nature17162</a>","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."},"publist_id":"7953","date_created":"2018-12-11T11:44:38Z","doi":"10.1038/nature17162","_id":"101","external_id":{"arxiv":["1603.03217"]},"abstract":[{"text":"Majorana zero modes are quasiparticle excitations in condensed matter systems that have been proposed as building blocks of fault-tolerant quantum computers. They are expected to exhibit non-Abelian particle statistics, in contrast to the usual statistics of fermions and bosons, enabling quantum operations to be performed by braiding isolated modes around one another. Quantum braiding operations are topologically protected insofar as these modes are pinned near zero energy, with the departure from zero expected to be exponentially small as the modes become spatially separated. Following theoretical proposals, several experiments have identified signatures of Majorana modes in nanowires with proximity-induced superconductivity and atomic chains, with small amounts of mode splitting potentially explained by hybridization of Majorana modes. Here, we use Coulomb-blockade spectroscopy in an InAs nanowire segment with epitaxial aluminium, which forms a proximity-induced superconducting Coulomb island (a â ∼ Majorana islandâ (tm)) that is isolated from normal-metal leads by tunnel barriers, to measure the splitting of near-zero-energy Majorana modes. We observe exponential suppression of energy splitting with increasing wire length. For short devices of a few hundred nanometres, sub-gap state energies oscillate as the magnetic field is varied, as is expected for hybridized Majorana modes. Splitting decreases by a factor of about ten for each half a micrometre of increased wire length. For devices longer than about one micrometre, transport in strong magnetic fields occurs through a zero-energy state that is energetically isolated from a continuum, yielding uniformly spaced Coulomb-blockade conductance peaks, consistent with teleportation via Majorana modes. Our results help to explain the trivial-to-topological transition in finite systems and to quantify the scaling of topological protection with end-mode separation.","lang":"eng"}],"publication_status":"published","publisher":"Nature Publishing Group","date_published":"2016-03-10T00:00:00Z","page":"206 - 209","extern":"1","quality_controlled":"1","volume":531,"intvolume":"       531","date_updated":"2021-01-12T06:47:37Z","oa":1,"issue":"7593","title":"Exponential protection of zero modes in Majorana islands","publication":"Nature","language":[{"iso":"eng"}],"month":"03","day":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.03217"}],"oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Albrecht","full_name":"Albrecht, S M","first_name":"S M"},{"full_name":"Higginbotham, Andrew P","first_name":"Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363"},{"full_name":"Jespersen, Thomas","first_name":"Thomas","last_name":"Jespersen"},{"last_name":"Madsen","full_name":"Madsen, Morten","first_name":"Morten"},{"last_name":"Kuemmeth","full_name":"Kuemmeth, Ferdinand","first_name":"Ferdinand"},{"last_name":"Nygård","first_name":"Jesper","full_name":"Nygård, Jesper"},{"first_name":"Peter","full_name":"Krogstrup, Peter","last_name":"Krogstrup"},{"first_name":"Charles","full_name":"Marcus, Charles","last_name":"Marcus"}],"arxiv":1,"type":"journal_article","status":"public"},{"title":"Approaching a topological phase transition in Majorana nanowires","issue":"24","date_updated":"2021-01-12T06:47:42Z","oa":1,"intvolume":"        93","language":[{"iso":"eng"}],"publication":"Physical Review B","arxiv":1,"author":[{"first_name":"Ryan","full_name":"Mishmash, Ryan","last_name":"Mishmash"},{"last_name":"Aasen","full_name":"Aasen, David","first_name":"David"},{"last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","first_name":"Andrew P"},{"last_name":"Alicea","first_name":"Jason","full_name":"Alicea, Jason"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.07908"}],"day":"08","oa_version":"Preprint","month":"06","type":"journal_article","status":"public","citation":{"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>","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>.","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>"},"publist_id":"7952","date_created":"2018-12-11T11:44:38Z","year":"2016","article_number":"245404","_id":"102","doi":"10.1103/PhysRevB.93.245404","publication_status":"published","abstract":[{"lang":"eng","text":"Recent experiments have produced mounting evidence of Majorana zero modes in nanowire-superconductor hybrids. Signatures of an expected topological phase transition accompanying the onset of these modes nevertheless remain elusive. We investigate a fundamental question concerning this issue: Do well-formed Majorana modes necessarily entail a sharp phase transition in these setups? Assuming reasonable parameters, we argue that finite-size effects can dramatically smooth this putative transition into a crossover, even in systems large enough to support well-localized Majorana modes. We propose overcoming such finite-size effects by examining the behavior of low-lying excited states through tunneling spectroscopy. In particular, the excited-state energies exhibit characteristic field and density dependence, and scaling with system size, that expose an approaching topological phase transition. We suggest several experiments for extracting the predicted behavior. As a useful byproduct, the protocols also allow one to measure the wire's spin-orbit coupling directly in its superconducting environment."}],"external_id":{"arxiv":["1601.07908"]},"quality_controlled":"1","volume":93,"extern":"1","date_published":"2016-06-08T00:00:00Z","publisher":"American Physical Society"},{"publication":"The Journal of Chemical Physics","language":[{"iso":"eng"}],"intvolume":"       145","scopus_import":"1","article_processing_charge":"No","issue":"21","date_updated":"2021-11-29T10:33:11Z","oa":1,"title":"Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation","status":"public","type":"journal_article","pmid":1,"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"month":"12","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02320"}],"oa_version":"Preprint","arxiv":1,"author":[{"first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139"},{"full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T.","last_name":"Michaels"},{"first_name":"Alessio","full_name":"Zaccone, Alessio","last_name":"Zaccone"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."},{"last_name":"Frenkel","first_name":"Daan","full_name":"Frenkel, Daan"}],"doi":"10.1063/1.4965040","article_type":"original","_id":"10376","article_number":"211926","year":"2016","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.).","keyword":["physical and theoretical chemistry","general physics and astronomy"],"date_created":"2021-11-29T10:01:57Z","citation":{"apa":"Šarić, A., Michaels, T. C. T., Zaccone, A., Knowles, T. P. J., &#38; Frenkel, D. (2016). Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation. <i>The Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4965040\">https://doi.org/10.1063/1.4965040</a>","ieee":"A. Šarić, T. C. T. Michaels, A. Zaccone, T. P. J. Knowles, and D. Frenkel, “Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation,” <i>The Journal of Chemical Physics</i>, vol. 145, no. 21. American Institute of Physics, 2016.","ama":"Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation. <i>The Journal of Chemical Physics</i>. 2016;145(21). doi:<a href=\"https://doi.org/10.1063/1.4965040\">10.1063/1.4965040</a>","short":"A. Šarić, T.C.T. Michaels, A. Zaccone, T.P.J. Knowles, D. Frenkel, The Journal of Chemical Physics 145 (2016).","ista":"Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. 2016. Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation. The Journal of Chemical Physics. 145(21), 211926.","chicago":"Šarić, Anđela, Thomas C. T. Michaels, Alessio Zaccone, Tuomas P. J. Knowles, and Daan Frenkel. “Kinetics of Spontaneous Filament Nucleation via Oligomers: Insights from Theory and Simulation.” <i>The Journal of Chemical Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1063/1.4965040\">https://doi.org/10.1063/1.4965040</a>.","mla":"Šarić, Anđela, et al. “Kinetics of Spontaneous Filament Nucleation via Oligomers: Insights from Theory and Simulation.” <i>The Journal of Chemical Physics</i>, vol. 145, no. 21, 211926, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1063/1.4965040\">10.1063/1.4965040</a>."},"date_published":"2016-12-01T00:00:00Z","publisher":"American Institute of Physics","volume":145,"quality_controlled":"1","extern":"1","abstract":[{"lang":"eng","text":"Nucleation processes are at the heart of a large number of phenomena, from cloud formation to protein crystallization. A recently emerging area where nucleation is highly relevant is the initiation of filamentous protein self-assembly, a process that has broad implications in many research areas ranging from medicine to nanotechnology. As such, spontaneous nucleation of protein fibrils has received much attention in recent years with many theoretical and experimental studies focusing on the underlying physical principles. In this paper we make a step forward in this direction and explore the early time behaviour of filamentous protein growth in the context of nucleation theory. We first provide an overview of the thermodynamics and kinetics of spontaneous nucleation of protein filaments in the presence of one relevant degree of freedom, namely the cluster size. In this case, we review how key kinetic observables, such as the reaction order of spontaneous nucleation, are directly related to the physical size of the critical nucleus. We then focus on the increasingly prominent case of filament nucleation that includes a conformational conversion of the nucleating building-block as an additional slow step in the nucleation process. Using computer simulations, we study the concentration dependence of the nucleation rate. We find that, under these circumstances, the reaction order of spontaneous nucleation with respect to the free monomer does no longer relate to the overall physical size of the nucleating aggregate but rather to the portion of the aggregate that actively participates in the conformational conversion. Our results thus provide a novel interpretation of the common kinetic descriptors of protein filament formation, including the reaction order of the nucleation step or the scaling exponent of lag times, and put into perspective current theoretical descriptions of protein aggregation."}],"external_id":{"pmid":["28799382"],"arxiv":["1610.02320"]},"publication_status":"published"},{"publication_status":"published","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"}],"external_id":{"pmid":["27618764"],"arxiv":["1603.04644"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["540"],"quality_controlled":"1","volume":6,"extern":"1","date_published":"2016-09-13T00:00:00Z","publisher":"Springer Nature","keyword":["multidisciplinary"],"date_created":"2021-11-29T10:34:08Z","citation":{"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>","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.","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>.","short":"C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, D.J. Kraft, Scientific Reports 6 (2016).","ieee":"C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, and D. J. Kraft, “Lipid membrane-mediated attraction between curvature inducing objects,” <i>Scientific Reports</i>, vol. 6, no. 1. Springer Nature, 2016.","ama":"van der Wel C, Vahid A, Šarić A, Idema T, Heinrich D, Kraft DJ. Lipid membrane-mediated attraction between curvature inducing objects. <i>Scientific Reports</i>. 2016;6(1). doi:<a href=\"https://doi.org/10.1038/srep32825\">10.1038/srep32825</a>"},"year":"2016","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.","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/srep37382"}]},"article_number":"32825","article_type":"original","_id":"10377","file_date_updated":"2021-11-29T10:50:00Z","doi":"10.1038/srep32825","arxiv":1,"author":[{"first_name":"Casper","full_name":"van der Wel, Casper","last_name":"van der Wel"},{"first_name":"Afshin","full_name":"Vahid, Afshin","last_name":"Vahid"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela"},{"first_name":"Timon","full_name":"Idema, Timon","last_name":"Idema"},{"last_name":"Heinrich","first_name":"Doris","full_name":"Heinrich, Doris"},{"first_name":"Daniela J.","full_name":"Kraft, Daniela J.","last_name":"Kraft"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"date_updated":"2021-11-29T10:50:00Z","date_created":"2021-11-29T10:50:00Z","checksum":"d6cf16dd511e15726b001e7cc287cf1d","file_id":"10379","file_name":"2016_SciRep_vanderWel.pdf","success":1,"relation":"main_file","file_size":1598289,"access_level":"open_access","content_type":"application/pdf","creator":"cchlebak"}],"day":"13","main_file_link":[{"url":"https://www.nature.com/articles/srep32825","open_access":"1"}],"oa_version":"Published Version","publication_identifier":{"issn":["2045-2322"]},"month":"09","status":"public","type":"journal_article","pmid":1,"title":"Lipid membrane-mediated attraction between curvature inducing objects","issue":"1","article_processing_charge":"No","oa":1,"date_updated":"2021-11-29T11:08:15Z","intvolume":"         6","has_accepted_license":"1","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Scientific Reports"},{"quality_controlled":"1","volume":12,"page":"874-880","extern":"1","date_published":"2016-07-18T00:00:00Z","publisher":"Springer Nature","abstract":[{"lang":"eng","text":"The ability of biological molecules to replicate themselves is the foundation of life, requiring a complex cellular machinery. However, a range of aberrant processes involve the self-replication of pathological protein structures without any additional assistance. One example is the autocatalytic generation of pathological protein aggregates, including amyloid fibrils, involved in neurodegenerative disorders. Here, we use computer simulations to identify the necessary requirements for the self-replication of fibrillar assemblies of proteins. We establish that a key physical determinant for this process is the affinity of proteins for the surfaces of fibrils. We find that self-replication can take place only in a very narrow regime of inter-protein interactions, implying a high level of sensitivity to system parameters and experimental conditions. We then compare our theoretical predictions with kinetic and biosensor measurements of fibrils formed from the Aβ peptide associated with Alzheimer’s disease. Our results show a quantitative connection between the kinetics of self-replication and the surface coverage of fibrils by monomeric proteins. These findings reveal the fundamental physical requirements for the formation of supra-molecular structures able to replicate themselves, and shed light on mechanisms in play in the proliferation of protein aggregates in nature."}],"external_id":{"pmid":["31031819"]},"publication_status":"published","doi":"10.1038/nphys3828","_id":"10378","article_type":"original","keyword":["general physics and astronomy"],"date_created":"2021-11-29T10:36:11Z","citation":{"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.","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.","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>"},"year":"2016","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.).","status":"public","type":"journal_article","pmid":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"18","oa_version":"Preprint","main_file_link":[{"url":"https://discovery.ucl.ac.uk/id/eprint/1517406/","open_access":"1"}],"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"month":"07","author":[{"full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139"},{"full_name":"Buell, Alexander K.","first_name":"Alexander K.","last_name":"Buell"},{"full_name":"Meisl, Georg","first_name":"Georg","last_name":"Meisl"},{"last_name":"Michaels","first_name":"Thomas C. T.","full_name":"Michaels, Thomas C. T."},{"first_name":"Christopher M.","full_name":"Dobson, Christopher M.","last_name":"Dobson"},{"last_name":"Linse","first_name":"Sara","full_name":"Linse, Sara"},{"last_name":"Knowles","full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J."},{"first_name":"Daan","full_name":"Frenkel, Daan","last_name":"Frenkel"}],"publication":"Nature Physics","language":[{"iso":"eng"}],"intvolume":"        12","scopus_import":"1","title":"Physical determinants of the self-replication of protein fibrils","article_processing_charge":"No","issue":"9","date_updated":"2021-11-29T11:07:25Z","oa":1},{"keyword":["physical and theoretical chemistry","general physics and astronomy"],"citation":{"short":"P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, D. Frenkel, The Journal of Chemical Physics 144 (2016).","ama":"Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. Non-equilibrium simulations of thermally induced electric fields in water. <i>The Journal of Chemical Physics</i>. 2016;144(22). doi:<a href=\"https://doi.org/10.1063/1.4953036\">10.1063/1.4953036</a>","ieee":"P. Wirnsberger, D. Fijan, A. Šarić, M. Neumann, C. Dellago, and D. Frenkel, “Non-equilibrium simulations of thermally induced electric fields in water,” <i>The Journal of Chemical Physics</i>, vol. 144, no. 22. American Institute of Physics, 2016.","chicago":"Wirnsberger, P., D. Fijan, Anđela Šarić, M. Neumann, C. Dellago, and D. Frenkel. “Non-Equilibrium Simulations of Thermally Induced Electric Fields in Water.” <i>The Journal of Chemical Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1063/1.4953036\">https://doi.org/10.1063/1.4953036</a>.","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.","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>.","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>"},"date_created":"2021-11-29T11:08:52Z","year":"2016","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).","article_number":"224102","_id":"10380","article_type":"original","doi":"10.1063/1.4953036","publication_status":"published","abstract":[{"lang":"eng","text":"Using non-equilibrium molecular dynamics simulations, it has been recently demonstrated that water molecules align in response to an imposed temperature gradient, resulting in an effective electric field. Here, we investigate how thermally induced fields depend on the underlying treatment of long-ranged interactions. For the short-ranged Wolf method and Ewald summation, we find the peak strength of the field to range between 2 × 107 and 5 × 107 V/m for a temperature gradient of 5.2 K/Å. Our value for the Wolf method is therefore an order of magnitude lower than the literature value [J. A. Armstrong and F. Bresme, J. Chem. Phys. 139, 014504 (2013); J. Armstrong et al., J. Chem. Phys. 143, 036101 (2015)]. We show that this discrepancy can be traced back to the use of an incorrect kernel in the calculation of the electrostatic field. More seriously, we find that the Wolf method fails to predict correct molecular orientations, resulting in dipole densities with opposite sign to those computed using Ewald summation. By considering two different multipole expansions, we show that, for inhomogeneous polarisations, the quadrupole contribution can be significant and even outweigh the dipole contribution to the field. Finally, we propose a more accurate way of calculating the electrostatic potential and the field. In particular, we show that averaging the microscopic field analytically to obtain the macroscopic Maxwell field reduces the error bars by up to an order of magnitude. As a consequence, the simulation times required to reach a given statistical accuracy decrease by up to two orders of magnitude."}],"external_id":{"arxiv":["1602.02734"],"pmid":["27305991"]},"quality_controlled":"1","volume":144,"extern":"1","date_published":"2016-06-10T00:00:00Z","publisher":"American Institute of Physics","title":"Non-equilibrium simulations of thermally induced electric fields in water","issue":"22","article_processing_charge":"No","date_updated":"2021-11-29T13:09:08Z","oa":1,"intvolume":"       144","scopus_import":"1","language":[{"iso":"eng"}],"publication":"The Journal of Chemical Physics","arxiv":1,"author":[{"full_name":"Wirnsberger, P.","first_name":"P.","last_name":"Wirnsberger"},{"first_name":"D.","full_name":"Fijan, D.","last_name":"Fijan"},{"first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić"},{"last_name":"Neumann","first_name":"M.","full_name":"Neumann, M."},{"last_name":"Dellago","first_name":"C.","full_name":"Dellago, C."},{"full_name":"Frenkel, D.","first_name":"D.","last_name":"Frenkel"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"url":"https://arxiv.org/abs/1602.02734","open_access":"1"}],"oa_version":"Preprint","day":"10","month":"06","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"type":"journal_article","status":"public","pmid":1},{"pmid":1,"type":"journal_article","status":"public","author":[{"full_name":"Bachmann, Stephan Jan","first_name":"Stephan Jan","last_name":"Bachmann"},{"last_name":"Kotar","first_name":"Jurij","full_name":"Kotar, Jurij"},{"full_name":"Parolini, Lucia","first_name":"Lucia","last_name":"Parolini"},{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela"},{"first_name":"Pietro","full_name":"Cicuta, Pietro","last_name":"Cicuta"},{"first_name":"Lorenzo","full_name":"Di Michele, Lorenzo","last_name":"Di Michele"},{"last_name":"Mognetti","first_name":"Bortolo Matteo","full_name":"Mognetti, Bortolo Matteo"}],"arxiv":1,"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"month":"08","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.05788"}],"day":"19","oa_version":"Preprint","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"publication":"Soft Matter","oa":1,"date_updated":"2021-11-29T13:09:00Z","issue":"37","article_processing_charge":"No","title":"Melting transition in lipid vesicles functionalised by mobile DNA linkers","intvolume":"        12","scopus_import":"1","publisher":"Royal Society of Chemistry","date_published":"2016-08-19T00:00:00Z","extern":"1","page":"7804-7817","volume":12,"quality_controlled":"1","publication_status":"published","external_id":{"pmid":["27722701"],"arxiv":["1608.05788"]},"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"}],"article_type":"original","_id":"10381","doi":"10.1039/c6sm01515h","year":"2016","date_created":"2021-11-29T11:09:55Z","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>","chicago":"Bachmann, Stephan Jan, Jurij Kotar, Lucia Parolini, Anđela Šarić, Pietro Cicuta, Lorenzo Di Michele, and Bortolo Matteo Mognetti. “Melting Transition in Lipid Vesicles Functionalised by Mobile DNA Linkers.” <i>Soft Matter</i>. Royal Society of Chemistry, 2016. <a href=\"https://doi.org/10.1039/c6sm01515h\">https://doi.org/10.1039/c6sm01515h</a>.","mla":"Bachmann, Stephan Jan, et al. “Melting Transition in Lipid Vesicles Functionalised by Mobile DNA Linkers.” <i>Soft Matter</i>, vol. 12, no. 37, Royal Society of Chemistry, 2016, pp. 7804–17, doi:<a href=\"https://doi.org/10.1039/c6sm01515h\">10.1039/c6sm01515h</a>.","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.","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.","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."},"keyword":["condensed matter physics","general chemistry"]},{"publication":"Nature Photonics","doi":"10.1038/nphoton.2015.266","_id":"1057","language":[{"iso":"eng"}],"intvolume":"        10","issue":"2","article_processing_charge":"No","year":"2016","acknowledgement":"We thank T. Gilat and E. Rothermel (both MPI) for help with preparing samples, and J. Keller for discussion. J.G.D. acknowledges support by the European Union through a Marie Curie fellowship PIEF-GA-2011-299283. S.W.H. acknowledges support by the Körber Foundation.","date_updated":"2021-01-12T06:47:58Z","title":"Coordinate-targeted fluorescence nanoscopy with multiple off states","date_created":"2018-12-11T11:49:55Z","publist_id":"6331","citation":{"apa":"Danzl, J. G., Sidenstein, S., Gregor, C., Urban, N., Ilgen, P., Jakobs, S., &#38; Hell, S. (2016). Coordinate-targeted fluorescence nanoscopy with multiple off states. <i>Nature Photonics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nphoton.2015.266\">https://doi.org/10.1038/nphoton.2015.266</a>","ista":"Danzl JG, Sidenstein S, Gregor C, Urban N, Ilgen P, Jakobs S, Hell S. 2016. Coordinate-targeted fluorescence nanoscopy with multiple off states. Nature Photonics. 10(2), 122–128.","chicago":"Danzl, Johann G, Sven Sidenstein, Carola Gregor, Nicolai Urban, Peter Ilgen, Stefan Jakobs, and Stefan Hell. “Coordinate-Targeted Fluorescence Nanoscopy with Multiple off States.” <i>Nature Photonics</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nphoton.2015.266\">https://doi.org/10.1038/nphoton.2015.266</a>.","mla":"Danzl, Johann G., et al. “Coordinate-Targeted Fluorescence Nanoscopy with Multiple off States.” <i>Nature Photonics</i>, vol. 10, no. 2, Nature Publishing Group, 2016, pp. 122–28, doi:<a href=\"https://doi.org/10.1038/nphoton.2015.266\">10.1038/nphoton.2015.266</a>.","short":"J.G. Danzl, S. Sidenstein, C. Gregor, N. Urban, P. Ilgen, S. Jakobs, S. Hell, Nature Photonics 10 (2016) 122–128.","ieee":"J. G. Danzl <i>et al.</i>, “Coordinate-targeted fluorescence nanoscopy with multiple off states,” <i>Nature Photonics</i>, vol. 10, no. 2. Nature Publishing Group, pp. 122–128, 2016.","ama":"Danzl JG, Sidenstein S, Gregor C, et al. Coordinate-targeted fluorescence nanoscopy with multiple off states. <i>Nature Photonics</i>. 2016;10(2):122-128. doi:<a href=\"https://doi.org/10.1038/nphoton.2015.266\">10.1038/nphoton.2015.266</a>"},"date_published":"2016-02-01T00:00:00Z","type":"journal_article","status":"public","publisher":"Nature Publishing Group","volume":10,"extern":"1","page":"122 - 128","month":"02","abstract":[{"lang":"eng","text":"Far-field super-resolution fluorescence microscopy discerns fluorophores residing closer than the diffraction barrier by briefly transferring them in different (typically ON and OFF) states before detection. In coordinate-targeted super-resolution variants, such as stimulated emission depletion (STED) microscopy, this state difference is created by the intensity minima and maxima of an optical pattern, causing all fluorophores to assume the off state, for instance, except at the minima. Although strong spatial confinement of the on state enables high resolution, it also subjects the fluorophores to excess intensities and state cycles at the maxima. Here, we address these issues by driving the fluorophores into a second off state that is inert to the excess light. By using reversibly switchable fluorescent proteins as labels, our approach reduces bleaching and enhances resolution and contrast in live-cell STED microscopy. Using two or more transitions to off states is a useful strategy for augmenting the power of coordinate-targeted super-resolution microscopy."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","day":"01","publication_status":"published","author":[{"full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"},{"full_name":"Sidenstein, Sven","first_name":"Sven","last_name":"Sidenstein"},{"full_name":"Gregor, Carola","first_name":"Carola","last_name":"Gregor"},{"first_name":"Nicolai","full_name":"Urban, Nicolai","last_name":"Urban"},{"last_name":"Ilgen","full_name":"Ilgen, Peter","first_name":"Peter"},{"full_name":"Jakobs, Stefan","first_name":"Stefan","last_name":"Jakobs"},{"first_name":"Stefan","full_name":"Hell, Stefan","last_name":"Hell"}]},{"citation":{"ieee":"A. Butkevich <i>et al.</i>, “Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells,” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 10. Wiley-Blackwell, pp. 3290–3294, 2016.","ama":"Butkevich A, Mitronova G, Sidenstein S, et al. Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells. <i>Angewandte Chemie - International Edition</i>. 2016;55(10):3290-3294. doi:<a href=\"https://doi.org/10.1002/anie.201511018\">10.1002/anie.201511018</a>","short":"A. Butkevich, G. Mitronova, S. Sidenstein, J. Klocke, D. Kamin, D. Meineke, E. D’Este, P. Kraemer, J.G. Danzl, V. Belov, S. Hell, Angewandte Chemie - International Edition 55 (2016) 3290–3294.","mla":"Butkevich, Alexey, et al. “Fluorescent Rhodamines and Fluorogenic Carbopyronines for Super-Resolution STED Microscopy in Living Cells.” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 10, Wiley-Blackwell, 2016, pp. 3290–94, doi:<a href=\"https://doi.org/10.1002/anie.201511018\">10.1002/anie.201511018</a>.","ista":"Butkevich A, Mitronova G, Sidenstein S, Klocke J, Kamin D, Meineke D, D’Este E, Kraemer P, Danzl JG, Belov V, Hell S. 2016. Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells. Angewandte Chemie - International Edition. 55(10), 3290–3294.","chicago":"Butkevich, Alexey, Gyuzel Mitronova, Sven Sidenstein, Jessica Klocke, Dirk Kamin, Dirk Meineke, Elisa D’Este, et al. “Fluorescent Rhodamines and Fluorogenic Carbopyronines for Super-Resolution STED Microscopy in Living Cells.” <i>Angewandte Chemie - International Edition</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1002/anie.201511018\">https://doi.org/10.1002/anie.201511018</a>.","apa":"Butkevich, A., Mitronova, G., Sidenstein, S., Klocke, J., Kamin, D., Meineke, D., … Hell, S. (2016). Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells. <i>Angewandte Chemie - International Edition</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/anie.201511018\">https://doi.org/10.1002/anie.201511018</a>"},"publist_id":"6330","date_created":"2018-12-11T11:49:55Z","title":"Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells","acknowledgement":"We thank Prof. Y. Okada (RIKEN Quantitative Biology Center, Osaka, Japan) for the gift of β-tubulin-Halo plasmid, T. Gilat and Dr. E. Rothermel (MPIBPC, Göttingen, Germany) for cell culture and transfection, M. Pulst, J. Bienert (MPIBPC), Dr. M. John, Dr. H. Frauendorf, and co-workers (Institut für Organische und Biomolekulare Chemie, Georg-August-Universität, Göttingen, Germany) for UV/Vis, NMR, and ESI-MS spectra, Prof. M. L. Bossi (University of Buenos-Aires, Argentina) for measuring fluorescence lifetimes, and Dr. S. Vos and Prof. P. Cramer (MPIBPC) for access to a Tecan microplate reader. S.W.H. acknowledges a grant from the Bundesministerium für Bildung und Forschung (BMBF 513) within the program “Optische Technologien für Biowissenschaften und Gesundheit” (FKZ 13N11066). J.G.D. was supported by funds from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013; REA grant agreement PIEF-GA-2011-299283).","date_updated":"2021-01-12T06:47:59Z","article_processing_charge":"No","issue":"10","year":"2016","intvolume":"        55","language":[{"iso":"eng"}],"_id":"1059","doi":"10.1002/anie.201511018","publication":"Angewandte Chemie - International Edition","publication_status":"published","author":[{"first_name":"Alexey","full_name":"Butkevich, Alexey","last_name":"Butkevich"},{"last_name":"Mitronova","first_name":"Gyuzel","full_name":"Mitronova, Gyuzel"},{"full_name":"Sidenstein, Sven","first_name":"Sven","last_name":"Sidenstein"},{"first_name":"Jessica","full_name":"Klocke, Jessica","last_name":"Klocke"},{"first_name":"Dirk","full_name":"Kamin, Dirk","last_name":"Kamin"},{"first_name":"Dirk","full_name":"Meineke, Dirk","last_name":"Meineke"},{"first_name":"Elisa","full_name":"D'Este, Elisa","last_name":"D'Este"},{"first_name":"Philip","full_name":"Kraemer, Philip","last_name":"Kraemer"},{"full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl"},{"first_name":"Vladimir","full_name":"Belov, Vladimir","last_name":"Belov"},{"full_name":"Hell, Stefan","first_name":"Stefan","last_name":"Hell"}],"oa_version":"None","day":"01","abstract":[{"lang":"eng","text":"A range of bright and photostable rhodamines and carbopyronines with absorption maxima in the range of λ=500-630 nm were prepared, and enabled the specific labeling of cytoskeletal filaments using HaloTag technology followed by staining with 1 μm solutions of the dye-ligand conjugates. The synthesis, photophysical parameters, fluorogenic behavior, and structure-property relationships of the new dyes are discussed. Light microscopy with stimulated emission depletion (STED) provided one- and two-color images of living cells with an optical resolution of 40-60 nm."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"month":"03","extern":"1","page":"3290 - 3294","volume":55,"publisher":"Wiley-Blackwell","date_published":"2016-03-01T00:00:00Z","type":"journal_article","status":"public"},{"publist_id":"6329","date_created":"2018-12-11T11:49:56Z","citation":{"short":"S. Sidenstein, E. D’Este, M. Böhm, J.G. Danzl, V. Belov, S. Hell, Scientific Reports 6 (2016) 1–8.","ama":"Sidenstein S, D’Este E, Böhm M, Danzl JG, Belov V, Hell S. Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses. <i>Scientific Reports</i>. 2016;6:1-8. doi:<a href=\"https://doi.org/10.1038/srep26725\">10.1038/srep26725</a>","ieee":"S. Sidenstein, E. D’Este, M. Böhm, J. G. Danzl, V. Belov, and S. Hell, “Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, pp. 1–8, 2016.","ista":"Sidenstein S, D’Este E, Böhm M, Danzl JG, Belov V, Hell S. 2016. Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses. Scientific Reports. 6, 1–8.","mla":"Sidenstein, Sven, et al. “Multicolour Multilevel STED Nanoscopy of Actin/Spectrin Organization at Synapses.” <i>Scientific Reports</i>, vol. 6, Nature Publishing Group, 2016, pp. 1–8, doi:<a href=\"https://doi.org/10.1038/srep26725\">10.1038/srep26725</a>.","chicago":"Sidenstein, Sven, Elisa D’Este, Marvin Böhm, Johann G Danzl, Vladimir Belov, and Stefan Hell. “Multicolour Multilevel STED Nanoscopy of Actin/Spectrin Organization at Synapses.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep26725\">https://doi.org/10.1038/srep26725</a>.","apa":"Sidenstein, S., D’Este, E., Böhm, M., Danzl, J. G., Belov, V., &#38; Hell, S. (2016). Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep26725\">https://doi.org/10.1038/srep26725</a>"},"title":"Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses","article_processing_charge":"No","year":"2016","date_updated":"2021-01-12T06:47:59Z","acknowledgement":"We acknowledge the assistance of I. Herfort with neuron preparation, and of J. Bienert and K. Müller with analyses of the dye 540R derivatives. We thank T. Gilat and E. Rothermel for sample preparation as well as J. Keller, F. Winter (all MPI-BPC) and C.A. Wurm (Abberior Instruments) for helpful discussion, and S.J. Sahl (MPI-BPC) for a critical reading of the manuscript.","intvolume":"         6","language":[{"iso":"eng"}],"_id":"1060","doi":"10.1038/srep26725","publication":"Scientific Reports","publication_status":"published","author":[{"first_name":"Sven","full_name":"Sidenstein, Sven","last_name":"Sidenstein"},{"first_name":"Elisa","full_name":"D'Este, Elisa","last_name":"D'Este"},{"last_name":"Böhm","first_name":"Marvin","full_name":"Böhm, Marvin"},{"first_name":"Johann G","full_name":"Danzl, Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"},{"last_name":"Belov","first_name":"Vladimir","full_name":"Belov, Vladimir"},{"full_name":"Hell, Stefan","first_name":"Stefan","last_name":"Hell"}],"abstract":[{"lang":"eng","text":"Superresolution fluorescence microscopy of multiple fluorophores still requires development. Here we present simultaneous three-colour stimulated emission depletion (STED) nanoscopy relying on a single STED beam at 620 nm. Toggling the STED beam between two or more power levels (&quot;multilevelSTEDv) optimizes resolution and contrast in all colour channels, which are intrinsically co-aligned and well separated. Three-colour recording is demonstrated by imaging the nanoscale cytoskeletal organization in cultured hippocampal neurons. The down to ∼35 nm resolution identified periodic actin/betaII spectrin lattices along dendrites and spines; however, at presynaptic and postsynaptic sites, these patterns were found to be absent. Both our multicolour scheme and the 620 nm STED line should be attractive for routine STED microscopy applications."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","day":"25","month":"05","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":6,"extern":"1","page":"1 - 8","date_published":"2016-05-25T00:00:00Z","type":"journal_article","status":"public","publisher":"Nature Publishing Group"},{"alternative_title":["LIPIcs"],"type":"conference","status":"public","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dvorák","full_name":"Dvorák, Wolfgang","first_name":"Wolfgang"},{"orcid":"0000-0002-5008-6530","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"first_name":"Veronika","full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer"}],"conference":{"start_date":"2016-08-22","name":"MFCS: Mathematical Foundations of Computer Science (SG)","end_date":"2016-08-26","location":"Krakow, Poland"},"month":"08","day":"01","oa_version":"Published Version","file":[{"file_name":"IST-2017-779-v1+1_LIPIcs-MFCS-2016-25.pdf","file_id":"5187","date_created":"2018-12-12T10:16:02Z","date_updated":"2018-12-12T10:16:02Z","creator":"system","file_size":632786,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"oa":1,"date_updated":"2025-06-02T08:53:50Z","pubrep_id":"779","article_processing_charge":"No","title":"Conditionally optimal algorithms for generalized Büchi Games","scopus_import":"1","has_accepted_license":"1","intvolume":"        58","project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_published":"2016-08-01T00:00:00Z","department":[{"_id":"KrCh"}],"quality_controlled":"1","volume":58,"publication_status":"published","ddc":["000","004","006"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"abstract":[{"lang":"eng","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}. "}],"file_date_updated":"2018-12-12T10:16:02Z","_id":"1068","doi":"10.4230/LIPIcs.MFCS.2016.25","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","year":"2016","date_created":"2018-12-11T11:49:58Z","publist_id":"6317","citation":{"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>.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","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>","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.","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>"},"ec_funded":1,"article_number":"25"},{"author":[{"full_name":"Chonev, Ventsislav K","first_name":"Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Chonev"},{"last_name":"Ouaknine","first_name":"Joël","full_name":"Ouaknine, Joël"},{"last_name":"Worrell","full_name":"Worrell, James","first_name":"James"}],"month":"08","conference":{"name":"ICALP: Automata, Languages and Programming","start_date":"2016-07-12","location":"Rome, Italy","end_date":"2016-07-15"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2018-12-12T10:16:26Z","date_created":"2018-12-12T10:16:26Z","file_id":"5213","file_name":"IST-2017-778-v1+1_LIPIcs-ICALP-2016-100.pdf","file_size":521415,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"system"}],"oa_version":"Published Version","day":"01","status":"public","type":"conference","alternative_title":["LIPIcs"],"pubrep_id":"778","date_updated":"2021-01-12T06:48:03Z","oa":1,"title":"On the skolem problem for continuous linear dynamical systems","has_accepted_license":"1","intvolume":"        55","scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["004","006"],"abstract":[{"lang":"eng","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."}],"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"}],"date_published":"2016-08-01T00:00:00Z","publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik","volume":55,"quality_controlled":"1","department":[{"_id":"KrCh"}],"year":"2016","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).","citation":{"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>","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>","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.","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.","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>.","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>."},"publist_id":"6314","date_created":"2018-12-11T11:49:59Z","article_number":"100","ec_funded":1,"_id":"1069","file_date_updated":"2018-12-12T10:16:26Z","doi":"10.4230/LIPIcs.ICALP.2016.100"},{"language":[{"iso":"eng"}],"intvolume":"        55","has_accepted_license":"1","scopus_import":1,"oa":1,"pubrep_id":"812","date_updated":"2021-01-12T06:48:03Z","title":"Computation tree logic for synchronization properties","alternative_title":["LIPIcs"],"type":"conference","status":"public","conference":{"end_date":"2016-07-15","location":"Rome, Italy","start_date":"2016-07-12","name":"ICALP: Automata, Languages and Programming"},"month":"01","day":"01","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","relation":"main_file","file_size":546133,"access_level":"open_access","file_name":"IST-2017-812-v1+1_LIPIcs-ICALP-2016-98.pdf","file_id":"4714","date_updated":"2018-12-12T10:08:52Z","date_created":"2018-12-12T10:08:52Z"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"}],"doi":"10.4230/LIPIcs.ICALP.2016.98","file_date_updated":"2018-12-12T10:08:52Z","_id":"1070","ec_funded":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","year":"2016","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.","short":"K. Chatterjee, L. Doyen, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016.","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>","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.","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>"},"date_created":"2018-12-11T11:49:59Z","publist_id":"6313","publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik","date_published":"2016-01-01T00:00:00Z","department":[{"_id":"KrCh"}],"volume":55,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"ddc":["005"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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. "}],"publication_status":"published"},{"_id":"1071","file_date_updated":"2018-12-12T10:14:31Z","doi":"10.4230/LIPIcs.ESA.2016.28","year":"2016","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).","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>","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2016. Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs. ESA: European Symposium on Algorithms, LIPIcs, vol. 57, 28.","mla":"Chatterjee, Krishnendu, et al. <i>Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant Treewidth Graphs</i>. Vol. 57, 28, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">10.4230/LIPIcs.ESA.2016.28</a>.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant Treewidth Graphs,” Vol. 57. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016. <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>","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.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016."},"date_created":"2018-12-11T11:49:59Z","publist_id":"6312","related_material":{"record":[{"id":"821","relation":"dissertation_contains","status":"public"}]},"article_number":"28","ec_funded":1,"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"date_published":"2016-08-01T00:00:00Z","publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik","quality_controlled":"1","volume":57,"department":[{"_id":"KrCh"}],"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["004","006"],"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. "}],"language":[{"iso":"eng"}],"date_updated":"2023-09-07T12:01:58Z","oa":1,"pubrep_id":"777","title":"Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs","scopus_import":1,"has_accepted_license":"1","intvolume":"        57","type":"conference","status":"public","alternative_title":["LIPIcs"],"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"}],"month":"08","conference":{"name":"ESA: European Symposium on Algorithms","start_date":"2016-08-22","location":"Aarhus, Denmark","end_date":"2016-08-24"},"file":[{"date_updated":"2018-12-12T10:14:31Z","date_created":"2018-12-12T10:14:31Z","file_id":"5084","file_name":"IST-2017-777-v1+1_LIPIcs-ESA-2016-28.pdf","access_level":"open_access","file_size":579225,"content_type":"application/pdf","relation":"main_file","creator":"system"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","day":"01"},{"publication":"APS March Meeting 2016","language":[{"iso":"eng"}],"intvolume":"        61","issue":"2","article_processing_charge":"No","date_updated":"2022-02-08T10:44:06Z","oa":1,"title":"Study of vortex states and dynamics in mesoscopic superconducting samples with MFM","status":"public","type":"conference","alternative_title":["Bulletin of the American Physical Society"],"month":"03","publication_identifier":{"issn":["0003-0503"]},"conference":{"location":"Baltimore, MD, United States","end_date":"2016-03-18","name":"APS: American Physical Society","start_date":"2016-03-14"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","main_file_link":[{"url":"https://meetings.aps.org/Meeting/MAR16/Session/E25.7","open_access":"1"}],"day":"01","author":[{"first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"full_name":"Naibert, Tyler","first_name":"Tyler","last_name":"Naibert"},{"full_name":"Chua, Victor","first_name":"Victor","last_name":"Chua"},{"last_name":"Budakian","full_name":"Budakian, Raffi","first_name":"Raffi"}],"_id":"10746","article_number":"E25.00007","year":"2016","citation":{"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.","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.","chicago":"Polshyn, Hryhoriy, Tyler Naibert, Victor Chua, and Raffi Budakian. “Study of Vortex States and Dynamics in Mesoscopic Superconducting Samples with MFM.” In <i>APS March Meeting 2016</i>, Vol. 61. American Physical Society, 2016.","ama":"Polshyn H, Naibert T, Chua V, Budakian R. Study of vortex states and dynamics in mesoscopic superconducting samples with MFM. In: <i>APS March Meeting 2016</i>. Vol 61. American Physical Society; 2016.","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."},"date_created":"2022-02-08T09:55:09Z","date_published":"2016-03-01T00:00:00Z","publisher":"American Physical Society","quality_controlled":"1","volume":61,"extern":"1","abstract":[{"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.","lang":"eng"}],"publication_status":"published"},{"publisher":"American Physical Society","date_published":"2016-03-01T00:00:00Z","extern":"1","quality_controlled":"1","volume":61,"publication_status":"published","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"}],"_id":"10747","year":"2016","citation":{"ista":"Naibert T, Polshyn H, Wolin B, Durkin M, Garrido Menacho R, Shem IM, Chua V, Hughes T, Mason N, Budakian R. 2016. Stochastic resonance magnetic force microscopy imaging of Josephson arrays. APS March Meeting 2016. APS: American Physical Society, Bulletin of the American Physical Society, vol. 61, H25.00006.","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.","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.","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."},"date_created":"2022-02-08T10:10:39Z","article_number":"H25.00006","alternative_title":["Bulletin of the American Physical Society"],"type":"conference","status":"public","author":[{"last_name":"Naibert","first_name":"Tyler","full_name":"Naibert, Tyler"},{"first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"last_name":"Wolin","first_name":"Brian","full_name":"Wolin, Brian"},{"full_name":"Durkin, Malcolm","first_name":"Malcolm","last_name":"Durkin"},{"last_name":"Garrido Menacho","first_name":"Rita","full_name":"Garrido Menacho, Rita"},{"last_name":"Shem","full_name":"Shem, Ian Mondragon","first_name":"Ian Mondragon"},{"first_name":"Victor","full_name":"Chua, Victor","last_name":"Chua"},{"last_name":"Hughes","first_name":"Taylor","full_name":"Hughes, Taylor"},{"last_name":"Mason","first_name":"Nadya","full_name":"Mason, Nadya"},{"last_name":"Budakian","full_name":"Budakian, Raffi","first_name":"Raffi"}],"conference":{"name":"APS: American Physical Society","start_date":"2016-03-14","location":"Baltimore, MD, United States","end_date":"2016-03-18"},"month":"03","publication_identifier":{"issn":["0003-0503"]},"main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR16/Session/H25.6"}],"oa_version":"Published Version","day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"publication":"APS March Meeting 2016","date_updated":"2022-02-08T10:43:33Z","oa":1,"issue":"2","article_processing_charge":"No","title":"Stochastic resonance magnetic force microscopy imaging of Josephson arrays","intvolume":"        61"}]