[{"scopus_import":"1","citation":{"chicago":"Cheng, Bingqing, Christoph Dellago, and Michele Ceriotti. “Theoretical Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics and Kinetics.” <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry, 2018. <a href=\"https://doi.org/10.1039/c8cp04561e\">https://doi.org/10.1039/c8cp04561e</a>.","short":"B. Cheng, C. Dellago, M. Ceriotti, Physical Chemistry Chemical Physics 20 (2018) 28732–28740.","apa":"Cheng, B., Dellago, C., &#38; Ceriotti, M. (2018). Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c8cp04561e\">https://doi.org/10.1039/c8cp04561e</a>","ama":"Cheng B, Dellago C, Ceriotti M. Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. <i>Physical Chemistry Chemical Physics</i>. 2018;20(45):28732-28740. doi:<a href=\"https://doi.org/10.1039/c8cp04561e\">10.1039/c8cp04561e</a>","ista":"Cheng B, Dellago C, Ceriotti M. 2018. Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. 20(45), 28732–28740.","mla":"Cheng, Bingqing, et al. “Theoretical Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics and Kinetics.” <i>Physical Chemistry Chemical Physics</i>, vol. 20, no. 45, Royal Society of Chemistry, 2018, pp. 28732–40, doi:<a href=\"https://doi.org/10.1039/c8cp04561e\">10.1039/c8cp04561e</a>.","ieee":"B. Cheng, C. Dellago, and M. Ceriotti, “Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics,” <i>Physical Chemistry Chemical Physics</i>, vol. 20, no. 45. Royal Society of Chemistry, pp. 28732–28740, 2018."},"intvolume":"        20","abstract":[{"lang":"eng","text":"Estimating the homogeneous ice nucleation rate from undercooled liquid water is crucial for understanding many important physical phenomena and technological applications, and challenging for both experiments and theory. From a theoretical point of view, difficulties arise due to the long time scales required, as well as the numerous nucleation pathways involved to form ice nuclei with different stacking disorders. We computed the homogeneous ice nucleation rate at a physically relevant undercooling for a single-site water model, taking into account the diffuse nature of ice–water interfaces, stacking disorders in ice nuclei, and the addition rate of particles to the critical nucleus. We disentangled and investigated the relative importance of all the terms, including interfacial free energy, entropic contributions and the kinetic prefactor, that contribute to the overall nucleation rate. Breaking down the problem into pieces not only provides physical insights into ice nucleation, but also sheds light on the long-standing discrepancy between different theoretical predictions, as well as between theoretical and experimental determinations of the nucleation rate. Moreover, we pinpoint the main shortcomings and suggest strategies to systematically improve the existing simulation methods."}],"external_id":{"pmid":["30412211"],"arxiv":["1807.05551"]},"issue":"45","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"journal_article","publisher":"Royal Society of Chemistry","oa_version":"Preprint","author":[{"first_name":"Bingqing","full_name":"Cheng, Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"},{"last_name":"Dellago","first_name":"Christoph","full_name":"Dellago, Christoph"},{"first_name":"Michele","full_name":"Ceriotti, Michele","last_name":"Ceriotti"}],"article_type":"original","extern":"1","article_processing_charge":"No","publication_status":"published","publication_identifier":{"eissn":["1463-9084"],"issn":["1463-9076"]},"quality_controlled":"1","arxiv":1,"language":[{"iso":"eng"}],"date_published":"2018-12-07T00:00:00Z","page":"28732-28740","date_created":"2021-07-15T12:51:44Z","date_updated":"2021-08-09T12:36:47Z","title":"Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics","year":"2018","_id":"9668","publication":"Physical Chemistry Chemical Physics","pmid":1,"doi":"10.1039/c8cp04561e","month":"12","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1807.05551","open_access":"1"}],"volume":20,"day":"07"},{"citation":{"ista":"Cheng B, Ceriotti M. 2018. Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. 97(5), 054102.","ieee":"B. Cheng and M. Ceriotti, “Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids,” <i>Physical Review B</i>, vol. 97, no. 5. American Physical Society, 2018.","mla":"Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids.” <i>Physical Review B</i>, vol. 97, no. 5, 054102, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/physrevb.97.054102\">10.1103/physrevb.97.054102</a>.","short":"B. Cheng, M. Ceriotti, Physical Review B 97 (2018).","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids.” <i>Physical Review B</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/physrevb.97.054102\">https://doi.org/10.1103/physrevb.97.054102</a>.","ama":"Cheng B, Ceriotti M. Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. <i>Physical Review B</i>. 2018;97(5). doi:<a href=\"https://doi.org/10.1103/physrevb.97.054102\">10.1103/physrevb.97.054102</a>","apa":"Cheng, B., &#38; Ceriotti, M. (2018). Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.97.054102\">https://doi.org/10.1103/physrevb.97.054102</a>"},"scopus_import":"1","abstract":[{"lang":"eng","text":"The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from trivial, so the potential energy of a system is often used as a proxy. In this paper, we use a combination of thermodynamic integration methods to accurately evaluate the Gibbs free energies associated with defects in crystals, including the vacancy formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron, and cobalt. We quantify the importance of entropic and anharmonic effects in determining the free energies of defects at high temperatures, and show that the potential energy approximation as well as the harmonic approximation may produce inaccurate or even qualitatively wrong results. Our calculations manifest the necessity to employ accurate free energy methods such as thermodynamic integration to estimate the stability of crystallographic defects at high temperatures."}],"intvolume":"        97","external_id":{"arxiv":["1710.02815"]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"journal_article","issue":"5","oa":1,"publisher":"American Physical Society","oa_version":"Preprint","author":[{"last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing","full_name":"Cheng, Bingqing"},{"last_name":"Ceriotti","first_name":"Michele","full_name":"Ceriotti, Michele"}],"article_type":"original","extern":"1","article_processing_charge":"No","article_number":"054102","publication_status":"published","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"quality_controlled":"1","arxiv":1,"language":[{"iso":"eng"}],"date_published":"2018-02-01T00:00:00Z","date_created":"2021-07-19T09:39:48Z","date_updated":"2021-08-09T12:38:26Z","title":"Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids","publication":"Physical Review B","year":"2018","_id":"9687","doi":"10.1103/physrevb.97.054102","month":"02","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.02815"}],"status":"public","day":"01","volume":97},{"day":"21","status":"public","month":"11","doi":"10.15479/AT:ISTA:th1057","_id":"10","year":"2018","degree_awarded":"PhD","file_date_updated":"2021-02-11T11:17:16Z","title":"Role of genomic imprinting in cerebral cortex development","supervisor":[{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"date_created":"2018-12-11T11:44:08Z","date_updated":"2023-09-07T12:40:44Z","page":"1 - 139","date_published":"2018-11-21T00:00:00Z","language":[{"iso":"eng"}],"ddc":["570"],"pubrep_id":"1057","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","article_processing_charge":"No","file":[{"file_name":"Thesis_LaukoterSusanne_FINAL.docx","file_id":"6396","creator":"dernst","embargo_to":"open_access","checksum":"41fdbf5fdce312802935d88a8ad9932c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-05-10T07:47:04Z","access_level":"closed","relation":"source_file","date_updated":"2019-11-23T23:30:03Z","file_size":17949175},{"file_id":"6397","embargo":"2019-11-21","file_name":"Thesis_LaukoterSusanne_FINAL.pdf","content_type":"application/pdf","checksum":"53001a9a0c9e570e598d861bb0af28aa","file_size":21187245,"access_level":"open_access","date_updated":"2021-02-11T11:17:16Z","relation":"main_file","date_created":"2019-05-10T07:47:04Z","creator":"dernst"}],"author":[{"full_name":"Laukoter, Susanne","first_name":"Susanne","last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","oa":1,"department":[{"_id":"SiHi"}],"abstract":[{"text":"Genomic imprinting is an epigenetic process that leads to parent of origin-specific gene expression in a subset of genes. Imprinted genes are essential for brain development, and deregulation of imprinting is associated with neurodevelopmental diseases and the pathogenesis of psychiatric disorders. However, the cell-type specificity of imprinting at single cell resolution, and how imprinting and thus gene dosage regulates neuronal circuit assembly is still largely unknown. Here, MADM (Mosaic Analysis with Double Markers) technology was employed to assess genomic imprinting at single cell level. By visualizing MADM-induced uniparental disomies (UPDs) in distinct colors at single cell level in genetic mosaic animals, this experimental paradigm provides a unique quantitative platform to systematically assay the UPD-mediated imbalances in imprinted gene expression at unprecedented resolution. An experimental pipeline based on FACS, RNA-seq and bioinformatics analysis was established and applied to systematically map cell-type-specific ‘imprintomes’ in the mouse brain. The results revealed that parental-specific expression of imprinted genes per se is rarely cell-type-specific even at the individual cell level. Conversely, when we extended the comparison to downstream responses resulting from imbalanced imprinted gene expression, we discovered an unexpectedly high degree of cell-type specificity. Furthermore, we determined a novel function of genomic imprinting in cortical astrocyte production and in olfactory bulb (OB) granule cell generation. These results suggest important functional implication of genomic imprinting for generating cell-type diversity in the brain. In addition, MADM provides a powerful tool to study candidate genes by concomitant genetic manipulation and fluorescent labelling of single cells. MADM-based candidate gene approach was utilized to identify potential imprinted genes involved in the generation of cortical astrocytes and OB granule cells. We investigated p57Kip2, a maternally expressed gene and known cell cycle regulator. Although we found that p57Kip2 does not play a role in these processes, we detected an unexpected function of the paternal allele previously thought to be silent. Finally, we took advantage of a key property of MADM which is to allow unambiguous investigation of environmental impact on single cells. The experimental pipeline based on FACS and RNA-seq analysis of MADM-labeled cells was established to probe the functional differences of single cell loss of gene function compared to global loss of function on a transcriptional level. With this method, both common and distinct responses were isolated due to cell-autonomous and non-autonomous effects acting on genotypically identical cells. As a result, transcriptional changes were identified which result solely from the surrounding environment. Using the MADM technology to study genomic imprinting at single cell resolution, we have identified cell-type-specific gene expression, novel gene function and the impact of environment on single cell transcriptomes. Together, these provide important insights to the understanding of mechanisms regulating cell-type specificity and thus diversity in the brain.","lang":"eng"}],"has_accepted_license":"1","publist_id":"8046","citation":{"ista":"Laukoter S. 2018. Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria.","ieee":"S. Laukoter, “Role of genomic imprinting in cerebral cortex development,” Institute of Science and Technology Austria, 2018.","mla":"Laukoter, Susanne. <i>Role of Genomic Imprinting in Cerebral Cortex Development</i>. Institute of Science and Technology Austria, 2018, pp. 1–139, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1057\">10.15479/AT:ISTA:th1057</a>.","short":"S. Laukoter, Role of Genomic Imprinting in Cerebral Cortex Development, Institute of Science and Technology Austria, 2018.","chicago":"Laukoter, Susanne. “Role of Genomic Imprinting in Cerebral Cortex Development.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1057\">https://doi.org/10.15479/AT:ISTA:th1057</a>.","ama":"Laukoter S. Role of genomic imprinting in cerebral cortex development. 2018:1-139. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1057\">10.15479/AT:ISTA:th1057</a>","apa":"Laukoter, S. (2018). <i>Role of genomic imprinting in cerebral cortex development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1057\">https://doi.org/10.15479/AT:ISTA:th1057</a>"}},{"type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"issue":"10","publisher":"Oxford University Press","oa_version":"Preprint","author":[{"first_name":"László","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"first_name":"Dominik J","full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","orcid":"0000-0002-2904-1856"}],"ec_funded":1,"citation":{"ieee":"L. Erdös and D. J. Schröder, “Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues,” <i>International Mathematics Research Notices</i>, vol. 2018, no. 10. Oxford University Press, pp. 3255–3298, 2018.","mla":"Erdös, László, and Dominik J. Schröder. “Fluctuations of Rectangular Young Diagrams of Interlacing Wigner Eigenvalues.” <i>International Mathematics Research Notices</i>, vol. 2018, no. 10, Oxford University Press, 2018, pp. 3255–98, doi:<a href=\"https://doi.org/10.1093/imrn/rnw330\">10.1093/imrn/rnw330</a>.","ista":"Erdös L, Schröder DJ. 2018. Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. International Mathematics Research Notices. 2018(10), 3255–3298.","apa":"Erdös, L., &#38; Schröder, D. J. (2018). Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rnw330\">https://doi.org/10.1093/imrn/rnw330</a>","ama":"Erdös L, Schröder DJ. Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. <i>International Mathematics Research Notices</i>. 2018;2018(10):3255-3298. doi:<a href=\"https://doi.org/10.1093/imrn/rnw330\">10.1093/imrn/rnw330</a>","short":"L. Erdös, D.J. Schröder, International Mathematics Research Notices 2018 (2018) 3255–3298.","chicago":"Erdös, László, and Dominik J Schröder. “Fluctuations of Rectangular Young Diagrams of Interlacing Wigner Eigenvalues.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/imrn/rnw330\">https://doi.org/10.1093/imrn/rnw330</a>."},"scopus_import":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"6179","status":"public"}]},"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"publist_id":"6383","abstract":[{"text":"We prove a new central limit theorem (CLT) for the difference of linear eigenvalue statistics of a Wigner random matrix H and its minor H and find that the fluctuation is much smaller than the fluctuations of the individual linear statistics, as a consequence of the strong correlation between the eigenvalues of H and H. In particular, our theorem identifies the fluctuation of Kerov's rectangular Young diagrams, defined by the interlacing eigenvalues ofH and H, around their asymptotic shape, the Vershik'Kerov'Logan'Shepp curve. Young diagrams equipped with the Plancherel measure follow the same limiting shape. For this, algebraically motivated, ensemble a CLT has been obtained in Ivanov and Olshanski [20] which is structurally similar to our result but the variance is different, indicating that the analogy between the two models has its limitations. Moreover, our theorem shows that Borodin's result [7] on the convergence of the spectral distribution of Wigner matrices to a Gaussian free field also holds in derivative sense.","lang":"eng"}],"intvolume":"      2018","external_id":{"isi":["000441668300009"],"arxiv":["1608.05163"]},"department":[{"_id":"LaEr"}],"title":"Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues","publication":"International Mathematics Research Notices","year":"2018","_id":"1012","doi":"10.1093/imrn/rnw330","month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.05163"}],"status":"public","volume":2018,"day":"18","article_processing_charge":"No","publication_status":"published","isi":1,"publication_identifier":{"issn":["10737928"]},"arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"page":"3255-3298","date_published":"2018-05-18T00:00:00Z","date_created":"2018-12-11T11:49:41Z","date_updated":"2023-09-22T09:44:21Z"},{"publication_identifier":{"eissn":["2569-2925"]},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["000"],"article_processing_charge":"No","publication_status":"published","page":"214-242","date_published":"2018-01-01T00:00:00Z","date_created":"2021-11-14T23:01:25Z","date_updated":"2021-11-15T10:48:49Z","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.13154/tches.v2018.i3.214-242","file_date_updated":"2021-11-15T10:27:29Z","title":"Evaluation and monitoring of free running oscillators serving as source of randomness","publication":"IACR Transactions on Cryptographic Hardware and Embedded Systems","license":"https://creativecommons.org/licenses/by/4.0/","_id":"10286","year":"2018","status":"public","volume":2018,"day":"01","month":"01","citation":{"apa":"Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., &#38; Fischer, V. (2018). Evaluation and monitoring of free running oscillators serving as source of randomness. <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>. International Association for Cryptologic Research. <a href=\"https://doi.org/10.13154/tches.v2018.i3.214-242\">https://doi.org/10.13154/tches.v2018.i3.214-242</a>","ama":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and monitoring of free running oscillators serving as source of randomness. <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>. 2018;2018(3):214-242. doi:<a href=\"https://doi.org/10.13154/tches.v2018.i3.214-242\">10.13154/tches.v2018.i3.214-242</a>","chicago":"Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>. International Association for Cryptologic Research, 2018. <a href=\"https://doi.org/10.13154/tches.v2018.i3.214-242\">https://doi.org/10.13154/tches.v2018.i3.214-242</a>.","short":"E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.","mla":"Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>, vol. 2018, no. 3, International Association for Cryptologic Research, 2018, pp. 214–42, doi:<a href=\"https://doi.org/10.13154/tches.v2018.i3.214-242\">10.13154/tches.v2018.i3.214-242</a>.","ieee":"E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer, “Evaluation and monitoring of free running oscillators serving as source of randomness,” <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>, vol. 2018, no. 3. International Association for Cryptologic Research, pp. 214–242, 2018.","ista":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242."},"scopus_import":"1","department":[{"_id":"KrPi"}],"abstract":[{"lang":"eng","text":"In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied."}],"has_accepted_license":"1","intvolume":"      2018","oa_version":"Published Version","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"issue":"3","publisher":"International Association for Cryptologic Research","article_type":"original","file":[{"date_created":"2021-11-15T10:27:29Z","relation":"main_file","date_updated":"2021-11-15T10:27:29Z","access_level":"open_access","file_size":955755,"checksum":"b816b848f046c48a8357700d9305dce5","content_type":"application/pdf","creator":"cchlebak","success":1,"file_id":"10289","file_name":"2018_IACR_Allini.pdf"}],"author":[{"full_name":"Allini, Elie Noumon","first_name":"Elie Noumon","last_name":"Allini"},{"last_name":"Skórski","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","full_name":"Skórski, Maciej"},{"last_name":"Petura","full_name":"Petura, Oto","first_name":"Oto"},{"last_name":"Bernard","full_name":"Bernard, Florent","first_name":"Florent"},{"full_name":"Laban, Marek","first_name":"Marek","last_name":"Laban"},{"first_name":"Viktor","full_name":"Fischer, Viktor","last_name":"Fischer"}]},{"pmid":1,"doi":"10.1021/acs.jpcb.8b07805","title":"Statistical mechanics of globular oligomer formation by protein molecules","_id":"10357","year":"2018","publication":"The Journal of Physical Chemistry B","status":"public","volume":122,"day":"18","month":"10","publication_identifier":{"eissn":["1520-5207"],"issn":["1520-6106"]},"article_processing_charge":"No","extern":"1","publication_status":"published","date_published":"2018-10-18T00:00:00Z","page":"11721-11730","date_created":"2021-11-26T11:55:12Z","date_updated":"2021-11-26T12:40:02Z","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"None","issue":"49","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"American Chemical Society","article_type":"original","author":[{"first_name":"Alexander J.","full_name":"Dear, Alexander J.","last_name":"Dear"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"},{"full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T.","last_name":"Michaels"},{"last_name":"Dobson","first_name":"Christopher M.","full_name":"Dobson, Christopher M."},{"first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J.","last_name":"Knowles"}],"scopus_import":"1","acknowledgement":"We acknowledge support from the Schiff Foundation (A.J.D.), the Royal Society (A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Wellcome Trust (T.P.J.K.), the Cambridge Centre for Misfolding Diseases (T.P.J.K.), the BBSRC (T.P.J.K.), the Frances and Augustus Newman foundation (T.P.J.K.). The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (Grant FP7/2007-2013) through the ERC Grant PhysProt (Agreement No. 337969). We thank Daan Frenkel for several useful discussions.","citation":{"ista":"Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. 2018. Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. 122(49), 11721–11730.","ieee":"A. J. Dear, A. Šarić, T. C. T. Michaels, C. M. Dobson, and T. P. J. Knowles, “Statistical mechanics of globular oligomer formation by protein molecules,” <i>The Journal of Physical Chemistry B</i>, vol. 122, no. 49. American Chemical Society, pp. 11721–11730, 2018.","mla":"Dear, Alexander J., et al. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” <i>The Journal of Physical Chemistry B</i>, vol. 122, no. 49, American Chemical Society, 2018, pp. 11721–30, doi:<a href=\"https://doi.org/10.1021/acs.jpcb.8b07805\">10.1021/acs.jpcb.8b07805</a>.","short":"A.J. Dear, A. Šarić, T.C.T. Michaels, C.M. Dobson, T.P.J. Knowles, The Journal of Physical Chemistry B 122 (2018) 11721–11730.","chicago":"Dear, Alexander J., Anđela Šarić, Thomas C. T. Michaels, Christopher M. Dobson, and Tuomas P. J. Knowles. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” <i>The Journal of Physical Chemistry B</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acs.jpcb.8b07805\">https://doi.org/10.1021/acs.jpcb.8b07805</a>.","apa":"Dear, A. J., Šarić, A., Michaels, T. C. T., Dobson, C. M., &#38; Knowles, T. P. J. (2018). Statistical mechanics of globular oligomer formation by protein molecules. <i>The Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpcb.8b07805\">https://doi.org/10.1021/acs.jpcb.8b07805</a>","ama":"Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. Statistical mechanics of globular oligomer formation by protein molecules. <i>The Journal of Physical Chemistry B</i>. 2018;122(49):11721-11730. doi:<a href=\"https://doi.org/10.1021/acs.jpcb.8b07805\">10.1021/acs.jpcb.8b07805</a>"},"keyword":["materials chemistry"],"external_id":{"pmid":["30336667"]},"intvolume":"       122","abstract":[{"lang":"eng","text":"The misfolding and aggregation of proteins into linear fibrils is widespread in human biology, for example, in connection with amyloid formation and the pathology of neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. The oligomeric species that are formed in the early stages of protein aggregation are of great interest, having been linked with the cellular toxicity associated with these conditions. However, these species are not characterized in any detail experimentally, and their properties are not well understood. Many of these species have been found to have approximately spherical morphology and to be held together by hydrophobic interactions. We present here an analytical statistical mechanical model of globular oligomer formation from simple idealized amphiphilic protein monomers and show that this correlates well with Monte Carlo simulations of oligomer formation. We identify the controlling parameters of the model, which are closely related to simple quantities that may be fitted directly from experiment. We predict that globular oligomers are unlikely to form at equilibrium in many polypeptide systems but instead form transiently in the early stages of amyloid formation. We contrast the globular model of oligomer formation to a well-established model of linear oligomer formation, highlighting how the differing ensemble properties of linear and globular oligomers offer a potential strategy for characterizing oligomers from experimental measurements."}]},{"publisher":"Taylor & Francis","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","issue":"21-22","oa":1,"oa_version":"Preprint","author":[{"last_name":"Michaels","full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T."},{"first_name":"Lucie X.","full_name":"Liu, Lucie X.","last_name":"Liu"},{"first_name":"Samo","full_name":"Curk, Samo","last_name":"Curk"},{"full_name":"Bolhuis, Peter G.","first_name":"Peter G.","last_name":"Bolhuis"},{"full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"},{"last_name":"Knowles","full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J."}],"article_type":"original","acknowledgement":"We thank Claudia Flandoli for the help with illustrations.","citation":{"ama":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. Reaction rate theory for supramolecular kinetics: application to protein aggregation. <i>Molecular Physics</i>. 2018;116(21-22):3055-3065. doi:<a href=\"https://doi.org/10.1080/00268976.2018.1474280\">10.1080/00268976.2018.1474280</a>","apa":"Michaels, T. C. T., Liu, L. X., Curk, S., Bolhuis, P. G., Šarić, A., &#38; Knowles, T. P. J. (2018). Reaction rate theory for supramolecular kinetics: application to protein aggregation. <i>Molecular Physics</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/00268976.2018.1474280\">https://doi.org/10.1080/00268976.2018.1474280</a>","short":"T.C.T. Michaels, L.X. Liu, S. Curk, P.G. Bolhuis, A. Šarić, T.P.J. Knowles, Molecular Physics 116 (2018) 3055–3065.","chicago":"Michaels, Thomas C. T., Lucie X. Liu, Samo Curk, Peter G. Bolhuis, Anđela Šarić, and Tuomas P. J. Knowles. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” <i>Molecular Physics</i>. Taylor &#38; Francis, 2018. <a href=\"https://doi.org/10.1080/00268976.2018.1474280\">https://doi.org/10.1080/00268976.2018.1474280</a>.","ieee":"T. C. T. Michaels, L. X. Liu, S. Curk, P. G. Bolhuis, A. Šarić, and T. P. J. Knowles, “Reaction rate theory for supramolecular kinetics: application to protein aggregation,” <i>Molecular Physics</i>, vol. 116, no. 21–22. Taylor &#38; Francis, pp. 3055–3065, 2018.","mla":"Michaels, Thomas C. T., et al. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” <i>Molecular Physics</i>, vol. 116, no. 21–22, Taylor &#38; Francis, 2018, pp. 3055–65, doi:<a href=\"https://doi.org/10.1080/00268976.2018.1474280\">10.1080/00268976.2018.1474280</a>.","ista":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. 2018. Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. 116(21–22), 3055–3065."},"scopus_import":"1","abstract":[{"lang":"eng","text":"Probing reaction mechanisms of supramolecular processes in soft and biological matter, such as protein aggregation, is inherently challenging. This is because these processes involve multiple molecular mechanisms that are associated with the rearrangement of large numbers of weak bonds, resulting in complex free energy landscapes with many kinetic barriers. Reaction rate measurements at different temperatures can offer unprecedented insights into the underlying molecular mechanisms. However, to be able to interpret such measurements, a key challenge is to establish which properties of the complex free energy landscapes are probed by the reaction rate. Here, we present a reaction rate theory for supramolecular kinetics based on Kramers theory of diffusive reactions over multiple kinetic barriers. We find that reaction rates for protein aggregation are of the Arrhenius–Eyring type and that the associated activation energies probe only one relevant barrier along the respective free energy landscapes. We apply this advancement to interpret, in experiments and in coarse-grained computer simulations, reaction rates of amyloid aggregation in terms of molecular mechanisms and associated thermodynamic signatures. These results suggest a practical extension of the concept of rate-determining steps for complex supramolecular processes and establish a general platform for probing the underlying energy landscape using kinetic measurements."}],"intvolume":"       116","external_id":{"arxiv":["1803.04851"]},"keyword":["physical chemistry"],"publication":"Molecular Physics","_id":"10358","year":"2018","title":"Reaction rate theory for supramolecular kinetics: application to protein aggregation","doi":"10.1080/00268976.2018.1474280","month":"05","volume":116,"day":"24","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.04851"}],"status":"public","publication_status":"published","extern":"1","article_processing_charge":"No","publication_identifier":{"issn":["0026-8976"],"eissn":["1362-3028"]},"language":[{"iso":"eng"}],"arxiv":1,"quality_controlled":"1","date_updated":"2021-11-26T12:39:58Z","date_created":"2021-11-26T12:08:02Z","page":"3055-3065","date_published":"2018-05-24T00:00:00Z"},{"volume":18,"day":"18","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.10147"}],"status":"public","month":"04","pmid":1,"doi":"10.1021/acs.nanolett.8b00786","_id":"10359","year":"2018","publication":"Nano Letters","title":"Controlling cargo trafficking in multicomponent membranes","date_created":"2021-11-26T12:15:47Z","date_updated":"2021-11-26T15:14:08Z","date_published":"2018-04-18T00:00:00Z","page":"5350-5356","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"publication_status":"published","article_processing_charge":"No","extern":"1","article_type":"original","author":[{"first_name":"Tine","full_name":"Curk, Tine","last_name":"Curk"},{"last_name":"Wirnsberger","full_name":"Wirnsberger, Peter","first_name":"Peter"},{"full_name":"Dobnikar, Jure","first_name":"Jure","last_name":"Dobnikar"},{"last_name":"Frenkel","first_name":"Daan","full_name":"Frenkel, Daan"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela"}],"oa_version":"Preprint","publisher":"American Chemical Society","oa":1,"issue":"9","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","external_id":{"pmid":["29667410"]},"keyword":["mechanical engineering","condensed matter physics"],"intvolume":"        18","abstract":[{"text":"Biological membranes typically contain a large number of different components dispersed in small concentrations in the main membrane phase, including proteins, sugars, and lipids of varying geometrical properties. Most of these components do not bind the cargo. Here, we show that such “inert” components can be crucial for the precise control of cross-membrane trafficking. Using a statistical mechanics model and molecular dynamics simulations, we demonstrate that the presence of inert membrane components of small isotropic curvatures dramatically influences cargo endocytosis, even if the total spontaneous curvature of such a membrane remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically included proteins and tethered sugars can, therefore, actively participate in the control of the membrane trafficking of nanoscopic cargo. We find that even a low-level expression of curved inert membrane components can determine the membrane selectivity toward the cargo size and can be used to selectively target membranes of certain compositions. Our results suggest a robust and general method of controlling cargo trafficking by adjusting the membrane composition without needing to alter the concentration of receptors or the average membrane curvature. This study indicates that cells can prepare for any trafficking event by incorporating curved inert components in either of the membrane leaflets.","lang":"eng"}],"scopus_import":"1","citation":{"ista":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. 2018. Controlling cargo trafficking in multicomponent membranes. Nano Letters. 18(9), 5350–5356.","ieee":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, and A. Šarić, “Controlling cargo trafficking in multicomponent membranes,” <i>Nano Letters</i>, vol. 18, no. 9. American Chemical Society, pp. 5350–5356, 2018.","mla":"Curk, Tine, et al. “Controlling Cargo Trafficking in Multicomponent Membranes.” <i>Nano Letters</i>, vol. 18, no. 9, American Chemical Society, 2018, pp. 5350–56, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.8b00786\">10.1021/acs.nanolett.8b00786</a>.","short":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, A. Šarić, Nano Letters 18 (2018) 5350–5356.","chicago":"Curk, Tine, Peter Wirnsberger, Jure Dobnikar, Daan Frenkel, and Anđela Šarić. “Controlling Cargo Trafficking in Multicomponent Membranes.” <i>Nano Letters</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acs.nanolett.8b00786\">https://doi.org/10.1021/acs.nanolett.8b00786</a>.","apa":"Curk, T., Wirnsberger, P., Dobnikar, J., Frenkel, D., &#38; Šarić, A. (2018). Controlling cargo trafficking in multicomponent membranes. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.8b00786\">https://doi.org/10.1021/acs.nanolett.8b00786</a>","ama":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. Controlling cargo trafficking in multicomponent membranes. <i>Nano Letters</i>. 2018;18(9):5350-5356. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.8b00786\">10.1021/acs.nanolett.8b00786</a>"},"acknowledgement":"We acknowledge discussions with Giuseppe Battaglia as well as support from the Herchel Smith scholarship (T.C.), the CAS PIFI fellowship (T.C.), the UCL Institute for the Physics of Living Systems (T.C. and A.Š.), the Austrian Academy of Sciences through a DOC fellowship (P.W.), the European Union Horizon 2020 programme under ETN grant no. 674979-NANOTRANS and FET grant no. 766972-NANOPHLOW (J.D. and D.F.), the Engineering and Physical Sciences Research Council (D.F. and A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (A.Š.). We thank Claudia Flandoli for help with Figure 1."},{"citation":{"short":"S.I.A. Cohen, R. Cukalevski, T.C.T. Michaels, A. Šarić, M. Törnquist, M. Vendruscolo, C.M. Dobson, A.K. Buell, T.P.J. Knowles, S. Linse, Nature Chemistry 10 (2018) 523–531.","chicago":"Cohen, Samuel I. A., Risto Cukalevski, Thomas C. T. Michaels, Anđela Šarić, Mattias Törnquist, Michele Vendruscolo, Christopher M. Dobson, Alexander K. Buell, Tuomas P. J. Knowles, and Sara Linse. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” <i>Nature Chemistry</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41557-018-0023-x\">https://doi.org/10.1038/s41557-018-0023-x</a>.","ama":"Cohen SIA, Cukalevski R, Michaels TCT, et al. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. <i>Nature Chemistry</i>. 2018;10(5):523-531. doi:<a href=\"https://doi.org/10.1038/s41557-018-0023-x\">10.1038/s41557-018-0023-x</a>","apa":"Cohen, S. I. A., Cukalevski, R., Michaels, T. C. T., Šarić, A., Törnquist, M., Vendruscolo, M., … Linse, S. (2018). Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-018-0023-x\">https://doi.org/10.1038/s41557-018-0023-x</a>","ista":"Cohen SIA, Cukalevski R, Michaels TCT, Šarić A, Törnquist M, Vendruscolo M, Dobson CM, Buell AK, Knowles TPJ, Linse S. 2018. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. 10(5), 523–531.","ieee":"S. I. A. Cohen <i>et al.</i>, “Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide,” <i>Nature Chemistry</i>, vol. 10, no. 5. Springer Nature, pp. 523–531, 2018.","mla":"Cohen, Samuel I. A., et al. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” <i>Nature Chemistry</i>, vol. 10, no. 5, Springer Nature, 2018, pp. 523–31, doi:<a href=\"https://doi.org/10.1038/s41557-018-0023-x\">10.1038/s41557-018-0023-x</a>."},"acknowledgement":"We thank B. Jönsson and I. André for helpful discussions. We acknowledge financial support from the Schiff Foundation (S.I.A.C.), St John’s College, Cambridge (S.I.A.C.), the Royal Physiographic Society (R.C.), the Research School FLÄK of Lund University (S.L., R.C.), the Swedish Research Council (S.L.) and its Linneaus Centre Organizing Molecular Matter (S.L.), the Crafoord Foundation (S.L.), Alzheimerfonden (S.L.), the European Research Council (S.L.), NanoLund (S.L.), Knut and Alice Wallenberg Foundation (S.L.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science Foundation (T.C.T.M.), Magdalene College, Cambridge (A.K.B.), the Leverhulme Trust (A.K.B.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the Wellcome Trust (C.M.D., T.P.J.K., A.Š.), and the Centre for Misfolding Diseases (C.M.D., T.P.J.K, M.V.). A.K.B. thanks the Alzheimer Forschung Initiative (AFI).","scopus_import":"1","abstract":[{"text":"Mapping free-energy landscapes has proved to be a powerful tool for studying reaction mechanisms. Many complex biomolecular assembly processes, however, have remained challenging to access using this approach, including the aggregation of peptides and proteins into amyloid fibrils implicated in a range of disorders. Here, we generalize the strategy used to probe free-energy landscapes in protein folding to determine the activation energies and entropies that characterize each of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which is associated with Alzheimer’s disease. Our results reveal that interactions between monomeric Aβ42 and amyloid fibrils during fibril-dependent secondary nucleation fundamentally reverse the thermodynamic signature of this process relative to primary nucleation, even though both processes generate aggregates from soluble peptides. By mapping the energetic and entropic contributions along the reaction trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results from the enthalpic stabilization of adsorbing peptides in conformations amenable to nucleation, resulting in a dramatic lowering of the activation energy for nucleation.","lang":"eng"}],"intvolume":"        10","external_id":{"pmid":["29581486"]},"keyword":["general chemical engineering","general chemistry"],"publisher":"Springer Nature","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"5","oa_version":"None","author":[{"first_name":"Samuel I. A.","full_name":"Cohen, Samuel I. A.","last_name":"Cohen"},{"first_name":"Risto","full_name":"Cukalevski, Risto","last_name":"Cukalevski"},{"last_name":"Michaels","first_name":"Thomas C. T.","full_name":"Michaels, Thomas C. T."},{"full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139"},{"full_name":"Törnquist, Mattias","first_name":"Mattias","last_name":"Törnquist"},{"first_name":"Michele","full_name":"Vendruscolo, Michele","last_name":"Vendruscolo"},{"last_name":"Dobson","first_name":"Christopher M.","full_name":"Dobson, Christopher M."},{"full_name":"Buell, Alexander K.","first_name":"Alexander K.","last_name":"Buell"},{"full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J.","last_name":"Knowles"},{"last_name":"Linse","full_name":"Linse, Sara","first_name":"Sara"}],"article_type":"original","publication_status":"published","extern":"1","article_processing_charge":"No","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2021-11-26T12:41:38Z","date_updated":"2021-11-26T15:14:00Z","page":"523-531","date_published":"2018-03-26T00:00:00Z","publication":"Nature Chemistry","_id":"10360","year":"2018","title":"Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide","doi":"10.1038/s41557-018-0023-x","pmid":1,"month":"03","volume":10,"day":"26","status":"public"},{"publication_identifier":{"eissn":["1545-1593"],"issn":["0066-426X"]},"publication_status":"published","extern":"1","article_processing_charge":"No","date_created":"2021-11-26T12:52:12Z","date_updated":"2021-11-26T15:58:19Z","date_published":"2018-02-28T00:00:00Z","page":"273-298","language":[{"iso":"eng"}],"quality_controlled":"1","pmid":1,"doi":"10.1146/annurev-physchem-050317-021322","_id":"10361","year":"2018","publication":"Annual Review of Physical Chemistry","title":"Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation","volume":69,"day":"28","status":"public","month":"02","scopus_import":"1","citation":{"ama":"Michaels TCT, Šarić A, Habchi J, et al. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. <i>Annual Review of Physical Chemistry</i>. 2018;69(1):273-298. doi:<a href=\"https://doi.org/10.1146/annurev-physchem-050317-021322\">10.1146/annurev-physchem-050317-021322</a>","apa":"Michaels, T. C. T., Šarić, A., Habchi, J., Chia, S., Meisl, G., Vendruscolo, M., … Knowles, T. P. J. (2018). Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. <i>Annual Review of Physical Chemistry</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-physchem-050317-021322\">https://doi.org/10.1146/annurev-physchem-050317-021322</a>","chicago":"Michaels, Thomas C.T., Anđela Šarić, Johnny Habchi, Sean Chia, Georg Meisl, Michele Vendruscolo, Christopher M. Dobson, and Tuomas P.J. Knowles. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” <i>Annual Review of Physical Chemistry</i>. Annual Reviews, 2018. <a href=\"https://doi.org/10.1146/annurev-physchem-050317-021322\">https://doi.org/10.1146/annurev-physchem-050317-021322</a>.","short":"T.C.T. Michaels, A. Šarić, J. Habchi, S. Chia, G. Meisl, M. Vendruscolo, C.M. Dobson, T.P.J. Knowles, Annual Review of Physical Chemistry 69 (2018) 273–298.","ieee":"T. C. T. Michaels <i>et al.</i>, “Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation,” <i>Annual Review of Physical Chemistry</i>, vol. 69, no. 1. Annual Reviews, pp. 273–298, 2018.","mla":"Michaels, Thomas C. T., et al. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” <i>Annual Review of Physical Chemistry</i>, vol. 69, no. 1, Annual Reviews, 2018, pp. 273–98, doi:<a href=\"https://doi.org/10.1146/annurev-physchem-050317-021322\">10.1146/annurev-physchem-050317-021322</a>.","ista":"Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM, Knowles TPJ. 2018. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. 69(1), 273–298."},"acknowledgement":"We acknowledge support from the Swiss National Science Foundation (T.C.T.M.); Peterhouse,\r\nCambridge (T.C.T.M.); the Royal Society (A.S.); the Academy of Medical Sciences (A.S.); the\r\nWellcome Trust (A.S., M.V., C.M.D., T.P.J.K.); the Cambridge Centre for Misfolding Diseases\r\n(M.V., C.M.D., T.P.J.K.); the Biotechnology and Biological Sciences Research Council (C.M.D.,\r\nT.P.J.K.); and the Frances and Augustus Newman Foundation (T.P.J.K.). The research leading\r\nto these results has received funding from the European Research Council (ERC) under the\r\nEuropean Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant\r\nPhysProt (337969).","external_id":{"pmid":["29490200"]},"keyword":["physical and theoretical chemistry"],"intvolume":"        69","abstract":[{"lang":"eng","text":"Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation."}],"oa_version":"None","publisher":"Annual Reviews","issue":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","article_type":"original","author":[{"first_name":"Thomas C.T.","full_name":"Michaels, Thomas C.T.","last_name":"Michaels"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela"},{"last_name":"Habchi","first_name":"Johnny","full_name":"Habchi, Johnny"},{"first_name":"Sean","full_name":"Chia, Sean","last_name":"Chia"},{"full_name":"Meisl, Georg","first_name":"Georg","last_name":"Meisl"},{"first_name":"Michele","full_name":"Vendruscolo, Michele","last_name":"Vendruscolo"},{"first_name":"Christopher M.","full_name":"Dobson, Christopher M.","last_name":"Dobson"},{"first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J.","last_name":"Knowles"}]},{"scopus_import":"1","citation":{"mla":"Fisher, Patrick D. Ellis, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” <i>ACS Nano</i>, vol. 12, no. 2, American Chemical Society, 2018, pp. 1508–18, doi:<a href=\"https://doi.org/10.1021/acsnano.7b08044\">10.1021/acsnano.7b08044</a>.","ieee":"P. D. E. Fisher <i>et al.</i>, “A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement,” <i>ACS Nano</i>, vol. 12, no. 2. American Chemical Society, pp. 1508–1518, 2018.","ista":"Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia TJ, Hoogenboom BW, Lin C, Lusk CP. 2018. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. 12(2), 1508–1518.","ama":"Fisher PDE, Shen Q, Akpinar B, et al. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. <i>ACS Nano</i>. 2018;12(2):1508-1518. doi:<a href=\"https://doi.org/10.1021/acsnano.7b08044\">10.1021/acsnano.7b08044</a>","apa":"Fisher, P. D. E., Shen, Q., Akpinar, B., Davis, L. K., Chung, K. K. H., Baddeley, D., … Lusk, C. P. (2018). A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.7b08044\">https://doi.org/10.1021/acsnano.7b08044</a>","short":"P.D.E. Fisher, Q. Shen, B. Akpinar, L.K. Davis, K.K.H. Chung, D. Baddeley, A. Šarić, T.J. Melia, B.W. Hoogenboom, C. Lin, C.P. Lusk, ACS Nano 12 (2018) 1508–1518.","chicago":"Fisher, Patrick D. Ellis, Qi Shen, Bernice Akpinar, Luke K. Davis, Kenny Kwok Hin Chung, David Baddeley, Anđela Šarić, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” <i>ACS Nano</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acsnano.7b08044\">https://doi.org/10.1021/acsnano.7b08044</a>."},"acknowledgement":"We thank J. Edel and members of the Lusk, Lin and Hoogenboom lab for discussion and acknowledge A. Pyne and R. Thorogate for support carrying out the AFM experiments. This work was funded by the NIH (R21GM109466 to CPL, CL and TJM, DP2GM114830 to CL, RO1GM105672 to CPL, and T32GM007223 to PDEF) and the UK Engineering and Physical Sciences Research Council (EP/L015277/1, EP/L504889/1, and EP/M028100/1).","external_id":{"pmid":["29350911"]},"keyword":["general physics and astronomy"],"intvolume":"        12","abstract":[{"text":"Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties.","lang":"eng"}],"oa_version":"None","publisher":"American Chemical Society","issue":"2","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","article_type":"original","author":[{"last_name":"Fisher","first_name":"Patrick D. Ellis","full_name":"Fisher, Patrick D. Ellis"},{"first_name":"Qi","full_name":"Shen, Qi","last_name":"Shen"},{"full_name":"Akpinar, Bernice","first_name":"Bernice","last_name":"Akpinar"},{"full_name":"Davis, Luke K.","first_name":"Luke K.","last_name":"Davis"},{"full_name":"Chung, Kenny Kwok Hin","first_name":"Kenny Kwok Hin","last_name":"Chung"},{"first_name":"David","full_name":"Baddeley, David","last_name":"Baddeley"},{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela"},{"last_name":"Melia","full_name":"Melia, Thomas J.","first_name":"Thomas J."},{"last_name":"Hoogenboom","full_name":"Hoogenboom, Bart W.","first_name":"Bart W."},{"first_name":"Chenxiang","full_name":"Lin, Chenxiang","last_name":"Lin"},{"last_name":"Lusk","first_name":"C. Patrick","full_name":"Lusk, C. Patrick"}],"publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"publication_status":"published","article_processing_charge":"No","extern":"1","date_updated":"2021-11-26T15:57:02Z","date_created":"2021-11-26T15:15:00Z","date_published":"2018-01-19T00:00:00Z","page":"1508-1518","language":[{"iso":"eng"}],"quality_controlled":"1","pmid":1,"doi":"10.1021/acsnano.7b08044","_id":"10362","year":"2018","publication":"ACS Nano","title":"A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement","volume":12,"day":"19","status":"public","month":"01"},{"issue":"10","oa":1,"type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","oa_version":"Published Version","author":[{"last_name":"Seitner","full_name":"Seitner, Denise","first_name":"Denise"},{"full_name":"Uhse, Simon","first_name":"Simon","last_name":"Uhse"},{"last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","first_name":"Michelle C","full_name":"Gallei, Michelle C"},{"first_name":"Armin","full_name":"Djamei, Armin","last_name":"Djamei"}],"file":[{"file_name":"2018_MolecPlantPath_Seitner.pdf","file_id":"5740","success":1,"creator":"dernst","date_created":"2018-12-18T09:46:00Z","date_updated":"2018-12-18T09:46:00Z","access_level":"open_access","relation":"main_file","file_size":682335,"content_type":"application/pdf"}],"scopus_import":"1","citation":{"apa":"Seitner, D., Uhse, S., Gallei, M. C., &#38; Djamei, A. (2018). The core effector Cce1 is required for early infection of maize by Ustilago maydis. <i>Molecular Plant Pathology</i>. Wiley. <a href=\"https://doi.org/10.1111/mpp.12698\">https://doi.org/10.1111/mpp.12698</a>","ama":"Seitner D, Uhse S, Gallei MC, Djamei A. The core effector Cce1 is required for early infection of maize by Ustilago maydis. <i>Molecular Plant Pathology</i>. 2018;19(10):2277-2287. doi:<a href=\"https://doi.org/10.1111/mpp.12698\">10.1111/mpp.12698</a>","short":"D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19 (2018) 2277–2287.","chicago":"Seitner, Denise, Simon Uhse, Michelle C Gallei, and Armin Djamei. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” <i>Molecular Plant Pathology</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/mpp.12698\">https://doi.org/10.1111/mpp.12698</a>.","ieee":"D. Seitner, S. Uhse, M. C. Gallei, and A. Djamei, “The core effector Cce1 is required for early infection of maize by Ustilago maydis,” <i>Molecular Plant Pathology</i>, vol. 19, no. 10. Wiley, pp. 2277–2287, 2018.","mla":"Seitner, Denise, et al. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” <i>Molecular Plant Pathology</i>, vol. 19, no. 10, Wiley, 2018, pp. 2277–87, doi:<a href=\"https://doi.org/10.1111/mpp.12698\">10.1111/mpp.12698</a>.","ista":"Seitner D, Uhse S, Gallei MC, Djamei A. 2018. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 19(10), 2277–2287."},"acknowledgement":"the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22], and the Austrian Academy of Science (OEAW).","publist_id":"7950","intvolume":"        19","has_accepted_license":"1","abstract":[{"lang":"eng","text":"The biotrophic pathogen Ustilago maydis, the causative agent of corn smut disease, infects one of the most important crops worldwide – Zea mays. To successfully colonize its host, U. maydis secretes proteins, known as effectors, that suppress plant defense responses and facilitate the establishment of biotrophy. In this work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence and is upregulated during infection. Through microscopic analysis and in vitro assays, we show that Cce1 is secreted from hyphae during filamentous growth of the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection and induce callose deposition as a plant defense response. Cce1 is highly conserved among smut fungi and the Ustilago bromivora ortholog complemented the virulence defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core effector with apoplastic localization that is essential for U. maydis to infect its host."}],"department":[{"_id":"GradSch"}],"external_id":{"isi":["000445624100006"]},"title":"The core effector Cce1 is required for early infection of maize by Ustilago maydis","file_date_updated":"2018-12-18T09:46:00Z","_id":"104","year":"2018","publication":"Molecular Plant Pathology","doi":"10.1111/mpp.12698","month":"10","status":"public","volume":19,"day":"01","article_processing_charge":"No","isi":1,"publication_status":"published","ddc":["580"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2018-10-01T00:00:00Z","page":"2277 - 2287","date_created":"2018-12-11T11:44:39Z","date_updated":"2023-09-19T10:06:42Z"},{"language":[{"iso":"eng"}],"arxiv":1,"quality_controlled":"1","date_updated":"2023-09-13T08:49:16Z","date_created":"2018-12-11T11:44:40Z","page":"26 - 31","date_published":"2018-09-01T00:00:00Z","publication_status":"published","isi":1,"article_processing_charge":"No","month":"09","volume":40,"day":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.05172"}],"status":"public","publication":"Mathematical Intelligencer","_id":"106","year":"2018","title":"Long geodesics on convex surfaces","doi":"10.1007/s00283-018-9795-5","abstract":[{"lang":"eng","text":"The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below."}],"intvolume":"        40","external_id":{"isi":["000444141200005"],"arxiv":["1702.05172"]},"department":[{"_id":"HeEd"}],"citation":{"short":"A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.","chicago":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” <i>Mathematical Intelligencer</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00283-018-9795-5\">https://doi.org/10.1007/s00283-018-9795-5</a>.","ama":"Akopyan A, Petrunin A. Long geodesics on convex surfaces. <i>Mathematical Intelligencer</i>. 2018;40(3):26-31. doi:<a href=\"https://doi.org/10.1007/s00283-018-9795-5\">10.1007/s00283-018-9795-5</a>","apa":"Akopyan, A., &#38; Petrunin, A. (2018). Long geodesics on convex surfaces. <i>Mathematical Intelligencer</i>. Springer. <a href=\"https://doi.org/10.1007/s00283-018-9795-5\">https://doi.org/10.1007/s00283-018-9795-5</a>","ista":"Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 26–31.","mla":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” <i>Mathematical Intelligencer</i>, vol. 40, no. 3, Springer, 2018, pp. 26–31, doi:<a href=\"https://doi.org/10.1007/s00283-018-9795-5\">10.1007/s00283-018-9795-5</a>.","ieee":"A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” <i>Mathematical Intelligencer</i>, vol. 40, no. 3. Springer, pp. 26–31, 2018."},"scopus_import":"1","publist_id":"7948","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","first_name":"Arseniy"},{"last_name":"Petrunin","full_name":"Petrunin, Anton","first_name":"Anton"}],"publisher":"Springer","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","issue":"3","oa":1,"oa_version":"Preprint"},{"article_type":"original","author":[{"orcid":"0000-0001-8223-8896","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy"},{"full_name":"Zhou, H.","first_name":"H.","last_name":"Zhou"},{"first_name":"E. M.","full_name":"Spanton, E. M.","last_name":"Spanton"},{"last_name":"Taniguchi","first_name":"T.","full_name":"Taniguchi, T."},{"first_name":"K.","full_name":"Watanabe, K.","last_name":"Watanabe"},{"last_name":"Young","full_name":"Young, A. F.","first_name":"A. F."}],"oa_version":"Preprint","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"22","oa":1,"publisher":"American Physical Society","keyword":["general physics and astronomy"],"external_id":{"arxiv":["1805.04199"]},"abstract":[{"text":"Owing to their wide tunability, multiple internal degrees of freedom, and low disorder, graphene heterostructures are emerging as a promising experimental platform for fractional quantum Hall (FQH) studies. Here, we report FQH thermal activation gap measurements in dual graphite-gated monolayer graphene devices fabricated in an edgeless Corbino geometry. In devices with substrate-induced sublattice splitting, we find a tunable crossover between single- and multicomponent FQH states in the zero energy Landau level. Activation gaps in the single-component regime show excellent agreement with numerical calculations using a single broadening parameter \r\nΓ≈7.2K. In the first excited Landau level, in contrast, FQH gaps are strongly influenced by Landau level mixing, and we observe an unexpected valley-ordered state at integer filling ν=−4.","lang":"eng"}],"intvolume":"       121","citation":{"ama":"Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. <i>Physical Review Letters</i>. 2018;121(22). doi:<a href=\"https://doi.org/10.1103/physrevlett.121.226801\">10.1103/physrevlett.121.226801</a>","apa":"Polshyn, H., Zhou, H., Spanton, E. M., Taniguchi, T., Watanabe, K., &#38; Young, A. F. (2018). Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.121.226801\">https://doi.org/10.1103/physrevlett.121.226801</a>","chicago":"Polshyn, Hryhoriy, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” <i>Physical Review Letters</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/physrevlett.121.226801\">https://doi.org/10.1103/physrevlett.121.226801</a>.","short":"H. Polshyn, H. Zhou, E.M. Spanton, T. Taniguchi, K. Watanabe, A.F. Young, Physical Review Letters 121 (2018).","ieee":"H. Polshyn, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young, “Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices,” <i>Physical Review Letters</i>, vol. 121, no. 22. American Physical Society, 2018.","mla":"Polshyn, Hryhoriy, et al. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” <i>Physical Review Letters</i>, vol. 121, no. 22, 226801, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/physrevlett.121.226801\">10.1103/physrevlett.121.226801</a>.","ista":"Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. 2018. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. 121(22), 226801."},"acknowledgement":"We thank Cory Dean, S. Chen, Y. Zeng, M. Yankowitz, and J. Li for discussing their unpublished data and for sharing the stack inversion technique. The authors acknowledge further discussions of the results with I. Sodemann, M. Zaletel, C. Nayak, and J. Jain. A. F. Y., H. P., H. Z., and E. M. S. were supported by the ARO under awards 69188PHH and MURI W911NF-17-1-0323. A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by National Science Foundation Cooperative Agreement No. DMR-1644779 and the State of Florida. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan, and JSPS KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Prize Fellowship in Science of the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard Foundation.","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.04199"}],"status":"public","volume":121,"day":"28","month":"11","doi":"10.1103/physrevlett.121.226801","title":"Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices","publication":"Physical Review Letters","_id":"10626","year":"2018","date_published":"2018-11-28T00:00:00Z","date_updated":"2022-01-14T13:48:35Z","date_created":"2022-01-14T12:15:47Z","arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"extern":"1","article_processing_charge":"No","publication_status":"published","article_number":"226801"},{"language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"date_created":"2022-01-14T13:48:47Z","date_updated":"2022-01-14T13:58:24Z","date_published":"2018-05-08T00:00:00Z","article_number":"184501","publication_status":"published","extern":"1","article_processing_charge":"No","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"05","day":"08","volume":97,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.08184"}],"status":"public","publication":"Physical Review B","year":"2018","_id":"10627","title":"Imaging phase slip dynamics in micron-size superconducting rings","doi":"10.1103/physrevb.97.184501","abstract":[{"text":"We present a scanning probe technique for measuring the dynamics of individual fluxoid transitions in multiply connected superconducting structures. In these measurements, a small magnetic particle attached to the tip of a silicon cantilever is scanned over a micron-size superconducting ring fabricated from a thin aluminum film. We find that near the superconducting transition temperature of the aluminum, the dissipation and frequency of the cantilever changes significantly at particular locations where the tip-induced magnetic flux penetrating the ring causes the two lowest-energy fluxoid states to become nearly degenerate. In this regime, we show that changes in the cantilever frequency and dissipation are well-described by a stochastic resonance (SR) process, wherein small oscillations of the cantilever in the presence of thermally activated phase slips (TAPS) in the ring give rise to a dynamical force that modifies the mechanical properties of the cantilever. Using the SR model, we calculate the average fluctuation rate of the TAPS as a function of temperature over a 32-dB range in frequency, and we compare it to the Langer-Ambegaokar-McCumber-Halperin theory for TAPS in one-dimensional superconducting structures.","lang":"eng"}],"intvolume":"        97","external_id":{"arxiv":["1703.08184"]},"acknowledgement":"We are grateful to Nadya Mason for useful discussions. This work was supported by the DOE Basic Energy Sciences under Contract No. DE-SC0012649, the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois.\r\n","citation":{"ista":"Polshyn H, Naibert TR, Budakian R. 2018. Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. 97(18), 184501.","ieee":"H. Polshyn, T. R. Naibert, and R. Budakian, “Imaging phase slip dynamics in micron-size superconducting rings,” <i>Physical Review B</i>, vol. 97, no. 18. American Physical Society, 2018.","mla":"Polshyn, Hryhoriy, et al. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” <i>Physical Review B</i>, vol. 97, no. 18, 184501, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/physrevb.97.184501\">10.1103/physrevb.97.184501</a>.","short":"H. Polshyn, T.R. Naibert, R. Budakian, Physical Review B 97 (2018).","chicago":"Polshyn, Hryhoriy, Tyler R. Naibert, and Raffi Budakian. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” <i>Physical Review B</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/physrevb.97.184501\">https://doi.org/10.1103/physrevb.97.184501</a>.","apa":"Polshyn, H., Naibert, T. R., &#38; Budakian, R. (2018). Imaging phase slip dynamics in micron-size superconducting rings. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.97.184501\">https://doi.org/10.1103/physrevb.97.184501</a>","ama":"Polshyn H, Naibert TR, Budakian R. Imaging phase slip dynamics in micron-size superconducting rings. <i>Physical Review B</i>. 2018;97(18). doi:<a href=\"https://doi.org/10.1103/physrevb.97.184501\">10.1103/physrevb.97.184501</a>"},"scopus_import":"1","author":[{"full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn"},{"full_name":"Naibert, Tyler R.","first_name":"Tyler R.","last_name":"Naibert"},{"full_name":"Budakian, Raffi","first_name":"Raffi","last_name":"Budakian"}],"article_type":"original","publisher":"American Physical Society","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"issue":"18","oa_version":"Preprint"},{"isi":1,"publication_status":"published","article_processing_charge":"Yes (via OA deal)","ddc":["516","000"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2018-12-11T11:49:57Z","date_updated":"2023-09-20T12:08:51Z","date_published":"2018-06-01T00:00:00Z","page":"1001-1009","year":"2018","_id":"1064","publication":"Discrete & Computational Geometry","title":"On the circle covering theorem by A.W. Goodman and R.E. Goodman","file_date_updated":"2019-01-18T09:27:36Z","doi":"10.1007/s00454-017-9883-x","month":"06","volume":59,"day":"01","status":"public","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"scopus_import":"1","citation":{"apa":"Akopyan, A., Balitskiy, A., &#38; Grigorev, M. (2018). On the circle covering theorem by A.W. Goodman and R.E. Goodman. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-017-9883-x\">https://doi.org/10.1007/s00454-017-9883-x</a>","ama":"Akopyan A, Balitskiy A, Grigorev M. On the circle covering theorem by A.W. Goodman and R.E. Goodman. <i>Discrete &#38; Computational Geometry</i>. 2018;59(4):1001-1009. doi:<a href=\"https://doi.org/10.1007/s00454-017-9883-x\">10.1007/s00454-017-9883-x</a>","chicago":"Akopyan, Arseniy, Alexey Balitskiy, and Mikhail Grigorev. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00454-017-9883-x\">https://doi.org/10.1007/s00454-017-9883-x</a>.","short":"A. Akopyan, A. Balitskiy, M. Grigorev, Discrete &#38; Computational Geometry 59 (2018) 1001–1009.","ieee":"A. Akopyan, A. Balitskiy, and M. Grigorev, “On the circle covering theorem by A.W. Goodman and R.E. Goodman,” <i>Discrete &#38; Computational Geometry</i>, vol. 59, no. 4. Springer, pp. 1001–1009, 2018.","mla":"Akopyan, Arseniy, et al. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” <i>Discrete &#38; Computational Geometry</i>, vol. 59, no. 4, Springer, 2018, pp. 1001–09, doi:<a href=\"https://doi.org/10.1007/s00454-017-9883-x\">10.1007/s00454-017-9883-x</a>.","ista":"Akopyan A, Balitskiy A, Grigorev M. 2018. On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete &#38; Computational Geometry. 59(4), 1001–1009."},"publist_id":"6324","intvolume":"        59","has_accepted_license":"1","abstract":[{"text":"In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot be separated into two subfamilies by a straight line disjoint from the disks. In this note we show that essentially the same idea may work for different analogues and generalizations of their result. In particular, we prove the following: Given a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane disjoint from the homothets.","lang":"eng"}],"department":[{"_id":"HeEd"}],"external_id":{"isi":["000432205500011"]},"publisher":"Springer","issue":"4","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","oa_version":"Published Version","ec_funded":1,"author":[{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy"},{"last_name":"Balitskiy","full_name":"Balitskiy, Alexey","first_name":"Alexey"},{"full_name":"Grigorev, Mikhail","first_name":"Mikhail","last_name":"Grigorev"}],"file":[{"content_type":"application/pdf","file_size":482518,"relation":"main_file","date_updated":"2019-01-18T09:27:36Z","date_created":"2019-01-18T09:27:36Z","access_level":"open_access","success":1,"creator":"dernst","file_id":"5844","file_name":"2018_DiscreteComp_Akopyan.pdf"}],"article_type":"original"},{"month":"08","main_file_link":[{"open_access":"1","url":"https://doi.org/10.4230/LIPIcs.ESA.2018.39"}],"status":"public","volume":112,"day":"14","title":"A tree structure for dynamic facility location","publication":"26th Annual European Symposium on Algorithms","year":"2018","_id":"11827","doi":"10.4230/LIPICS.ESA.2018.39","conference":{"location":"Helsinki, Finland","end_date":"2018-08-22","name":"ESA: Annual European Symposium on Algorithms","start_date":"2018-08-20"},"arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2018-08-14T00:00:00Z","date_created":"2022-08-12T08:20:57Z","date_updated":"2023-02-16T10:50:51Z","article_processing_charge":"No","extern":"1","article_number":"39","publication_status":"published","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959770811"]},"author":[{"last_name":"Goranci","first_name":"Gramoz ","full_name":"Goranci, Gramoz "},{"first_name":"Monika H","full_name":"Henzinger, Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Leniowski","first_name":"Dariusz","full_name":"Leniowski, Dariusz"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LIPIcs"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We study the metric facility location problem with client insertions and deletions. This setting differs from the classic dynamic facility location problem, where the set of clients remains the same, but the metric space can change over time. We show a deterministic algorithm that maintains a constant factor approximation to the optimal solution in worst-case time O~(2^{O(kappa^2)}) per client insertion or deletion in metric spaces while answering queries about the cost in O(1) time, where kappa denotes the doubling dimension of the metric. For metric spaces with bounded doubling dimension, the update time is polylogarithmic in the parameters of the problem."}],"intvolume":"       112","external_id":{"arxiv":["1909.06653"]},"citation":{"short":"G. Goranci, M.H. Henzinger, D. Leniowski, in:, 26th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","chicago":"Goranci, Gramoz , Monika H Henzinger, and Dariusz Leniowski. “A Tree Structure for Dynamic Facility Location.” In <i>26th Annual European Symposium on Algorithms</i>, Vol. 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPICS.ESA.2018.39\">https://doi.org/10.4230/LIPICS.ESA.2018.39</a>.","ama":"Goranci G, Henzinger MH, Leniowski D. A tree structure for dynamic facility location. In: <i>26th Annual European Symposium on Algorithms</i>. Vol 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPICS.ESA.2018.39\">10.4230/LIPICS.ESA.2018.39</a>","apa":"Goranci, G., Henzinger, M. H., &#38; Leniowski, D. (2018). A tree structure for dynamic facility location. In <i>26th Annual European Symposium on Algorithms</i> (Vol. 112). Helsinki, Finland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.ESA.2018.39\">https://doi.org/10.4230/LIPICS.ESA.2018.39</a>","ista":"Goranci G, Henzinger MH, Leniowski D. 2018. A tree structure for dynamic facility location. 26th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 112, 39.","ieee":"G. Goranci, M. H. Henzinger, and D. Leniowski, “A tree structure for dynamic facility location,” in <i>26th Annual European Symposium on Algorithms</i>, Helsinki, Finland, 2018, vol. 112.","mla":"Goranci, Gramoz, et al. “A Tree Structure for Dynamic Facility Location.” <i>26th Annual European Symposium on Algorithms</i>, vol. 112, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPICS.ESA.2018.39\">10.4230/LIPICS.ESA.2018.39</a>."},"scopus_import":"1"},{"status":"public","main_file_link":[{"url":"https://doi.org/10.4230/LIPIcs.ESA.2018.40","open_access":"1"}],"volume":112,"day":"14","month":"08","doi":"10.4230/LIPICS.ESA.2018.40","conference":{"location":"Helsinki, Finland","end_date":"2018-08-22","name":"ESA: Annual European Symposium on Algorithms","start_date":"2018-08-20"},"title":"Dynamic effective resistances and approximate schur complement on separable graphs","publication":"26th Annual European Symposium on Algorithms","year":"2018","_id":"11828","date_published":"2018-08-14T00:00:00Z","date_updated":"2023-02-16T11:08:08Z","date_created":"2022-08-12T08:26:42Z","arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783959770811"],"issn":["1868-8969"]},"extern":"1","article_processing_charge":"No","article_number":"40","publication_status":"published","author":[{"last_name":"Goranci","first_name":"Gramoz","full_name":"Goranci, Gramoz"},{"first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530"},{"last_name":"Peng","first_name":"Pan","full_name":"Peng, Pan"}],"oa_version":"Published Version","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LIPIcs"],"external_id":{"arxiv":["1802.09111"]},"abstract":[{"lang":"eng","text":"We consider the problem of dynamically maintaining (approximate) all-pairs effective resistances in separable graphs, which are those that admit an n^{c}-separator theorem for some c<1. We give a fully dynamic algorithm that maintains (1+epsilon)-approximations of the all-pairs effective resistances of an n-vertex graph G undergoing edge insertions and deletions with O~(sqrt{n}/epsilon^2) worst-case update time and O~(sqrt{n}/epsilon^2) worst-case query time, if G is guaranteed to be sqrt{n}-separable (i.e., it is taken from a class satisfying a sqrt{n}-separator theorem) and its separator can be computed in O~(n) time. Our algorithm is built upon a dynamic algorithm for maintaining approximate Schur complement that approximately preserves pairwise effective resistances among a set of terminals for separable graphs, which might be of independent interest.\r\nWe complement our result by proving that for any two fixed vertices s and t, no incremental or decremental algorithm can maintain the s-t effective resistance for sqrt{n}-separable graphs with worst-case update time O(n^{1/2-delta}) and query time O(n^{1-delta}) for any delta>0, unless the Online Matrix Vector Multiplication (OMv) conjecture is false.\r\nWe further show that for general graphs, no incremental or decremental algorithm can maintain the s-t effective resistance problem with worst-case update time O(n^{1-delta}) and query-time O(n^{2-delta}) for any delta >0, unless the OMv conjecture is false."}],"intvolume":"       112","citation":{"short":"G. Goranci, M.H. Henzinger, P. Peng, in:, 26th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","chicago":"Goranci, Gramoz, Monika H Henzinger, and Pan Peng. “Dynamic Effective Resistances and Approximate Schur Complement on Separable Graphs.” In <i>26th Annual European Symposium on Algorithms</i>, Vol. 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPICS.ESA.2018.40\">https://doi.org/10.4230/LIPICS.ESA.2018.40</a>.","ama":"Goranci G, Henzinger MH, Peng P. Dynamic effective resistances and approximate schur complement on separable graphs. In: <i>26th Annual European Symposium on Algorithms</i>. Vol 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPICS.ESA.2018.40\">10.4230/LIPICS.ESA.2018.40</a>","apa":"Goranci, G., Henzinger, M. H., &#38; Peng, P. (2018). Dynamic effective resistances and approximate schur complement on separable graphs. In <i>26th Annual European Symposium on Algorithms</i> (Vol. 112). Helsinki, Finland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.ESA.2018.40\">https://doi.org/10.4230/LIPICS.ESA.2018.40</a>","ista":"Goranci G, Henzinger MH, Peng P. 2018. Dynamic effective resistances and approximate schur complement on separable graphs. 26th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 112, 40.","ieee":"G. Goranci, M. H. Henzinger, and P. Peng, “Dynamic effective resistances and approximate schur complement on separable graphs,” in <i>26th Annual European Symposium on Algorithms</i>, Helsinki, Finland, 2018, vol. 112.","mla":"Goranci, Gramoz, et al. “Dynamic Effective Resistances and Approximate Schur Complement on Separable Graphs.” <i>26th Annual European Symposium on Algorithms</i>, vol. 112, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPICS.ESA.2018.40\">10.4230/LIPICS.ESA.2018.40</a>."},"scopus_import":"1"},{"title":"Dynamic algorithms for graph coloring","year":"2018","_id":"11872","publication":"29th Annual ACM-SIAM Symposium on Discrete Algorithms","doi":"10.1137/1.9781611975031.1","conference":{"end_date":"2018-01-10","name":"SODA: Symposium on Discrete Algorithms","start_date":"2018-01-07","location":"New Orleans, LA, United States"},"month":"01","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1711.04355","open_access":"1"}],"day":"01","extern":"1","article_processing_charge":"No","publication_status":"published","publication_identifier":{"eisbn":["978-161197503-1"]},"arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2018-01-01T00:00:00Z","page":"1 - 20","date_created":"2022-08-16T12:07:14Z","date_updated":"2023-02-17T11:39:01Z","oa":1,"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Society for Industrial and Applied Mathematics","oa_version":"Preprint","author":[{"first_name":"Sayan","full_name":"Bhattacharya, Sayan","last_name":"Bhattacharya"},{"full_name":"Chakrabarty, Deeparnab","first_name":"Deeparnab","last_name":"Chakrabarty"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"first_name":"Danupon","full_name":"Nanongkai, Danupon","last_name":"Nanongkai"}],"scopus_import":"1","citation":{"ieee":"S. Bhattacharya, D. Chakrabarty, M. H. Henzinger, and D. Nanongkai, “Dynamic algorithms for graph coloring,” in <i>29th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, New Orleans, LA, United States, 2018, pp. 1–20.","mla":"Bhattacharya, Sayan, et al. “Dynamic Algorithms for Graph Coloring.” <i>29th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Society for Industrial and Applied Mathematics, 2018, pp. 1–20, doi:<a href=\"https://doi.org/10.1137/1.9781611975031.1\">10.1137/1.9781611975031.1</a>.","ista":"Bhattacharya S, Chakrabarty D, Henzinger MH, Nanongkai D. 2018. Dynamic algorithms for graph coloring. 29th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1–20.","apa":"Bhattacharya, S., Chakrabarty, D., Henzinger, M. H., &#38; Nanongkai, D. (2018). Dynamic algorithms for graph coloring. In <i>29th Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 1–20). New Orleans, LA, United States: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611975031.1\">https://doi.org/10.1137/1.9781611975031.1</a>","ama":"Bhattacharya S, Chakrabarty D, Henzinger MH, Nanongkai D. Dynamic algorithms for graph coloring. In: <i>29th Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 2018:1-20. doi:<a href=\"https://doi.org/10.1137/1.9781611975031.1\">10.1137/1.9781611975031.1</a>","chicago":"Bhattacharya, Sayan, Deeparnab Chakrabarty, Monika H Henzinger, and Danupon Nanongkai. “Dynamic Algorithms for Graph Coloring.” In <i>29th Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 1–20. Society for Industrial and Applied Mathematics, 2018. <a href=\"https://doi.org/10.1137/1.9781611975031.1\">https://doi.org/10.1137/1.9781611975031.1</a>.","short":"S. Bhattacharya, D. Chakrabarty, M.H. Henzinger, D. Nanongkai, in:, 29th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2018, pp. 1–20."},"abstract":[{"lang":"eng","text":"We design fast dynamic algorithms for proper vertex and edge colorings in a graph undergoing edge insertions and deletions. In the static setting, there are simple linear time algorithms for (Δ + 1)- vertex coloring and (2Δ – 1)-edge coloring in a graph with maximum degree Δ. It is natural to ask if we can efficiently maintain such colorings in the dynamic setting as well. We get the following three results. (1) We present a randomized algorithm which maintains a (Δ + 1)-vertex coloring with O(log Δ) expected amortized update time. (2) We present a deterministic algorithm which maintains a (1 + o(1)Δ-vertex coloring with O(polylog Δ) amortized update time. (3) We present a simple, deterministic algorithm which maintains a (2Δ – 1)-edge coloring with O(log Δ) worst-case update time. This improves the recent O(Δ)-edge coloring algorithm with  worst-case update time [4]."}],"external_id":{"arxiv":["1711.04355"]}},{"author":[{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"last_name":"Noe","full_name":"Noe, Alexander","first_name":"Alexander"},{"full_name":"Schulz, Christian","first_name":"Christian","last_name":"Schulz"},{"full_name":"Strash, Darren","first_name":"Darren","last_name":"Strash"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","publisher":"Society for Industrial and Applied Mathematics","oa_version":"Preprint","abstract":[{"lang":"eng","text":"The minimum cut problem for an undirected edge-weighted graph asks us to divide its set of nodes into two blocks while minimizing the weight sum of the cut edges. Here, we introduce a linear-time algorithm to compute near-minimum cuts. Our algorithm is based on cluster contraction using label propagation and Padberg and Rinaldi's contraction heuristics [SIAM Review, 1991]. We give both sequential and shared-memory parallel implementations of our algorithm. Extensive experiments on both real-world and generated instances show that our algorithm finds the optimal cut on nearly all instances significantly faster than other state-of-the-art exact algorithms, and our error rate is lower than that of other heuristic algorithms. In addition, our parallel algorithm shows good scalability."}],"external_id":{"arxiv":["1708.06127"]},"scopus_import":"1","citation":{"ista":"Henzinger MH, Noe A, Schulz C, Strash D. 2018. Practical minimum cut algorithms. 20th Workshop on Algorithm Engineering and Experiments. ALENEX: Symposium on Algorithm Engineering and Experiments, 48–61.","ieee":"M. H. Henzinger, A. Noe, C. Schulz, and D. Strash, “Practical minimum cut algorithms,” in <i>20th Workshop on Algorithm Engineering and Experiments</i>, New Orleans, LA, United States, 2018, pp. 48–61.","mla":"Henzinger, Monika H., et al. “Practical Minimum Cut Algorithms.” <i>20th Workshop on Algorithm Engineering and Experiments</i>, Society for Industrial and Applied Mathematics, 2018, pp. 48–61, doi:<a href=\"https://doi.org/10.1137/1.9781611975055.5\">10.1137/1.9781611975055.5</a>.","short":"M.H. Henzinger, A. Noe, C. Schulz, D. Strash, in:, 20th Workshop on Algorithm Engineering and Experiments, Society for Industrial and Applied Mathematics, 2018, pp. 48–61.","chicago":"Henzinger, Monika H, Alexander Noe, Christian Schulz, and Darren Strash. “Practical Minimum Cut Algorithms.” In <i>20th Workshop on Algorithm Engineering and Experiments</i>, 48–61. Society for Industrial and Applied Mathematics, 2018. <a href=\"https://doi.org/10.1137/1.9781611975055.5\">https://doi.org/10.1137/1.9781611975055.5</a>.","apa":"Henzinger, M. H., Noe, A., Schulz, C., &#38; Strash, D. (2018). Practical minimum cut algorithms. In <i>20th Workshop on Algorithm Engineering and Experiments</i> (pp. 48–61). New Orleans, LA, United States: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611975055.5\">https://doi.org/10.1137/1.9781611975055.5</a>","ama":"Henzinger MH, Noe A, Schulz C, Strash D. Practical minimum cut algorithms. In: <i>20th Workshop on Algorithm Engineering and Experiments</i>. Society for Industrial and Applied Mathematics; 2018:48-61. doi:<a href=\"https://doi.org/10.1137/1.9781611975055.5\">10.1137/1.9781611975055.5</a>"},"month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.06127"}],"status":"public","day":"01","title":"Practical minimum cut algorithms","year":"2018","_id":"11882","publication":"20th Workshop on Algorithm Engineering and Experiments","doi":"10.1137/1.9781611975055.5","conference":{"start_date":"2018-01-07","end_date":"2018-01-08","name":"ALENEX: Symposium on Algorithm Engineering and Experiments","location":"New Orleans, LA, United States"},"quality_controlled":"1","arxiv":1,"language":[{"iso":"eng"}],"date_published":"2018-01-01T00:00:00Z","page":"48-61","date_created":"2022-08-17T07:04:57Z","date_updated":"2023-02-17T14:03:39Z","article_processing_charge":"No","extern":"1","publication_status":"published","publication_identifier":{"eisbn":["978-1-61197-505-5"]}}]