Journal ArticleDOI
Multiple time scale dynamics of distance fluctuations in a semiflexible polymer: A one-dimensional generalized Langevin equation treatment
TLDR
The calculations demonstrate that C(t) is well approximated by a Mittag-Leffler function and K( t) by a power-law decay on time scales of several decades.Abstract:
Time-dependent fluctuations in the distance x(t) between two segments along a polymer are one measure of its overall conformational dynamics. The dynamics of x(t), modeled as the coordinate of a particle moving in a one-dimensional potential well in thermal contact with a reservoir, is treated with a generalized Langevin equation whose memory kernel K(t) can be calculated from the time-correlation function of distance fluctuations C(t)≡⟨x(0)x(t)⟩. We compute C(t) for a semiflexible continuum model of the polymer and use it to determine K(t) via the GLE. The calculations demonstrate that C(t) is well approximated by a Mittag-Leffler function and K(t) by a power-law decay on time scales of several decades. Both functions depend on a number of parameters characterizing the polymer, including chain length, degree of stiffness, and the number of intervening residues between the two segments. The calculations are compared with the recent observation of a nonexponential C(t) and a power law K(t) in the conformat...read more
Citations
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疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Journal ArticleDOI
Fluctuating enzymes: lessons from single-molecule studies.
TL;DR: A theoretical model based on the generalized Langevin equation (GLE) treatment of Kramers' barrier crossing problem for chemical reactions accounts naturally for the observation of dynamic disorder and highly dispersed kinetics.
Journal ArticleDOI
Multiscale complex network of protein conformational fluctuations in single-molecule time series
TL;DR: The scheme to extract a multiscale state space network (SSN) from a single-molecule time series is presented and it is shown that the topographical features of the SSNs depend on the time scale of observation; the longer the time Scale, the simpler the underlying SSN becomes, leading to a transition of the dynamics from anomalous diffusion to normal Brownian diffusion.
Journal ArticleDOI
Polymer translocation through a nanopore: A showcase of anomalous diffusion
TL;DR: The comparison of the analytic results with data derived from extensive Monte Carlo simulations reveals very good agreement and proves that the diffusion dynamics of unbiased translocation through a nanopore is anomalous in its nature.
Journal ArticleDOI
Complex chemical kinetics in single enzyme molecules: Kramers’s model with fractional Gaussian noise
TL;DR: Analysis of Kramers's flux-over-population method yields analytic expressions for the time-dependent transmission coefficient and the distribution of waiting times for barrier crossing that reproduce the observed trends in recent simulations and experiments.
References
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疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Journal ArticleDOI
Fractional Brownian Motions, Fractional Noises and Applications
Journal ArticleDOI
Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm.
Peter E. Wright,H. Jane Dyson +1 more
TL;DR: Many proteins that lack intrinsic globular structure under physiological conditions have now been recognized, and it appears likely that their rapid turnover, aided by their unstructured nature in the unbound state, provides a level of control that allows rapid and accurate responses of the cell to changing environmental conditions.
Book
Nonequilibrium statistical mechanics
TL;DR: The paradoxes of irreversibility as mentioned in this paper is a well-known problem in nonlinear problems, and it has been studied extensively in the literature for a long time, e.g. in the context of projection operators.
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