Journal ArticleDOI
Quasielastic neutron scattering and relaxation processes in proteins: analytical and simulation-based models
TLDR
An overview of analytical and simulation approaches to describe the relaxation dynamics of proteins and recent developments of theoretical models, such as fractional Brownian dynamics, are emphasised.Abstract:
The present article gives an overview of analytical and simulation approaches to describe the relaxation dynamics of proteins. Particularly emphasised are recent developments of theoretical models, such as fractional Brownian dynamics. The latter connects dynamical events seen on the pico- to nanoscond time scale, accessible to quasielastic neutron scattering, and functional dynamics of proteins on much longer time scales.read more
Citations
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Journal ArticleDOI
Stochastic Processes in Physics and Chemistry
TL;DR: Van Kampen as mentioned in this paper provides an extensive graduate-level introduction which is clear, cautious, interesting and readable, and could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes.
Journal ArticleDOI
Lectures on Theoretical Physics
TL;DR: In this article, Sommerfeld presents a review of the theoretic aspects of Physik, including Mechanik, Elektrodynamik and Partielle Differentialgleichungen der Physik.
Book ChapterDOI
The Langevin Equation
TL;DR: The generalized Langevin equation as discussed by the authors describes processes in a mechanical system with both deterministic and random forces which have comparable magnitudes (i.e., neither the deterministic nor random part can be neglected) and the random force is a transformed white noise.
Journal ArticleDOI
Single-molecule force spectroscopy reveals signatures of glassy dynamics in the energy landscape of ubiquitin
TL;DR: In this article, the authors used single-molecule force-clamp spectroscopy to measure the kinetics of unfolding of the protein ubiquitin under a constant force and discovered a surprisingly broad distribution of unfolding rates that follows a power law with no characteristic mean.
Journal ArticleDOI
Critical exponent of the fractional Langevin equation.
Stanislav Burov,Eli Barkai +1 more
TL;DR: The dynamical phase diagram of the fractional Langevin equation is investigated and it is shown that critical exponents mark dynamical transitions in the behavior of the system.
References
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Journal ArticleDOI
Handbook of Mathematical Functions
Book
Computer Simulation of Liquids
Michael P. Allen,D. J. Tildesley +1 more
TL;DR: In this paper, the gear predictor -corrector is used to calculate forces and torques in a non-equilibrium molecular dynamics simulation using Monte Carlo methods. But it is not suitable for the gear prediction problem.
Book
Adaptive Filter Theory
TL;DR: In this paper, the authors propose a recursive least square adaptive filter (RLF) based on the Kalman filter, which is used as the unifying base for RLS Filters.
Journal ArticleDOI
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Wendy D. Cornell,Piotr Cieplak,Piotr Cieplak,Christopher I. Bayly,Christopher I. Bayly,Ian R. Gould,Ian R. Gould,Kenneth M. Merz,Kenneth M. Merz,David M. Ferguson,David M. Ferguson,David C. Spellmeyer,David C. Spellmeyer,Thomas R. Fox,James W. Caldwell,Peter A. Kollman +15 more
TL;DR: Weiner et al. as mentioned in this paper derived a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases.
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