Journal ArticleDOI
Positional time correlation function for one‐dimensional systems with barrier crossing: Memory function corrections to the optimized Rouse–Zimm approximation
TLDR
In this paper, the influence of barrier crossing processes on the positional time correlation function is studied. But the memory function of this correlation function was evaluated for a 2-4 potential as a function of the barrier height using the Mori continued fraction expansion and an equivalent but more efficient matrix formulation.Abstract:
The one‐variable Smoluchowski equation is used to study the influence of barrier crossing processes on the positional time correlation function. The memory function of this correlation function is evaluated for a 2–4 potential as a function of the barrier height using the Mori continued fraction expansion and an equivalent but more efficient matrix formulation. Higher orders in the expansions are required to obtain numerical convergence as the barrier height increases. An exact integral solution for the correlation time is derived and is compared with the approximations. A biexponential approximation, which describes the independent motion in a potential well and the transition between wells, is found to be very accurate for high barriers. Numerical simulations provide checks on the approximations to the correlation function for a barrier height of 2 kBT. The possibility of including the influence of more rapid barrier crossing processes into the many variable Smoluchowski description of long time polymer...read more
Citations
More filters
Journal ArticleDOI
Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations
TL;DR: In this article, a coarse molecular dynamics approach is used to study the kinetics and thermodynamics of a peptide fragment dissolved in water, where short bursts of appropriately initialized simulations are used to infer the deterministic and stochastic components of the peptide motion parametrized by an appropriate set of coarse variables.
Journal ArticleDOI
Enzyme millisecond conformational dynamics do not catalyze the chemical step
TL;DR: A renormalization approach is introduced that transforms the energetics and dynamics of the enzyme to an equivalent low-dimensional system, and allows us to simulate the dynamical coupling on a ms timescale, and establishes that the conformational dynamics is not remembered during the chemical step and does not contribute significantly to catalysis.
Journal ArticleDOI
Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics
TL;DR: In this article, the authors investigated the dynamics of the polymer backbone and found that the folding rate depends linearly on the solvent friction for high viscosity, but saturates at low viscosity because of internal friction.
Journal ArticleDOI
Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics
TL;DR: The motions involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, finding that the folding rate depends linearly on the solvent friction for high viscosity, but saturates at low viscosities because of internal friction.
Journal ArticleDOI
Synthesis, crystal structures, and nonlinear optical (NLO) properties of new Schiff-base nickel(II) complexes. Toward a new type of molecular switch?
Jean Pierre Costes,Jean François Lamère,Christine Lepetit,Pascal G. Lacroix,Françoise Dahan,Keitaro Nakatani +5 more
TL;DR: Qualitative ZINDO/SCI quantum chemical calculations indicate that, in [Ni(L)(MePhCHNH2)], the beta orientation strongly depends on the laser wavelength, raising the possibility for a new type of molecular switch.
References
More filters
Journal ArticleDOI
Brownian motion in a field of force and the diffusion model of chemical reactions
TL;DR: In this article, a particle which is caught in a potential hole and which, through the shuttling action of Brownian motion, can escape over a potential barrier yields a suitable model for elucidating the applicability of the transition state method for calculating the rate of chemical reactions.