Related papers: Solvent viscosity dependence for enzymatic reactio…
A realistic physical model for the so called rate promoting vibration (RPV) at enzyme action is constructed. The origin of the RPV is assumed to be an oscillating electric field produced by long-lived localized vibrational modes in protein…
Why reaction rate constants for enzymatic reactions are typically inversely proportional to fractional power exponents of solvent viscosity remains to be already a thirty years old puzzle. Available interpretations of the phenomenon invoke…
A relationship between the preexponent of the rate constant and the distribution over activation barrier energies for enzymatic/protein reactions is revealed. We consider an enzyme solution as an ensemble of individual molecules with…
We show that the vibrational response of a glassy liquid at finite frequencies can be described by continuum mechanics despite the vast degeneracy of the vibrational ground state; standard continuum elasticity assumes a unique ground state.…
We formulate frequency fluctuations of intramolecular vibrations of a solute by exploring the fluctuation of the electrostatic potential by solvents. We present a numerical methodology for estimating the frequency fluctuations; the…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
A growing amount of evidence points to the fact that many enzymes exhibit fluctuations in their catalytic activity, which are associated with conformational changes on a broad range of timescales. The experimental study of this phenomenon,…
Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent…
Viscoelasticity and rate-dependent adhesion of soft matter lead to difficulties in modeling the 'relatively simple' problem of a rigid sphere in contact with a viscoelastic half-space. For this reason, approximations in describing surface…
Molecular isomerization kinetics in liquid solvents are determined by a complex interplay between the friction acting on a rotating dihedral due to interactions with the solvent, internal dissipation effects (also known as internal…
We proposed in an earlier paper [arXiv:1108.6141] an empirical formula of the electrical conductivity which agrees with experiments within 20 percent for the most of pure elemental metals at room temperature ranges. This is obtained, in…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
The elastic response of an electron fluid at finite frequencies is defined by the electron viscosity $\eta(\omega)$. We determine $\eta(\omega)$ for graphene at the charge neutrality point in the collisionless regime, including the leading…
We determine the elastic moduli of two-dimensional assemblies of disks by computer simulations. The disks interact through elastic contact forces, that oppose the relative displacement at the contact points by means of a normal and a…
In order to realize the full potential of ion trap quantum computers, an improved understanding is required of the motional heating that trapped ions experience. Experimental studies of the temperature-, frequency-, and ion--electrode…
Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…
The mean-field dynamics of a molecule with an induced dipole moment (e.g., a homonuclear diatomic molecule) in a deterministic and a stochastic (fluctuating) electric field is solved to obtain the decoherence properties of the system. The…
Plasma turbulence is thought to be associated with various physical processes involved in solar flares, including magnetic reconnection, particle acceleration and transport. Using Ramaty High Energy Solar Spectroscopic Imager ({\it RHESSI})…
In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context…
Transport coefficients and dielectric relaxation in liquids are often treated as distinct manifestations of molecular dynamics. We show that, in polar liquids, orientational dipolar fluctuations generate a substantial contribution to the…