Related papers: Passage through fluctuating geometrical bottleneck…
Sub-Gaussian and subexponential distributions are introduced and applied to study the fluctuation-response relation out of equilibrium. A bound on the difference in expected values of an arbitrary sub-Gaussian or subexponential physical…
In this work the dynamics of a freely jointed random chain which fluctuates at constant temperature in some viscous medium is studied. The chain is regarded as a system of small particles which perform a brownian motion and are subjected to…
Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a…
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in…
We consider the generalization of the Kramers escape over a barrier problem to the case of a long chain molecule. It involves the motion of chain molecule of N segments across a region where the free energy per segment is higher, so that it…
For two molecules to react they first have to meet. Yet, reaction times are rarely on par with the first-passage times that govern such molecular encounters. A prime reason for this discrepancy is stochastic transitions between reactive and…
Fission transients describe the fission rate as it evolves towards the quasistationary value given by Kramers' formula. The nature of fission transients is dependent on the assumed initial distribution of the compound nuclei along the…
We consider the Ginzburg-Landau model, confined in an infinitely long rectangular wire of cross-section $L_{1}\times L_{2}$. Our approach is based on the Gaussian effective potential in the transverse unitarity gauge, which allows to treat…
A mechanism for relationship of solvent viscosity with reaction rate constant at enzyme action is suggested. It is based on fluctuations of electric field in enzyme active site produced by thermally equilibrium rocking (cranckshaft motion)…
An analytical approach, which develops the gauge model of the glass transition phenomenon, is suggested. It is based on the quantum field theory and critical dynamics methods. The suggested mechanism of glass transition is based on the…
Enzyme-based systems have been shown to undergo directional motion in response to their substrate gradient. Here, we formulate a kinetic model to analyze the directional movement of an ensemble of protein molecules in response to a gradient…
Gas slippage occurs when the mean free path of the gas molecules is in the order of the characteristic pore size of a porous medium. This phenomenon leads to the Klinkenberg's effect where the measured permeability of a gas (apparent…
We develop a fluctuation framework to quantify the free energy difference between two equilibrium states connected by nonequilibrium processes under arbitrary dynamics and system-environment coupling. For an open system described by the…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
We develop an analytical diffusion-equation-type approximation scheme for the one-dimensional coagulation reaction A+A->A with partial reaction probability on particle encounters which are otherwise hard-core. The new approximation…
This paper reviews recent Monte Carlo simulation studies of the glassy behavior in thin polymer films. The simulations employ a version of the bond-fluctuation lattice model, in which the glass transition is driven by the competition…
Recent experiments and computer simulations show that supercooled liquids around the glass transition temperature are "dynamically heterogeneous" [1]. Such heterogeneity is expected from the random first order transition theory of the glass…
We study a lattice model describing the non-equilibrium dynamics emerging from the pulling of a tracer particle through a disordered medium occupied by randomly placed obstacles. The model is considered in a restricted geometry pertinent…
We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided…
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…