相关论文: Passage through fluctuating geometrical bottleneck…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
The classical theory of chemical reactions can be understood in terms of diffusive barrier crossing, where the rate of a reaction is determined by the inverse of the mean first passage time (FPT) to cross a free energy barrier. Whenever a…
We study the diffusive behavior of biased Brownian particles in a two dimensional confined geometry filled with the freezing obstacles. The transport properties of these particles are investigated for various values of the obstacles density…
We study a gas of hard rods on a ring, driven by an external thermostat, with either elastic or inelastic collisions, which exhibits sub-diffusive behavior $<x^2 > \sim t^{1/2}$. We show the validity of the usual Fluctuation-Dissipation…
In this paper we consider a superconducting film modeled by the Ginzburg-Landau model, confined between two parallel planes a distance $L$ apart from one another. Our approach is based on the Gaussian effective potential in the transverse…
In the diffusion-collision model, the unfolding or backward rates are given by the likelihood of secondary structural cluster dissociation. In this work, we introduce a backward rate calculation modeled from a Kramers-type thermal tunneling…
In this article we obtain the equilibrium fluctuations of a symmetric exclusion process in $\mathbb{Z}$ with long jumps. The transition probability of the jump from $x$ to $y$ is proportional to $|x-y|^{-\gamma-1}$. Here we restrict to the…
A fluctuation theorem is examined for the first-passage time of a biomolecular machine (e.g., a motor protein or an enzyme) in a nonequilibrium steady-state. For such machines in which the driven, observable process is coupled to a hidden…
The temperature dependence of the diffusion coefficient of particles is studied on lattices with disorder. A model is investigated with both trap and barrier disorder that was introduced before by Limoge and Bocquet (1990 Phys. Rev. Lett.…
The position $x(t)$ of a particle diffusing in a one-dimensional uncorrelated and time dependent random medium is simply Gaussian distributed in the typical direction, i.e. along the ray $x=v_0 t$, where $v_0$ is the average drift. However,…
We study the deterministic diffusion coefficient of the two-dimensional periodic Lorentz gas as a function of the density of scatterers. Results obtained from computer simulations are compared to the analytical approximation of Machta and…
A sharp change in apparent mobility at a characteristic temperature that depends on the observation time has been reported in experiments and simulations of hydrated proteins. Such behavior is often discussed in the context of the protein…
Small separation between reactants, not exceeding $10^{-8}-10^{-7}cm$, is the necessary condition for various chemical reactions. It is shown that random advection and stretching by turbulence leads to formation of scalar-enriched sheets of…
We study the effect of confinement on diffusion limited bimolecular reactions within a lattice model where a small number of reactants diffuse amongst a much larger number of inert particles. When the number of inert particles is held…
We study the decay rate $\theta(a)$ that characterizes the late time exponential decay of the first-passage probability density $F_a(t|0) \sim e^{-\theta(a)\, t}$ of a diffusing particle in a one dimensional confining potential $U(x)$,…
The time needed for a particle to exit a confining domain through a small window, called the narrow escape time (NET), is a limiting factor of various processes, such as some biochemical reactions in cells. Obtaining an estimate of the mean…
In the past the study of reaction-diffusion systems has greatly contributed to our understanding of the behavior of many-body systems far from equilibrium. In this paper we aim at characterizing the properties of diffusion limited reactions…
We show that a fluid under strong spatially periodic confinement displays a glass transition within mode-coupling theory (MCT) at a much lower density than the corresponding bulk system. We use fluctuating hydrodynamics, with confinement…
A molecular theory of the glass transition of network forming liquids is developed using a combination of self-consistent phonon and liquid state approaches. Both the dynamical transition and the entropy crisis characteristic of random…
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…