Related papers: Relaxation in a perfect funnel
We consider the diffusion constant, D, of a probe particle coupled to the East model, extending previous numerical results for this model to encompass a total of twelve orders of magnitude in relaxation time, {\tau}. Our considerations thus…
We deal with a system of two coupled differential equations, describing the evolution of a first order phase transition. In particular, we have two non-linear parabolic equations: the first one is deduced from a balance law for entropy and…
We study thermally activated, low temperature equilibrium dynamics of elastic systems pinned by disorder using one loop functional renormalization group (FRG). Through a series of increasingly complete approximations, we investigate how the…
We show that for any liquid or solid with strong correlation between its $NVT$ virial and potential-energy equilibrium fluctuations, the temperature is a product of a function of excess entropy per particle and a function of density,…
A new method for investigating relaxation phenomena for charge carriers hopping between localized tail states has been developed. It allows us to consider both charge and energy {\it dispersive} transport. The method is based on the idea of…
The near-native free energy landscape of protein G is investigated through 0.4 microseconds-long atomistic molecular dynamics simulations in explicit solvent. A theoretical and computational framework is used to assess the time-dependence…
The probability distribution of sequences with maximum entropy that satisfies a given amino acid composition at each site and a given pairwise amino acid frequency at each site pair is a Boltzmann distribution with $\exp(-\psi_N)$, where…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…
Amorphous solids or glasses are known to exhibit stretched-exponential decay over broad time intervals in several of their macroscopic observables: intermediate scattering function, dielectric relaxation modulus, time-elastic modulus etc.…
Generic glass formers exhibit at least two characteristic changes in their relaxation behavior, first to an Arrhenius-type relaxation at some characteristic temperature, and then at a lower characteristic temperature to a super-Arrhenius…
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…
Stretched-exponential relaxation is a widely observed phenomenon found in ordered ferromagnets as well as glassy systems. One modeling approach connects this behavior to a droplet dynamics described by an effective Langevin equation for the…
Exactly solvable models provide an opportunity to study different aspects of reduced quantum dynamics in detail. We consider the reduced dynamics of a single spin in finite XX and XY spin 1/2 chains. First we introduce a general expression…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
A novel Information Theory based method for determining the density of states from prior information is presented. The energy dependence of the density of states is determined from the observed number of states per energy interval and model…
We discuss a nonlinear model for the relaxation by energy redistribution within an isolated, closed system composed of non-interacting identical particles with energy levels e_i with i=1,2,...,N. The time-dependent occupation probabilities…
We introduce an exactly solvable model for glassy dynamics with many relaxational modes, each one characterized by a different relaxational time-scale. Analytical solution of the aging dynamics at low temperatures shows that a…
We investigate the deconfinement transition driven by excitations in long-range spin models. At low temperatures, these models exhibit a confined phase where domain-wall (or kinks) are localized. As temperature increases, kinks interact and…
We study the mass dependence of various quantities (like the average and maximum density, collision rate, participant-spectator matter, temperature as well as time zones for higher density) by simulating the reactions at the energy of…