Related papers: Relaxation in a perfect funnel
We address a recent conjecture according to which the relaxation time $\tau$ of a viscous liquid obeys density scaling ($\tau=F(\rho^\gamma/T)$ where $\rho$ is density) if the liquid is ``strongly correlating,'' i.e., has almost 100%…
Using molecular dynamics simulation, we calculate fluctuations and response for steadily sheared hard spheres over a wide range of packing fractions $\phi$ and shear strain rates $\gamma$, using two different methods to dissipate energy. To…
We obtain a nonequilibrium theory for a simple model of a generic class of active dense systems consisting of self-propelled particles with a self-propulsion force, $f_0$, and persistence time, $\tau_p$, of their motion. We consider two…
The dynamics of folding of proteins is studied by means of a phenomenological master equation. The energy distribution is taken as a truncated exponential for the misfolded states plus a native state sitting below the continuum. The…
In biological systems, expression dynamics to shape a fitted phenotype for function has evolved through mutations to genes, as observed in the evolution of funnel landscape in protein. We study this evolutionary process with a…
We try to improve the Thomas-Fermi model for the total energy and electron density of atoms and molecules by directly modifying the Euler equation for the electron density, which we argue is less affected by nonlocal corrections. Here we…
The time dependence of deviations from the Gaussian state in a freely cooling homogeneous system of smooth inelastically colliding spheres is investigated by kinetic theory. We determine the full time dependence of the coefficients of an…
A coarse grained model of a random polypeptide chain, with only discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues is shown to display stretched exponential relaxation under Metropolis…
We study numerically the relaxation of a driven elastic string in a two dimensional pinning landscape. The relaxation of the string, initially flat, is governed by a growing length $L(t)$ separating the short steady-state equilibrated…
The relativistic generalization of a free Brownian motion theory is presented. The global characteristics of the relaxation are {\it explicitly} found for the velocity and momentum (stochastic) kinetics. It is shown that the thermal…
We have simulated energy relaxation and equilibrium dynamics in Coulomb Glasses using the random energy lattice model. We show that in a temperature range where the Coulomb Gap is already well developed, (T=0.03-0.1) the system still…
Ozawa et. al [1] presented numerical results for the configurational entropy density, $s_c$, of a model glass-forming liquid in the presence of random pinning. The location of a "phase boundary" in the pin density ($c$) - temperature ($T$)…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
In the present work, we provide a dielectric study on two differently concentrated aqueous lysozyme solutions in the frequency range from 1 MHz to 40 GHz and for temperatures from 275 to 330 K. We analyze the three dispersion regions,…
Free-energy landscape theory is often used to describe complex molecular systems. Here, a microscopic description of water structure and dynamics based on configuration-space-networks and molecular dynamics simulations of the TIP4P/2005…
We discuss the relaxation time (inverse spectral gap) of the one dimensional $O(N)$ model, for all $N$ and with two types of boundary conditions. We see how its low temperature asymptotic behavior is affected by the topology. The…
A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory…
The nonexponential relaxation ocurring in complex dynamics manifested in a wide variety of systems is analyzed through a simple model of diffusion in phase space. It is found that the inability of the system to find its equilibrium state in…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
We examine the structural relaxation of glassy materials at finite temperatures, considering the effect of activated rearrangements and long-range elastic interactions. Our three-dimensional mesoscopic relaxation model shows how the…