Related papers: Glassy Dynamics of Protein Folding
We report on quantitative comparisons between simulation results of a bead-spring model and mode-coupling theory calculations for the structural and conformational dynamics of a supercooled, unentangled polymer melt. We find…
We show that the interplay between excluded volume effects, hydrophobicity, and hydrogen bonding of a tube-like representation of a polypeptide chain gives rise to free energy landscapes that exhibit a small number of metastable minima…
The question of whether glass continues to relax at low temperature is of fundamental and practical interest. Here, we report a novel atomistic simulation method allowing us to directly access the long-term dynamics of glass relaxation at…
We introduce a new model for the dynamics of a wormlike chain in an environment that gives rise to a rough free energy landscape, which we baptise the glassy wormlike chain. It is obtained from the common wormlike chain by an exponential…
The folding kinetics of a number of sequences for off-lattice continuum model of proteins is studied using Langevin simulations at two values of the friction coefficient. We show that there is a remarkable correlation between folding times,…
We construct a framework for the study of fluctuations in the nonequilibrium relaxation of glassy systems with and without quenched disorder. We study two types of two-time local correlators with the aim of characterizing the heterogeneous…
We study dynamics of freely cooling granular gases in two-dimensions using large-scale molecular dynamics simulations. We find that for dilute systems the typical kinetic energy decays algebraically with time, E(t) ~ t^{-1}, in the long…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
In this work, we study the dynamics of complex systems with time-dependent transition rates, focusing on $p$-adic analysis in modeling such systems. Starting from the master equation that governs the stochastic dynamics of a system with a…
Energy landscapes are high-dimensional surfaces representing the dependence of system energy on variable configurations, which determine crucially the system's emergent behavior but are difficult to be analyzed due to their high-dimensional…
We analyze a simple dynamical model of glasses, based on the idea that each particle is trapped in a local potential well, which itself evolves due to hopping of neighbouring particles. The glass transition is signalled by the fact that the…
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence of local interactions, native structure formation does not…
We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable…
A method for reconstructing the energy landscape of simple polypeptidic chains is described. We show that we can construct an equivalent representation of the energy landscape by a suitable directed graph. Its topological and dynamical…
In the free energy landscape picture of glassy systems, the slow dynamics characteristic of these systems is believed to be due to the existence of a complicated free-energy landscape with many local minima. We show here that for a…
The zero temperature relaxational dynamics of a particle in a short range correlated random potential is addressed. We derive a set of "two-times" mean-field dynamical equations, accounting for a possible mean displacement of the particle…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
We consider the problem of slow activation dynamics in glassy systems undergoing a random first order phase transition. Using an effective potential approach to supercooled liquids, we determine the spectrum of activation barriers for…
Epithelial cell tissues have a slow relaxation dynamics resembling that of supercooled liquids. Yet, they also have distinguishing features. These include an extended short-time sub-diffusive transient, as observed in some experiments and…
Quantitative topological analogies between the flexibilities of optimized inorganic glasses, small biological molecules, and proteins suggest that mean field estimates of internal stress are useful in identifying mechanisms supporting…