Related papers: Glassy Dynamics of Protein Folding
We endow a system of interacting particles with two distinct, local, Markovian and reversible microscopic dynamics. Using common field-theoretic techniques used to investigate the presence of a glass transition, we find that while the…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
We present a three-dimensional lattice-gas model with trivial thermodynamics, but nontrivial dynamics. The model is characterized by each particle having its own random energy landscape. The equilibrium dynamics of the model were…
We study the stochastic relaxation dynamics of the Ising p-spin model on a random graph, a well-known model with glassy dynamics at low temperatures. We introduce and discuss a new closure scheme for the master equation governing the…
We develop a framework for understanding the difference between strong and fragile behavior in the dynamics of glass-forming liquids from the properties of the potential energy landscape. Our approach is based on a master equation…
We numerically simulate a thermalization process in an energy landscape with hierarchically organized metastable states. The initial configuration is chosen to have a large energy excess, relative to the thermal equilibrium value at the…
It is common to study polymer physics through the use of idealized single-chain models, and the most popular of these is the freely jointed chain model. In certain thermodynamic ensembles, statistical mechanical treatment of this model is…
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective…
We perform an analytic study on the stochastic thermodynamics of a small classical particle trapped in a time dependent single-well potential in the highly underdamped limit. It is shown that the nonequilibrium probability density function…
A system is glassy when the observation time is much smaller than the equilibration time. A unifying thermodynamic picture of the glassy state is presented. Slow configurational modes are in quasi-equilibrium at an effective temperature. It…
We study a minimal extension of the worm-like chain to describe polypeptides having alpha-helical secondary structure. In this model presence/absence of secondary structure enters as a scalar variable that controls the local chain bending…
The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein…
Simulations are used to examine the microscopic origins of strain hardening in polymer glasses. While stress-strain curves for a wide range of temperature can be fit to the functional form predicted by entropic network models, many other…
Folding channels and free-energy landscapes of hydrophobic-polar heteropolymers are discussed on the basis of a minimalistic off-lattice coarse-grained model. We investigate how rearrangements of hydrophobic and polar monomers in a…
A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative…
A conceptual difficulty in the Hooke's-law description of ideal Gaussian polymer-chain elasticity is sometimes apparent in analyses of experimental data or in physical models designed to simulate the behavior of biopolymers. The problem,…
Kinetically constrained models (KCM) generically have trivial thermodynamics and yet manifest rich glassy dynamics. In order to resolve the thermodynamics-dynamics disconnect in KCMs, we derive a KCM by coarse-graining a non-trivial…
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…
We incorporate hydrodynamic interactions (HI) in a coarse-grained and structure-based model of proteins by employing the Rotne-Prager hydrodynamic tensor. We study several small proteins and demonstrate that HI facilitate folding. We also…
In this paper we extend the earlier treatment of out-of-equilibrium mesoscopic fluctuations in glassy systems in several significant ways. First, via extensive simulations, we demonstrate that models of glassy behavior without quenched…