Related papers: Glassy Dynamics of Protein Folding
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
In this paper, a statistical physical derivation of thermodynamically consistent fluid mechanical equations is presented for non-isothermal viscous molecular fluids. The coarse-graining process is based on (i) the adiabatic expansion of the…
We analyze the slow, glassy structural relaxation as measured through collective and tagged-particle density correlation functions obtained from Brownian dynamics simulations for a polydisperse system of quasi-hard spheres in the framework…
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…
It is generally believed that the intrinsic properties of glasses are intimately related to potential-energy landscapes (PELs). However, little is known about the PELs of glasses below the glass transition temperature (Tg). Taking advantage…
A few years ago it was showed that some systems that have very similar local structure, as quantified by the pair correlation function, exhibit vastly different slowing down upon supercooling [L. Berthier and G. Tarjus, Phys. Rev. Lett.…
How useful it is to think about the potential energy landscape of a complex many-body system depends in large measure on how direct the connection is to the system's dynamics. In this paper we show that, within what we call the potential…
We study the dynamics of a single semiflexible filament coupled to a Hookean spring at its boundary. The spring produces a fluctuating tensile force on the filament, whose value depends on the filament's instantaneous end-to-end length. The…
We consider the thermally activated fragmentation of a homopolymer chain. In our simple model the dynamics of the intact chain is a Rouse one until a bond breaks and bond breakdown is considered as a first passage problem over a barrier to…
The binary hard-sphere mixture is one of the simplest representations of a many-body system with competing time and length scales. This model is relevant to fundamentally understand both the structural and dynamical properties of materials,…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
We study the folding thermodynamics of a beta-hairpin and two three-stranded beta-sheet peptides using a simplified sequence-based all-atom model, in which folding is driven mainly by backbone hydrogen bonding and effective hydrophobic…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
Numerical simulations of hydrated proteins show that protein hydration shells are polarized into a ferroelectric cluster with a large magnitude of its average dipole moment. The emergence of this new mesophase dramatically alters the…
Using molecular dynamics simulations we examine the dynamics of a family of model polymers with varying chain length and torsional potential barriers. We focus on features of the dynamics of polymers that are seen experimentally but absent…
We consider a frustrated spin model with a glassy dynamics characterized by a slow component and a fast component in the relaxation process. The slow process involves variables with critical behavior at finite temperature T_p and has a…
We introduce a stochastic generalisation of the classical deterministic Floquet-East model, a discrete circuit with the same kinetic constraint as the East model of glasses. We prove exactly that, in the limit of long time and large size,…
In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are…
The dynamics of structural relaxation in a model polymer glass subject to spatially-homogeneous, time-periodic shear deformation is investigated using molecular dynamics simulations. We study a coarse-grained bead-spring model of short…
We compare dynamical heterogeneities in equilibrated supercooled liquids and in the nonequilibrium glassy state within the framework of the random first order transition theory. Fluctuating mobility generation and transport in the glass are…