Related papers: Glassy Dynamics of Protein Folding
Molecular-dynamics simulations are presented for two correlation functions formed with the partial density fluctuations of binary hard-sphere mixtures in order to explore the effects of mixing on the evolution of glassy dynamics upon…
The dynamics of many glassy systems are known to exhibit string-like hopping motions each consisting of a line of particles displacing one and other. By using molecular dynamics simulations of glassy polymers, we show that these motions…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
Taking into account the nonequivalence of fixed-force and fixed-length ensembles in the weak-force regime, equations of state are derived that describe the equilibrium extension or compression of an ideal Gaussian polymer chain in response…
In polymers melts and supercooled liquids, the glassy dynamics is characterized by the rattling of monomers or particles in the cage formed by their neighbors. Recently, a direct correlation in such systems, described by a universal scaling…
There has been renewed interest in the frequency dependent specific heat of supercooled liquids in recent years with computer simulation studies exploring the whole frequency range of relaxation. The simulation studies can thus supplement…
We propose a new class of phenomenological models for dynamic glass transitions. The system consists of an ensemble of mesoscopic regions to which local energies are allocated. At each time step, a region is randomly chosen and a new local…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
We analyze the properties of a Lennard-Jones system at the level of the potential energy landscape. After an exhaustive investigation of the topological features of the landscape of the systems, obtained studying small size sample, we…
We numerically study dynamical properties of the one-component Gaussian Core Model in the supercooled states. We find that nucleation is suppressed as density increases. Concomitantly the system exhibits glassy slow dynamics characterized…
The free energy landscape of a protein-like chain in a fluid was studied by combining discontinuous molecular dynamics and parallel tempering. The model protein is a repeating sequence of four different beads, with interactions mimicking…
We study the geometric properties of the energy landscape of coarse-grained, off-lattice models of polymers by endowing the configuration space with a suitable metric, depending on the potential energy function, such that the dynamical…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
We present a simple mathematical framework for the description of the dynamics of glassy systems in terms of a random walk in a complex energy landscape pictured as a network of minima. We show how to use the tools developed for the study…
Prompted by results that showed that a simple protein model, the frustrated G\=o model, appears to exhibit a transition reminiscent of the protein dynamical transition, we examine the validity of this model to describe the low-temperature…
We study at- and out-of-equilibrium dynamics of a single homopolymer chain at low temperature using molecular dynamics simulations. The main quantities of interest are the average root mean square displacement of the monomers below the…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…
Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…
We investigate the near-surface relaxation of freestanding atactic \glsdesc{ps} films with molecular dynamics simulations. As in previous coarse-grained simulations, relaxation times for backbone segments and phenyl rings are linked to…
The folding of naturally occurring, single domain proteins is usually well-described as a simple, single exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this…