Related papers: Glassy Dynamics of Protein Folding
The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Proteins are aminoacid chains that diffusively fold or unfold depending on the thermal and chemical environmental conditions. While sophisticated models account for detailed aspects of real proteins, finding traits that unify protein…
We study the dynamics of a one-dimensional fluid of orientable hard rectangles with a non-coarse-grained microscopic mechanism of facilitation. The length occupied by a rectangle depends on its orientation, which is coupled to an external…
We present results of temperature dependent measurements of dynamics of micellar nanoparticle - polymer composites of fixed volume fraction and variable polymer chain grafting density. For nanoparticles with lower grafting density we…
We discuss the stochastic thermodynamics of systems that are described by a time-dependent density field, for example simple liquids and colloidal suspensions. For a time-dependent change of external parameters, we show that the Jarzynski…
This article delves into the micro-macro modeling of polymeric fluids, considering various microscopic potential energies, including the classical Hookean potential, as well as newly proposed modified Morse and Elastic-plastic potentials.…
We have exactly solved the relaxational dynamics of a model protein which possesses a kinetically perfect funnel-like energy landscape. We find that the dependence of the relaxation time, $\tau$, on the density of states (DOS) and the…
Inspired by experiments on dynamic extensile gels of biofilaments and motors, we propose a model of a network of linear springs with a kinetics consisting of growth at a prescribed rate, death after a lifetime drawn from a distribution, and…
An instructive and apparently simple model of fully-coupled rotators, the so-called Hamiltonian Mean Field (HMF) model, together with a generalized version with variable interaction range, have revealed a very complex out-of-equilibrium…
We study the role of fluctuations on the thermodynamic glassy properties of plaquette spin models, more specifically on the transition involving an overlap order parameter in the presence of an attractive coupling between different replicas…
We investigate the behavior of energy fluctuations in several models of granular gases maintained in a non-equilibrium steady state. In the case of a gas heated from a boundary, the inhomogeneities of the system play a predominant role.…
We present a numerical study of the statistical properties of the potential energy landscape of a simple model for strong network-forming liquids. The model is a system of spherical particles interacting through a square well potential,…
The near-native free energy landscape of protein G is investigated through 0.4 microseconds-long atomistic molecular dynamics simulations in explicit solvent. A theoretical and computational framework is used to assess the time-dependence…
We analyze the stretching elasticity of a wormlike chain with a tension discontinuity resulting from a Hookean spring connecting its backbone to a fixed point. The elasticity of isolated semiflexible filaments has been the subject in a…
We consider the dynamics of spin facilitated models of glasses in the non-equilibrium aging regime following a sudden quench from high to low temperatures. We briefly review known results obtained for the broad class of kinetically…
Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging…
Temporal relaxation of density fluctuations in supercooled liquids near the glass transition occurs in multiple steps. The short-time $\beta$-relaxation is generally attributed to spatially local processes involving the rattling motion of a…
We present two simplified models of protein dynamics based on Langevin's equation of motion in a viscous medium. We explore the effect of the potential energy function's symmetry on the kinetics and thermodynamics of simulated folding. We…
The dynamics of individual colloidal particles in random potential energy landscapes were investigated experimentally and by Monte Carlo simulations. The value of the potential at each point in the two-dimensional energy landscape follows a…