Related papers: Protein Folding and Spin Glass

One of the most remarkable predictions to emerge out of the exact infinite-dimensional solution of the glass problem is the Gardner transition. Although this transition was first theoretically proposed a generation ago for certain…

Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…

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…

We offer simple solutions to three kinematic problems that occur in the folding of proteins. We show how to construct suitably local elementary Monte Carlo moves, how to close a loop, and how to fold a loop without breaking the bond that…

Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…

An introduction and overview is given of the theory of spin glasses and its application.

The glass transition is the most enduring grand-challenge problem in contemporary condensed matter physics. Here, we review the contribution of colloid experiments to our understanding of this problem. First, we briefly outline the success…

We consider the stationary state of a fluid comprised of inelastic hard spheres or disks under the influence of a random, momentum-conserving external force. Starting from the microscopic description of the dynamics, we derive a nonlinear…

We present a modified version of our "sliding model", where chain arcs, between two contacts at the surface, may move if all the barriers along the arc are weaker than a certain threshold.An important advance of the revised model is that…

We study the glass transition by exploring a broad class of kinetic rules that can significantly modify the normal dynamics of super-cooled liquids, while maintaining thermal equilibrium. Beyond the usual dynamics of liquids, this class…

First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…

As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…

We study the glass transition in fluids where particles are endowed with spins, such that magnetic and positional degrees of freedom are coupled. Novel results for slowing down in the spin time-correlation functions are described, and the…

The free-energy landscape of two peptides is evaluated at various temperatures and an estimate for its fractal dimension at these temperatures calculated. We show that monitoring this quantity as a function of temperature allows to…

In this letter we study a lattice gas system that undergoes a glassy transition. When we approach the glass transition we find both a divergence of a point to set correlation length and the vanishing of the thermodynamic potential. These…

The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…

We propose a method to study quantitatively the glass transition in a system of interacting particles. In spite of the absence of any quenched disorder, we introduce a replicated version of the hypernetted chain equations. The solution of…

A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…

Protein folding is a phenomenon that has been studied for about 50 years and still remains as an unsolved problem. The main feature of this process is that it occurs as an all or none process, so a protein, can jump directly between folded…

Spin glasses are a longstanding model for the sluggish dynamics that appears at the glass transition. However, spin glasses differ from structural glasses for a crucial feature: they enjoy a time reversal symmetry. This symmetry can be…