Related papers: Protein Folding and Spin Glass
A novel approach to protein folding dynamics is presented. We suggest that folding of protein may be mediated via interaction with solitons which propagate along the molecular chain. A simple toy model is presented in which a Sine-Gordon…
We use computer simulations to investigate the static properties of a simple glass-forming fluid in which the positions of a finite fraction of the particles has been frozen in. By probing the equilibrium distribution of the overlap between…
The description of thermodynamic phase transitions in terms of percolation transitions of suitably defined clusters has a long tradition and boasts a number of important successes, the most prominent ones being in ferromagnetic lattice…
Extending mode-coupling theory, we elaborate a microscopic theory for the glass transition of liquids confined between two parallel flat hard walls. The theory contains the standard MCT equations in bulk and in two dimensions as limiting…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
Globular proteins are expected to assume folds with fixed secondary structures, alpha-helices and beta-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to…
The folding of the cholesterol trapping apolipoprotein A1 in aqueous solution at increasing ionic strength is studied using atomically detailed molecular dynamics simulations. We calculate various structural properties to characterize the…
Numerical simulations on Ising Spin Glasses show that spin glass transitions do not obey the usual universality rules which hold at canonical second order transitions. On the other hand the dynamics at the approach to the transition appear…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
As one increases the concentration of a colloidal suspension, the system exhibits a dramatic increase in viscosity. Structurally, the system resembles a liquid, yet motions within the suspension are slow enough that it can be considered…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
We give a brief introduction to the mode-coupling theory of the glass transition, a theory which was proposed a while ago to describe the dynamics of supercooled liquids. After presenting the basic equations of the theory, we review some of…
Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter…
Glass forming liquids exhibit a rich phenomenology upon confinement. This is often related to the effects arising from wall-fluid interactions. Here we focus on the interesting limit where the separation of the confining walls becomes of…
The glass transition is considered within two toys models, a mean field spin glass and a directed polymer in a correlated random potential. In the spin glass model there occurs a dynamical transition, where the system condenses in a state…
We consider here the percolation problem in thin films, both in the direction normal to the film and in the direction parallel to the film. We thereby describe here the cross-over between 2D and 3D percolation, which we do on cubic and…
Quantitative topological analogies between the flexibilities of optimized inorganic glasses, small biological molecules, and proteins suggest that mean field estimates of internal stress are useful in identifying mechanisms supporting…
The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is…
We propose a connection between self-similar, focusing dynamics in nonlinear partial differential equations (PDEs) and macroscopic dynamic features of the glass transition. In particular, we explore the divergence of the appropriate…