Related papers: Protein Folding and Spin Glass
Thermodynamics and kinetics are thought to be linked in glass transitions. The quantitative predictions of -relaxation activation barriers provided by the theory of glasses based on random first order transitions are compared with…
Theory of multi-dimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in…
The glass transition is described in terms of thermally activated local structural rearrangements, the secondary relaxations of the glass phase. The interaction between these secondary relaxations leads to a much faster and much more…
We consider a simplified model of protein folding, with binary degrees of freedom, whose equilibrium thermodynamics is exactly solvable. Based on this exact solution, the kinetics is studied in the framework of a local equilibrium approach,…
Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of two monomer types. Although these chains…
Protein folding, which dictates the protein structure from its amino acid sequence, is half a century old problem of biology. The function of the protein correlates with its structure, emphasizing the need of understanding protein folding…
The prediction of the biologically active native conformation of a protein is one of the fundamental challenges of structural biology. This problem remains yet unsolved mainly due to three factors: the partial knowledge of the effective…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
Pinning a fraction of particles from an equilibrium configuration in supercooled liquids has been recently proposed as a way to induce a new kind of glass transition, the Random Pinning Glass Transition (RPGT). The RPGT has been predicted…
The p-spin spin-glass model has been studied extensively at mean-field level because of the insights which it provides into the mode-coupling approach to structural glasses and the nature of the glass transition. We demonstrate explicitly…
We propose a novel computational strategy to study the glass transition of molecular fluids. Our approach combines the construction of simple yet realistic models with the development of Monte Carlo algorithms to accelerate equilibration…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
An analytical approach, which develops the gauge model of the glass transition phenomenon, is suggested. It is based on the quantum field theory and critical dynamics methods. The suggested mechanism of glass transition is based on the…
This review presents various aspects of a mean-field spin glass model known as the p-spin spherical spin glass model, which has raised a lot of interest in the study of spin glasses, and also for its possible links with a mean-field theory…
We present numerical simulations of the 4D Edwards Anderson Ising spin glass with binary couplings. Our results, in the midst of strong finite size effects, suggest the existence of a spin glass phase transition. We present a preliminar…
We show that finite size scaling techniques can be employed to study the glass transition. Our results follow from the postulate of a diverging correlation length at the glass transition whose physical manifestation is the presence of…
We introduce and analytically study a generalized p-spin glass like model that captures some of the main features of attractive glasses, recently found by Mode Coupling investigations, such as a glass/glass transition line and dynamical…
In this paper we study the critical properties of a finite dimensional generalization of the p-spin model. We find evidence that in dimension three, contrary to its mean field limit, the glass transition is associated to a diverging…
The microcanonical analysis is shown to be a powerful tool to characterize the protein folding transition and to neatly distinguish between good and bad folders. An off-lattice model with parameter chosen to represent polymers of these two…
We show that a fluid under strong spatially periodic confinement displays a glass transition within mode-coupling theory (MCT) at a much lower density than the corresponding bulk system. We use fluctuating hydrodynamics, with confinement…