Related papers: Protein Folding and Spin Glass
This paper first describes, from a high level viewpoint, the main challenges that had to be solved in order to develop a theory of spin glasses in the last fifty years. It then explains how important inference problems, notably those…
We study the glass transition of binary mixtures of dipolar particles in two dimensions within the framework of mode-coupling theory, focusing in particular on the influence of composition changes. In a first step, we demonstrate that the…
Colloids are suspensions of small solid particles in a liquid, and exhibit glassy behavior when the particle concentration is high. In these samples, the particles are roughly analogous to individual molecules in a traditional glass. This…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
A spin-glass transition occurs both in and out of the limit of validity of mean-field theory on a diluted one dimensional chain of Ising spins where exchange bonds occur with a probability decaying as the inverse power of the distance.…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…
The glass transition is considered as a phase transition in the system of topologically protected excitations in matter structure. The critical behavior of the system is considered both in statics and dynamics cases. It is shown in the…
The glass transition is a long-standing problem in physics. Identifying the structural origin of the transition may lead to the ultimate solution to the problem. Here, for the first time, we discover such a structural origin by proposing a…
In this talk, after a short phenomenological introduction on glasses, I will describe some recent progresses that have been done in glasses using the replica method in the definition and in the evaluation of the configurational entropy (or…
Apparent critical phenomena, typically indicated by growing correlation lengths and dynamical slowing-down, are ubiquitous in non-equilibrium systems such as supercooled liquids, amorphous solids, active matter and spin glasses. It is often…
For hard ellipsoids of revolution we calculate the phase diagram for the idealized glass transition. Our equations cover the glass physics in the full phase space, for all packing fractions and all aspect ratios X$_0$. With increasing…
To determine the 3D conformation of proteins is a necessity to understand their functions or interactions with other molecules. It is commonly admitted that, when proteins fold from their primary linear structures to their final 3D…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
Dynamical connectivity graphs, which describe dynamical transition rates between local energy minima of a system, can be displayed against the background of a disconnectivity graph which represents the energy landscape of the system. The…
We point out that the correlation between folding times and $\sigma = (T_{\theta } - T_{f})/T_{\theta }$ in protein-like heteropolymer models where $T_{\theta }$ and $T_{f}$ are the collapse and folding transition temperatures was already…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…