Related papers: Protein Folding and Spin Glass
A current focus in studies of the glass transition is the role of dynamic heterogeneities. Although these efforts may clarify the origin of the spectacular change in properties of liquids approaching vitrification, we point out that a…
As in the preceding paper we aim at identifying the effective theory that describes the fluctuations of the local overlap with an equilibrium reference configuration close to a putative thermodynamic glass transition. We focus here on the…
Recent studies on the spin and the chirality orderings of the three-dimensional Heisenberg spin glass and related systems are reviewed with particular emphasis on the possible spin-chirality decoupling phenomena. Chirality scenario of real…
Spin glasses are magnetic systems exhibiting both quenched disorder and frustration, and have often been cited as examples of `complex systems.' In this talk I review some of the basic notions of spin glass physics, and discuss how some of…
Phase transitions in spin glass type systems and, more recently, in related computational problems have gained broad interest in disparate arenas. In the current work, we focus on the "community detection" problem when cast in terms of a…
The interconnected processes of protein folding, mutations, epistasis, and evolution have all been the subject of extensive analysis throughout the years due to their significance for structural and evolutionary biology. The origin…
In this note we present numerical simulations of binary mixtures and we find indications for a thermodynamic transition to a glassy phase. We find that below the transition point the off equilibrium correlation functions and response…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
We study a recently introduced model of one-component glass-forming liquids whose constituents interact with anisotropic potential. This system is interesting per-se and as a model of liquids like glycerol (interacting via hydrogen bonds)…
One of the main concerns of Anfinsen was to reveal the connection between the amino acid sequence and their biologically active conformation. This search gave rise to two crucial questions in structural biology, namely, why the proteins…
We study the protein folding problem on the base of the quantum approach we proposed recently by considering the model of protein chain with nine amino-acid residues. We introduced the concept of distance space and its projections on a…
Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as…
Recent experiments have demonstrated that the glass transition temperature of thin polymer films can be shifted as compared to the same polymer in the bulk, the amplitude and the sign of this effect depending on the interaction between the…
We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding…
It is frequently assumed that in the limit of vanishing cooling rate, the glass transition phenomenon becomes a thermodynamic transition at a temperature $T_{K}$. However, with any finite cooling rate, the system falls out of equilibrium at…
The energy for protein folding arises from multiple sources and is not large in total. In spite of the many specific successes of energy landscape and other approaches, there still seems to be some missing guiding factor that explains how…
A three-dimensional $\pm J$ XY spin-glass model is investigated by a nonequilibrium relaxation method. We have introduced a new criterion for the finite-time scaling analysis. A transition temperature is obtained by a crossing point of…
We use the Popov-Fedotov representation of spin operators to construct an effective action for a Kondo lattice model with quenched disorder at finite temperatures. We study the competition between the Kondo effect and frozen spin order in…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…