Related papers: Protein Folding and Spin Glass
We review recent findings on spin glass models. Both the equilibrium properties and the dynamic properties are covered. We focus on progress in theoretical, in particular numerical, studies, while its relationship to real magnetic materials…
The synergetic approach proposed here is based on characteristic instability of chemical bonding in the form of the bond wave considered as the spatiotemporal correlation between the elementary acts of bond exchange. In frames of the model,…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
A spin glass is a diluted magnetic material in which the magnetic moments are randomly interacting, with a huge number of metastable states which prevent reaching equilibrium. Spin-glass models are conceptually simple, but require very…
We study the influence of composition changes on the glass transition of binary hard disc and hard sphere mixtures in the framework of mode coupling theory. We derive a general expression for the slope of a glass transition line. Applied to…
Kinetics of folding of a protein held in a force-clamp are compared to an unconstrained folding. The comparison is made within a simple topology-based dynamical model of ubiquitin. We demonstrate that the experimentally observed variations…
Comparisons and analogies are drawn between materials ferroic glasses and conventional spin glasses, in terms of both experiment and theoretical modelling, with inter-system conceptual transfers leading to suggestions of further issues to…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
The glass transition temperature and its connection to statistical properties of confined and free-standing polymer films of varying thickness containing unentangled to highly entangled bead-spring chains are studied by molecular dynamics…
The recently proposed strategy for studying the equilibrium thermodynamics of the glass phase using a molecular liquid is reviewed and tested in details on the solvable case of the $p$-spin model. We derive the general phase diagram, and…
One of the most puzzling and unsolved challenges in molecular biology is understanding how proteins fold. Despite having advanced predictive tools that can accurately estimate the native structures of proteins, we still lack a comprehensive…
The glass transition is investigated in three dimensions for single and double Yukawa potentials for the full range of control parameters. For vanishing screening parameter, the limit of the one-component plasma is obtained; for large…
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins.…
The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
Understanding glass formation is a challenge because the existence of a true glass state, distinct from liquid and solid, remains elusive: Glasses are liquids that have become too viscous to flow. An old idea, as yet unproven…