相关论文: Cooperativity in Protein Folding: From Lattice Mod…
Predicting the change in binding free energy ($\Delta \Delta G$) is crucial for understanding and modulating protein-protein interactions, which are critical in drug design. Due to the scarcity of experimental $\Delta \Delta G$ data,…
We examine the dynamics of hard spheres and discs at high packing fractions in two and three dimensions, modeling the simplest systems exhibiting a glass transition. As it is well known, cooperativity and dynamic heterogeneity arise as…
We have performed parallel tempering Monte Carlo simulations using a simple continuum heteropolymer model for proteins. All ten heteropolymer sequences which we have studied have shown first-order transitions at low temperature to ordered…
Strongly-coupled gauge theories are an important ingredient in the construction of many extensions of the standard model, particularly for models of electroweak symmetry breaking in which the Higgs boson is a composite object. There is a…
We compute the c/a lattice strain versus temperature for nonmagnetic hcp iron at high pressures using both first-principles linear response quasiharmonic calculations based on the full potential linear-muffin-tin-orbital (LMTO) method and…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
The aim of this paper is to show that one can achieve convergence rates of $N^{-\alpha+ \delta}$ for $\alpha > 1/2$ (and for $\delta > 0$ arbitrarily small) for nonperiodic $\alpha$-smooth cosine series using lattice rules without random…
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,…
In the standard approach to lattice proteins the models based on nearest neighbor interaction are used. In this kind of models it is difficult to explain the existence of secondary structures --- special preferred conformations of protein…
[abridged] Background: The distribution of chemical species in an open system at metastable equilibrium can be expressed as a function of environmental variables which can include temperature, oxidation-reduction potential and others.…
Pressure-induced phase transitions of spin-crossover materials were simulated by a Monte Carlo simulation in the constant pressure ensemble for the first time. Here, as the origin of the cooperative interaction, we adopt elastic interaction…
In order to elucidate the role of the native state topology and the stability of subdomains in protein folding, we investigate free energy landscape of human lysozyme, which is composed of two subdomains, by Monte Carlo simulations. A…
A transfer-matrix formalism is introduced to evaluate exactly the partition function of the Munoz-Eaton model, relating the folding kinetics of proteins of known structure to their thermodynamics and topology. This technique can be used for…
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…
Cooperative adsorption of gases by porous frameworks permits more efficient uptake and removal than does the more usual non-cooperative (Langmuir-type) adsorption. Cooperativity, signaled by a step-like isotherm, is usually attributed to a…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
We study numerically a lattice model of semiflexible homopolymers with nearest neighbor attraction and energetic preference for straight joints between bonded monomers. For this we use a new algorithm, the "Pruned-Enriched Rosenbluth…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
We consider in this review the statistical mechanical description of a very general microscopic lattice model of a compressible and interacting multi-component mixture of linear polymers of fixed lengths. The model contains several…