相关论文: Ab initio study of alanine polypeptide chains twis…

The interface states appearing in polyacetylene-polyvinylfluoride and polyethylene-polyvinylfluoride are determined via an ab initio self consistent field technique based on Green matrix formalism. Different properties of these states are…

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…

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…

Prediction of the functions of riboswitches requires a quantitative description of the folding landscape so that the barriers and time scales for the conformational change in the switching region in the aptamer can be estimated. Using a…

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…

We present a first principles-quality potential energy surface (PES) describing the inter-atomic forces for hydrogen atoms interacting with free-standing graphene. The PES is a high-dimensional neural network potential that has been…

Encoding the complex features of an energy landscape is a challenging task, and often chemists pursue the most salient features (minima and barriers) along a highly reduced space, i.e. 2- or 3-dimensions. Even though disconnectivity graphs…

The mechanical unfolding of an engineered protein composed of eight domains of Ig27 is investigated by using atomic force microscopy. Exploiting a fluctuation relation, the equilibrium free energy as a function of the molecule elongation is…

We present a microscopic variational theory for the free energy surface of a fast folding protein that allows folding kinetics to be resolved to the residue level using Debye-Waller factors as local order parameters. We apply the method to…

A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory…

The free energy landscape of a protein-like chain in a fluid was studied by combining discontinuous molecular dynamics and parallel tempering. The model protein is a repeating sequence of four different beads, with interactions mimicking…

We report on total-energy electronic structure calculations in the density-functional theory performed for the ultra-thin atomic layers of Si on Ag(111) surfaces. We find several distinct stable silicene structures:…

A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…

The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling…

We report results from multicanonical simulations of poly-alanine. Homopolymers of up to 30 amino acids were considered and various thermodynamic quantities as a function of temperature calculated. We study the nature of the observed…

We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…

Two proteins, one belonging to the mainly alpha class and the other belonging to the alpha/beta class, are selected to test a kinetic mechanism for protein folding. Targeted molecular dynamics is applied to generate folding pathways for…

We use the torsional angles of the protein chain as generalized coordinates in the canonical formalism, derive canonical equations of motion, and investigate the coordinate dependence of the kinetic energy expressed in terms of the…

We perform Monte Carlo simulations to study the elastic properties of the helix-coil worm-like chain model of alpha-helical polypeptides. In this model the secondary structure enters as a scalar (Ising like) variable that controls the local…