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Shape transformations in driven and damped molecular chains are considered. Closed chains of weakly coupled molecular subunits under the action of spatially homogeneous time-periodic external field are studied. The coupling between the…
Relations between the thermodynamics and dynamics of supercooled liquids approaching a glass transition have been proposed over many years. The potential energy surface of model liquids has been increasingly studied since it provides a…
A surface model with skeletons is investigated by using the canonical Monte Carlo simulations. The skeleton is composed of linear chains, which are joined to each other at the rigid junctions. A one-dimensional bending energy is defined on…
We propose the conformon as a quantum of conformational change for energy transfer in alpha-helical proteins. The underlying mechanism of interaction between the quantum of excitation and the conformational degrees of freedom is nonlinear…
We consider random walk model of a semi-flexible polymer chain on a square and a cubic lattice to enumerate conformations of the polymer chain in two and three dimensions, respectively. The bending energy of the chain is assumed as the key…
Polyampholytes (PA) are charged polymers composed of positively and negatively charged monomers along their backbone. The sequence of the charged monomers and the bending of the chain significantly influence the conformation and dynamical…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
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…
We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to…
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…
A method to reconstruct the energy landscape of small peptides is presented with reference to a 2d off--lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly…
A self consistent field theory for compressible polymer mixtures is developed by introducing elements of classical density functional theory into the framework of the Helfand theory. It is then applied to study free surfaces of binary (A,B)…
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…
We propose a new backbone-torsion-energy term in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, the backbone dihedral angles phi and psi. It gives a natural…
De novo prediction of protein folding is an open scientific challenge. Many folding models and force fields have been developed, yet all face difficulties converging to native conformations. Hydrophobicity scales (HSs) play a crucial role…
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 study the adsorption-desorption transition of polyelectrolyte chains onto planar, cylindrical and spherical surfaces with arbitrarily high surface charge densities by massive Monte Carlo computer simulations. We examine in detail how the…
Energy levels, radiative rates and lifetimes are calculated among the lowest 98 levels of the n <= 4 configurations of Be-like Al X. The GRASP (General-purpose Relativistic Atomic Structure Package) is adopted and data are provided for all…
A general approach to the design of accurate classical potentials for protein folding is described. It includes the introduction of a meaningful statistical measure of the differences between approximations of the same potential energy, the…