Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from...

Structural water molecules within protein active sites are relevant for ligand-protein recognition because they modify the active site geometry and contribute to binding affinity. In this work an analysis of the interactions between 23 ligands and dimeric HIV-1 protease is reported. The X-ray structures of these complexes show the presence of four types of structural water molecules: water 301 ...

The Hofmeister effect describes how different ions make solutes more or less hydrophobic. The effect is thought to occur due to structural changes in the solvent induced by the ion's presence, particularly in water. In this study, the structural changes in water due to the presence of ions are investigated by molecular dynamics simulations of various monatomic ions in the SPC/E water model. Str...

A simultaneous improvement of the diffusion and dielectric properties of the simple point charge (SPC) model for liquid water appears to be very difficult with conventional reparametrization of the commonly used Lennard-Jones and Coulomb interaction functions and without including a self-energy correction in the effective pair-potential as is done in the SPC/E model. Here, a different approach ...

We study the statistical properties of the potential energy landscape of a system of particles interacting via a very short-range square-well potential (of depth -u0) as a function of the range of attraction Delta to provide thermodynamic insights of the Noro and Frenkel [M. G. Noro and D. Frenkel, J. Chem. Phys. 113, 2941 (2000)] scaling. We exactly evaluate the basin free energy and show that...

We introduce a two-dimensional (2D) multisurface reaction free energy description of the catalytic cycle that explicitly connects the recently observed multi-time-scale conformational dynamics as well as dispersed enzymatic kinetics to the classical Michaelis-Menten equation. A slow conformational motion on a collective enzyme coordinate Q facilitates the catalytic reaction along the intrinsic ...

Knowledge-based potential functions for protein structure prediction assume that the frequency of occurrence of a given structure or a contact in the protein database is a measure of its free energy. Here, we put this assumption to test by comparing the results obtained from sequence-structure cluster analysis with those obtained from long all-atom molecular dynamics simulations. Sixty-four eig...

We find the exact quasiparticle spectrum for the continuum Kondo problem of k species of electrons coupled to an impurity of spin S. In this description, the impurity becomes an immobile quasiparticle sitting on the boundary. The particles are “kinks”, which can be thought of as field configurations interpolating between adjacent wells of a potential with k + 1 degenerate minima. For the oversc...