We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the folding of a small peptide is a multistage process associated with two characteristic temperatures, the collapse temperature Ttheta and the folding temperat...

The two-phase thermodynamic (2PT) model is generalized to determine the thermodynamic properties of mixtures. In this method, the vibrational density of states (DoS), obtained from the Fourier transform of the velocity autocorrelation function, and quantum statistics are combined to determine the entropy and free energy from the trajectory of a molecular dynamics simulation. In particular, the ...

This article highlights my group’s recent progress in developing a new class of computer simulation tools for studying the equilibrium self-assembly and thermodynamic properties of complex polymeric fluids. Our approach utilizes well known formal methods for converting ‘‘particle-based’’ statistical mechanical models of fluids into field theories, but builds on the formalism to develop practica...

A stochastic biogeochemical model has been developed to simulate the transformation and degradation of natural organic matter (NOM) using an agent-based algorithm which treats each molecule as a separate and potentially unique entity. Molecules react when a pseudo-random number is lower than the calculated reaction probability in a given time step; repeated time steps simulate the transformatio...

Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity ...

The two-phase thermodynamic (2PT) model is generalized to determine the thermodynamic properties of mixtures. In this method, the vibrational density of states (DoS), obtained from the Fourier transform of the velocity autocorrelation function, and quantum statistics are combined to determine the entropy and free energy from the trajectory of a molecular dynamics simulation. In particular, the ...

Water contributes significantly to the binding of small molecules to proteins in biochemical systems. Molecular dynamics (MD) simulation based programs such as WaterMap and WATsite have been used to probe the locations and thermodynamic properties of hydration sites at the surface or in the binding site of proteins generating important information for structure-based drug design. However, quest...