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The results of molecular dynamics simulations of the bovine pancreatic trypsin inhibitor (BPTI) in water with force fields that explicitly include polarization for both the protein and the water are presented. The findings reveal that the solvating water's relaxation is most affected when both the protein and the water models are polarizable.

A new approach is developed to study the dynamics of the localized process in solution and other condensed phase system. The approach employs a fluctuating elastic boundary (FEB) model, which encloses the simulated system in an elastic bag that mimics the effects of the bulk solvent.

This article discusses quantum mechanical and mixed quantum-classical approaches for studying vibrational energy relaxation function in condensed phase systems. Results indicate that vibronic absorption spectrum depends on both electronic transitions and vibrational relaxation.

A study was conducted to analyze the fluctuating charge, fluctuating dipole and combined models for substituted benzenes. A general linear response framework containing both fluctuating charges and dipoles was formulated. An electrostatic model was then completed by adding fixed charges fit to the zero-field quantum chemical electrostatic potential. Results indicated the accuracy of the many-body response of the peptide models and was in good agreement with ab initio computations of the changes in the electrostatic potential.

Molecular dynamics simulations are used for studying the temperature dependence of hydrophobic association and drying transition of large-scale solutes. The deviations of the predicted have emerged due to increased fluctuations, characterizing finite systems, as the temperature has increased.

The efficiency of newly developed replica exchange with solute tempering (REST) was assessed by applying it to three large solvated peptide systems ([alpha]-helix, [beta]-hairpin, TrpCage). It was found that the original implementation of REST, with the protein as the central group, performs poorly on systems where the folded (F) and unfolded (U) conformations have vastly different structural energies.

An investigation on the effect of salts on the solvent-induced interactions between hydrophobic particles dispersed in explicit aqueous solution is conducted as a function of the salt's ionic charge density by molecular dynamics simulations. The aggregate is found to form a 'micelle-like' structure, in which the ions are preferentially adsorbed at the surface of the aggregate, at low concentrations of low charge density ions.

The hydrophobic aided replica exchange method (HAREM) is introduced to accelerate the simulation of all-atom protein folding in explicit solvent. The method is applied to a small representative protein, the alpha-helix 3K(I), and it is found that the HAREM method successfully folds the protein with 4 ns, while the regular replicas exchange method does not fold the same protein within 5 ns, even with many more replicas.

The fluctuating elastic boundary (FEB) model is extended for molecular dynamics simulation of bulk water and solvated alanine dipeptide. The applicability of this FEB model to biomolecular simulations is examined through the analysis of conformational population distribution of solvated alanine dipeptide.

Molecular dynamics simulations are performed to study the dynamics of interfacial water confined in the interdomain region of a two-domain protein, BphC enzyme. The results show that near the protein surface the water diffusion constant is much smaller and the water-water hydrogen bond lifetime is much longer than that in bulk.

A modified Delphi model combined with a molecular dynamics method is devised to calculate the free energy landscape of a small protein. Based on the replica exchange method (REM), the molecular dynamics method is used to sample the conformational space of the beta-hairpin, the C-terminus beta-hairpin of protein G, as before.

A general method to calculate the self-diffusion coefficient tensor from molecular dynamics (MD) in a finite region is proposed. The results revealed that far from the interface the diffusion tensor is found of distance as expected, and the diffusion coefficient has the value D approximately is 0.22 A degree 2/ps, in agreement with what is found in the bulk liquid.

Molecular dynamics simulations of 1-buthyl-3 methylimidazolium hexafluorophosphate ([bmim][PF6]) is presented. Radial distribution functions, average density, and mean-square displacements for the individual ions are computed.

The short-time dynamics of loop unfolding and hydrogen bond formation and breaking in the alanine pentapeptide at room temperature is studied using several constant-energy molecular dynamics simulations of about 4 ns of duration. The results are analyzed in terms of time histories of 'core' alpha-carbon dihedral angles.

A study was conducted, using a diatomic in molecules semiempirical ligand field (DIMSELF) method, to calculate ground and excited many-body potential energy surfaces for an arbitrary transition metal ion in an arbitrary complex system. The result shows how the ligand field theory and diatomics in molecules can be connected to generate ground and excited electronic potential energy surfaces of complex systems with transition metal ions.