Abstract: Methods for modeling solvent-solute thermal interactions in molecular dynamics simulations are described. The methods, which employ impulses to achieve transfer of thermal energy between solvent and solute, are particularly useful in simulations which make use of an implicit solvent model.

Abstract: Methods of obtaining directional information of a solvent-accessible surface of an atom or molecule are described. Also disclosed are methods for simulating the kinetic behavior of a solute molecule in a solvent are also described. The methods utilize a representation of the solvent-accessible surface of the solute molecule which includes information on the geometric orientation of the surface relative to the molecule, and using the representation in a corrected kinetic model to simulate the kinetic behavior of the solute molecule in the solvent.