Introduction

In this chapter, the focus is on presenting the fundamentals of molecular simulations, particularly molecular dynamics (MD) and its derivatives, particularly nonequilibrium molecular dynamics (NEMD), or MD in a system that is exposed to an external field. The number of molecular simulation tools has grown substantially over the last few years, and it would be impossible to mention all the applications that have appeared in the literature. MD simulations have been used in a variety of ways; four of the most important ways in the context of this text that such calculations have been used are as follows:

• Calculating transport properties of new fluids and mixtures for which such properties have not been measured or as a test of the accuracy of such experimental measurements

• Predicting the equilibrium conformation of complex biomolecules and polymers

• Verifying fluid dynamics boundary conditions (Koplik et al., 1989)

• Predicting the flow of pure fluids and complex mixtures in very small channels and circular pores, where the continuum approximation may break down and where direct experimental measurements are not available

Indeed, it is the last class of problems that is of particular interest in this chapter. It is certainly to be noted that while restricted to very short length and time scales, molecular simulations provide information that cannot be found any other way.

As has been seen throughout this book, ionic and biomolecular transport devices are now being used for drug development and delivery, single molecule manipulation, detection and transport, and rapid molecular analysis.