Molecular dynamics (MD) simulations are performed to elucidate the physics surrounding secondary ion mass spectrometry (SIMS). During SIMS, an energetic projectile is bombarded against a surface, and material is lifted off the surface and analyzed. MD simulations provide a mesoscopic view of this process in order to gather a better understanding of the underlying physics. Significant work has already been performed to explore the effects of atomic and cluster projectiles, cluster sizes at low energies, and polymer chain length on the resulting ejection dynamics.;This thesis has three objectives. The first is to redefine the best conceptual model for understanding cluster bombardment. We propose a model which likens cluster projectiles to a single large particle moving through a solid. The energy decay of cluster projectiles during the bombardment process is shown to follow a friction equation at short times. In addition, the projectile motion, energy deposition, and reaction dynamics are compared between a cluster projectile and single large bead to examine the accuracy of this model.;Secondly, the optimal experimental parameters for maximizing ejection yield while reducing sample damage are investigated. The effect of incident angle and cluster projectile size is examined for multiple cluster types including a series of fullerenes, Au3, benzene, and naphthalene. The results are compared with experimental data to determine which parameters contribute to the greatest quality of data.;Lastly, the reaction dynamics of a dissociative water sample following C60 and Au3 bombardment is modeled. The sample is able to dissociate into OH-, H+, and O2- ions, which has a very high activation energy. Therefore, we use this sample as an indicator of where a broad range of reactions can occur for molecular sample.