We report herein on a model built to analyze and optimize nanoparticle (NP) dimer formation. The rationale for this work stems from our interest in building effective NP dimer-based tagging systems for surface enhanced Raman scattering (SERS)-based detection. This model takes into account the behavior of the NPs in solution and the molecules on their surface, to provide a coherent and physically constrained system. The kinetics of formation of dimers and larger assemblies are investigated on suspensions of varying concentrations through a coarse-grained ad hoc computer simulation based on a Molecular Dynamics-like approach. Several different effects are considered, including the behavior and interaction of surface molecules, the interactions between the latter and the NPs, and between NPs. The surface molecules are treated as rigid structures that can occupy specific binding sites. A Brownian model is used to both integrate the particle trajectory and provide random thermal forces. These systems show a NP concentration-dependent behavior with respect to the formation of dimers versus larger assemblies over the timescale of the simulation. The simulations also indicate that these systems form low-density aggregates as opposed to the close packed formations reported previously. A dependence on the properties and the concentration of the linkers is also demonstrated. (C) 2011 Elsevier Inc. All rights reserved.