Understanding the surface orientation and interactions between biomolecules and nanoparticles is important in order to determine their effects on the final structure and activity. At present, limited analytical techniques are available to probe these interactions, especially for materials dispersed in solution. We recently demonstrated that arginine, a simple amino acid, is able to bind to the surface of Au nanoparticles in a segregated pattern, which produces an electronic dipole across the structure. As a result, the formation of linear chains of Au nanoparticles occurred that was dependent upon of the concentration of arginine. Here, we present new information concerning the mechanism of assembly and demonstrate unique reaction conditions that can be used to directly control the assembly rate, and thus the size of the final superstructure that is produced. The assembly process was modulated by the arginine/Au nanoparticle ratio, the temperature of the system, the dielectric of the solvent, and the solution ionic strength, all of which can be used in combination to control the process. These effects were monitored using UV-vis spectroscopy, transmission electron microscopy, and dynamic light scattering. From these results, it is suggested that the second step of the assembly process, which is the formation of nanoparticle chains mediated by Brownian motion, controls the overall assembly rate and thus the size and orientation of the final superstructure produced. Furthermore, the reaction kinetics of the system have been studied from which rate constants and activity energies have been extracted for electrostatic-based nanoparticle assembly. This analysis indicates that the assembly/organization step is likely broken into two substeps with the formation of nanoparticle dimers occurring in solution first, followed by the oligomerization of the dimers to form the linear and branched chains. The dimerization step follows traditional second-order kinetics and is relatively fast, while the oligomerization process is quite complex and is anticipated to be slower than the dimerization step. These results are important, as they lay the basis for the subsequent use of this technique for the possible fabrication of electronic device components or as sensitive assays to probe the surface structure of nanomaterials.