Self-Assembly in the context of micro-scale integration refers to a developing set of techniques which exploit phenomena resulting in the spontaneous integration of micro-scale components into designed systems. Self-Assembly may be leveraged most effectively in parallel assembly processes. This thesis studies the modeling of micro-scale self-assembly processes as stochastic processes. The researchers propose that self-assembly processes may be modeled as Markov chains. In order to develop these models a Self-Assembly test system was created and trials were conducted using this system. Initial tests into the hypothesis that variables contributing to the transition probabilities include the kinetic energy of the assembly interaction, the energy minimized during assembly, and the area fraction of bonding sites on the assembly surface are tested.

Rous Sarcoma Virus (RSV) is an avian retrovirus with an enclosing capsid protein (CA) shell. RSV CA is studied due to its similar molecular structure to other retrovirus capsid proteins such as Human Immunodeficiency Virus (HIV). In this project, turbidity assay is used to track the assembly process of RSV CA, while solid state nuclear magnetic resonance (ssNMR) is used to probe the CA structure at a site specific level and investigate the morphology of the spherical structure of the I190V mutated strain of RSV CA. The I190V mutant is a naturally occurring mutation and is able to form into roughly uniform spheres, where the wild type RSV CA cannot form as pure spheres as possible. Turbidity assay results of the mutated RSV CA revealed a lack of a noticeable lag time before assembly began, as well as, a prolonged time period to reach saturation when compared to the wild-type RSV CA. Using ssNMR, and the TALOS-N program the torsion angles of the protein backbone were found. Using Ramachandran plots, it was found that the mutation of the 190th residue from Isoleucine to Valine caused a changed in the secondary structure of residues, from α-helix to β-sheet and vice versa. These changes were concentrated at the loops between select interfaces of helices that make up the structure of RSV CA. In particular, between helices 4 (residues 65-85), 8 (residues 165-177), and 11 (residues 215-225). The differing secondary structure in the mutant RSV CA was supported by the overlaying of the NMR spectra of the wild-type RSV CA on to the spherically assembled mutant RSV CA. It can be concluded that the spherical assembly of the mutated RSV CA displays noticeable differences in assembly and overall structure when compared to the wild-type RSV CA.