Computational investigations of organic materials for hybrid nanodevice and optoelectronic applications

This dissertation examines two organic material systems, biotinylated microtubule filaments and thiophene.;Biotinylated microtubule filaments partially coated with streptavidin and gliding on surface-adhered kinesin motor proteins converge to form linear "nanowire" and circular "nanospool" structures. We present a cellular automaton simulation tool that models the dynamics of microtubule gliding and interactions. In this method, each microtubule is composed of a head, body, and tail segments. The microtubule surface density, lengths, persistence length, and modes of interaction are dictated by the user. The microtubules are randomly arranged and move across a hexagonal lattice surface with the direction of motion of the head segment being determined probabilistically: the body and tail segments follow the path of the head. The analysis of the motion and interactions allow statistically meaningful data to be obtained regarding the number of generated spools, radial distribution in the distance between spools, and the average spool circumference lengths which can be compared to experimental results. This technique will aid in predictions of the formation process of nanowires and nanospools. Information regarding the kinetics and microstructure of any system can be extracted through this tool by the manipulation in the time and space dimensions.;Chemical reactions of thiophene with organic molecules are of interest to chemically modify thermally deposited coatings or thin films of conductive polymers. Energy barriers are identified for reactive systems involving thiophene and small hydrocarbon radicals. The transition states for these reactive systems occurred through hydrogen abstraction. The results provide quantum mechanical level insights into the chemical processes that occur in the chemical modification processes described above, such as Surface Polymerization by Ion-Assisted Deposition (SPIAD), electropolymerization, and ion beam deposition. Enthalpies of formation are calculated for organic molecules using B3LYP, BMK, and B98 hybrid functionals. G3 and CBS-QB3 are used as standards in conjunction, due to their accurate thermochemistry parameters, with experimental values. The BMK functional proves to perform best with the selected organic molecules.