Date of Award


Document Type


Degree Name

Master of Science


Department of Electrical and Computer Engineering

First Advisor

Keith A. Shomper, PhD


Molecular docking aids in the design of materials supporting the current and future needs of the warfighter by simulating the real-world results of combining molecules. Specifically, it supports research and development in novel non-linear optical materials for laser-hardening and other advanced optical applications. Potential uses for these materials range from personnel and optical system laser protection to holographic information displays. DOCKER, our baseline docking system, minimizes the computational overhead of the simulation by modeling the molecules as rigid objects. This simplification can cause DOCKER's solutions to disagree with the real-world results, because molecules flex as they react to one another and to other external influences, such as heat or the presence of a solvent. Our research adds flexibility to the DOCKER model by articulating it in response to the interactive atomic forces. We anticipate this addition will improve the model's predictive capability by improving its overall fidelity. Articulation also provides a basis for other extensions. These extensions include thermal effects and computation of barrier energy along a reaction path.

AFIT Designator


DTIC Accession Number