This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Combinatorics and geometry have been among the most active areas of mathematics over the past few years because of newly discovered inter-relations between them and their potential for applications. In this project, the authors set out to identify problems in physics, chemistry, and biology where these methods could impact significantly. In particular, the experience suggested that the areas of unitary symmetry and discrete dynamical systems could be brought more strongly under the purview of combinatorial methods. Unitary symmetry deals with the detailed description of the quantum mechanics of many-particle systems, and discrete dynamical systems with chaotic systems. The depth and complexity of the mathematics in these physical areas of research suggested that not only could significant advances be made in these areas, but also that here would be a fertile feedback of concept and structure to enrich combinatorics itself by setting new directions. During the three years of this project, the goals have been realized beyond expectation, and in this report the authors set forth these advancements and justify their optimism.