Abstract of Disclosure A computer-based system is described that provides users with the ability to develop high-fidelity digital quantitative representations of physical and chemical phenomena, and to employ an optimization-based approach to control associated physiochemical processes. The system includes a computational environment, intuitive user interface(s), integrated software libraries, analytical tools, and visualization / rendering engine that together provide an integrated framework for nanoscale modeling, analysis, simulation, and synthesis. Additionally, the system includes an optimal linear control synthesis methodology that incorporates a first order dynamic mathematical representation (of the conceptual molecular system) suitable for applying various pragmatic control system techniques including optimization of structured singular values, linear quadratic performance functions, Lyapunov criteria, or similar, for the purposes of nanoscale fabrication and molecular assembly.