Bio-CAD Tools for DNA Computing

The project objective is to develop an integrated software environment for hierarchical prototyping/analysis of hardware for DNA computers and DNA self-assembly. Emerging interdisciplinary field of biomolecular computing explores new paradigms to perform calculations and to design computing architectures at the molecular level. The use of biomaterials in the fabrication and operation of high performance, intelligent systems will present opportunities to make dramatic improvement in system autonomy, radiation hardness and extreme low power operations. Simulation/design tools are required for development of the molecular computing algorithms and its biophysical bio/nanotechnology implementation. Phase I research has resulted in a preliminary version of a prototyping/research software environment for DNA computer. We have developed (1) a state-of-the-art DNA code synthesis method that captures key aspects of the nearest neighbor thermodynamic model; (2) built multiphysics models and software for a device-level simulation of microfluidic-based DNA computer; and (3) demonstrated feasibility of these tools for system-level and large-scale simulations of DNA computer. Phase II research will focus on generalization the proposed methodologies with emphasis on development of the mature computational tools that will address the complete chain of the DNA computer design issues: synthesis of the DNA code; device-level multiphysics/biochemistry high-fidelity modeling; and system-level simulations of DNA computer based on an electric-equivalent-circuit reduced-order model. We will demonstrate the tools on the information technology problems of interest to the AF and validate them with laboratory experiments.