Bio-CAD Tools for DNA Computing

Emerging interdisciplinary field of biomolecular computing explores new paradigms to perform calculations using molecules. Simulation/design tools are required for development of the molecular computing algorithms and its biophysical bio/nanotechnology implementation. In Phase I, CFDRC together with Prof. A. Macula will develop the Bio-CAD tools for this innovative field, starting from our commercial ACE+ software already successfully used for biotechnology problems. The ACE+ software has incorporated coupled multiphysics solvers and CAD capabilities including excellent geometry creation, visualization and GUI tools. New developments will include multiphysics model of hybrid bio-electronic DNA-silicon interface, model-based extraction of time constants for molecular computing processes: DNA transport, mixing, immobilization, hybridization, washout, PCR, new powerful method of DNA library generation, spatio-temporal model of dielectric properties of multicomponent DNA solution (for dielectric spectroscopy untagged electronic readout), physical model of ultrafast DNA hybridization using short (high-frequency) electric pulse. We will demonstrate the tools on the data mining problem of identification of maximal frequent sets and simulation of simple computing operations using nanoslot DNA-silicon interface. In Phase II, CFDRC with UC Berkeley will perform experimental demonstration of simple operations involved in DNA computing in DNA-silicon chip. CFDRC and Prof. A. Macula will develop compact models for system-level simulations.