SPICE for modeling biochemical networks

The Simulation Program for Integrated Circuit Engineering (SPICE) has been used successfully for many years to aid semiconductor circuit design. This tool represents circuits as networks of basic devices with interacting parameters (current, voltage, etc.). SPICE then models these interactions as systems of partial differential equations. Biological systems are roughly similar, in that they consist of networks of interacting biochemical cycles whose resulting chemical concentrations can also be modeled by partial differential equations. In the present work, we used SPICE 3f5 to model an optically-accessed protein-based 3D memory. This is a prelude to our future research thrusts in developing protein-based optical memory, and in building biologically-based computation engines in support of the cell-like entity (CLE) program