Towards Practical Biomolecular Computers Using Microfluidic Deoxyribozyme Logic Gate Networks

We propose a new way of implementing a biomolecular computer in the laboratory, using deoxyribozyme logic gates inside a microfluidic reaction chamber. We build upon our previous work, which simulated the operation of a deoxyribozymebased flip-flop and oscillator in a continuous stirred-tank reactor (CSTR); unfortunately, using these logic gates in a laboratory-size CSTR is too expensive because the reagent volume is too large. For a realistic microfluidic design, the properties of microfluidic flow and mixing have to be taken into account. We describe the differences between a macrofluidic system such as the CSTR and the microfluidic setting. Liquid in a microfluidic setting exhibits laminar flow, and is more difficult to mix than in the CSTR. We use a rotary mixer, and examine how it operates so that we may properly model it. We discuss the details of our mixer simulation, including our diffusion model. We discuss why having discrete phases of influx/efflux (“charging”) and mixing is a necessary, and how it changes the kinetics of the system. We then show the result of simulating both a flip-flop and an oscillator inside our rotary mixing chamber, and discuss the differences in results from the CSTR