We propose a 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 deoxyribozyme-based flip-flop and oscillator in a continuous stirred-tank reactor (CSTR). Unfortunately, using these logic gates in a laboratory-size CSTR is prohibitively expensive, because the reagent quantities are too large. A desire to reduce the cost of open-reactor experiments using these gates motivated our decision to design a microfluidic system. 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 a microfluidic setting. Liquid in a microfluidic setting exhibits laminar flow, and is more difficult to mix than in a CSTR. We would like to use a rotary mixer, and so we 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 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 setting.