A major opportunity in the development of medical diagnostic instrumentation is the highly inefficient design of conventional polymerase chain reaction (PCR) thermocycling hardware. Operation of such hardware is slow, expensive, and consumes considerable electrical power to repeatedly heat and cool the reagent mixture. An alternative thermocycling approach is to harness natural convection to perform rapid DNA amplification via the PCR. The proposed design makes use of natural convection, is inherently simple, and consumes minimal electrical power making it well suited for portable applications. This research is aimed at understanding the fundamental processes that underlie thermally driven biochemical reactions in convective flow fields. The underlying structure of these flows is characterized by rich complexity because of operation in a transition regime associated with the onset of buoyancy driven turbulence. This regime has not been extensively probed owing to challenges associated with the inherently chaotic motion. The research involves detailed 3D characterization of velocity and temperature fields inside PCR reactors using coordinated particle image velocimetry and laser induced fluorescence of dispersed thermochromic seed particles. Computational fluid dynamic studies will determine the extent to which the observed phenomena can be captured. These results will (1) guide development of improved computational techniques and constitutive models which in turn will (2) enable the design of new convective thermocycling devices for ultra rapid PCR. Intellectual Merit: The experimental and computational capabilities developed will deliver new insights and innovations by probing complex single and multiphase flows at the micro and nanoscales with a level of spatial and temporal resolution that is currently unavailable. Broader Impacts: The potential to achieve an order of magnitude increase in reaction speed will spur development of portable, inexpensive, and rugged DNA analysis instrumentation. In addition to the commercial impact associated with making PCR more affordable, this technology will spawn new ways to teach physics and molecular biology through the development of educational experiences for undergraduates at the interface between the physical, chemical, and life sciences. The underlying principles of this technology are highly relatable (for example, the flow is established in the same way as in a lava lamp), making it ideal to target K12 audiences in addition to undergraduate students. This will provide an innovative way for students to see how fundamental knowledge can be applied to produce real, working products.
