Three Dimensional Simulation of Rayleigh-Bénard Convection for Rapid Microscale Polymerase Chain Reaction

Abstract

Rayleigh-Bénard convection has been extensively studied in literature owing to its ubiquitous nature. However, most of the studies have been confined to geometries where the aspect ratio of the cylinder was less than 1. Here we study the motion of fluid in geometries with aspect ratio greater than 1, with particular application to use of such motion to actuate biochemical reactions, such as the polymerase chain reaction. We show that it is possible to accelerate the rate of reaction by using a geometry that promotes chaotic motion versus a geometry that promotes quasi- periodic motion. We also simulate chemical kinetics using the fluid motion as a starting point and we prove that chaotic motion indeed enhances the rate of the reaction. We also provide qualitative and quantitative measures for chaotic motion in a fluid flow, which helps to distinguish between different types of fluid motion. We highlight the transitions between different types of flow that are possible with Rayleigh-Bénard convection. Finally, we compare our simulations against experimental data obtained from particle image velocimetry, laser induced fluorescence and optical microscopic visualization.