CFD-Enabled Optimization of Polymerase Chain Reaction Thermal Flow Systems

Microfluidic flow systems with precise thermal control are required in many important practical applications, such as in heat sink cooling of electronics, droplet freezing systems to determine environmental pollution levels and in efficient chemical processing [1, 2, 3]. This study focuses on the thermal microfluidic flows arising in Polymerase Chain Reaction (PCR) thermal cycling systems used for rapid diagnostic screening and testing [4]. PCR systems have been widely studied and numerous design features have been proposed to regulate the temperature distribution to provide the required thermal environment for effective amplification of DNA needed to complete the process [3]. Microfluidics are very useful for such systems since they can reduce the reagent consumption and the thermal mass, which enables the temperature to be manipulated rapidly within the various temperature zones needed for the denaturation, annealing, and extension components of the PCR process. Computational Fluid Dynamics is used to explore the effect of microfluidic geometry and operating conditions on the thermal and hydraulic conditions within each of the three temperature zones. COMSOL Multiphysics® 5.4 coupled with MATLAB codes are used to solve a novel series of optimization problems that enable the most effective thermal conditions for the process of DNA amplification to be identified. The study focuses on a prototype serpentine microfluidic geometry that enables multiple cycles of denaturation, annealing, and extension to be carried out within a single microfluidic chip