Optimal Design of Microfluidic Platforms for Diffusion-Based PCR for “One-Pot” Analysis of Cells

Abstract Polymerase chain reaction (PCR) is routinely used for analysis of genes from targeted cells leading to an understanding of the fundamental molecular biology involved in cellular events and for detecting abnormal pathways involved in disease development. In a previous paper we argued that the three commonly known strategies to alleviate the impact of cell pretreatment on PCR had serious shortcomings. Furthermore microfluidic strategies that permit simple operation, simple device design and are compatible with Taq polymerase are highly in demand. In this paper, we discuss optimization of microfluidic platform designs, which may be more efficient than the current one we have developed. The microfluidic reactor modelled in this paper relies on the diffusion of molecules from the loading chambers into a small reaction chamber. This results show that diffusion into the reaction chamber can be modified using different loading chamber geometries. Based on the results we have began to develop a mixed integer optimization model to automatically design the geometry to meet the desired transport rates of species in PCR.