Performance of convective polymerase chain reaction by doubling time

We report in this article a novel computational methodology to estimate the doubling time, which is proposed as an effective performance evaluation tool for a convective polymerase chain reactor (cPCR). The method is a high-fidelity, in silico simulation for the development of a low-cost, robust, and portable cPCR intended for point-of-care applications. Our in-house computer code, based on the well-established OpenFOAM solver, outputs the number of generated double-stranded DNA copies and the doubling times by solving for the concentration species. For this purpose, a three-dimensional, conjugate heat and momentum transport model is developed. In the first step, a simulation of a steady, circulating flow, due to convection, is computed by solving the coupled Navier-Stokes and heat transfer equations. Flow and temperature fields are then used to obtain the concentrations of the double-stranded, the primal annealed, and the single-stranded DNAs while solving the convection-diffusion-reaction equations. The methodology is demonstrated through multiple design cases and validated by experimental results. The results strongly suggest that the performance of a cPCR reactor can be measured by computing the doubling time, and such an approach reduces the otherwise needed extensive experimental efforts to a minimum. (C) 2019 Elsevier Ltd. All rights reserved.