Thermal Modeling for Design Optimization of a Microfluidic Device for Continuous Flow Polymerase Chain Reaction (PCR)

Polymerase Chain Reaction (PCR) is a molecular biological method for the in vitro amplification of nucleic acid molecules which has wide applications in the area of genetics, medicine and biochemistry. The typical three step PCR cycle consists of heating the sample to 90–94 °C to denature double-stranded DNA, cooling down to 50–54 °C to anneal the specific primers to the single stranded DNA and finally increasing the temperature to 70–75 °C for extension of the primers with thermostable DNA polymerase. The temperature sensitivity of the reaction requires precise temperature control and proper thermal isolation of these three zones. In this paper we present the design of a continuous flow PCR microfluidic device with the channels fabricated in (poly) dimethylsiloxane (PDMS) and thin film Platinum Resistance Temperature Detector (RTD) elements fabricated on glass substrate to define the three different temperature zones. The fluidic arrangement has a water jacket layer to minimize evaporation from the porous PDMS walls. A detailed thermo fluidic model of the device is presented to predict the performance and efficacy of the proposed design. Numerical simulations are carried out to find the temperature distribution and temperature gradients in the device and a parametric study is done by varying flow rate, heat flux and channel dimensions in order to optimize the design for achieving temperature isolation and sharp temperature gradients between different zones.