Numerical simulation of heat transfer to optimize DNA amplification in Polymerase Chain Reaction

Polymerase Chain Reaction (PCR) is a biomedical technique for forensic laboratory sciences in which small amount of DNA is amplified through repeated thermal cycles. It has become a powerful technique for clinical, biological, medical, forensic and genetic analysis and other areas of life science. This process actively increases the quantity of DNA by repetition of three-step procedure i.e. denaturation, annealing and extension which are performed at 95°C, 55°C and 72°C respectively. The reaction temperature sensitivity requires precise temperature control and appropriate thermal insulation of the three reaction zones. Three dimensional simulation of heat transfer is carried out for a continuous flow PCR based model to study the heat transfer effect on the temperature distribution and thermal gradients in a PCR device. For improving the computational time, one pass simulation model is used. Isothermal boundary conditions are applied using heaters of 8mm and 9mm lengths in the reaction zones. Air gaps of 0.5mm, 1mm and 1.5mm are introduced in the glass substrate for improving the temperature uniformity of the extension zone. It has been observed that the air gaps improves the temperature uniformity in the PCR channel extension zone but size of the air gaps has a negligible effect on temperature uniformity. The effect of heat loss via convection is also observed and it is shown that the thermal isolation of glass domain from outside improves the temperature distribution in the reaction zones. ANSYS CFX 15 is used to perform computational fluid dynamics (CFD) simulations by varying the velocity to study the effect of fluid convection on the temperature distribution in the flow channel and to estimate the residence time of the fluid to attain efficient DNA amplification.