Simulation Based Design of Polymerace Chain Reaction (PCR) Thermal Block

Abstract

The static chamber microfluidic device (thermal cycler) is a laboratory apparatus of crucial significance in the field of biomedical sciences, such as its use in medical diagnostics. The device being developed in this work aims to increase the carriage capacity of commercially available devices from 30 microliters per well to 50 microliters per well – with 48 wells in total – while remaining cost-effective. The sample polymerase chain reaction (PCR) block is inspired by similar works in literature to retain a level of intercompatibility. A polymerase chain reaction consists of three steps; denaturation of the double stranded DNA (carried out at 92–98 oC), the primers annealing (at 50–60 oC) and the extension of the single strand of DNA to double stranded DNA (at 68–72 oC). For effective and correct progression of the polymerase chain reaction, the temperatures corresponding to each step of the reaction must be controlled precisely. To that end, a thermoelectric cooler (Peltier device) is attached to the microfluidic device along with a heat sink for efficient functioning. The complete assembly is analyzed thermally using steady and transient finite element simulations. Heat generation within the device is modeled using a thermal-electric module while heat transfer is approximated using a finite element scheme. The device design is contingent upon performance parameters such as heat loads, temperatures at the cold and hot side of the Peltier, input current and voltage, as well as coefficient of performances (COP) for all three steps of the PCR. The performance parameters of the thermo-electric cooler are analyzed for hot side temperatures of 95 oC, 55 oC and 75 oC, which are required for the three steps of PCR. Special care is taken in designing the rectangular plate fin heat sink, which is studied both analytically and numerically to accurately estimate the forced convection coefficient required to dissipate the heat produce at the cold side of the Peltier (in order to maintain the delta in temperature between the hot and cold side). Furthermore, the entire system is numerically and mathematically validated with good accuracy. Additionally, the methods prescribed herein are equally applicable to other Peltier devices as well.