Three-dimensional heat transfer analysis of a disposable, continuous-flow polymerase chain reaction device

Polymerase Chain Reaction (PCR) is a process which amplifies a specific segment of DNA through a thermal cycling protocol. PCR is largely used in diagnostics, but also has applications in the defense industry and many others. The PCR industry is shifting its focus towards micro-scale devices, and away from macro-scale systems due to i) the micro-scale sample size requiring less blood from patients, ii) total reaction times on the order of minutes opposed to hours and iii) the cost advantages as many microfluidic devices are manufactured from inexpensive polymers. In general, polymers have many advantages including minimal microfabrication processes during manufacturing, wide availability and low cost. This work presents the manufacturing process as well as simulations and testing results of a disposable polycarbonate (PC) device capable of achieving PCR in less than 7 minutes by thermally cycling the sample through an established temperature gradient in a serpentine channel. This device also features a unique laser manufacturing process eliminating the need for a microfabrication facility. Two-dimensional (2D) and three-dimensional (3D) simulations were created to analyze the heat transfer and fluid dynamics throughout the device. Simulations were created both in the flow plane, to analyze the reaction temperatures occurring in each bend of the serpentine channel, and the out of flow plane, to observe the amount of heat leaving the system. Although the 2D simulations did not produce the same values as the 3D models, the same trends were exhibited so qualitative observations could still be made. Experiments were performed to validate the simulations by comparing the measured device surface temperature from an IR camera to those values from the 3D simulations. It was found that the device produces fluid temperature results within the reaction limits for several flow rates with specific heater temperature settings. An end point PCR melting analysis was also completed on reactants to determine if PCR was achieved. These results were unsuccessful, due to highly inconsistent flow rates observed during the experiments. Although PCR was not achieved, with slight changes to increase flow rate accuracy, PCR is expected to be successful since the IR images suggest that the fluid is reaching the reaction temperatures.