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This paper describes the use of thermal modelling tools in the design and characterisation of a multi-function silicon microreactor polymerase chain reaction (PCR) thermocycler system for rapid DNA diagnostic assays. MEMS technologies have been successfully applied to this application and the miniaturization of devices offers several advantages; including reduced assay times, reduced amounts of expensive reagents required as well as allowing rapid heating/cooling rates due to the lower thermal mass. This technique involves repetitive cycling at three different temperatures and requires rapid and accurate temperature changes. However, the direct measurement and monitoring of the temperature distribution on the nanostructures is still a challenge. Thus, this paper describes the use of static and transient thermal modeling to analyse the thermal performance of the system. The CFD code Flotherm was used to construct a 3D model of the PCR system. The system included assisted fan cooling in the thermal cycling chamber. Static thermal analysis was undertaken to simulate the temperature profile within the overall system and thus determine the fan characteristics needed to maintain system temperatures within operating requirements.Secondly, the PCR system operation involves repetitive thermal cycling of DNA at three different temperatures and requires rapid and accurate temperature changes. The thermal modeling results were used to determine the input power levels needed to obtain this required temperature/time profile.

A silicon microreactor consisting of an integrated heater, temperature sensor and thermal isolation chamber has been described. The thermal characteristics of the device have been studied by computer simulation and a rapid heating rate (20 degrees C--95 degrees C in less than 2 s) has been achieved. The fabrication process, consisting of microelectromechanical systems (MEMS) fabrication techniques has been established. The design features of this device, in particular the integrated heater and temperature sensor and the thermal isolation chamber allows fast heating/cooling rates and therefore enables efficient thermocycling suitable for DNA amplification.