Thermal Performance Analysis of a Silicon Microreactor for Rapid DNA Analysis

Abstract

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.

Miniaturized PCR chips for nucleic acid amplification and analysis: latest advances and future trends

“…During the past two years, the miniaturization of such PCR devices has been of growing interest. In general, they can be classified as single chamber stationary PCR chip ( Figure 1A) (10,(12)(13)(14)(15)(16)18,21,22,24,26,27,29,32,37,39,40,43,45,46,48,(51)(52)(53)57,62,63,(68)(69)(70) and multi chamber stationary PCR chip ( Figure 1B) (11,17,19,20,25,28,31,(33)(34)(35)(36)38,47,49,54,78). The former can perform very well in terms of fluidic and thermal controls and offer beneficial properties such as reduced thermal and fluidic crosstalk between chambers.…”

Three-Dimensional Transient Thermal Analysis for a Silicon PCR Microreactor

“…Air trenches around the reactor are etched out of the silicon wafer to provide thermal isolation between the microreactor and the surrounding chip [14,19]. Moreover, the inlet and outlet channels were wound around the chamber to further decrease the heat loss [6].…”

“…A more intense amplification was successfully obtained for a microfabricated cavity with pillars [17]. Several numerical modeling studies were used for the thermal characterization of PCR microreactors [8,[18][19][20]. Jones et al studied the effect of pillars and the effect of isolation gap size during steady-state [15].…”

Brain Peptides Update. Volume 1.

“…The first PCR chip developed by Northrup et al in 1993 was based on such a stationary chamber (84). In general, they can be classified as single chamber stationary PCR chip ( Figure 1A) (10,(12)(13)(14)(15)(16)18,21,22,24,26,27,29,32,37,39,40,43,45,46,48,(51)(52)(53)57,62,63,(68)(69)(70) and multi chamber stationary PCR chip ( Figure 1B) (11,17,19,20,25,28,31,(33)(34)(35)(36)38,47,49,54,78). During the past two years, the miniaturization of such PCR dev...…”

“…Within the past two years, this approach has been widely used on the chamber-based stationary PCR chips (10,(12)(13)(14)20,21,24,25,36,39,51,70). Moreover, direct measurement cannot provide any static and/or dynamic information on temperature/fluid before micromachining of PCR chips.…”