Polymerase chain reaction (PCR) is widely used in biochemical analysis to amplify DNA and RNA in vitro. The PCR process is highly temperature sensitive, and thermal management has in important role in PCR operation in reaching the required temperature set points at each step of the process. The goal of this research is to achieve a thermal technique to rapidly increase the heating/cooling thermal cycling speed while maintaining a uniform temperature distribution throughout the substrate containing the aqueous nucleic acid sample. In this work, an innovative microfluidic PCR. thermal cycler, which Utilizes a properly arranged configuration filled with a porous medium, is investigated. Various effective parameters that are relevant in optimizing this flexible heat exchanger are investigated such as heat exchanger geometry, flow rate, conductive plate, the porous matrix material, and utilization of thermal grease. An optimized case is established based on the effects of the cited parameters oil the temperature distribution and the required power for circulating the fluid in the heat exchanger. The results indicate that the heating/cooling temperature ramp of the proposed PCR heat exchanger is considerably higher (150.82 degrees C/s) than those ill the literature. In addition, the proposed PCR offers a very uniform temperature in the Substrate while utilizing a low power. (C) 2007 Elsevier Ltd. All rights reserved.