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This paper presents thermal analysis simulation and verification of a 50-nanoliter-reactor PCR (Polymerase Chain Reaction) well for application in silicon arrays, allowing 5×5 chamber matrix to be fitted on a 1cm2 square. Every reactor cell is equipped with an integrated heater, temperature sensor and a photodetector. Each well forms a separate unit independently controlled and thermally insulated from the rest. Through micromachining the thermal capacity of each chamber is minimized, enabling rapid (8 - 10 cycles per minute) PCR cycling. To characterize the thermal behavior, an equivalent lumped element electrical circuit was defined and the results were compared to those obtained by Finite Element Method (FEM) analysis with CoventorWare™. The proposed structure was implemented on a silicon substrate using a standard CMOS process and post-processing. Experiments were performed for verification of the model. Analysis shows that a temperature of about 95°C can be reached (starting from 55°C) by applying 1.5 W of electrical power in the integrated heater over a period of less than 2.5 seconds. The cooling (not active - self cooling) of the device is done in about 1.5 second.