The thermocouple inside the chip has been placed to provide accurate temperature readings. These data are very useful for control purposes, but they only reflect the temperature of a small and localized region in the PCR chamber, while the sample covers a relatively large volume. To obtain substantial DNA amplification it is important to minimize temperature differences within the sample.
A thermal simulation software has been developed for obtaining a better understanding of how heat is produced by the resistor and how it propagates through the chip to the sample. The simulation software uses a custom implementation of the FEM (finite element method), which is used to solve the 3D heat transmission equation. By doing this, it is possible to simulate how the temperature will evolve at every point of the chip and the sample.
Although many other commercial FEM software programs already exist, ours has been customized with the intention of making it easy to use. With just a few steps, it's possible to define the geometry and the thermal properties of our structure (heater, chip and sample) and obtain graphical results describing the temperature distribution.