Method for thermal cycling of microfluidic samples

A method of operating a thermal cycler for a microfluidic device, the thermal cycler having a heat sink, a heating element in thermal communication with the heat sink, and a thermal chuck in thermal communication with the heating element, the method comprising:

• a) providing a target temperature profile for the microfluidic device and initializing a counter i to a predetermined initial value;
• b) determining a target temperature for the microfluidic device for an increment of time associated with the counter i;
• c) measuring operating temperatures;
• d) computing a temperature profile for the thermal chuck;
• e) computing a plurality of possible temperature profiles, each associated with one of a plurality of power levels for the heating element;
• f) adjusting each of the plurality of possible temperature profiles for heat contribution and heat loss;
• g) comparing each of the plurality of adjusted possible temperature profiles to the temperature profile for the thermal chuck;
• h) determining that a minimum difference is present between a selected one of the plurality of adjusted possible temperature profiles and the temperature profile for the thermal chuck, wherein the selected one of the plurality of adjusted possible temperature profiles is associated with a selected one of the plurality of power levels for the heating element;
• j) defining a power level for the heating element equal to the selected one of the plurality of power levels for the heating element;
• k) sending the power level for the heating element to the heating element;
• l) incrementing the counter i;
• and
• m) repeating b) through l) until the counter i has reached a predetermined final value.