A microfluidic chip includes one or more reaction chambers to hold fluids for chemical or biochemical reactions, such as PCR. A non-contact heat source heats the reaction chamber and the fluid, such that the heat source does not contact the reaction chamber or the fluid. The heat source can heat the reaction chamber and the fluid separately, where the reaction chamber and the fluid separately absorb heat radiation from the heat source. A temperature sensor acquires a temperature of the reaction chamber and/or the fluid. Control circuitry controls the heat source according to a cycling profile for the reaction in the fluid to cycle the heat source between heating and not heating the reaction chamber and the fluid based on the temperature acquired by the temperature sensor. Cooling can be provided passively or actively.

Methods and devices for conducting chemical or biochemical reactions that require multiple reaction temperatures are described. The methods involve moving one or more reaction droplets or reaction volumes through various reaction zones having different temperatures on a microfluidics apparatus. The devices comprise a microfluidics apparatus comprising appropriate actuators capable of moving reaction droplets or reaction volumes through the various reaction zones.

Thermal systems and methods including cooling and heating fixtures for use with flow cells and other analytic substrates. The cooling fixture includes a turbulent air flow cavity with an array of air flow diverters that facilitates fast, accurate, and uniform cooling of a flow cell or other substrate positioned across an opening of the cavity. The heating fixture includes an array of light emitting diodes that are spaced apart from and configured to provide overlapping radiation intensity profiles that facilitate fast, accurate, and uniform heating of the flow cell or other substrate positioned relative to the LED array.

Provided is photoactivated selective release (or PHASR) of droplets from a microwell array enabled by a photoresponsive polymer layer integrated into the microfluidic device. This photoresponsive layer is placed in between a microwell array that traps a large number of droplets and a monolithic flow chamber that can be used for recovery. By using focused light, the photoresponsive layer can either be punctured or induced to create local heating to selectively release droplets. The type of photoacoustic dye and the physical properties of the photoresponsive layer can be engineered to induce either puncture of the membrane or pushing of droplets out of the microwells with low thermal impact on the droplets. This approach has broad application in the field of soft lithography-based microfluidic devices for various applications including photoresponsive valves as well as high throughput single cell sequencing.