Abstract: This invention provides microfluidic devices that comprise a fluidics layer having microfluidic channels and one or more regulating layers that regulate the movement of fluid in the channels. The microfluidic devices can be used to mix one or more fluids. At least a portion of the fluidics layer can be isolated from the regulating layer, for example in the form of a shelf. Such isolated portions can be used as areas in which the temperature of liquids is controlled. Also provided are instruments including thermal control devices into which the microfluidic device is engaged so that the thermal control device controls temperature in the isolated portion, and a movable magnetic assembly including magnets with shields so that a focused magnetic field can be applied to or withdrawn from the isolated portion or any other portion of the microfluidic device. Also provided are methods of mixing fluids.