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Separation and extraction
Digital microfluidics can be used for separation and extraction of target analytes, including through the microscale application of widely used separation techniques such as liquid-liquid extraction, solid-phase extraction, and filtration , together with more specialized methods such as the use of magnetic particles,       optical tweezers, and hydrodynamic effects.

Liquid-liquid extraction
Liquid-liquid extractions can be carried out on digital microfluidic device by taking advantage of immiscible liquids. Two droplets, one containing the analyte in aqueous phase, and the other an immiscible ionic liquid are present on the electrode array. The two droplets are mixed and the ionic liquid extracts the analyte, and the droplets are easily separable.

Solid-Phase Extraction
Solid-phase extractions (SPE) can also be performed in digital microfluidic devices. While there are many various approaches to do this, all revolve around the core concept of SPE, namely the use of a solid stationary phase that separates chemical compounds from a liquid mobile phase through its increased affinity for those compounds. While the form of the solid phase varies widely in DMF applications, the mobile phase is typically in the form of manipulable droplets. The stationary phase can then be washed with a suitable liquid eluent which subsequently allows both reuse of the stationary phase as well as further manipulation of the extracted compounds. Furthermore, the amount of eluent used can be manipulated to achieve much higher concentrations of the resulting solution, which can be particularly useful in terms of manipulating droplet size in the DMF device to allow the use of channels and tubing of various sizes within a single device. .

In implementing solid-phase extraction in digital microfluidics specifically, there is a wide range of possible methods to incorporate the solid phase into the device. This includes coated fibers (used in solid phase microextraction specifically), surface-functionalized microchannels , packed beads , and freestanding monoliths , using stationary phases ranging from polymers   to functionalized magnetic beads. As such, there are a variety of ways that solid-phase extraction methods can be incorporated into digital microfluidic devices depending on the specifications and uses of the device in question.

Filtration
There are also various methods of applying the basic principle of filtration to digital microfluidic devices to achieve separations in such. Suitable filters for this application can be made from membranes, silicon , and polymers , as well as a variety of other materials. Droplets can be moved through the filter in a number of ways, including effusion or manipulation by electrowetting. Filtration in DMF devices is particularly useful for the extraction of analytes from complex samples, such as the extraction of plasma directly from blood samples.

Due to the appeal of digital microfluidic devices in allowing for portable chemical analysis, such methods are of interest in terms of potential medical applications, and as such are noteworthy for their relative ease of maintenance and use, particularly in cases where the filter is made to be easily replaceable, since fouling of the filter is an issue in this method.

Magnetic particles
For magnetic particle separations a droplet of solution containing the analyte of interest is placed on a digital microfluidics electrode array and moved by the changes in the charges of the electrodes. The droplet is moved to an electrode with a magnet on one side of the array with magnetic particles functionalized to bind to the analyte. Then it is moved over the electrode, the magnetic field is removed and the particles are suspended in the droplet. The droplet is swirled on the electrode array to ensure mixing. The magnet is reintroduced and the particles are immobilized while the droplet is moved away. This process is repeated with wash and elution buffers to extract the analyte.

Magnetic particles coated with antihuman serum albumin antibodies have been used to isolate human serum albumin, as proof of concept work for immunoprecipitation using digital microfluidics. DNA extraction from a whole blood sample has also been performed with digital microfluidics. The procedure follows the general methodology as the magnetic particles, but includes pre-treatment on the digital microfluidic platform to lyse the cells prior to DNA extraction.

Optical tweezers
Optical tweezers, or the use of lasers to manipulate droplets, have also been used to separate cells in droplets. Two droplets are mixed on an electrode array, one containing the cells, and the other with nutrients or drugs. The droplets are mixed and then optical tweezers are used to move the cells to one side of the larger droplet before it is split. For a more detailed explanation on the underlying principles, see Optical tweezers.

Hydrodynamic separation
Particles have been applied for use outside of magnetic separation, with hydrodynamic forces being used to separate particles from the bulk of a droplet. This is performed on electrode arrays with a central electrode that is then surrounded by electrode ‘slices’ surrounding it. Droplets are added onto the array and swirled in a circular pattern so that the hydrodynamic forces generated cause the particles to aggregate onto the central electrode.