The molecular gate is a deceptively simple construct that has high functional complexity. It involves two microfluidic domains or channels that are separated by nanopores. Flow from one microfluidic domain to the other, mediated by nanofluidic pores, is by electrokinetic flow (electrical potentials applied in the microfluidic domains drive fluids through the nanopores).

The essential aspects of the nanopores are that (a) the pore radius is of the same order or smaller than the Debye (electrical shielding) length within the fluid, and (b) the length of the pore is much, much larger than the radius. When these two conditions are met, the flow through the pore is completely mediated by its walls.

By controlling the pore walls, the flow from one micro domain to another is controlled by the nanofluidic interconnect. The interconnect becomes, then, a gate that controls the molecules that pass through it. Molecular gates, therefore, are similar to electronic gates, but with decided differences.

Electrons are indistinguishable from one another and do not change their nature passing though an electronic gate. Molecules, however, can be very different from each other, can undergo reactions and can change their nature in the process. This added complexity allows us to use the molecular gates to control chemical reactions in extremely small volumes, or confined spaces, which in turn changes the transport phenomena through the gates.