A method and system for separating a selected molecule from a heterogeneous mixture of molecules in aqueous solution are described. The method comprises (a) providing a separation device comprising a loading reservoir and a receiving reservoir coupled by a channel bearing immobilized microtubules aligned parallel to the longitudinal axis thereof the channel; (b) placing an aqueous solution containing the heterogeneous mixture of molecules in the loading reservoir; (c) adding a motor-ligand composition and ATP to the aqueous solution, wherein the motor-ligand composition comprises a motor protein for attaching to microtubules and moving therealong in the presence of ATP and the ligand is capable of binding the selected molecule, such that the ligand binds the selected molecule to form a complex and the complex moves along the immobilized microtubules to the receiving reservoir; and (d) removing the selected molecule from the receiving chamber.