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We present a new method for introducing stable non-equilibrium concentration gradients in molecular dynamics simulations of mixtures. This method extends earlier Reverse Non-Equilibrium Molecular Dynamics (RNEMD) methods which use kinetic energy scaling moves to create temperature or velocity gradients. In the new scaled particle flux (SPF-RNEMD) algorithm, energies and forces are computed simultaneously for a molecule existing in two non-adjacent regions of a simulation box, and the system evolves under a linear combination of these interactions. A continuously increasing particle scaling variable is responsible for migration of the molecule between the regions as the simulation progresses, allowing for simulations under an applied particle flux. To test the method, we investigate diffusivity in mixtures of identical, but distinguishable particles, and in a simple mixture of multiple Lennard-Jones particles. The resulting concentration gradients provide Fick diffusion constants for mixtures. We also discuss using the new method to obtain coupled transport properties using simultaneous particle \textit{and} thermal fluxes to compute the temperature dependence of the diffusion coefficient and activation energies for diffusion from a single simulation. Lastly, we demonstrate the use of this new method in interfacial systems by computing the diffusive permeability for a molecular fluid moving through a nanoporous graphene membrane.