In this article we introduce a novel coupled algorithm for massively parallel direct numerical simulations of electrophoresis in microfluidic flows. This multiphysics algorithm employs an Eulerian description of fluid and ions, combined with a Lagrangian representation of moving charged particles. The fixed grid facilitates efficient solvers and the employed lattice Boltzmann method can efficiently handle complex geometries. Validation experiments with more than 70 000 time steps are presented, together with scaling experiments with over 4 · 10 6 particles and 1.96 · 10 11 grid cells for both hydrodynamics and electric potential. We achieve excellent performance and scaling on up to 65 536 cores of a current supercomputer.At the finest level of resolution, fluid, ions, and particles are simulated by Lagrangian approaches. These explicit solvent methods [37] typically apply coarse-grained molecular dynamics (MD) models to describe the motion of fluid molecules and incorporate Brownian motion [38]. The mesoscale dissipative particle dynamics method is applied in [39] to simulate electrophoresis of a polyelectrolyte in a nanochannel. Another explicit solvent method is presented in [40] for simulating DNA electrophoresis, modeling DNA as a polymer. In both methods the polymer is represented by bead-spring chains with beads represented by a truncated Lennard-Jones potential and connected by elastic spring potentials. Explicit solvent models, however, are computationally very expensive, especially for large numbers of fluid molecules due to pairwise interactions [40]. Moreover, the resolution of solvent, macromolecules, and ions on the same scale limits the maximal problem sizes that can be simulated [41]. Also the mapping of measurable properties from colloidal suspensions to these particle-based methods is problematic [37]. The high computational effort is significantly reduced in implicit particle-based methods that incorporate hydrodynamic interactions into the inter-particle forces. Such methods are applied in [37] and [42] to simulate electrophoretic deposition under consideration of Brownian motion and van der Waals forces. Nevertheless, these methods are restricted to few particle shapes and hydrodynamic interactions in Stokes flow.Euler-Lagrange methods constitute the intermediate level of resolution. These approaches employ Eulerian methods to simulate the fluid phase, whereas the motion of individual particles is described by Newtonian mechanics. For simulations of particles in steady-state motion, the resolved particles can be modeled as fixed while the moving fluid is modeled by an Eulerian approach. In [43] the finite volume method is applied to simulate electrophoresis of up to two stagnant toroids in a moving fluid, employing the Hückel approximation for a fixed ζ-potential and different electrical double layer thicknesses. The steady-state electrophoretic motion of particles with low surface potentials under a weak applied electric field in a charged cylindrical pore is simulated in [44] for a single c...