Electrokinetic phenomena in nanopore sensors and microfluidic devices require accurate simulation of coupled fluid-electrostatic interactions in geometrically complex domains with irregular boundaries and adaptive mesh refinement. We develop an equal-order virtual element method for the Stokes–Poisson–Boltzmann equations that naturally handles general polygonal meshes, including meshes with hanging nodes, without requiring special treatment or remeshing. The key innovation is a residual-based pressure stabilization scheme derived by reformulating the Laplacian drag force in the momentum equation as a weighted advection term involving the nonlinear Poisson–Boltzmann equation, thereby eliminating second-order derivative terms while maintaining theoretical rigor. Well-posedness of the coupled stabilized problem is established using the Banach and Brouwer fixed-point theorems under sufficiently small data assumptions, and optimal a priori error estimates are derived in the energy norm with convergence rates of order for approximation degree . Numerical experiments on diverse polygonal meshes – including distorted elements, non-convex polygons, Voronoi tessellations, and configurations with hanging nodes – confirm optimal convergence rates, validating theoretical predictions. Applications to electro-osmotic flows in nanopore sensors with complex obstacle geometries illustrate the method’s practical utility for engineering simulations. Compared to Taylor–Hood finite element formulations, the equal-order approach simplifies implementation through uniform polynomial treatment of all fields and offers native support for general polygonal elements.

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