Treffer: Simulation of coupled fluid-ion transport through a biological nanopore on graphics processing units.

Nanoscale fluid-ion transport is investigated in biophysical chemistry, drug delivery, protein sequencing, etc. Currently, fast three-dimensional models for fluid-ion transport through biological nanopores are unavailable. This study, therefore, focuses on the simulation and parallelization of nanoscale fluid-ion transport on multiple graphics processing units (GPUs). Nanoscale fluid-ion transport is described through the fourth-order Poisson-Nernst-Planck-Bikerman model coupled with the Navier-Stokes equations. The model incorporates the effect of ionic and non-ionic interactions, ion solvation, nonlocal electrostatics, and the finite size of particles. Governing equations are discretized using the lattice Boltzmann method (LBM). For complex geometries, the immersed boundary method has been incorporated with the LBM. To demonstrate the applicability of the developed model, electro-osmotic flow through a relatively large biological nanopore has been simulated. Parallelization on multiple GPUs has enabled us to perform simulations for a full three-dimensional channel geometry. Results showed a good match with the published data. We captured local variations in concentration and fluid flow in both axial and radial directions. Furthermore, flow circulation around the channel was also observed. The impact of external potential difference and the finite size of the particles on the flow has also been assessed. Using our in-house code, we achieved a performance of 1982 × 106 lattice updates per second on 8 A100 80 gigabyte GPUs. The methodology presented here provides an accurate and fast simulation methodology for characterizing symmetric/asymmetric nanopore properties. This model can help in enhancing the fundamental understanding of nanofluidics and characterization of the nanopores.
(© 2025 Author(s). Published under an exclusive license by AIP Publishing.)