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In principle, different physical models can be applied to simulate ion currents through nanopores. These include the continuum Poisson-Nernst-Planck (PNP) equations, Brownian dynamics (BD) and molecular dynamics (MD). In practice however, it is infeasible to perform molecular dynamics simulations long enough to simulate a sufficient amount of ion translocation events to determine a current, and even Brownian dynamics is often computationally too demanding to model the access resistance of a nanopore in a realistic way. As a consequence, nanopores are generally modeled using the PNP equations, even though this model does not always accurately describe the ionic movement within the nanopore itself, as ions are not treated as discrete entities and water is regarded as a static continuum. The former issue can be solved by both Brownian and molecular dynamics, the latter only by molecular dynamics. Therefore, realistic simulations of ionic currents may be feasible if the PNP equations in the reservoirs are combined with Brownian and/or molecular dynamics within the nanopore. Here, we will focus on the combination of PNP with Brownian dynamics.

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