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Ion Channel Simulations by the TR-PNP Model and the Excess Chemical Potential Approach

S. Hu and K. Hess
Beckman Institute, University of Illinois at Urbana-Champaign, US

Keywords:
ion channel, Poisson-Nernst-Planck, PNP, excess chemical potential, ECP

Abstract:
We describe a new method referred to as TR-PNP model to study general types of nanostructure ion channels. Our method extends the common continuum methods to include particle like properties, such as the ion trapping and release effects. Methods of estimating the characteristic parameters used in the TR-PNP model are discussed. The rate theory is used to estimate the ion release coefficient. We implement a simple toy channel model with a single binding site in terms of both the TR-PNP model and the previous ECP method respectively, and show the equivalence of both approaches under steady state. One of the conditions required for their equivalence is quantitatively determined by an equation relating the TR-PNP parameters to the value of the ECP. Furthermore, we perform a time-dependent study including one to several binding sites inside the pore by using TR-PNP. The transient simulation results quantitatively illustrate the hopping process of ions from one site to the other producing huge currents over short distances within short periods of time. This method can also handle a time scale of microseconds. It is therefore a good candidate to be integrated into a multi-scale simulation framework to provide a bridge between continuum and particle methods.

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