Three-Dimensional Simulation of Biological Ion Channels Under Mechanical, Thermal and Fluid Forces

TL;DR

This paper presents a comprehensive 3D multi-physics simulation of biological ion channels, integrating electrochemical, thermal, fluid, and mechanical effects to better understand their complex behavior.

Contribution

It introduces the first self-consistent continuum-based model combining ion electrodiffusion, fluid motion, thermal effects, and mechanical deformation for ion channels.

Findings

Fluid and thermal effects are negligible without mechanical deformation.

Mechanical stress significantly alters ion distributions and channel response.

Model predictions align with biophysical theories on protein conformation influence.

Abstract

In this article we address the three-dimensional modeling and simulation of biological ion channels using a continuum-based approach. Our multi-physics formulation self-consistently combines, to the best of our knowledge for the first time, ion electrodiffusion, channel fluid motion, thermal self-heating and mechanical deformation. The resulting system of nonlinearly coupled partial differential equations in conservation form is discretized using the Galerkin Finite Element Method. The validation of the proposed computational model is carried out with the simulation of a cylindrical voltage operated ion nanochannel with K+ and Na+ ions. We first investigate the coupling between electrochemical and fluid-dynamical effects. Then, we enrich the modeling picture by investigating the influence of a thermal gradient. Finally, we add a mechanical stress responsible for channel deformation and investigate its effect on the functional response of the channel. Results show that fluid and thermal fields have no influence in absence of mechanical deformation whereas ion distributions and channel functional response are significantly modified if mechanical stress is included in the model. These predictions agree with biophysical conjectures on the importance of protein conformation in the modulation of channel electrochemical properties.