Three-Dimensional Simulation of Biological Ion Channels Under Mechanical, Thermal and Fluid Forces
For researchers studying ion channel biophysics, this work provides a comprehensive simulation tool that confirms the importance of mechanical deformation in modulating channel behavior.
This paper presents a novel continuum-based multi-physics model for biological ion channels that couples ion electrodiffusion, fluid motion, thermal effects, and mechanical deformation. Simulations show that mechanical deformation significantly alters ion distributions and channel functional response, while fluid and thermal fields have negligible effect without deformation.
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.