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Parallel Adaptive Finite Element Algorithms for Solving the Coupled Electro-diffusion Equations

Yan XieJie ChengBenzhuo LuLinbo Zhang — 2013

Molecular Based Mathematical Biology

rithms for solving the 3D electro-diffusion equations such as the Poisson-Nernst-Planck equations and the size-modified Poisson-Nernst-Planck equations in simulations of biomolecular systems in ionic liquid. A set of transformation methods based on the generalized Slotboom variables is used to solve the coupled equations. Calculations of the diffusion-reaction rate coefficients, electrostatic potential and ion concentrations for various systems verify the method’s validity and stability. The iterations...

Membrane-Channel Protein System Mesh Construction for Finite Element Simulations

Tiantian LiuShiyang BaiBin TuMinxin ChenBenzhuo Lu — 2015

Molecular Based Mathematical Biology

We present a method of constructing the volume meshes of the membrane-channel protein system for finite element simulation of ion channels. The membrane channel system consists of the solvent region and the membrane-protein region. Our method focuses on labeling the tetrahedra in the solvent and membrane-protein regions and collecting the interface triangles between different regions. It contains two stages. Firstly, a volume mesh conforming the surface of the channel protein is generated by the...

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