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Modeling and Simulating Asymmetrical Conductance Changes in Gramicidin Pores

Shixin XuMinxin ChenSheereen MajdXingye YueChun Liu — 2014

Molecular Based Mathematical Biology

Gramicidin A is a small and well characterized peptide that forms an ion channel in lipid membranes. An important feature of gramicidin A (gA) pore is that its conductance is affected by the electric charges near the its entrance. This property has led to the application of gramicidin A as a biochemical sensor for monitoring and quantifying a number of chemical and enzymatic reactions. Here, a mathematical model of conductance changes of gramicidin A pores in response to the presence of electrical...

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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