Modeling and Simulating Asymmetrical Conductance Changes in Gramicidin Pores

Xu, S

Chen, M

Majd, S

Yue, X

Liu, C

2023-08-29T15:41:08Z

2023-08-29T15:41:08Z

2014-01-01

2023-08-29T15:41:07Z

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 charges near its entrance, either on membrane surface or attached to gramicidin A itself, is presented. In this numerical simulation, a two dimensional computational domain is set to mimic the structure of a gramicidin A channel in the bilayer surrounded by electrolyte. The transport of ions through the channel is modeled by the Poisson-Nernst-Planck (PNP) equations that are solved by Finite Element Method (FEM). Preliminary numerical simulations of this mathematical model are in qualitative agreement with the experimental results in the literature. In addition to the model and simulations, we also present the analysis of the stability of the solution to the boundary conditions and the convergence of FEM method for the two dimensional PNP equations in our model.

2544-7297

https://hdl.handle.net/10161/28789

Walter de Gruyter GmbH

Computational and Mathematical Biophysics

10.2478/mlbmb-2014-0003

Modeling and Simulating Asymmetrical Conductance Changes in Gramicidin Pores

Journal article

Xu, S|0000-0002-8207-7313

34

55

1

Duke

Duke Kunshan University

DKU Faculty

Published

2