Modeling and Simulating Asymmetrical Conductance Changes in Gramicidin Pores

Shixin Xu; Minxin Chen; Sheereen Majd; Xingye Yue; Chun Liu

Molecular Based Mathematical Biology (2014)

  • Volume: 2, Issue: 1, page 34-55, electronic only
  • ISSN: 2299-3266

Abstract

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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.

How to cite

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Shixin Xu, et al. "Modeling and Simulating Asymmetrical Conductance Changes in Gramicidin Pores." Molecular Based Mathematical Biology 2.1 (2014): 34-55, electronic only. <http://eudml.org/doc/267362>.

@article{ShixinXu2014,
abstract = {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.},
author = {Shixin Xu, Minxin Chen, Sheereen Majd, Xingye Yue, Chun Liu},
journal = {Molecular Based Mathematical Biology},
keywords = {Gramicidin; conductance change; finite element method; Poisson-Nernst-Planck (PNP) equation; ion channels; gramicidin},
language = {eng},
number = {1},
pages = {34-55, electronic only},
title = {Modeling and Simulating Asymmetrical Conductance Changes in Gramicidin Pores},
url = {http://eudml.org/doc/267362},
volume = {2},
year = {2014},
}

TY - JOUR
AU - Shixin Xu
AU - Minxin Chen
AU - Sheereen Majd
AU - Xingye Yue
AU - Chun Liu
TI - Modeling and Simulating Asymmetrical Conductance Changes in Gramicidin Pores
JO - Molecular Based Mathematical Biology
PY - 2014
VL - 2
IS - 1
SP - 34
EP - 55, electronic only
AB - 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.
LA - eng
KW - Gramicidin; conductance change; finite element method; Poisson-Nernst-Planck (PNP) equation; ion channels; gramicidin
UR - http://eudml.org/doc/267362
ER -

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