Modeling and Simulating Asymmetrical Conductance Changes in Gramicidin Pores

• Autorzy: Shixin Xu , Minxin Chen , Sheereen Majd , Xingye Yue , Chun Liu
• Języki publikacji: EN

Abstrakty

EN

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.

Słowa kluczowe

EN

Gramicidin; conductance change; finite element method; Poisson-Nernst-Planck (PNP) equation; ion channels

• Wydawca: De Gruyter Open
• Czasopismo: Molecular Based Mathematical Biology
• Rocznik: 2014
• Tom: 2
• Numer: 1

Daty

wydano

2014-01-01

otrzymano

2013-12-20

zaakceptowano

2014-03-21

online

2014-04-24

Twórcy

autor

Shixin Xu

• Center for System Biology, Department of Mathematics, Soochow University, Suzhou 215006, China

autor

Minxin Chen

• Center for System Biology, Department of Mathematics, Soochow University, Suzhou 215006, China

autor

Sheereen Majd

• Department of Bioengineering, Department of Engineering Science and Mechanics Pennsylvania State University, University Park, PA 16802, US

autor

Xingye Yue

• Center for System Biology, Department of Mathematics, Soochow University, Suzhou 215006, China

autor

Chun Liu

• Department of Mathematics, Pennsylvania State University, University Park, PA 16802, US

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Identyfikatory

DOI

10.2478/mlbmb-2014-0003