Membrane-Channel Protein System Mesh Construction for Finite Element Simulations

Tiantian Liu; Shiyang Bai; Bin Tu; Minxin Chen; Benzhuo Lu

Molecular Based Mathematical Biology (2015)

  • Volume: 3, Issue: 1
  • ISSN: 2299-3266

Abstract

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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 surface and volume mesh generation tools: TMSmesh and TetGen. Then a walk-and-detect algorithm is used to identify the pore region to embed the membrane correctly. This method is shown to be robust because of its independence of the pore structure of the ion channels. In addition, we can also get the information of whether the ion channel is open or closed by the walk-and-detect algorithm. An on-line meshing procedure will be available at our website www.continuummodel.org.

How to cite

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Tiantian Liu, et al. "Membrane-Channel Protein System Mesh Construction for Finite Element Simulations." Molecular Based Mathematical Biology 3.1 (2015): null. <http://eudml.org/doc/275995>.

@article{TiantianLiu2015,
abstract = {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 surface and volume mesh generation tools: TMSmesh and TetGen. Then a walk-and-detect algorithm is used to identify the pore region to embed the membrane correctly. This method is shown to be robust because of its independence of the pore structure of the ion channels. In addition, we can also get the information of whether the ion channel is open or closed by the walk-and-detect algorithm. An on-line meshing procedure will be available at our website www.continuummodel.org.},
author = {Tiantian Liu, Shiyang Bai, Bin Tu, Minxin Chen, Benzhuo Lu},
journal = {Molecular Based Mathematical Biology},
keywords = {membrane; ion channel; tetrahedral mesh construction; walk-and-detect},
language = {eng},
number = {1},
pages = {null},
title = {Membrane-Channel Protein System Mesh Construction for Finite Element Simulations},
url = {http://eudml.org/doc/275995},
volume = {3},
year = {2015},
}

TY - JOUR
AU - Tiantian Liu
AU - Shiyang Bai
AU - Bin Tu
AU - Minxin Chen
AU - Benzhuo Lu
TI - Membrane-Channel Protein System Mesh Construction for Finite Element Simulations
JO - Molecular Based Mathematical Biology
PY - 2015
VL - 3
IS - 1
SP - null
AB - 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 surface and volume mesh generation tools: TMSmesh and TetGen. Then a walk-and-detect algorithm is used to identify the pore region to embed the membrane correctly. This method is shown to be robust because of its independence of the pore structure of the ion channels. In addition, we can also get the information of whether the ion channel is open or closed by the walk-and-detect algorithm. An on-line meshing procedure will be available at our website www.continuummodel.org.
LA - eng
KW - membrane; ion channel; tetrahedral mesh construction; walk-and-detect
UR - http://eudml.org/doc/275995
ER -

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