Membrane-Channel Protein System Mesh Construction for Finite Element Simulations

• Autorzy: Tiantian Liu , Shiyang Bai , Bin Tu , Minxin Chen , Benzhuo Lu
• Języki publikacji: EN

Abstrakty

EN

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.

Słowa kluczowe

EN

membrane; ion channel; tetrahedral mesh construction; walk-and-detect

• Wydawca: De Gruyter Open
• Czasopismo: Molecular Based Mathematical Biology
• Rocznik: 2015
• Tom: 3
• Numer: 1

Daty

otrzymano

2015-08-01

zaakceptowano

2015-10-20

online

2015-11-06

Twórcy

autor

Tiantian Liu

• State Key Laboratory of Scientific and Engineering Computing, Academy of Mathematics and Systems Science,
  National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing 100190, China

autor

Shiyang Bai

• State Key Laboratory of Scientific and Engineering Computing, Academy of Mathematics and Systems Science,
  National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing 100190, China

autor

Bin Tu

• National Center for NanoScience and Technology, Chinese Academy of Sciences, Beijing 100190, China

autor

Minxin Chen

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

autor

Benzhuo Lu

• State Key Laboratory of Scientific and Engineering Computing, Academy of Mathematics and Systems Science,
  National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing 100190, China

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Identyfikatory

DOI

10.1515/mlbmb-2015-0008