Geometric Model

2. Geometric Model

  • Mesh model of neuro-muscular junction: We shall use the mesh model of a part of the neuro-muscular junction provided by Dr. Tom Bartol of SALK Inst. The visualization of the mesh can be seen in the figure below. The mesh can be downloaded from http://cvcweb.ices.utexas.edu/ccv/meshing/NMJ. The lower contorted surface is of cell membrane and the volume enclosed by the two is the synaptic cleft.
    A sketch of neuro-muscular junction. Mesh model of the cell membrane.
  • Molecules: There are two sets of molecules we need to deal with in this modeling exercise. First set consists of the AchR molecules (PDBID 2BG9) and the second set consists of AchE (PDBID 1C2B).

The goal is to:

  1. Devise an automatic way of placing the AchR molecules in the thickened surface of the cell membrane. The parameters are the densities of these molecules and their orientations which might differ from molecule to molecule.
  2. Devise an automatic way of placing the AchE molecules in the synaptic cleft. Again, the parameters guide the density and orientations of these molecules.
    In the next section we list some of the detailed steps and the routines/algorithms that one might want to use/design to create the spatially realistic model of a neuro-muscular junction.