The Membrane GroupThe following is an overview of the list of requirements for the membrane part of the project.- Input: mesh of NMJ. We shall work on a 512^3 cube.- Output: location and orientation of each molecule (AchR and AchE)in a volume.- Steps: (1) Generate SDF from the given mesh. (Sangmin).(2) Separate the nerve membrane from the cell membrane, and separate the vertical membrane from the horizontal membrane. (Sangmin) (3) Classify each cell (in the 512^3 cube) into several types: (Zeyun) a). Cells containing nerve membrane. b). Cells containing cell membrane (both vertical and horizontal). c). Cells between nerve membrane and cell membrane. d). All other cells (of no interest here).(4) Design the distribution functions of AchR and AchE mathematically. (Shaolieand Fred work together on this)(5) Place the molecules (AchR and AchE) into the mesh based on their distribution functions. (Zeyun, but may need help from others team members if unexpected difficulty is encountered).(6) The output of (5) will be the location and orientation of each AchR and AchE,which will be the input of Vinay's team.Work progress so far and initial ideas:1) Generating the given mesh (Sangmin). Done 2a) Separating the nerve membrane from the cell membrane (Sangmin)Idea:Since the cell membrane is flatter than the nerve membrane and it is parallel to theXY plane, we can shoot rays from the top of the volume (+Z direction) until they hit the cell membrane surface.Algorithm Pseudo Codes: For all voxels on the XY plane at Z=Max (the top surface of the volume to the +Z direction) shoot a ray to the -Z direction until it hits a zero surface. The hit surface is classified into the cell membrane surface.2b) Separating the vertical membrane from the horizontal membrane (Sangmin)Idea:Since the horizontal membrane is very close to the cell membrane, we can use orthogonal distance to the detected cell membrane surface in the previous algorithm.4) Designing the distribution functions of AchR and AchE mathematically (Shaolie and Fred) .As suggested by Samrat, as an initial approximation, the size of the total membrane boundary can be taken to be 900 square-microns (literatures say it's between 400-1300 - we just took something in between) and the density of AchR in the top part to be 7250 per square micron and in the gorge to be 70% less. Density of AchE is same all through out the basal lamina and it is 1800 per square-micron.Shaolie and Fred are developing a diffusion formula that is both time and locationdepth dependent. They have located a chapter on Monte Carlo Methods for Simulation Realistic Synaptic Microphysiology Using Mcell written by Joel Stiles and Thomas M. Bartol, in the book Computational Neuroscience (Edited by Erik De Schutter) and some other references as well and have been looking at
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