Dear Fred, Sangmin, Shaolie, and Zeyun

Thank you for the draft of your sub-project requirements report.
My suggestions are below. Please incorporate them into your revision, adding
details of the substeps.
(a) Calibrate and build a combined NMJ gridded domain Abstract data structure
(ADS) or class Object with associated methods (see (d)) with a 2-level octree
search index.

NMJ domain data includes pre-synaptic membrane, postsynaptic membrane, AChR and
AChE molecule clusters, enclosed within a bounding rectangular gridded box,
so that the grid voxel size in nanometers (nm) determined.
(Ques: Why is 512^3 the correct grid resoln ?, and for this what is the voxel
size in nm ?).

(b) The grid cells of the overall NMJ domain grid
 should be classified into the groups:
  (i) above pre-synaptic membrane (intra-nerve cellular domain)
  (ii) pre-synaptic nerve cell membrane
  (iii) between pre- and post-synaptic membranes,post-synaptic membrane (cleft
subdomain which is the diffusion region and the region for locating the
molecules),
  (iv) the post-synaptic muscle membrane
  (v) below post-synaptic muscle membrane
(c) ray-shooting is not required for the classification . Instead use a
gridding/classification library of functions that Vinay has developed.

(d) the various addtl steps are to be implemented as methods to the NMJ gridded
domain ADS (or class) of step (a). Methods should be implemented for
(i) locating points in each of the classified  grid cells, or grid faces,
inside the NMJ domain
(ii) specifying various functions (molecular densities, solvent densities, mol.
properties (electro-pot, charge density etc) on the grid vertices
(iii) summation, min, max operations on the functions defined on the grid
(iv) derivatives of functions
(v) contouring of functions defined on the grid

Please email Samrat and I, by Tue eve (at the latest) with your revised report.
We shall collect the individual sub-group reports, link them on the web, and
then discuss them in class on Wed, and establish interdependencies between the
groups.

Please also let Samrat and I, know if you have further questions
chandrajit