On 11/5/05, chandrajit bajaj <bajaj@cs.utexas.edu> wrote:

    Dear Rick, Robin, Vinay

    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.

    During the NMJ model construction phase the requirements of
    the Molecular group interfaces with the Membrane Group as well as the
    Properties group as follows.

    The NMJ domain is a gridded classified volume, with multiple associated
    volumetric functions (mol/membrane density, electron charge density,
    hydrophobicity, electro-potentials), defined on grid vertices.
    The NMJ domain with a vector of attributed function values per grid vertex,
    should be thought of as an abstract data structure
    (ADS) or class Object that your group would be reading into the player.
    The gridded volume shall be classified into cells
    (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
    The volumetric properties for the combined NMJ
    domain include
    (a) electric charge density
    (b) hydrophobicity
    (c) electrostatics potential
    These volumetric properties need to be computed for two different states
    (i) before activation of AChR-channels
    (ii) after depolarization of post-synaptic membrane (post ion-permeation)

    The molecular group thus needs to compute
    (A) the molecular electron densities for AChR and AChE-clusters as a multi-res
    mip-maps (three or four levels) and for two different states (AChR -- open
    and closed, AChE -clusters in ACh-bound/ACh-unbound). An item we should discuss
    but dont forget to include your ideas here.
    (B) water molecules, ions, could be approx as tiny spheres and located
    in NMJ domain grid cells of type (i), (iii) and (V), while AChR and
    AChE-clusters are located in grid cells of type (iii).

    All  mip-map sub-volumes of (A) are located/ rotated and aligned with the type
    (iii) grid cells of the NMJ domain i.e. the atoms of AChR and AChE are
    transformed and then the NMJ grid regions are specified for the computation
    of the mip-map sub-volumes.

    Subvolumes of (B) are computed / blurred to form electron density functions on
    grid
    cells of type (i), (iii) and (V)

    (C) molecular surfaces need to be computed as well for two states of
    AChE-clusters
    as they provide dilectric interfaces for the electro-potential properties
    calculations. Furthermore, some collagen stalk attachements would also need
    to be included. Finally motion of the clusters could be incorporated.

    (D) molecular/membrane surfaces for AChR merged with local membrane geometry
    would need to be computed.

    (E) motion of the ACh would be needed for "visually - simulated diffusion".
    Your ideas need to be included here.

    (F) use of texture-maps for mol. rendering, would be a great feature. Item that
    needs to be discussed, but again dont hesitate to include your ideas here.

    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
    cb

    --
    Chandrajit Bajaj

    Department of Computer Sciences,
    Computational Visualization Center (CVC),
    Institute of Computational Engineering and Sciences (ICES)
    The University of Texas at Austin,
    201 East 24th Street, ACES 2.324A,
    1 University Station, C0200
    Austin, TX 78712-0027
    Tel: 512-471-8870    FAX: 512-471-0982

    http://www.cs.utexas.edu/~bajaj
    http://www.ices.utexas.edu/CVC