High Performance Computer/innovative research

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From: Richard Gordon <gordonr@B9zudHRuMXvYxJjCmxOpLtZszw5c1QPaI1tMh7TXjhAXpvrvbiN48doA7hHDvzcjZxNjT4YI9uoz6scIZYEKZt0.yahoo.invalid>

Dr. Peter C.J. Graham
Department of Computer Science, University of Manitoba
556 Machray Hall
Winnipeg MB R3T 2N2, Canada
Phone: (204) 474-8837, Fax: (204) 474-7609
E-mail: pgraham@J8UcBAFRipBMrTru_FnsdU0ZsttlAalS9HzaeGkKBeZ_VvfNNbXpBQ4I6VUBDSRyw8lFjnuGZMROyVvQqP5m1Q.yahoo.invalid (Peter C.J. Graham)

Dear Peter,
You asked about projects requiring your proposed High Performance Computer
(HPC) at the University of Manitoba. Here's a list, which I'm ccing to my
collaborators.
Yours, -Dick

"I would ask that each of you think about what additional or new
*innovative* research might be possible with access to an HPC facility.
Please do not constrain yourselves to only your current research. Feel free
to speculate a little."

In Vivo: simulation of the motion, polymerization, and chemistry of all the
macromolecules in whole cells, to be tested against live immunofluorescence
microscopy video recordings. Applications include: the spindle apparatus,
which separates chromosomes; the cell state splitter, which may be involved
in cell differentiation; protein trafficking; cell motility; and asymmetric
cell division, all involving cell tensegrity structures.

Cyberworm: simulation of the embryonic development of a nematode worm
(Caenorhabditis elegans) at the macromolecular level, using the sequence of
its DNA, now fully known, starting from the fertilized egg. This would link
to databases on the genome and known spatial coordinates of each cell
during development in both normal animals and mutants. Simulation of
nematode behavior and evolution are also contemplated.

Axolotl embryonic development: simulation of the physics of cleavage and
differentiation waves during early development of the salamander Ambystoma
mexicanum, based on time lapse observations of the whole surface.
Simulation of neural tube defects (spina bifida and anencephaly), the most
common human birth defects, would also be done.

Embryo EIT: imaging of electrical resistance and generated electrical
fields in the axolotl embryo, versus developmental time. EIT (electrical
impedance tomography) algorithms would have to be generalized to include
internal current sources and anisotropic impedance.

Breast screening by CT: simulation of a high resolution computed tomography
(CT) scanner for detection of breast tumors prior to metastasis. Each image
would be up to 64GB in size, and reconstructed from multiple projection
datasets of 50MB each. Purpose is to optimize machine design to maximize
image quality while minimizing total x-ray dose. Some CT algorithms to be
tested involve imaging from one photon at a time, of up to 10^15 photons.

Breast screening by EIT: simulation of a high resolution electrical
impedance tomography (EIT) scanner for detection of breast tumors prior to
metastasis. Each image would be up to 64GB in size, and reconstructed from
multiple voltage measurements over the surface of the breast, each
measurement involving multiplexed subliminal electric current injection via
a different pair of electrodes. Optimal placement and number of electrodes
for high resolution imaging has to be determined.

3D registration for breast screening: point for point matching of up to
64GB 3D images of breast, obtained by CT, EIT, or MRI (magnetic resonance
imaging). By registering and subtracting two images of the same breast,
taken at two different times, small tumors growing in the interim should be
detectable.

Skin scanner: robotic scanning of all skin on a person, to detect any
changes, especially early melanoma. Registration with previous images,
collected in visible and/or infrared, with depth imaging by
transillumination and visible light/IR CT, would be used to detect small,
growing tumors.

Whole body scanning: at high resolution, for detection of all changes in
the body, by EIT or MRI. The above imaging and registration methods would
be applied to the whole body, for early detection and preventative medicine
for a variety of diseases, especially cancer.

Dr. Richard Gordon, Radiology, U. Manitoba, HSC, 820 Sherbrook Street,
Winnipeg R3A 1R9 Canada, Phone: (204) 789-3828, fax: (204) 787-2080/ Book
just out: The Hierarchical Genome & Differentiation Waves: Novel
Unification of Development, Genetics & Evolution:
http://www.wspc.com.sg/books/lifesci/2755.html, E-mail:
GordonR@xn9QihG8KIvb1NfD1lgnJaxhAA3ByQ4ShI3W_-ntvZ8_o8b6Jb6R4zE9XMqWVeN5diYMGOSkx3MKxUFXJjRQ.yahoo.invalid