CS 384R (#52590), CAM 395T (#65115), BME 383J (#52590)
FALL 2010 MW 9:30 – 11:00am WEL 4.224
Geometric (Bio-) Modeling and Visualization
Image consists of Ribosome, Virus, Human body, Brain, NMJ(Neuromuscular
junction), and Universe
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Office |
ACES 2.324 |
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Phone |
512-471-8870 |
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Office hours |
Mon,Wed 3:00 - 4:00p or by appt. via suzanne@ices.utexas.edu |
CS384R, CAM395T, BME383J Course Outline
The course will teach you the basic algorithms, techniques
and tools of geometric modeling and visualization with applications in the
biomedical sciences and engineering. Bio-medical modeling (or Biomodeling) and visualization has roots in medical
illustration and communication for the health sciences, with branches of
application to mathematical modeling and computer simulation of artificial
life. In this course we shall emphasize computational image processing,
computational topology, computational algebraic and differential geometry,
polynomial spline approximations, computer graphics,
together with aesthetic choices involved in producing effective scientific
animations. The emphasis shall be on spatial realism, and the programmatic use
of physiological simulation and visualization to quantitatively depict
"how things work" at the molecular, cellular, tissue, and organ level
scales.
Exercises on domain and physiological modeling and visualization at multiple
scales, shall be drawn from virology (viral envelopes, capsids,
proteins, nucleic acids), and neurology (brain, hippocampus, neuropil, axons, dendrites, glial
cells, ion-channels, neurotransmitters), and their interactions (molecular energetics and force fields, molecular flexibility,
synaptic transmission, synaptic spillover).
Lecture Topics
Models: algebraic curves, surfaces, splines, parametrization,
intersection manifolds, singularities, topology,
Maps: x-ray diffraction, electron
microscopy, CT/MRI imaging, reconstruction
Maps2Models:
filtering, contrast enhancement, classification, symmetry detection,
segmentation, skeletonization,
clustering, matching, compression, reconstruction
Models2Analytics
I: surfaces, finite element meshing, spline
representations, feature identification, symmetry detection, shape
segmentation, matching & complementary docking, flexibility
Models2Analytics
II: bonded and non-bonded molecular energetics,
forces, numerical quadrature, cubature, fast multiple
methods, discrete differential operators, de-Rham
diagrams, integral equations
Analytics2Informatics/Visualization
I: differential/integral/topological/combinatorial properties, active
sites, pockets, tunnels, regions of interest, contour trees, comparative
structural analysis
Analytics2Informatics/Visualization
II: multi-dimensional transfer functions, visible surface and volume
rendering, function on surface, capturing uncertainity
Case Studies: molecular recognition, electrical
signaling amongst neurons, cardio electrophysiology
Grading
You will be graded on bi-weekly homework assignments (50%), a semester programming project (30%), and a final exam (20%).
Lectures
Exercises:
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1 (Sept. 13) |
Exercise 1 Algebraic Curve, Surface Splines - I Solution 1 |
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2 (Oct. 7)) |
Exercise 2 Algebraic Curve, Surface Splines - II Solution 2 |
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3 (Oct. 28) |
Exercise 3 Spline Finite Elements Interpolation, Meshing /span> Solution 3 |
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4 (Nov. 19) |
Exercise 4 Spline Finite Elements and Image Processing Solution 4 |
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5 (Dec. 3) |
Final Exercise Molecular Models and Differential Properties Final Solution |
Suggested Projects
I Molecular Forces and
Recognition
II Neuronal Structure and
Plasticity
III Cardio Deformations and
Electrophysiology
Pictures and Animations
Suggested Reading
Links