Name 

Office 
ACES 2.324 


Phone 
5124718870 
Office hours 
Wed 9:00 am  12:00 am or by appt. via suzanne@ices.utexas.edu 
CS384R, CAM395T, BME385J 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. Biomedical 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, ionchannels, neurotransmitters), and their interactions (molecular energetics
and force fields, molecular flexibility, synaptic transmission, synaptic spillover).
Lecture Topics
Grading
You will be graded on weekly homework assignments (70%) and a final exam (30%).
Lectures
DATE 
LECTURES 
August 30 

September 4 

September 6 

September 18 

October 23 

October 30 

November 6 
Boundary & Finite Element Meshed Models III: Topologically Accurate NonLinear Elements 
November 12 
Finite Elements from Imaging I & II: Active Contouring, Segmentation, Reconstruction 
November 27 
Geometric Partial Differential Equations: NonLinear Surface & Volume Diffusion 
December 12 
Integrals & Integral Equations: Molecular Energetics & Forces 
Exercises:
1 
Exercise 1 Algebraic Curve, Surface Splines  I Solution 1 
2 
Exercise 2 Algebraic Curve, Surface Splines  II Solution 2 
3 
Exercise 3 Algebraic Curve, Surface Splines  III Solution 3 
4 
Exercise 4 Algebraic Curve, Surface Splines  IV: Molecular Models Solution 4 
5 
Exercise 5 Finite Element Meshing  I: Linear Elemen Solution 5 
6 
Exercise 6 Finite Element Meshing II  NonLinear Elements Solution 6 
7 
Exercise 7 Geometric Modeling and Visualization Final Solution 7 
Pictures and Animations
Suggested Reading
Links