CS/CAM/BME 395T - #56630,#66537

FALL 2006     Wed 2:00 – 5:00pm    BUR 116

Multi-scale Bio-Modeling and Visualization


Picture is from [5] under suggested reading



Chandrajit Bajaj


ACES 2.324





Office hours

By appt. via robert@ices.utexas.edu

CS 395T Course Outline

Biomedical modeling 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, and modeling algorithms with emphasis on spatial realism, and the programmatic use of simulation and visualization to quantitatively depict "how things work" at the molecular, cellular, tissue, and organ level scales. Computational methods shall include multi-scale geometry representations, image filtering, contrast enhancement, segmentation, fusion, boundary and finite element meshing, spline interpolants and approximants and, their use in integral and differential equation solving, quadrature and cubature formulas, volumetric contouring, volumetric rendering, volumetric texture-based image and geometry composition, combinatorial, topological and integral/differential metric quantitation. Practical exercises on computational domain and physiological modeling and visualization at multiple scales, shall be drawn from cardiology (heart, cardiac tissue, myocytes,ion-channels), and neurology (brain, spinal cord, neurons, Schwann cells, neurotransmitters), and their interactions (synaptic  transmission at the neuro-muscular junction).


You will be graded on the successful completion and presentation of  the assigned project.

There shall also be two reports due:

  • a mid-semester report on the project
  • and a final report (and additionally a demo),  summarizing results obtained and lessons learned




August 30

Model and Visualize “How Things Work” spanning Organ, Tissue, Cell, Molecular Scales

  Producing Effective Bio-Animations

September  6

Multiscale Domain modeling I – atomic resolution models from PDB, VIPER

  Demo of TexMol Molecular Modeling/Visualization Software

September  13

Multiscale Domain modeling II  ---  Segmentation of 3D EM maps from EBI, structure elucidation from Imagin

  Demo of VolRover 3D Image Proc/Viz Software

September  20

Multiscale BEM-FEM Domain Modeling III --- vol Contouring Gridding

  Demo of LBIE BEM/FEM Meshing Software

September 27

Multiscale BEM-FEM Domain  modeling IV --- Lofting/Tiling/Sweeping

  Demo of Cross-Section Tiling/Lofting Software

October  4

Multiscale Domain modeling V --- Fitting a Cloud of Points

  Demo of Prisms for smooth Patch Reconstruction

October  11

Multiscale Function Modeling I --- Molecular Energetics, Force Fields

  Molecular Mechanics, Binding/Drug Design

October  18

Multiscale Function Modeling II --- Electrostatics Potential, Mol.- Cell

Poisson, Boltzmann Equations

October  25

Multiscale Function Modeling III --- Diffusion and Drift

   Timed Smoluchowski Equation

November  1

Multiscale Function Modeling IV --- Diffusion and Reaction

   Rate Constants, Chemical Kinetics

November  8

Multiscale Function Modeling V - Interfacial Dynamics

  Stokesian Flows , Deformable Membranes

November  15

Multiscale Function Modeling VI - Acoustic Scattering

   Sound Localization

November  29

Multiscale Modeling of Synaptic Transmission at Neuro Muscular Junction



Constructing and visualizing computer models from the PDB, VIPER and assignments
TexMol download and tutorial
VMD download and tutorial


Segmentation and visualization and assignments



Project Presentations on December 6


  Molecular Modeling, Drug Binding, with TexMol


  Multiscale Molecular & Cell Electrostatics Models with LBIE-Mol


  Multiscale Isotropic & Anisotropic Diffusion


  Multiscale Drift & Diffusion Phenomena


  Stokesian Flows & Deformable Bio-Modeling with Tile Tools


  Acoustic Scattering, Sound Localization with Prism

Subsequent meetings shall also include discussions of assigned projects respectively. We shall discuss algorithms, data structures and system level issues pertaining to the projects.

Pictures and Animations


Suggested Reading (more to follow)

1.  Data Visualization Techniques, ed. C. Bajaj, John Wiley, 1999

2.  Finite Element Methods with B-splines, K. Hollig, SIAM Frontier in App. Math., 2003

3.  BioNanoTechnology, Lessons from Nature, D. Goodsell, Wiley-Liss, Inc, 2004

4.  On Growth and Form, D’Arcy Thompson, Dover, 1992

5.  Brain, Mind, and Behavior, F. Bloom, A. Lazerson, W. H. Freeman and Company,1999

6.  Biomechanics, Y. Fung, Springer Verlag, 1993

7.  Immunology, R. Coico, G. Sunshine, E. Benjamini, John Wiley, 2003

8.  Viruses and Human Disease, J. Strauss, E. Strauss, Academic Press, 2002

9.  Structural Aspects of Protein Synthesis, A. Liljas, World Scientific, 2004

10.  Introduction to Protein Structure, C. Branden & J. Tooze, Garland Pub., 1999

11.  Geometric Modeling and Quantitative Visualization of Virus Ultrastructure , C. Bajaj, 2005

12.  Geometric Processing of Reconstructed 3D Maps of Molecular Complexes, C. Bajaj & Z. Yu, 2005


Group Meeting Schedule