CS/CAM/BME 395T - #54303

FALL 2005     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 31

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

  Producing Effective Bio-Animations

September  7

Molecular modeling I – atomic resolution models from PDB, VIPER

  Multi-grid based molecular surfaces and Docking

September  14

Molecular modeling II  ---  3D EM maps from EBI, structure elucidation

  Structure-refinement techniques and tools

September  21

Molecular modeling III --- area/vol derivatives, energetics, force fields

  Generalized Born Solvation Energies and Forces

September 28

Cell  modeling I --- segmentation from 3d EM, free-form deformable models

  Poisson Boltzmann Solvation Energies and Force Calculations

October  5

Cell modeling II --- Hydrodynamics, Deformable Organelles

  Free-form modeling of Molecular and Cell Domains

October  12

Cell modeling III --- NMJ (putting cells +molecules together)

  Deformable free-form modeling of Intracellular Domains

October  19

Tissue modeling I --- Brains, neurons, schwann cells

  Filtering, Segmentation and Re-sampling of Multi-modal Imaging

October  26

Tissue modeling II --- Heart , myocardium, biomechanics

  Patient Specific Blood Vessel Extraction for Pulmonary Embolus Detection

November  2

Tissue modeling III – Putting tissue + cells +molecules

  Effective navigation for Interactive Animation Production

November  9

Organ modeling I --- Brain anatomy and function models

 Quality Meshing with Bounded Number of Elements

November  16

Organ modeling II --- Heart anatomy and function models

  Match and Fit Techiques for Anatomical Geometry with 3D Imaging

November  30

Organ modeling III --- Putting together organs +tissues+ cells +molecules

 Presentation on multiresolution modeling + visualization



Constructing and visualizing computer models from the PDB, VIPER and assignments


Segmentation and visualization and assignments


Spatially Realistic Modeling of the Neuro-Muscular Junction



                                     Presentations  on December 7


 Linking organelles + molecular models


 Linking cells + organelle models


 Linking tissue + cell models


 Linking organs + tissue models


  Modeling Organisms

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