CS 384R (#55830), CAM 395T (#67365)

FALL 2008 TTH 9:30 – 10:45am TAY 3.144

Geometric Modeling and Visualization

Image consists of Ribosome, Virus, Human body, Brain, NMJ(Neuromuscular junction), and Universe

Name	Chandrajit Bajaj
Office	ACES 2.324
Email	bajaj@cs.utexas.edu
Phone	512-471-8870
Office hours	Tue 1:30 - 3:00p Wed 2:30 pm - 3:30 pm or by appt. via suzanne@ices.utexas.edu

CS384R, CAM395T 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 and Maps: algebraic curves, surfaces, splines, parametrization, manifolds, singularities, topology, electron microscopy, CT/MRI imaging, reconstruction.

Maps2Models: filtering, contrast enhancement, classification, symmetry detection, segmentation, skeletonization, subunit identification, 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 energetics, forces, torques, dynamics, cubature, discrete differential operators, integral equations, sparsifiers, preconditioners, solvers.

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, VisPortal, MolSignatureDB.

Grading

You will be graded on weekly homework assignments (70%) and a final exam (30%).

Lectures

DATE	LECTURES
August 28	Preliminaries of Multiscale geometry; Multiscale imaging; Applications from Modeling Biology Interpretive Bio-Animations
September 2	Models/Maps: Discrete and Analytic Representations of Points(P), Curves(C), Surfaces(S), Spline Models I Ganith
September 4	Models/Maps: Discrete and Analytic Representations of Points(P), Curves(C), Surfaces(S), Spline Models II Ganith
September 9,11	Generation of Curves and Surface Splines from Scattered Points I: Volumetric 3D with applications to Molecular Modeling VolRover
September 16,18	Models/Maps: Extraction of affine invariant PCS from 3D Images (Geometry Elucidation) TexMol
September 23,25	Generation of Curves and Surface Splines from Scattered Points II: Surfaces immersed in 3D with applications to Tissue (Reconstruction) Modeling VolRover
September 30	Generation of Curves and Surface Splines from Scattered Points III: Contouring Scalar Functions VolRover
October 7,9	Generation of Surface Splines from Curves I: Sweeping with Applications to Cellular Organelles, Vasculature modeling Ganith
October 14,16	Generation of Surface Splines from Curves II: Lofting with Applications in Neuronal Cell Modeling VolRover
October 9	Generation of Surface Splines from Curvilinear Complex III: Patch Fitting with Applications to Organ modeling Prism
October 14	Generation of Surface Splines from Curvilinear Complex IV: Subdivision Schemes with Applications to Cell, Organs, Vessel modeling Prism
October 16	Generation of Surface Splines from Curvilinear Complex V: Geometric Flow with Applications to Hole Filling TexMol
October 21	Generation of Skeletons from Surface Models with Applications to Secondary/Tertiary Protein Structure Elucidation TexMol
October 23	Generation of Complementary Surface Features with Applications to Shape Matching TexMol
October 28	Construction of Adaptive Grids of Volumetric Domains with Boundaries TexMol
October 30	Construction of Adaptive Triangulations of Volumetric Domains with Boundaries LBIE
November 4	Construction of Adaptive Hexahedral Decompositions of Volumetric Domains with Boundaries LBIE
November 6	Geometric Matching and Docking I: Complementary Space Docking TexMol
November 11	Geometric Matching and Docking II: Flexible Docking TexMol
November 13	Geometric Matching and Docking III: Matching Geometry with Imaging VolRover
November 18	Multiscale Function Modeling I: Molecular Energetics, Solvation, Force Fields TexMol
November 20	Multiscale Function Modeling II: Generalized Born and Poisson Boltzmann TexMol
November 11	Multiscale Function Modeling III: Random Walks, Diffusion and Drift Chemical Synapses
November 18	Multiscale Function Modeling IV: Diffusion and Reaction Chemical Kinetics, Reactive Fluids
November 20	Multiscale Function Modeling V: Branching Processes Actin Polymerization, Vascular Networks
November 25	Multiscale Function Modeling V: Branching Processes Actin Polymerization, Vascular Networks
Decemeber 2	Multiscale Function Modeling VI: Interfacial Dynamics Stokesian Flows, Deformable Membranes
December 4	Multiscale Function Modeling VII: Acoustic , Light, EM Scattering Helmholtz and Maxwell Equations
December 4	Multiscale Visualization, Informatics I : Model and Map Resolutions, Errors and Uncertainity VisPortal
December 6	Multiscale Visualization, Informatics II: Molecular Signature Database

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 - Non-Linear Elements Solution 6
7	Exercise 7 Geometric Modeling and Visualization Final Solution 7

Pictures and Animations

Gallery

Suggested Reading

Papers Reading List

Links

Group Meeting Schedule