CS 384R (#56767), CAM 395T (#67597), BME 385J (#14608)
FALL
2007 TTH 9:30 – 11:00am
TAY 3.114
Geometric 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 |
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. 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
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
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LECTURES |
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August 31 |
Preliminaries of Multiscale geometry; Multiscale imaging; Applications from Modeling Biology
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September 4 |
Models/Maps: Discrete and Analytic Representations of Points(P), Curves(C), Surfaces(S), Spline Models
Models/Maps: Finite Element Splines (supplementary)
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September 6 |
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September 11 |
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September 13 |
Generation of Curves and Surface Splines from Scattered Points II: Surfaces
immersed in 3D with applications to Tissue (Reconstruction) Modeling
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September 18 |
Generation of Surface Splines from Curves I: Sweeping with Applications
to Cellular Organelles, Vasculature modeling |
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September 20 |
Generation of Surface Splines from Curves II: Lofting with Applications
in Neuronal Cell Modeling |
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September 25 |
Generation of Surface Splines from Curvilinear Complex III: Patch Fitting
with Applications to Organ modeling |
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September 27 |
Generation of Surface Splines from Curvilinear Complex IV: Subdivision
Schemes with Applications to Cell, Organs, Vessel modeling |
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October 2 |
Generation of Surface Splines from Curvilinear Complex V: Geometric
Flow with Applications to Hole Filling |
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October 4 |
Generation of Skeletons from Surface Models with Applications to Secondary/Tertiary
Protein Structure Elucidation |
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October 9 |
Generation of Complementary Surface Features with Applications to Shape
Matching |
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October 11 |
Construction of Adaptive Grids of Volumetric Domains with Boundaries
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October 16 |
Construction of Adaptive Triangulations of Volumetric Domains with Boundaries
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October 18 |
Construction of Adaptive Hexahedral Decompositions of Volumetric Domains
with Boundaries |
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October 23 |
Geometric Matching and Docking I: Complementary Space Docking |
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October 25 |
Geometric Matching and Docking II: Flexible Docking |
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October 30 |
Geometric Matching and Docking III: Matching Geometry with Imaging |
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November 1 |
Multiscale Function Modeling I: Molecular Energetics, Solvation, Force
Fields |
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November 6 |
Multiscale Function Modeling II: Generalized Born and Poisson Boltzmann
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November 8 |
Multiscale Function Modeling III: Random Walks, Diffusion and Drift
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November 13 |
Multiscale Function Modeling IV: Diffusion and Reaction |
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November 15 |
Multiscale Function Modeling V: Branching Processes |
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November 20 |
Multiscale Function Modeling V: Branching Processes
Actin Polymerization, Vascular Networks
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November 27 |
Multiscale Function Modeling VI: Interfacial Dynamics |
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November 29 |
Multiscale Function Modeling VII: Acoustic , Light, EM Scattering |
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December 4 |
Multiscale Visualization, Informatics I : Model and Map Resolutions,
Errors and Uncertainity |
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December 6 |
Multiscale Visualization, Informatics II: |
Exercises:
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1 |
Exercise 1 Algebraic Curve, Surface Splines - I Solution 1 |
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Exercise 2 Algebraic Curve, Surface Splines - II Solution 2 |
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Exercise 3 Algebraic Curve, Surface Splines - III Solution 3 |
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4 |
Exercise 4 Algebraic Curve, Surface Splines - IV: Molecular Models Solution 4 |
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Exercise 5 Finite Element Meshing - I: Linear Elemen Solution 5 |
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Exercise 6 Finite Element Meshing II - Non-Linear Elements Solution 6 |
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Exercise 7 Geometric Modeling and Visualization Final Solution 7 |
Pictures and Animations
Suggested Reading
Links