CS 384R (#53650), CSE 392 (#65334)

SPRING 2013     TTH 8:00 – 9:15am    RLM 7.116

Geometric (Bio-) Modeling and Visualization

 

(Top Row, left to right) Models of the HIV-Envelope Spike Multi-Protein; Electro-static potential (red = negative, blue = positive) via Poisson Boltzmann of the Machupo-Virus; Quality meshed models of a spiny Hippocampal dendrite (yellow) and axon (green);Visualization from a different view of the dendrite and axon, together with a slice of the ssTEM; (Bottom Row): Model of the inner workings of a cell with a collection of ribosomes and phage-29 at different stages of formation.

 

CS384R, CSE392 Course Outline

The course will teach you the basic mathematics, algorithms, techniques and tools of geometric and physiological 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, harmonic analysis, computational topology, computational geometry (algebraic and differential), group theory, polynomial spline approximations, computer graphics, data analysis, together with aesthetic choices involved in producing effective scientific animations. The emphasis shall be on spatial realism, and the programmatic use of multi-scale modeling, analysis and visualization to quantitatively depict "how things work" at the molecular,  and cellular scales.

Exercises on geometric and physiological modeling analysis 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

 

Mathematical Preliminaries: Linear algebra, Barycentric coordinates, Mean-value coordinates, Algebraic (polynomial) splines, Parametrization, Singularities, Differential forms,  Discrete exterior calculus, Motion groups, Radon and Fourier transforms

 

Models: Surface and Volumetric representations,  Point-based, Clouds, Weighted Delaunay triangulations, Voronoi diagrams, Octrees, Complementary Space (Pockets, Tunnels, Voids)

 

Maps: X-ray diffraction, Electron microscopy, CT/MRI,  Voxel  and Continuum Representations

 

Images & Maps: Forward and Inverse Problems,   Contrast Transfer Corrections, Symmetry and Anisotropy considerations, Compression

Maps2Models: Filtering, Contrast enhancement, Alignment, Classification, Symmetry detection, Static & active Contouring,  Segmentation, Medial axis, Skeletonization,  Clustering, Matching

Models2Analytics I: Point cloud and Cross-sectional Contour Reconstruction,  Surface and Volumetric finite element meshing,  Spline representations, Feature identification,  Symmetry detection, Shape segmentation, Matching & Complementary Docking,  Flexibility, Multi-component Assemblies & Reassembly, 

Models2Analytics II: Bonded and non-bonded Molecular Energetics, Forces,  Poisson-Boltzmann Electrostatics, Poisson-Nernst Planck ElectroDiffusion,  Electric Cable Models, Numerical Quadrature, Cubature,  Fast Multipole Methods, fast Fourier techniques, Discrete differential operators, de-Rham Diagrams, Integral equations

Analytics2Informatics/Visualization : Differential/integral/Topological/Combinatorial Properties, Active sites, Hydrogen bond Networks, Branching structures, Packings & Tilings, Contour trees, Comparative Structural analysis, Multi-dimensional Transfer Functions, Visible Surface and Volume rendering, Functions on Surface, Quantifying  Uncertainity

 

Case Studies: Molecular recognition, Electrical signaling amongst neurons.

 

Grading

You will be graded on periodic written homework assignments (60%), a research and/or programming project with a written report and final presentation (40%).

 

Lectures
 

DATE	LECTURES
Jan 15 (T)	Multiscale Imaging, Modeling, Informatics; Applications in Modeling Biology (Computational Drug Design, Discovery; Neuronal Electrical Circuits: Form and Function)
Jan 17 (TH)	Maps & Models I: Image Representations, Modalities, Capturing Molecular and Cellular Form
Jan 22 (T)	Maps & Models II: Mesh Representations, Regular Triangulations, Power Diagrams,
Jan 24(TH)	Maps & Models III: Barycentric Coordinates, Bernstein-Bezier Polynomials, Polynomial Splines
Jan 29  (T)	Maps & Models IV: Spline, Finite Element Representations of Molecular / Cellular Structure
Jan 31 (TH)	Images-&-Maps I: The Forward Problem for Electron Microscopy, and Computed Tomography
Feb 5  (T)	Images-&-Maps II: The Inverse Problem for Electron Microscopy, and Computed Tomography
Feb 7  (TH)	Maps2Models I: Image Processing 2D and 3D
Feb 12  (T)	Maps2Models II: Geometry Processing, Molecular and Cellular Structure Elucidation
Feb 14  (TH)	Maps2Models III: Geometry Processing, Skeletonization, Segmentation, Virus Ultrastructure, Reduced Neuronal Structures
Feb 19  (T)	Models2Analytics I: Point Cloud Reconstruction (Surface, Volumetric), Dynamic Packing Grids
Feb 21 (TH)	Models2Analytics II: Cross-Sectional Contour Reconstruction (Surface, Volumetric)
Feb 26  (T)	Models2Analytics III: Molecular Modeling: Hierarchical Structure Representations
Feb 28  (TH)	Models2Analytics IV: Molecular Surfaces, Complementary Regions  Structural Bioinformatics
March 5  (T)	Models2Analytics V: Molecular Recognition: Complementary Docking  (Cartesian and Spherical Fast Fourier Methods)
March 7  (TH)	Models2Analytics VI: Molecular Match & Fit (Cartesian and Spherical Fast Fourier Methods)
March 19  (T)	Models2Analytics VII: Molecular Bonded & Non-Bonded Energetics (Fast Algorithms)
March 21 (TH)	Models2Analytics VIII: Molecular Solvation Energetics - Generalized Born, Dispersion, Poisson Boltzmann
March 26  (T)	Models2Analytics IX: Forces, Normal Mode Analysis and Molecular Dynamics
March 28  (TH)	Models2Analytics X:Multi-Protein Docking, Molecular Assemblies, Tiling Theory & a>
April 2  (TH)	Models2Analytics XI: Neuronal Form: Spatially Realistic Cellular Connectomics
April 4  (T)	Models2Analytics XII: Neuronal Electrophysiology A – Cable Models
April 9  (TH)	Models2Analytics XIII: Neuronal Electrophysiology B - Electro-Diffusion
April 11  (T)	Models2Analytics XIV: Neuronal Electrophysiology C – Multi-scale Models
April 16   (TH)	Analytics2Informatics I: Contouring, Contour Spectrum
April 18  (T)	Analytics2Informatics II: Topological Contour Trees, Reeb Graphs
April 23  (TH)	Analytics2Informatics III: Comparative Structural Analysis
April 25  (T)	Analytics2Informatics IV: Quantifying UncertainityVerification & Validation
April 30  (T)	FINAL PROJECT PRESENTATIONS Gallery
May 2  (TH)	FINAL PROJECT PRESENTATIONS Gallery

 

Exercises:
 

Jan  22  (T)	Exercise 1 Computer Science & Mathematics Refresher Solution 1
Feb 5  (T)	Exercise 2 Image Processing 2D & 3D Solution 2
March 7  (T)	Exercise 3 Geometry Processing 2D & 3DSolution 3
March 26  (T)	Exercise 4 Quantitative Analysis, Informatics (Molecular and Cellular) Solution 4
April 9 (T)	FINAL PROJECTS  ASSIGNED

 

Primary Texts & References

 

1. C. Bajaj. Multi-scale BioImaging and Informatics, 2012 ()
2. C. Bajaj. Multi-scale BioModeling and Analysis, 2012 ()

 

Background Mathematical, Modeling References

1. C. Bajaj. Multi-scale Bio-Modeling and Visualization, Chapters 2, 3, 4 (pdf)
2. C. Bajaj. Computational Structural Bioinformatics II: Molecular Models. Chapters 2, 3, 4 (pdf)
3. C. Bajaj. Computational Structural Bioinformatics II: Molecular Models. Appendix (pdf)
4. C. Bajaj, A. Gillette. Polynomial Curves and Surfaces, Algebraic Spline Finite Elements , Chapter 1. (pdf)
5. C. Bajaj, A. Gillette. Operations on Polynomial Curves and Surfaces, Algebraic Spline Finite Elements , Chapter 2. (pdf)
6. C. Bajaj, A. Gillette. Piecewise Polynomial Curves and Surfaces, Algebraic Spline Finite Elements, Chapter 3. (pdf)
7. C. Bajaj, A. Gillette. Geometric Modeling, Algebraic Spline Finite Element , Chapter 4. (pdf)
8. C. Bajaj, A. Gillette. Derivatives and Integration, Algebraic Spline Finite Element, Chapter 5. (pdf)

 

 

Suggested Modeling, Analysis and Visualization Projects

 

I Molecular Forces and Recognition  (Computational Drug Design and Discovery)

 

II Neuronal Structure and Plasticity (Electrical Circuits in the Hippocampus: Form and Function)

 

Modeling, Analysis and Visualization Software

 

Graphical User Tools

• TexMol - Molecular modeling and visualization
• VolRover - Volumetric Image Processing and Visualization
• VolRoverN -  Spatial Realistic Modeling and Visualization of Neuronal Electrophysiology
• LBIE - Level Set Boundary-Interior-Exterior Meshing Tool.
• Prism - Geometric modeling using dual form Hermite Algebraic Surface Elements.
• GANITH – An Algebraic geometry toolkit.

Software Libraries and Command-Line Utilities

• MolSurf - Molecular surface generation and manipulation.
• MolEnergy - Molecular energetics computation.
• DPG - Dynamic packing grids.
• SSEP - Secondary structure elucidation package.
• Pocket/Tunnel - Protein pocket/tunnel extractor.
• QHM - Quality Quadrilateral/Hexahedral Mesh Generator. QTM - Quality Triangular/Tetrahedral Mesh Generator.  MDM - Multi-Domain Meshing.
• GPU Renderer - Surface/Volume Rendering Packages.

Server Based Codes

• F2Dock - Protein docking software.
• TRLIB - Texture-based Rendering Library.

Additional Suggested Reading

 

Books & Papers 

 

Useful Links

 

Other Relevant Course on Campus

 

Group Meeting Schedule