Class Information
Instructor
Location and Time
Class material
Office Hours
|
Amarda Shehu , Room #4422 ENG, amarda\AT\gmu.edu
ENT #276, R, 7:20pm - 10:00 pm
Lectures by instructor and chosen research articles
T 4-6 pm
|
Class Information
This class belongs to the AI/Database area. It presents geometric algorithms developed for modeling and
simulating physical and biological systems. The course will first
focus on algorithms for purely kinematic (robotic) systems, with an
emphasis on planning motions with geometric constraints. This
treatment will allow a seamless transition to algorithms for
simulation of motions of biological molecules with energetic
constraints.
Algorithms will be presented in the context of applications: (i)
simulating realistic motions of robotic kinematic chain for greater
autonomy; (ii) computing functionally-relevant motions of protein
chains for the design of novel therapeutics; (iii) computing
inter-molecular associations and assembly for the engineering of
molecular machines.
Class Reading
Material will be disseminated through research articles and lectures
developed by the instructor, which will be posted online prior to each
class.
Preliminary Class Syllabus
| Date |
Topic |
Chapters |
Assignments |
| Sep. 03 |
Course Overview and Introduction |
[pdf] |
|
| Sep. 10 |
Modeling and ForwardKinematics |
[pdf] |
Hw1 Out |
| Sep. 17 |
Inverse Kinematics |
[pdf] |
|
| Sep. 24 |
Loop Modeling |
[pdf] |
Hw1 Due |
|
|
Search Algorithms for High-dimensional Configuration Spaces
|
| Oct. 01 |
Probabilistic Roadmap |
Guest Lecturer |
|
| Oct. 08 |
Tree-based Exploration |
[pdf] |
Hw2 Out |
|
|
Algorithms for Computing Protein Structures
|
| Oct. 15 |
Trajectory-based Exploration |
[pdf] |
|
| Oct. 22 |
Fragment-based Assembly |
[pdf] |
Hw2 Due |
| Oct. 22 |
Research Article Highlight |
[pdf] |
Project Selection |
| Nov. 06 |
Docking Ligands, Docking Proteins |
[pdf] |
Hw3 Out |
|
|
Student Presentations of Research Articles
|
| Nov. 13 |
Group 1 |
|
|
| Nov. 13 |
Group 2 |
|
Hw3 Due |
| Nov. 27 |
Thanksgiving |
|
Turkey Time |
| Dec. 04 |
Complex Assembly |
[pdf] |
Progress Report |
| Dec. 11 |
Project Presentations |
|
Final Deliverables Due |
Grade Breakdown
- Class Participation: 5%
- Homeworks: 30% (10% each)
- Research Article Review and Presentation: 25%
- Project Completion and Presentation: 40%
Class Homepage
Latest lectures and other course materials will be available at
URL
http://www.cs.gmu.edu/~ashehu/?q=Fall2009