PHYS 847/492 - Quantitative Biology Stuff

Instructor: Eldon Emberly         Office: SCB9684      Phone: 3701        e-mail: eemberly_at_sfu_dot_ca

Syllabus

Reading List (To Be Updated)

Reference List

Possible Projects

Important Dates:

    Oct 13 - Thanksgiving

    Oct 14 - Make-up class 1

    Oct 20 - EE away

    Oct 22 - EE away

    Oct 28 - Make-up class 2

    Nov 26 & 28 - in-class presentations

    Dec 1 - Projects are due

Reading Questions:

Question set #1 (Discussion Sept. 12)

Question set #2 (Discussion Sept. 19)

Question set #3 (Discussion Sept. 29)

Question set #4 (Discussion Oct. 3)

Question set #5 (Discussion Oct. 10)

Question set #6 (Discussion Oct. 17)

Question set #7 (Discussion Oct. 28)

Question set #8 (Discussion Nov. 7)

Question set #9 (Discussion Nov. 14)

Question set #10 (Discussion Nov. 21)

Problem Sets:

Problem set #1 (Due Oct. 3)              PCA data 2D                PCA data 5D                   RNA folding primer

Problem set #2 (Due Oct. 31)     Gillespie Algorithm

Problem set #3 (Due Dec. 1)

Lecture Notes:

Week 1: Review of molecular biology (43 pages)  Cellular Estimates    Timescales

Week 2: RNA structure & function    RNA folding primer

Week 3: Protein Structure: Folding    Protein Structure: Modes and PCA

Week 4: Polymers: Random Walks

Week 5: Gene Logic: Cooperative Binding

Week 6: Genetic Switches

Week 7: Biological Oscillators

Week 7: Noise in Biological Systems (see handout)

Week 8: Diffusion in Biology

Week 9: Taking Space into Account: Reaction-diffusion

Week 10: Network epitome     Structure of large scale networks

Week 11: Large Network Dynamics: Boolean Nets