ELL 707, II semester 2019-20
This is the the webpage for ELL 707, II semester 2019-20
Systems Biology
Instructor
Shaunak Sen
E-mail: shaunak.sen@ee.iitd.ac.in
Lectures: MW 11:00-11:50am, Th 12:00-12:50pm
Room: LH 613
Announcements
Lectures
| S. No. | Date | Topic | Advised Reading | Lectures |
| 1 | Week 1
(Dec 30, Jan 1, 2) | Introduction
Oscillations
Examples in Polar Co-ordinates, Limit Cycle, Stability | DM 1, A 1.1, 1.2
S 1, 2, 3, 4
DM 3.3 | Dec 30
Jan 1
Jan 2 |
| 2 | Week 2
(Jan 6, 8, 9) | Bifurcations
Examples in Cartesian Co-ordinates, Simulations (pplane)
Examples of Biomolecular Oscillators (Videos), Quiz 1 | S 5, 6, 7, 8.0-8.3
DM 3.4 | Jan 6
Jan 8
Jan 9 |
| 3 | Week 3
(Jan 13, 16) | Repressilator, Repression, Activation
Law of Mass Action | DM 5.4, A 6.3
DM 2, A 1.3, 1.4, Appendix A | Jan 13
Jan 16
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| 4 | Week 4
(Jan 20, 22, 23) | Mathematical Models, ?, Quiz 2
Feedback, Negative, Delay
Negative Feedback, Faster Response Time | DM 2.1, 2.2, 2.3, 2.4, 2.5, A Appendix A & B
B. Novak & J. J. Tyson, 'Design Principles of Biochemical Oscillators’, Nat. Rev. Mol. Cell. Biol., 9(12), 2008., A 6.1
DM 5.2, A 2.4, 2.5 | Jan 20
Jan 22
Jan 23 |
| 5 | Week 5
(Jan 27, 29, 30) | Delay-induced Instability
code, Quiz 3
Solved Problem | | Jan 27
Jan 29
Jan 30 |
| 6 | Week 6
(Feb 4 - MINOR TEST 1) | | | |
| 7 | Week 7
(Feb 10, 12, 13) | Minor Test Solutions
Delay-induced Oscillations
Bendixson Criterion, Poincare-Bendixson Theorem, Mallet-Paret & Smith Generalization for Class of Cyclic Oscillators | DM 5.3, A 5.1.1, A 5.1.2, A 6.5
DM 3.3 | Feb 10
Feb 12
Feb 13 |
| 8 | Week 8
(Feb 19, 20, 22) | Quiz 4, Boundedness of Solutions
Equilibrium Points, Stability Analysis by Linearization
Quiz 5 |
DM 5.4, A 6.1, 6.2 | Feb 19
Feb 22
|
| 9 | Week 9
(Feb 24, 26, 27) | Root Locus
Homeostasis Robustness Adaptation
Example: a Feedforward Loop | DM 5.5, A 6.4
DM 3.1, 3.2 A 7.1
DM 5.6, A 3.1, 3.2, 3.3, 3.4, 3.7 | Feb 24
Feb 26
Feb 27 |
| 10 | Week 10
(Mar 2, 4, 5) | Transient Response
Fold-Change Detection Quiz 6
a Condition |
A 10.1, 10.4
A 10.5, 10.7 | Mar 2
Mar 4
Mar 5
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References
(DM) D. del Vecchio & R. M. Murray, Biomolecular Feedback Systems, Princeton University Press, 2014 (available online).
(A) U. Alon, An Introduction to Systems Biology, Chapman & Hall/ CRC Mathematical and Computational Biology, 2006.
(S) S. Strogatz, Nonlinear Dynamics and Chaos, Westview Press, 2001.
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