Physics 282: Spatiotemporal Dynamics in Biological Systems
| Instructor: | Prof. Terry Hwa; office: Urey 7222 phone: 4-7263; e-mail: TA: TBA |
| Time: | M W 9:30am – 10:50 am |
| Location: | 6120 Urey Hall |
| Office Hour: | after class or by appointment |
| Course URL: | this page (https://matisse.ucsd.edu/courses/f24-biodynamics/) |
| Grade | 3-4 problem sets and 1-2 group projects |
| Prerequisite: | a solid first course in ordinary differential equation; exposure to partial differential equation; interest in biological phenomena. |
Course description:
This course is aimed for advanced undergraduates and beginning graduate students in biophysics and bioengineering, and for quantitative-minded BIO students. The course teaches and applies basic concepts in dynamical systems (phase plots, stability analysis, Lyapunov function) and pattern formation in spatially extended systems (Fisher wave, Keller-Segel, Turing instability, excitable systems, etc) on topics taken from microbial ecology and evolution, and developmental biology. Lessons learned from the analysis will be gleaned for biological insight.
Course outline
- Introduction to bacterial growth, population dynamics, and ecology
- Lotka-Volterra model and its generalization: fixed points and phase diagrams
- Consumer-Resource model: coexistence and global stability
- Trophic interactions, cross-feeding, cooperation, and cheating
- Spatial range expansion: Fisher-Kolmogorov wave and the stability criterion
- Bacterial chemotaxis: coordination of migration and growth
- Turing instability and patterns in developmental biology
- Excitable systems: pulses and spiral waves
Tentative course outline:
| Date | Topics | assignment | |
| L1 | M, Sept 30 | course overview and intro to population dynamics; logistic equation; effect of predation [note] | |
| L2 | W, Oct 2 | two species interaction: fixed point, flow and phase diagram [note] | HW1 due Wed Oct 16 |
| L3 | M, Oct 7 | predator & prey; spread of infection [note] |