About
In our time together in the theory module of skills week, we’ll take a tour through the worlds of numerical thinking in biology and simple physical models of biological systems. We’ll try our hand at order-of-magnitude estimates and pen-and-paper models of phenomena like biological growth, diffusion, phase separation, polymerization, and more! For some topics, we’ll complement our calculations with Python simulations. You’ll also prepare and present an order-of-magnitude (‘Fermi’) estimate related to your own interests or research. Our main goal is to explore together how powerful (and fun!) numerical and physical thinking can be as a tool in understanding biology.
People
-
Hernan Garcia - Instructor
hggarcia@berkeley.edu
-
Christina Hueschen - Instructor
chueschen@ucsd.edu
-
Yovan Badal - TA
ybadal@berkeley.edu
Date |
Topics |
Materials |
Videos |
Monday |
-
A feeling for the numbers in biology.
-
Street-Fighting Mathematics: Order-of-magnitude estimates as a tool for discovery in the living world.
-
What sets the scale of X?
|
|
-
A Feeling for the Numbers in Biology (Video)
- How many porta potties do you need for an outdoor concert? (Video, Notes)
- What Sets the Scale of Mountain Height? (Video, Notes)
- mRNA vs protein size (Video, Notes)
- Sun vs Human Power (Video, Notes)
- Number of Genes in E. coli (Video, Notes)
- Most Abundant Cell Type (Video, Notes)
- Carbon Transporters in a Bacterium (Video, Notes)
- ATP Consumption per Volume of Cytoplasm (Video, Notes)
- Exhausting ATP Pool (Video, Notes)
- DNA Replication Error Rate (Video, Notes)
|
Monday |
-
Stuff(t) or the Protocol of Biological Dynamics.
- Time evolution in biology.
- Bacterial growth dynamics: Solving bacterial growth analytically and numerically.
|
|
|
Monday |
-
Diffusion as Biology's Null Hypothesis for Dynamics.
- Diffusion and axonal transport.
- Diffusion by coin flips.
|
|
|
Monday |
-
Null Hypotheses in Biology: The Poisson Distribution, Part I.
- The Great Probability Distributions of Biology
- The constitutive promoter.
|
|
|
Monday |
-
A Feeling for the Numbers in Biology: Your Turn.
- Prepare a 5 minute estimate you will present on Saturday.
- Christina and Hernan are around to help all week. Just Slack us!
|
|
|
Saturday |
-
Null Hypotheses in Biology: The Poisson Distribution, Part II.
- Chemical master equation of the constitutive promoter.
- The Poisson Distribution: Bombs over London, constitutive promoters, and sequencing the human genome.
- Synthetic transcriptomes and the single-cell sequencing revolution.
|
|
|
Saturday |
-
Phase Transitions in Biology.
- Entropy maximization.
- Free Energy Minimization.
- Drawing Phase Diagrams.
|
|
|
Saturday |
|
|
|
Saturday |
-
Physical Biology of the Cell.
|
|
|