Syllabus

Syllabus

Required text: Physical Biology of the Cell (2nd ed) by Phillips, Kondev, Theriot and Garcia (ISBN: 0815344503)

The syllabus (PDF) is tentative and subject to change. Refer to the list below for the prerecorded video lectures.

Date Topic
Week of Jan. 4 (#1)

1. Perspective, Vision, and Preliminaries

A feeling for the organism (04:42)
Order-of-magnitude thinking (08:51)
Transformative technologies (09:48)
Schrödinger's "What Is Life?" (22:08)
Doing physics to it (20:18)
Biological numeracy exam (16:54)
Week of Jan. 4 (#1)

2. A Feeling for the Organism

2.1 Rate of cell division
What sets the bacterial division time? (17:15)
Laws of cellular growth (23:01)
Rate limiting hypothesis: Proteomics (18:42)
Rate limiting hypothesis: Carbon transport (14:15)
Rate limiting hypothesis: ATP synthase (13:25)
Rate limiting hypothesis: Surface-to-volume ratio (07:18)
Rate limiting hypothesis: Transcription (16:15)
Rate limiting hypothesis: Ribosomes (07:21)
Rate limiting hypothesis: Summary (06:42)
Week of Jan. 11 (#2)
2.2 Scales and scaling
Interlude on passion (09:27)
Semantics on scale (18:12)
Scaling of diffusion time (16:46)
Diffusion time by the numbers (08:30)
Scaling of cellular structures (22:23)
Week of Jan. 11 (#2)

3. From Data to Insight: Thinking Big About Data

3.1 On the probability distributions
Biological puzzles and probabilistic thinking (11:39)
Carboxysomes and binomial partitioning (19:05)
Ion channels and exponential waiting time distriubtion (15:22)
mRNAs and Poisson distribution (16:49)
Interlude on Taylor series (17:50)
Every distribution has its moments (35:56)
Week of Jan. 11 (#2)
3.2 Bacterial size control
Bacterial size control: Timer (15:23)
Bacterial size control: Adder (09:40)
Week of Jan. 18 (#3)

4. The Dynamical Cell

4.1 Diffusion
Diffusion: Introduction (10:41)
Diffusion: Coin flips (19:14)
Diffusion: Continuum theory (22:10)
Diffusion: Master equation (17:45)
Week of Jan. 18 (#3)
4.2 Dynamics beyond diffusion
Introduction to dynamics beyond diffusion (15:40)
Rate equations for mRNA dynamics (19:24)
Dynamics of ligand-receptor binding (20:07)
Dynamics of enzymes (12:12)
On the literature (10:40)
Borges and you (11:34)
Rate equations for compartmentalized enzymes (15:07)
Statistical mechanics: Introduction (18:55)
Statistical mechanics: Binding (15:32)
Statistical mechanics: Binding cooperativity (22:55)
Week of Jan. 25 (#4)
4.2 Dynamics beyond diffusion (continued)
Introduction to gene networks (09:44)
Rate equations for auto-activation (15:35)
Rate equations for the mutual repression switch (20:11)
Mutual repression switch: Fixed points (13:07)
Stability analysis for the mutual repression switch (25:00)
Rate equations for genetic oscillators (15:26)
Reconciling thermodynamic and statistical mechanical views of binding (11:29)
Reconciling statistical mechanics and thermodynamics (continued) (08:49)
Rate equations for microtubule length control (19:48)
Why I am so boring (10:30)
Rate equations for pandemics (20:15)
Interlude on surprise (14:14)
Rate equations for the double negative regulation (13:10)
Double negative feedback hypothesis for the Aleutians (05:26)
On surprise in spectroscopy (05:06)
Week of Feb. 1 (#5)
4.2 Dynamics beyond diffusion (continued)
MWC model (24:33)
Closing the theory-experiment loop (19:32)
Week of Feb. 1 (#5)
4.3 Chemical master equation approaches to dynamics
Chemical master equation for the constitutive promoter (15:15)
Chemical master equation for the two-state model of transcription, part 1 (18:24)
Chemical master equation for the two-state model of transcription, part 2 (25:26)
Ode to precision (17:37)
Chemical master equation for the cytoskeleton (17:15)
Week of Feb. 1 (#5)
4.4 Linking time and space
On positional information (12:22)
Position information: Reaction-diffusion equation (19:50)
Position information: The French flag model (11:12)
Meeting Turing (19:07)
In the steps of Turing (31:11)
Turing ring of cells (25:02)
Continuous version of Turing (36:41)
Turing: Closing the loop (18:39)
Week of Feb. 8 (#6)

5. Life as Defiance

5.1 Defiance of diffusion
Life as defiance: Introduction (29:29)
Calculus of equilibrium (18:31)
Thermal energy scale (16:21)
Boltzmann as equilibrium recast (09:19)
Linear departure from equilibrium (12:54)
Phenomenology not a dirty word (13:41)
Cost of transport up a gradient (12:55)
Dissipation required to maintain a concentration gradient (17:43)
Drawing energy from a concentration gradient (18:12)
Proton motive force (09:50)
Cost of forming the Bicoid gradient (19:07)
Week of Feb. 8 (#6)

5. Life as Defiance

5.2 Adaptation as defiance of Boltzmann and Langmuir
Introduction to adaptation: Chemotaxis (15:42)
MWC model of chemoreceptors (22:54)
Sameness (18:28)
Chemotaxis adaptation (22:03)
Entropy production (13:08)
Week of Feb. 15 (#7)
5.3 Fidelity as defiance of Boltzmann
Fidelity as defiance (20:00)
Kinetic proofreading (18:27)
Week of Feb. 15 (#7)

6. Theory of Living Matter

Introduction to active matter (19:32)
What is field theory (22:56)
Week of Feb. 22 (#8)
Introduction to elasticity (15:19)
Stress and strain (32:10)
Elasticity of beams (31:14)
Gut folding (16:51)
Force balance in fluids (24:15)
Week of Mar. 1 (#9)
Stress in fluids (14:59)
Derivation of the Navier–Stokes equations (07:38)
Dimensionless Navier-Stokes, Reynolds number (12:42)
Introduction to cytoplasmic streaming in Chara (08:18)
Stokes equations for the cytoplasmic streaming in Chara (20:17)
Viscoelasticity in tissues (20:29)
Incompressibility (09:57)
Self-organization in Chara (08:58)
Week of Mar. 8 (#10)
The Real Biology (13:38)
C elegans actomyosin (18:08)
Membraneless organelles and phase separation (16:52)
Flory–Huggins theory (21:18)
Week of Mar. 8 (#10)

7. Final Thoughts

Night science (08:48)
Biological numeracy (17:44)
Musings on mechanism (18:07)
Grandeur in this view of life (02:44)
PBoC: Understanding (08:53)
Imposters, success and failure (10:15)
Course accomplishments (17:14)