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) Schrodinger's "What Is Life?" (22:08) Doing physics to it (20:18) Biological numeracy exam
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 Scaling of cellular structures (22:23)
Week of Jan. 11 (#2)	3. From Data to Insight: Thinking Big About Data Biological puzzles and probabilistic thinking (11:39) Carboxysomes and binomial partitioning Ion channels and exponential waiting time distribution (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 precisio (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 informtion: 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) Phenomenlogy 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	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)