Chronological table of course content. Readings, deadlines and links to files.
2025-2026 school year (2025W)
This will be updated (almost) daily as we go through the course. Please check here first if you need anything.
- Our meeting day/time is Wed, Fri at 10:00am-11:20am.
- Our meeting place is currently Hennings 309. (3rd floor, corner room with a huge board meeting table)
- Course credit breakdown is below. We’ll also discuss if this should be tweaked a bit.
| Date | Deadlines, tests and reminders | In-class topics and materials | Textbook readings |
|---|---|---|---|
| Week 1 Sept 10 (W) & Sept 12 (F) | HW 1 (due Sept 28) In-class worksheet for Lect 2 Video Recording Lect 1 Lecture 1 slides Video Recording Lect2 Lecture 2 slides Lecture 2 slides, annotated | – Understand the microscopic origins of friction – Understand the relationship between friction and the diffusion coefficient – Write a microscopic expression for the diffusion coefficient – Write and explain Fick’s law – Relate the thermal velocity of particles in solution to their temperature – Write and understand the Einstein equation relating the friction coefficient, diffusion constant, and the temperature – Understand the Reynolds number, and when it is small or large – Using dimensional analysis to find the relationship between the frictional drag force on a moving sphere | Textbook: 13.1 Diffusion in the cell 13.2 Concentration fields and diffusive flux Additional Materials: Nelson-Ch4.1 Rules_of_thumb-numbers Data Thief Tutorial for HW |
| Week 2 Sept 17 (W) & Sept 19 (F) | Video Recording Lect 3 Lecture 3 slides Lecture 3 slides, annotated Video Recording Lect 4 Lecture 4 slides Lecture 4 slides, annotated Lecture 4 slides Take 2, annotated | – Understand dimensional analysis and how to derive Stoke’s law – Understand the Gibbs-Boltzmann equation – Distinguish diffusive from drift flux and write equations for each – Derive the Einstein relation – Estimate diffusion coefficients of molecules – Derive the diffusion equation from continuity and from microtrajectories – Understand and use binomial probability distributions | Textbook: 13.2 The diffusion equation 13.2.1 Diffusion by summing over microtrajectories 13.2.5 The Einstein relation Video Tutorial 1 “6 easy pieces“ Einstein’s 1905 paper on diffusion! |
| Week 3 Sept 24 (W) & Sept 26 (F) | Lecture 5 slides Lecture 5 slides, annotated Video recording Lect 5 Lecture 6 slides Lecture 6 slides, annotated Video recording Lect 6 | – Probability distributions of random walkers for a large number of steps, in 1D, 2D, 3D. – Diffusion time – Biopolymer configurations as random walks – Return probability and probability of contact formation Transcriptome (RNA) sequencing Single-cell RNA sequencing SMART-seq | Textbook: 8.2.1 Random walk combinatorics 2.1 (pp 44-48) Binomial probabilities 8.2.4 Return probability for random walks – dimension dependence Picelli & Sandberg Nature Protocols 2014 “Full-length RNA-seq from single cells using Smart-seq2” |
| Week 4 Oct 1 (W) & Oct 3 (F) | HW 2 and materials Lecture 7 slides Lecture 7 slides, annotated Video Recording Lect 7 Lecture 8 slides Lecture 8 slides, annotated Video Recording Lect 8 | – Force-extension relationships for stretched polymers – Scaling law for the size of a stretched polymer – Understand the boundary conditions of confined particles vs. confined polymer distributions – Confined polymers; DNA conformations in the nucleus | Textbook: 14.2.4 (pp 561-562) Self-avoiding polymers; Flory exponent 8.3.2 Force-extension curves |
| Week 5 Oct 8 (W) & Oct 10 (F) | Lecture 9 slides Lecture 9 slides, annotated Video Recording Lect 9 Lecture 10 slides Lecture 10 slides, annotated Video Recording Lect 10 (sorry no audio and not sure why; I’ll doublecheck the mic set-up next time) | – Fractal dimensions – Fractal dimension of a random walk – Einstein derivation of the diffusion equation – Fluorescence Recovery After – Photobleaching (FRAP); Fourier expansion solutions of the diffusion equation | Textbook: 13.2.3 Diffusion in the cell–FRAP Youtube tutorial on non-linear curve fitting (in Matlab, Mathematica, R, and Python) |
| Week 6 Oct 15 (W) & Oct 17 (F) | Lecture 11 slides Lecture 11 slides, annotated Video Recording Lect 11 Lecture 12 slides Lecture 12 slides, annotated Video Recording Lect 12 | – Entropy of mixing – Flory-Huggins theory – Solvents, polymer melts, expansion & collapse – Condensates in mixtures; liquid-liquid phase separation | Flory-Huggins theory (reference in Lect 11 slides) See literature refs in slides |
| Week 7 Oct 22 (W) & Oct 24 (F) | HW3 and materials: Data for prob 1. Lecture 13 slides Lecture 13 slides, annotated Video Recording Lect 13 Lecture 14 slides Lecture 14 slides, annotated Video Recording Lect 14 | DNA structure — the crumpled globule; Gene regulation. – Pol II binding to promoters; probability of binding | Polymer scaling laws Ideal behavior of polymers in melts Phase diagrams of polymers in solvents Textbook: 6.1.2: Statistical mechanics of gene expression: RNA polymerase and promoter 19.1, 19.2.1 pages 813-814: Gene regulation and activators |
| Week 8 Oct 29 (W) & Oct 31 (F) | Lecture 15 slides Lecture 15 slides, annotated Video Tutorial on Activators and Repressors of Transcription Video Recording Lect 15 Lecture 16 slides Lecture 16 slides, annotated Video Recording Lect 16 | – Tethered activators and gene regulation – Activators and repressors in gene regulation – The regulatory factor F_reg – Fold change (FC) – Incoherent feed-forward regulation | Textbook: 19.1: Chemical and informational organization in the cell 19.2.1: The molecular implementation of regulation: Promoters, activators, and repressors 19.2 (all subsections): Genetic Networks: Doing the right thing at the right time |
| Week 9 Nov 5 (W) & Nov 7 (F) | Lecture 17 slides Lecture 17 slides, annotated Video Recording Lect 17 Lecture 18 slides (This lecture was pptx only) Video Recording Lect 18 | – The Lac operon and DNA looping in regulation. – DNA looping in repression; Nucleosome remodeling in gene regulation – Phase separation in transcription; super-enhancers In-situ hybridization, fluorescence in-situ hybridization (FISH), and immunofluorescence | Textbook: 4.4.1, 4.4.3: The Lac Operon 19.2 DNA looping in repression 6.4.3: Beyond simple ligand receptor binding: The Hill function Term project instructions |
| Nov 10-12 | HW 4 and materials: Oehler et al. 1994 fig19.27.xlsx operator_dist_vs_repress.xlsx | READING BREAK | |
| Week 10 Nov 14 (F only) | Lecture 19 slides Lecture 19 slides, annotated Video Recording Lect 19 | – Elastic Properties of polymers and cellular components – Young’s modulus, curvature, minimum energy conformations – Minimum energy conformations | Textbook: 10.1, 10.2 Beams are everywhere: From flagella to the cytoskeleton; Geometry and energetics of beam deformation 10.1, 10.2: Geometry and energetics of beam deformation |
| Week 11 Nov 19 (W) & Nov 21 (F) | Lecture 20 slides Lecture 20 slides, annotated Video Recording Lect 20 Lecture 21 slides Lecture 21 slides, annotated Video Recording Lect 21 | – Persistence length of polymers – The worm-like chain – Chromatin and nucleosomes – Nucleosomes in gene regulation | Textbook: 8.2.2: Random Walks; Persistence length 8.2.3: The The Geography of Chromosomes 10.2.2: Persistence Length 10.4.3: Energetics of Nucleosome wrapping 19.2.6: Nucleosomes in gene regulatory architectures |
| Week 12 Nov 26 (W) & Nov 28 (F) | Lecture 22 slides Lecture 22 slides, annotated Video Recording Lect 22 Lecture 23 slides Lecture 23 slides, annotated Video Recording Lect 23 | – Nucleosome Remodelling in gene transcription – Cis-reg architectures in yeast – nucleosome positioning – MNase-seq; Apparent nucleosome periodicity – Reconciling nucleosome periodicity and the absence of phase transitions in 1D systems – Embryonic development in multicellular animals – Anterior-Posterior patterning; Hox genes and segmentation. | Textbook: 10.4.3: Nucleosome unwrapping thermodynamics 19.2.6: Nucleosomes in gene regulatory architectures 21.3.3: MNase-seq; DNA Sequencing Reveals Patterns of Nucleosome Occupancy on Genomes 20.2.3 Spatial regulation 20.2 Morphogen gradients; The French Flag model |
| Week 13 Dec 3 (W) & Dec 5 (F) | Lecture 24 slides Lecture 24 slides, annotated Video Recording Lect 24 Lecture 25 slides Lecture 25 slides, annotated Video Recording Lect 25 | – Spatial patterning, The French flag model, pattern fidelity – Regulation of genes by enhancers – Cooperative regulation of Hb by Bcd; precision in spatial expression patterns – The problem of developmental fidelity – The Jarzynski equality for non-equilibrium processes | Textbook: 19.2.6: Cooperativity in Bicoid enhancement of the Hunchback gene 20.2.1-3: The French Flag model and thresholding; Statistical mechanics of Bicoid activation Papers: Jarzynski PRL 1997 Crooks PRE 1999 |
| Scientist Interviews Final Term Project | Interview papers: Takahashi_Sugimoto Wang_Cottle_Ha Interviews: Takahashi Cottle | Extra topics: – Role of crowding in cellular environments – Genomic fluorescence in-Situ Hybridization (FISH) by CRISPR (eSpCas9) + helicase (Rep-X) (sgGOLDFISH). – Understand stability points in phase portraits; vector fields – Linear stability analysis for the genetic switch – Genetic oscillators – Ligand receptor binding in cell signaling – Turing patterns – Vertebral segment formation – Notch-delta signaling – Genome structure – Phylogenetic trees; evolutionary mechanism | 19.3.5: Genetic switches, natural and synthetic 19.4 Cell Signalling 20.3 Reaction-Diffusion and Spatial patterns 20.4 Somitogenesis 20.5 Lateral inhibition 21.2 Gene structure; multiple sequence alignment Genome Structure |