All documents, labs and exercises in this plan are part of the curriculum if not otherwise stated.
Week plan
- Mon: Lecture and sometimes lab
- Thu: Lecture
W34 Introduction
- Book and papers
- Basic concepts: Heat, entropy, free energy, hydrophilic/phobic, membranes, protein folding,...
- Lectures
- Exercises: Nelson Yor turn 1A, Prob 1.3, 2.2, 2.5
W35 Passive and active walkers
- Book and papers
- Nelson: Ch. 4
- Einstein 1905 paper (background, not curriculum)
- Langevin 1908 paper (background, not curriculum)
- Notes on Physics of active and passive motion in biology
- Physics background:
- Nelson Ch. 3
- Probability and combinatorics, Lecture Fys2160: Tue 27 Aug
- Basic concepts: Diffusion, random walks, fluid friction
- Lectures:
- Lecture 2: Microscopy & image analysis
- Lecture 3: Image analysis, diffusion, fluid friction
- Lab: Brownian motion
- Exercises: Nelson Your Turn 4B, 4C, 4D, 4E, Numerical random walk
W36 Passive and active walkers
- Book and papers
- Nelson: Ch. 4 & 5
- Notes on Physics of active and passive motion in biology
- Basic concepts: Life at low Reynolds number
- Lectures:
- Lecture 4: Dimensional analysis, diffusion & friction
- Lecture 5:
- Lab: No
- Exercises: Nelson Your Turn 5 A-G
W37 Passive and active walkers
- Book and papers
- Basic concepts: Life at low Reynolds number, Active matter
- Lectures:
- Lecture 4: Students present Purcell's paper "Life at low Reynolds number"
- Lecture 5: Active matter
- Lab: No
- Exercises: Nelson Your Turn 5 A-G
W38 Passive and active walkers + Entropy
- Book and papers
- Basic concepts: Active matter, Viscek model
- Lab Monday: Viscek model simulations:
/studier/emner/matnat/fys/FYS4715/h24/ch3-5_motion/src/
- Lecture Thursday: Entropy
W39-43 Entropy, ions and membranes
- Book and papers
- Nelson: Ch. 6, 7, 11.1, 11.2,
- Notes on entropy
- Notes on processes at membranes
- Notes on transport through membranes
- Basic concepts: Entropy, free energy, osmotic force and flow, ions at membranes, Nernst potential, Donnan equilibrium, ion pumping, sodium anomaly, freezing cells,
- Exercise: Freezing cells
W43 Morphogenesis & mechanobiology
- Basic concepts: Active materials, self-organization, emergence, gastruloids / embryo models, light sheet microscopy, topological defects, glass / fluid states, quantitative phase imaging (QPI)
- Lecture Thursday 24 Oct:
W44 Morphogenesis & mechanobiology
- Papers and notes
- Basic concepts: mechanosensing, mechanotransduction, cytoskeleton, acto-myosin, cell-substrate adhesion
- Lectures:
- Monday: Basic concepts, mechanosensing, mechanotransduction
- Thursday part 1: Sections I-III of Physics of adherent cells
- Thursday part 2: Cellular Potts Model (CPM)
- Exercises: Read paper and notes.
W45 Morphogenesis & mechanobiology
- Papers and notes:
- Basic concepts: Differential adhesion
- Preparation: Install Morpheus SW and read papers!!
- Monday 12-16: "CPM lab": Cellular Potts Model (CPM)
- Thursday 12-14: Mechanobiology continued
- Sunday Nov 10: Deadline Report 2: Entropy ions and membranes
W46 Morphogenesis & mechanobiology
- Papers and notes: *
- Basic concepts:
- Lectures:
- Monday 14:15-16: Richard David Jun-Geet Ho: Building models of morphogenetic processes
- Thursday 12:15-13: Students present CPM results
- Thursday 13:15-14: Turing vs Wolpert
W47 Morphogenesis & mechanobiology
- Monday 12:15-16:00: Cell wet lab: epithelial monolayer dynamics
- Thursday 12:15-14:00: Students present analysis of epithelial monolayers
- Sunday: Deadline report 3: Morphogenesis and mechanobiology