| W | Theme | Ch. | Tue 10-16 | Wed 12-14 | Exercises | |
|---|---|---|---|---|---|---|
| 34 |
Introduction. Order from disorder. Statistical mechanics, ------------------------------------------------------ |
1,2 |
Lect 1, Notes ----------------------------------------------------------- |
Lect 2, diffusion,RandomWalks ----------------------------------------------------------- |
Your turn 1A, Prob 1.3, 2.2, 2.5 Random_walk_numerical |
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| 35 |
What's inside cells Brownian motion |
2,3 |
Cancelled |
Lect 3 |
Project 1: Active Passive walkers |
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| 36 |
Active and passive motion, low Reynolds world |
4,5 |
Lect 4, Luiza, Active matter Students: Purcell: Life at low Reynolds |
Project 1: Active Passive walkers | ||
| 37 | Entropy, temperature, free energy | 6 |
Lab: E coli experiment |
Lect 5, Biological examples diffusion, entropy, quizz | Project 1: Active Passive walkers | |
| 38 | Entropy, temperature, free energy | 6,7, 11.1,11.2 |
Lect 6, Osmotic pressure and osmotic flux. Problems 6.6, 6.7 |
Your turn 6A-I, Exercise 9 from Gaute |
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| 39 | Mechanobiology | Lect 8, Ion pumping, Physics of adherent cells, |
Lect 9, Physics of adherent cells, Fluorescence imaging, Notes and papers |
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| 40 |
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| 41 | Mechanobiology | Lect 10 Edna: "Single molecule talin stretching", quantitative imaging, Papers: Hu2016, Hu2017 |
Lect 11 From mechanobiology to Ising and Cellular Potts Models |
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| 42 | Cellular Potts Model and cell migration |
Lect 12 Alvaro: Lecture notes Alvaro: CPM Simulation project |
CPM |
Project 2: CPM and cell migration | ||
| 43 | Cellular Potts Model and cell migration |
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| 44 | Ultrasound and mechanobiology |
Lect 13, Bio-effects of ultrasound |
Seminar on US & mechanobiology |
Project 3: Ultrasound and mechanobiology | ||
| 45 |
Half of students not present Ions at membranes, membrane potentials to action potential |
11.1-2 12.1-2 |
Project 3: Ultrasound and mechanobiology | |||
| 46 |
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Lab, Thomas: Ultrasound experiment |
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| 47 | ||||||
| 48 |
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Curriculum FYS4715 Biological physics 2021
Philip Nelson "Biological Physics" chapters 1-7
Passive and active walkers
- Lab experiments, methods (microscopy & image analysis), results, discussion
- Random walk simulations
- Papers in detail: Langevin 1908, Purcell 1977
- Lecture notes
Mechanobiology
- Lecture notes (Dag & Edna)
- Papers (overview): DuFort 2011, Janmey 2011, Schwartz 2013 sec I-II, Hu2016, Hu2017
- Biological effects of ultrasound: lecture notes, group presentations and background (papers, simulations...) of presentation
- Maria and Karianne: Cooperativity in macromolecules (Nelson Ch 9), emphasis on presentation
Cellular Potts Model
- Lecture notes (Alvaro and Dag)
- Papers: Steinberg 2007, Chapter II.1 and II.2 in book Single-Cell-Based models in Biology and Medicine, Niculescu 2015
- Simulations, results and discussion of cell sorting and cell migration