Week 35
- Answers from students about Biological physics.
- Lecture notes: What's inside cells
Week 36:
- Lecture notes: Random walks, diffusion, Brownian motion
- Lecture (from FYS2160) on different models for diffusion
- Introduction to diffusion and random walks
- First Matlab exercises. Run the live script step-wise to get familiar with the syntax. We will make similar image analysis live scripts during the lectures.
- Papers on Brownian Motion
- Diffusion exercise (RW and molecular dynamics: self- and mutual diffusion)
- Brownian motion lab exercise
- After receiving reports I redid the experiments and wrote a "lab journal/internal report"
Week 37: Life at low Reynolds number
- E. M. Purcell: Life at low Reynolds number (1977)
- H.C. Berg & E.M. Purcell: Physics of chemisorption (1977)
- H.C. Berg: A Physicist Looks at Bacterial Chemotaxis (1988)
Week 38: Entropic forces at work
Monday: PPT and handwritten notes
Wednesday: handwritten notes
Week 39: Entropic forces at work, why cells are microscopic
Monday: Paper: Why cells are microscopic, handwritten notes
Wednesday: Exercise
Week 40 & 41: Midterm break
Week 42: Cellular Potts model (CPM)
Led by by Alvaro K?hn-Luque
Title: Modelling and simulation of multicellular systems using the cellular Potts model
In this part of the course the students will learn how to model and simulate multicellular and multiscale systems using the cellular Potts model and the software Morpheus: https://morpheus.gitlab.io/ It consists of a 90 minutes lecture followed by two hands-on sessions of 80 minutes each.
Lecture 14 Oct, 8:30-10:00: Modelling multicellular systems using the cellular Potts model.Hands-on sessions 16 Oct 8:30-12:00: Getting Started with Morpheus. Simulation and analysis of simple models.
Pre-Assignment:
1) Before the lecture, students should read at least Chapter II.2: The Cellular Potts Model and Biophysical Properties of Cells, Tissues and Morphogenesis
in this book: https://www.springer.com/gp/book/9783764381011 (free download from UiO)
I attach to this mail the whole section II of the book, which is all about the cellular Potts model, in case students have time and special interest in the topic.
2) For the practical sessions, students should install the software Morpheus (https://morpheus.gitlab.io/#download) and Gnuplot (https://sourceforge.net/projects/gnuplot/files/gnuplot/) in their own laptops. In case of problems, contact Alvaro K?hn-Luque (alvaro.kohn-luque@medisin.uio.no)
1. Cell sorting
2. Tumor growth (xml file)
3. Networks (movie)
Links about the CPM:
- Original 1992 CPM paper by Graner and Glacier in PRL: https://journals.aps.org/prl/pdf/10.1103/PhysRevLett.69.2013
- 1997 paper by Hogeweg extending the CPM to account for chemotaxis and applied to Dictyostelium social life: https://www.sciencedirect.com/science/article/pii/S0022519396902374
- Book including full section about CPM (free download from UiO). In particular, the first two chapters of that section (Magnetization to morphogenesis and CPM and Biophysical properties of cells) are specially interesting readings for a course in biophysics. https://www.springer.com/gp/book/9783764381011
- Morpheus software: https://morpheus.gitlab.io/, https://academic.oup.com/bioinformatics/article/30/9/1331/234757
- Morpheus tutorial by Walter de Back: https://gitlab.com/wdeback/Workshop-Morpheus/blob/master/tutorial-intro/README.md
- Introductory slides to multicellular models and Morpheus: https://gitlab.com/wdeback/Workshop-Morpheus/tree/master/slides
- CompuCell3D software: http://www.compucell3d.org/FrontPage, https://www.sciencedirect.com/science/article/pii/B9780123884039000138
- Cellular Potts modeling of complex multicellular behaviors
in tissue morphogenesis - Cellular Potts modeling of tumor growth, tumor invasion,
and tumor evolution
Week 43 & 44: Chemical forces and self assembly + finish CPM project
Lecture notes. Hemoglobin models. Recap on chemical potential. Recap on Gibbs factor and more on hemoglobin
Week 45: Ions at membranes, membrane potentials to action potential
Week 46: Calcium imaging
Review about the two-photon technique in neuroscience:
https://www.sciencedirect.com/science/article/pii/S0896627306004119
https://www.cell.com/neuron/comments/S0896-6273(12)00172-9
About the most used calcium sensor GCaMP 6:
https://www.nature.com/articles/nature12354
Monday: Lecture on fluorescence
Wednesday: Experiment
Week 47: Simulating nerve impulses
Led by Geir Halnes
Monday: Lecture
Wednesday: Simulation. Zip file with python code. Exercise.pdf & Python code
Week 48:
Monday: Repetition and exam projects given
Thursday: Exam