Stanford University - Winter 2013
It is well accepted that mechanistic/physical thinking can solve many mysteries in biology. This course intends to develop basic science to understand inner workings of biological systems at molecular and cellular levels using engineering principles. We will stress on learning to ask fundamental questions about biological systems in a quantitative way. While mastering new analytical tools introduced, we also expect students to develop physical intuition for the small world of living things.
Tentative Course Schedule:
Week 1 (1/08, 1/10)
What does Physical Biology mean?
Quantitative biology with numbers, “What, when and how many” of biological systems?
Measurements in Biology. What is lacking. How to read/process experimental data?
Tree of life, diversity in biological systems. Basic common principles of life as we know it. Information in biological systems, Central dogma.
“Life as we know it”
How to break living systems in quantitative numbers.
Exercise/in-class experiment: Molecular motors, Estimates of cytoplasmic streaming in Chara carolina
Reading: PBoC (Chapter 1)
Week 2 (1/15, 1/17)
Refresher of relevant physics concepts utilized throughout the course. Length/Time scales relevant to biological systems. Non-dimensional Analysis/Scaling Laws. Street fighting mathematics. Street fighting physics.
Entropy. Energy landscapes, equilibrium and non-equilibrium systems, Free energy. Thermodynamics review. Randomness, probability overview, Basic ideas from statistical mechanics. Work done in biological systems.
Exercise: Distinguish living and non-living systems. How does this connect with equilibrium systems.
Reading: PBoC (Chapter 5)
Week 3 (1/22, 1/24)
Statistical mechanics applied to macromolecules. Micro-macro states. Boltzman distribution. Examples - Origin of osmotic pressure, Ligand-receptor binding.
Reading: PBoC (Chapter 6)
Week 4 (1/29,1/31)
Polymer physics overview. Conformations of biological molecules, Examples for change in conformation (DNA, RNA), Scaling laws from polymer physics. Entropic springs.
Exercise: Probability of Knotting in a rope.
Reading: PBoC (Chapter 8)
Week 5 (2/05, 2/07)
Exercise: Biological ratchets.
Random walks, Diffusion, diffusion in confined volumes, Fick’s law.
Examples from experiments.
Selected Reading: Random Walks in Biology (Berg)
Class field trip!!!
We will be visiting several single molecule measurement setups across 4-5 labs at Stanford (one setup per group). This will be scheduled later during the term. You get to see how much technology/engineering it really takes to watch footsteps of molecules of life.
Week 6 (2/12, 2/14)
Multi-state systems, persistence of state
Molecular Crowding in biological systems, Confinement of biological molecules (example)
Week 7 (2/19, 2/21)
Exercise: soap bubbles.
Interfacial systems, surface energies
Biological membranes, effective two-dimension viscosity, diffusion in a membrane.
Phase transition in biological systems.
Reading: PBoC (Chapter 11)
Week 8 (2/26, 2/28)
Dynamic self-assembly, partition functions.
Designing macro-molecular self-assembling systems at atomistic scale.
Self assembly in biology.
Mathematics of viral capsid assembly.
Exercise/In class experiment: Self assembly (with exercise)
Week 9 (3/05, 3/07)
Exercise: Building scientific instruments..
Review of techniques in physical biochemistry. New Techniques for measurements in biological systems - design exercise in class. Combining physical models of biological systems with measurement techniques.
Open problems in measurement.
Week 10 (3/12, 3/14)
Exercise: Ciliary synchronization (life in a drop)
From Macromolecules to macro-machines. Emergent systems.
Ciliary motors - how cilia and flagella works. Flow of information. Control mechanisms?
Building a cilia. Macro-molecular assembly.
Open problems in physical biology. Where to go next.
Review of the class.
Take home final
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