Updates

• 25-Feb-2019 from 10-1200h: Mid semester exam in LHC201
• 13-Feb-2019: LAB02: The protocol has been uploaded for the Diffusion lab: Perrin's experiment.
• 07-Feb-2019: Quiz01: Fluid mechanics and life at low Reynolds numbers
• 31-Jan-2019: :LAB01: Reading and building: Testing the hand-powered centrifigue [ref: Bhamla et al. (2017) Nat. Biomed. Engg.]

This course, Biophysics II, will deal with molecules, cells and tissues in the contest of out of equilibrium processes.

We will begin with a detailed treatment of the one molecule that makes up the largest single population in biological systems- water. Given than most biological systems are in fact out of equilibrium, this course will touch upon some of the most recent theoretical and experimental approaches to understand the out of equilibrium aspects of biophysics. Nerve, muscle and stem-cells will be chosen for special attention as case studies for integration of the hierarchies of molecules and cells that appear to work so flawlessly in our macroscopic world from a biophysics perspective. Research paper reading will highlight case studies of the successful application of physics biological problems.

Continuous assessment will be through:

• Research paper reading
• Assignments
• Labs

1. Concepts in fluid dynamics as they apply to cellular scale life
2. Diffusion & Macromolecular crowding
3. Dynamics of macromolecules: Cytoskeleton
4. Molecular motors and Brownian Ratchets: Rate equation paradigm
5. Embryogenesis and the role of reaction diffusion patterns
6. Mechanics and development

Research paper reading assignments

1. Reynolds Number[24 Jan 2019]: Purcell 1977 Life at Low Reynolds Numbers. The famous reprint of a paper that appeared in a book "The Physics of our World"based on a talk given by E.M. Purcell at a Symposium in honour of Victor Weisskopf.
2. Centrifugation principles [31-Jan-2019]: Investigate the principles of cell-centrifugation by building one. We will follow the procedure described by Bhamla et al. (Manu Prakash's lab in Stanford) to assemble and test the "toy centrifuge", by constrasting the result against a motorized lab-centrifuge and a crank-power centrifuge. READING:Bhamla et al. (2017) Hand-powered ultralow-cost paper centrifuge. Nat. Biomed. Engg. 1: 0009. Basic protocol- assemble the centrifuge using the top lid of a 90x15 mm petri dish, assemble the harness using nylon fishing thread and mount the sample in burner-fused capillary tubes (TLC). Compare Hematocrit %age. Document your findings in a 1-page report to be uploaded in the GoogleClassroom.
3. Diffusion and measuring it: Conrad W. Mullineaux, Anja Nenninger, Nicola Ray, and Colin Robinson (2006) Diffusion of Green Fluorescent Protein in Three Cell Environments in Escherichia Coli. J. Bact. Vol. 188, No. 10, p. 3442- 3448 [PDF]
4. Crowding: [??-??-2019] McGuffee & Elcock (2010) Diffusion, crowding and protein stability in a dynamic molecular model of the bacterial cytoskeleton. PLoS Comp. Biol. Vol. 6, e1000694[PDF]
5. Brownian Ratchets [Paper reading: ??-??-2019] Astumian D. (1997). Thermodynamics and Kinetics of a Brownian Motor. Science 276.[PDF]
6. Protein folding Minton, A. P. (2000). Effect of a concentrated 'inert' macromolecular cosolute on the stability of a globular protein with respect to denaturation by heat and by chaotropes: a statistical-thermodynamic model. Biophys. J. 78, 101-109.[PDF]
7. Molecular motors: Bormuth et al. (2009). Protein friction limits diffusive and directed movement of kinesin motors on microtubules. Science 325, 870.[PDF] and supplementary material
8. Tissue mechanics: G Forgacs, R A Foty, Y Shafrir, and M S Steinberg (1998)Viscoelastic properties of living embryonic tissues: a quantitative study. Biophys J. 1998 May; 74(5): 2227-2234.
9. Stem cells: Engler et al 2004 The role of stiffness in stem cell differentiation.

Assignments

• Assignments will be announced on the google-classroom site.

Laboratory protocols

1. Building a paper centrifuge [31-Jan-2019] for hematocrit estimation: Based on the paper by Bhamla et al. (2017) The lab will involve critically evaluating the description of the device, claims made in the paper and attempting to reproduce the result- namely cell separation in 1.5 min. [LAB02-PROTOCOL][Python notebook for fitting]
2. Measuring diffusion (Perrin's experiment) [13-Feb-2019] [LAB01-PROTOCOL]
   • Date/Time of lab: 13 February 2019 @0940h
   • Submission date/time: 14-02-2019 (in class)
   • Python code for [1D Gaussian fitting]

1. Physical Biology of the Cell- Philips, Kondev, Theriot
2. Biological Physics- Philip Nelson
3. Mechanics of the Cell- David Boal
4. Biological Physics of the Developing Embryo. Gabor Forgacs and Stuart Newman
5. Mechanics of Motor Proteins and the Cytoskeleton- Jonathon Howard
6. Journals:
   • Physical Biology "Physical Biology publishes research on the quantitative characterization and understanding of biological systems at different levels of complexity."
   • Biophysical Journal "Biophysical Journal is the leading international journal for original research in molecular, cellular, and systems biophysics."
   • Soft Matter: Royal Society of Chemistry journal "Where physics meets chemistry meets biology..."