Cellular Biophysics II (Bio435): Out of equilibrium
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
Continuous assessment will be through:
A handy reference for lab-report
- Concepts in fluid dynamics as they apply to cellular scale
- Diffusion & Macromolecular crowding
- Dynamics of macromolecules: Cytoskeleton
- Molecular motors and Brownian Ratchets: Rate equation paradigm
- Embryogenesis and the role of reaction diffusion patterns
- Mechanics and development
Research paper reading assignments
- 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.
- 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.
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.
- 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]
- Crowding: [??-??-2019] McGuffee & Elcock (2010)
Diffusion, crowding and protein stability in a dynamic molecular
model of the bacterial cytoskeleton. PLoS Comp. Biol. Vol. 6,
- Brownian Ratchets [Paper reading: ??-??-2019] Astumian D.
(1997). Thermodynamics and Kinetics of a Brownian Motor. Science
- 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,
- 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
- 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.
- Stem cells: Engler et al 2004 The role of stiffness in stem
- Assignments will be announced on the google-classroom site.
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]
- 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
Plagiarism and fair use policy
For Bio435 and all submissions [PDF document]
- Physical Biology of the Cell- Philips, Kondev, Theriot
- Biological Physics- Philip Nelson
- Mechanics of the Cell- David Boal
- Biological Physics of the Developing Embryo. Gabor Forgacs and
- Mechanics of Motor Proteins and the Cytoskeleton- Jonathon
Biology "Physical Biology publishes research on the
quantitative characterization and understanding of biological
systems at different levels of complexity."
Journal "Biophysical Journal is the leading international
journal for original research in molecular, cellular, and
Matter: Royal Society of Chemistry journal "Where physics
meets chemistry meets biology..."
Additional watching (video-lectures)
2h per week
Dr. Chaitanya Athale-
Timings to meet coordinator: Thu 3-4pm
Mid-Semester Exam: 25 Feb-2019 at 1000h, ROOM: LHC201
Last updated: 18-Feb-2019 @0930h