Biophysics II: bio435

Classical and statistical mechanics of molecular motors, cells and development. Understanding biological phenomena and complexity with physical techniques, models and concepts.

Updated: 20-Apr-2012

Course contents

a)Mathematics of water:
Literature for discussion 18-Jan-2012 (contd. 24-Jan-2012)
- (i) [purcell1977],
- (ii) [Chen&Springer1999]
Additional reading:
- Shapere & Wilzek (1989) Geometry of Self-Propulsion at Low Reynolds Numbers
- Bell Model of adhesion and detachment
b) Macromolecular crowding
Literature for discussion 06/07-Feb-2012
- McGuffee & Elcock (2010) Diffusion, crowding and protein stability in a dynamic molecular model of the bacterial cytoskeleton. PLoS Comp. Biol. Vol. 6, e1000694[PDF]
- Konopka MC et al. (2006) Crowding and confinement effects on protein diffusion in vivo. J Bacteriol. 2006 Sep;188(17):6115 - 6123.[PDF]
Additional reading:
- Minton (2006) How can biochemical reactions within cells differ from those in test-tubes? J.Cell.Sci.119:2863 [PDF]
- Gernot Guigas et al. (2007) The degree of macromolecular crowding in the cytoplasm and nucleoplasm of mammalian cells is conserved. FEBS Letters 581 (2007) 5094 - 5098 [PDF]
Dynamics of macromolecules: Molecular motors, Cytoskeleton, Mechanics of transcriptional regulation, DNA packaging, Protein folding.
- Molecular motors
  Bormuth et al. (2009). Protein friction limits diffusive and directed movement of kinesin motors on microtubules. Science 325, 870.[PDF]
- Brownian Ratchets
  Astumian D. (1997). Thermodynamics and Kinetics of a Brownian Motor. Science 276.[PDF] [Paper reading: 21 Mar 2012]
- 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]
Non-equilibrium approaches: This topic will be introduced and dove-tailed with the biological themes
Biophysics of neurons, muscle cells and stem cells
- Neurons: Special lecture (2h) on physics of nerve condition by Dr. Pranay Goel. 20-22 Feb 2012.
- Muscle cells: Actin-myosin systems
- Stem cells: Engler et al 2004
Tissue dynamics and Development
Literature review
Term paper Propose and defend a 1 year project in biophysics.
Lab

Lecture slides

Laboratory

Lab Pages

Crowding and enzyme kinetics
FRAP in bacteria
Measuring the effect of crowding on diffusive motility
Spatial patterns by diffusion and aggregation

A handy reference for lab-report writing

References

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 Stuart Newman
Mechanics of Motor Proteins and the Cytoskeleton- Jonathon Howard
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."

Practicalities

2h per week

Mon 0930-1030h

Wed 0930-1030h

Venue: C301

Coordinator

Dr. Chaitanya Athale- timings: Fri 2-3pm

Contributors

Dr. Roop Malik (TIFR, Mumbai) - 2 lectures
Time: 0930-1130h, Date: 25 Jan 2012, Location: Sai Trinity (room C-306 'bio-tutorial room)
Dr. Pranay Goel on "Neurons, membrane potential and nerve conduction physics"
Date: 22 and 27 Feb 2012, Location: C301, HR4 lecture theatre, IISER main campus.

Mid-Semester Exam: 03-Mar-2012

End-Semester Exam: 25-Apr-2012, Time: 1430-1730h (2:30-5:30pm)

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