[IISER-p] [Instructor's webpage]

Bio322: Biophysics (Introduction to Physical Biology)

[ver. 2017]

Physical biology of molecules, cells and tissues at equilibrium.

Applying the very successful methods of thinking from classical and statistical-mechanics in physics to unravel problems in biology at the cellular scale. We use standard results from classical mechanics (springs, rods, pendula etc.) and examine how far we can use them for biological systems. We spend some time with Random Walk models and Boltzmann Statistics, and use these to derive theoretical results that connect energetics with the bulk-biochemistry. We intersperse this with a constant discussion of
  1. the number-scales
  2. experimental techniques
to test these validity of these theoretical pradigms. The emphasis is on usable theoretical models.

At the end of the course you should be able to understand and evaluate sensible theoretical models of cell-biological systems from a biophysics perspective.

Intructors:

Primary instructor: Dr. Chaitanya Athale (Div. of Biology @iiserpune)

Guest lectures: 2-3 lectures by Dr. Shiva Patil (Div. of Physics @iiserpune)

Assessment: Internal assesment (50%) includes evaluation of assignments, paper-reading and quizzes. Exam based assesment carries the remaining 50% of the score.

Course-Coordinator email: bio322 at the rat e student s dot ii serpune do t a c d o t in

You can also in case of urgent issues email me at cathale at the rate of iiser pune dot academia dot in.

News

  • Class on 18-September 2017 @1510h (3:10pm): Please come prepared to discuss the remaining 2 papers:
    1. You et al. (2006) FRET mapping
    2. Ryder et al. (2006) EMSA
    BRING a laptop or some electronic medium, so you can read the papers. The class will involve discussing these 2 papers uploaded on the Google-classroom site. Your contribution will be assessed in terms of the following:
    • (a) Explaining the experimental method
    • (b) Explaining the principle and equation(s) used to estimae Kd
    • (c) Explaining the strenghts/weaknesses of the method
  • Tue class: Summary of the semester
  • Topics covered until 19-Sep-2017 will be considered as material for the mid-semester exam

 Representative image: cells, springs, networks

Course Contents

  1. Introduction
  2. Dimensional analysis and order of magnitude estimates: developing a feeling for the numbers
  3. Energy of life: thermodynamics and entropy
  4. Minimization and optimality of physical systems: translating the biology
  5. Statistical mechanics and entropy: understanding molecular configuration
  6. Random walks and biopolymers
  7. Diffusion and capture
  8. Classical mechanics of beams and springs applied to DNA, proteins and membranes
  9. Cell mechanics and tissue shape
  10. Biophysical techniques (together with the relevant topics: reading)
    • Light
    • Measuring forces
    • Movement of cells and analysis
    • Bio-molecular kinetics
  11. Assignments: calculations, (python) computations and reading

Lecture notes

Assignments

The assignments page [link] contains all the assignmnts and their solutions as the deadline passes.


Scores will be scaled as y = e − x / 3 , (i.e. y= exp(-x/3)), where x=delay in days after date of submission, and y=score.

Policy on and membranes plagiarism [pdf]: A document of what is acceptable usage of existing resources. It particularly deals with what IS and IS NOT acceptable use of published, online, wikipedia, journal-article and other sources of information, figures, graphs and words.

Lecture notes (TBA)

Meeting times for the instructor

Wed 1600-1630h, Main Building, Biology Block, 2nd floor

Any other slot must be pre-arranged by appointment if you want to be sure to meet me.

For course and assignment related queries contact bio322 at the rate students stop iiserpune stop ac dot indiain

Course Reading

  • Nelson Philip: Biological Physics [free pdf] by Philip Nelson.
  • Philips, Kondev, Theriot: Physical Biology of the Cell [link]
  • Dill & Bromberg. Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics and Nanosceince. Garland Press. [link to publisher]
  • Berg Howard: Random Walks in Biology [link]
  • Sanjoy Mahajan:Order of Magnitude Physics [pdf]- a full course at Caltech
  • Thomas M. Nordlund (2011) Quantitative Understanding of Biosystems: An Introduction to Biophysics CRC Press.

Schedule

  • Quiz1
  • Quiz2
  • Mid-sem Exams
  • Quiz3
  • Quiz4
  • End-sem Exams

Additional reading

Statistical mechanics formalism applied to multi-molecular systems

Systems as diverse as ligand-receptor binding (e.g. Hemoglobin and O2), ion channels and protein dynamics and genetic evolution are reviewed in some of these following papers:
  1. Garcia et al. 2011 Thermodynamics of biological processes. 492:27
  2. Yoshida T, Dembo M. 1990 A thermodynamic model of hemoglobin suitable for physiological applications. Am. J Physiol. 1990 Mar;258(3 Pt 1):C563-77.
  3. Marzen S, Garcia HG, Phillips R. 2013 Statistical mechanics of Monod-Wyman-Changeux (MWC) models. J Mol Biol. 2013 May 13;425(9):1433-60. doi: 10.1016/j.jmb.2013.03.013. Epub 2013 Mar 14.
  4. Keller et al. 1986 Sodium Channels in Planar Lipid Bilayers Channel Gating Kinetics ofPurified Sodium Channels Modified by Batrachotoxin J. Gen. Physiol. 88:1
  5. Sella and Hirsh 2005 The application of statistical physics to evolutionary biology PNAS USA 102:9541
Historical accounts of Linus Pauling's work in biology
Newton Rules Biology by Pennycuick

Course calendar

Last updated: 18-Sep-2017