[IISER-p] [Instructor's webpage]

Bio315: Cellular Biophysics 1

[ver.2]

Physical biology of molecules, cells and tissues.

News

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 the following two aspects:
  1. the number-scales
  2. experimental techniques

Since most of our discussions will revolve around theory or standard models, the discussion will allow us to understand how one can seek to employ these theories as usable theoretical models by experimental validation or just reasoning through.

The phenomena that will be examined are:
  • Force spectroscopy of proteins and nucleic acids Cytoskeleton: Actin and microtubules Motor proteins
  • Protein diffusion, ligand-receptor binding and crowding effects Biomembrane mechanics
  • Red blood cells
  • Cell adhesion and migration
The models that will be invoked will build upon concepts from classical and statistical mechanics. At the end of the course the student will be expected to understand the following models in their application to cellular biophysics:
  • Mechanical forces Mass, stiffness and the damping of proteins
  • Thermal forces
  • Polymer mechanics
  • Molecular motor stepping
  • Membrane bending and vesicle formation
  • Simplest models of cell shape
Tutorials will involve a few computational and experimental exercises to complement theoretical concepts.

Paper reading of biophysical techniques will be evaluated in class.

Additional problem based assignments will intersperse the course. Regular quizzes will be conducted after the conclusion of substantial material. They will be announced and surprise, open- and closed-book.

Continuous assessment will constitute half the assessment, the other half being traditional exams.

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. The course will be complementary to Cell Biology (based on the book by B. Alberts et al. Mol. Biol. Cell).

Intructors:

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

Guest lectures: TBA

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.

Representative image: cells, springs, networks

Course Contents

  1. Introduction: aims of the course. Using order of magnitude estimates to develop a feeling for the numbers
  2. Minimization and optimality
  3. Mechanics: elasticity, viscosity and springs in cellular systems
  4. Rods, cantilevers and the basis for elasticity & cytoskeleton
  5. Membrane mechanics
  6. Statistical mechanics and entropy
  7. Diffusion and biological fluid mechanics
  8. Polymer mechanics
  9. Simple cells and their mechanobiology

Lecture notes (TBA)

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


Meeting times for the instructor


Weekly meedings: WED 1630-1730h in my office, biology wing, 2nd floor, central atrium. A meeting outside this 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 by Philip Nelson. [library copies available]
  • 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.
  • C. Ross Ethier & Craig A. Simmons (2007) Introductory Biomechanics : From Cells to Organisms. Cambridge Univ. Press [website]

Schedule

  • Quiz1:
  • Quiz2:
  • Mid-sem Exams: 24-Sep-2019 10-1200h LHC103
  • Quiz3
  • Quiz4
  • End-sem Exams

Additional reading

Order of magnitude estimates & numbers in cell biology

Book: John Tyler Bonner "Why size matters"

Book: Ron Milo and Rob (2015) Phillips Cell Biology by the Numbers. CRC Press.

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

Mechanics in Biology

  1. David Boal (2002) Mechanics of the Cell. Cambrdige Univ. Press
  2. Pennycuick C..J. (1992) Newton Rules Biology: Physical Approach to Biological Problems

Viscoelasticity

  1. Lakes R. (2010) Viscoelastic Materials. Cambridge Univ. Press.

Course calendar


Last updated: 06-Sep-2019