Course Details
Subject {L-T-P / C} : PH5102 : Biophysics { 3-0-0 / 3}
Subject Nature : Theory
Coordinator : Suryanarayan Dash
Syllabus
| Module 1 : |
(8 hrs) Biomolecular interactions and dynamics. Introduction to Biophysics, spatial and temporal scales. steric, van der Waals, Coulomb and hydrophobic interactions, protein structure and folding, molecular dynamics, Brownian dynamics
|
| Module 2 : |
(6 hrs) Diffusion. Life at low Reynol’ds number, random walks and diffusion, methods to measure the diffusion coefficient: single particle tracking, fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy, diffusion and cell signaling
|
| Module 3 : |
(8 hrs) Polymers. Introduction, freely jointed chain, freely rotating chain, Gaussian chain, Universality and Self-similarity, Scaling analysis
|
| Module 4 : |
(4 hrs) Understanding Chemical Kinetics for two-state system, From kinetics to thermodynamics, Michelis-Menten reaction
|
| Module 5 : |
(6 hrs) Equilibrium thermodynamics and statistical Mechanics. Laws of thermodynamics and entropy principle, microcanonical, canonical, grand canonical ensemble, ideal gas, phase transitions
|
| Module 6 : |
(3 hours) Fluid flows in biology, viscosity and Navier Stokes equation |
Course Objective
| 1 . |
To have a basic understanding of the protein structural hierarchy and forces governing biomolecular assembly and dynamics |
| 2 . |
To learn about diffusion in dilute and cellular environments |
| 3 . |
To understand the physical properties of long peptide chains |
| 4 . |
To understand the kinetics of biomolecular reactions |
| 5 . |
To understand why biological systems are marginally stable due to enthalpy-entropy balance |
| 6 . |
To learn about flow of fluids in biological systems |
Course Outcome
| 1 . |
At the end of course, students will be able to:
|
| 2 . |
CO2: Explain how cellular environment can influence diffusion of a tracer particle |
| 3 . |
CO3: Explain structural and dynamical characteristics of long peptide chains |
| 4 . |
CO4: Calculate biomolecular reaction rates and free energy changes |
| 5 . |
CO5: Analyze experimental and theoretical investigation biomolecular events |
Essential Reading
| 1 . |
Rob Phillips, Jane Kondev, Julie Theriot, Hernan Garcia, , Physical Biology of the Cell,, Garland Science; 2nd Edition (2012) |
| 2 . |
Philip Nelson, W.H.Freeman & Co Ltd, Biological Physics, Revised edition (2013) |
Supplementary Reading
| 1 . |
Ron Milo, Rob Phillips, Garland Science, Cell Biology by the Numbers, First edition (2015) |
| 2 . |
Howard C. Berg, Random Walks in Biology, Princeton University Press; Revised edition (1993) |
Journal and Conferences
| 1 . |