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Physics of Biological Systems

Physics of Biological Systems. Instructor: Prof. Mithun Mitra, Department of Physics, IIT Bombay. The application of physical principles to biological systems is an exciting and rapidly evolving field of research. Methods of equilibrium and non-equilibrium statistical physics, stochastic processes, nonlinear dynamics and polymer physics, among others have helped understand the guiding principles of a variety of biological processes. In this course, we will attempt to provide an introduction to the physics of biological systems using theoretical tools, with examples from diverse areas of biology such as pattern formation, low Reynolds number flows, cytoskeleton and motors and transport in cells, gene expression and chromatin organisation, among others. (from nptel.ac.in)

Lecture 01 - Introduction

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Lecture 01 - Introduction

Lecture 02 - DNA Packing and Structure

Lecture 03 - Shape and Function

Lecture 04 - Numbers and Sizes

Lecture 05 - Spatial Scales and System Variation

Lecture 06 - Timescales in Biology

Lecture 07 - Random Walks and Passive Diffusion

Lecture 08 - Random Walks to Model Biology

Lecture 09 - Derivation of FRAP Equations

Lecture 10 - Drift-Diffusion Equations

Lecture 11 - Solutions of the Drift-Diffusion Equations

Lecture 12 - The Cell Signaling Problem

Lecture 13 - Cell Signaling and Capture Probability of Absorbing Sphere

Lecture 14 - Capture Probability of Reflecting Sphere

Lecture 15 - Mean Capture Time

Lecture 16 - Introduction to Fluids, Viscosity and Reynolds Number

Lecture 17 - Introduction to the Navier-Stokes Equation

Lecture 18 - Understanding Reynolds Number

Lecture 19 - Life at Low Reynolds Number

Lecture 20 - Various Phenomena at Low Reynolds Number

Lecture 21 - Bacterial Flagellar Motion

Lecture 22 - Rotating Flagellum

Lecture 23 - Energy and Equilibrium

Lecture 24 - Binding Problems

Lecture 25 - Transcription and Translation

Lecture 26 - Internal States of Macromolecules

Lecture 27 - Protein Modification Problem

Lecture 28 - Haemoglobin-Oxygen Binding Problem

Lecture 29 - Freely Jointed Polymer Model

Lecture 30 - Entropic Strings and Persistence Length

Lecture 31 - Freely Rotating Chain Model and Radius of Gyration

Lecture 32 - The Hierarchical Chromatin Packing Model

Lecture 33 - FISH and DNA Looping

Lecture 34 - Nucleosomes as Barriers, Hi-C, and Contact Probabilities

Lecture 35 - Deriving the Full Force Extension Curve

Lecture 36 - Random Walk Models for Proteins

Lecture 37 - Hydrophobic Polar Protein Model

Lecture 38 - Diffusion in Crowded Environments

Lecture 39 - Depletion Interactions

Lecture 40 - Examples and Implications of Depletion Interactions

Lecture 41 - Introduction to Biological Dynamics

Lecture 42 - Introduction to Rate Equations

Lecture 43 - Separation of Timescales in Enzyme Kinetics

Lecture 44 - Structure and Treadmilling of Actin and Microtubules

Lecture 45 - Average Length of Polymers in Equilibrium

Lecture 46 - Growth Rate of Polymers

Lecture 47 - Dynamic Treadmilling in Microtubules

Lecture 48 - Introduction to Molecular Motors

Lecture 49 - Force Generation by Molecular Motors

Lecture 50 - Models of Motor Motion

Lecture 51 - Molecular Motors

Lecture 52 - Free Energies of Motor for Stepping

Lecture 53 - Two State Models

Lecture 54 - Cooperative Transport of Cargo

Lecture 55 - Cytoskeleton as a Motor

Lecture 56 - Translocation Ratchet

Lecture 57 - Spatial Pattern in Biology

Lecture 58 - Some Common Spatial Patterns in Biology

Lecture 59 - Reaction Diffusion and Spatial Pattern

Lecture 60 - Pattern Formation in Reaction Diffusion System with Stability

Lecture 61 - Condition for Destabilization in Pattern Formation

Lecture 62 - Schnakenberg Kinetics