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Course10210609360 lectures

Cellular Biophysics: a Framework for Quantitative Biology

Prof. Chaitanya A.Athale · IISER Pune

Start with lecture 1 At NPTEL

About

Given than most biological systems are in fact out of equilibrium, this course will touch upon some of the most recent theoretical and experimental approaches to understand the out of equilibrium aspects of biophysics. To this end we make a thermodynamics detour to answer the question posed by Schroedinger: “What is life?” We then consider a diversity of cell types to ask how the hierarchies of molecules and cells integrate. The question of how stochastic processes lead to deterministic outcomes will be briefly touched upon. Research paper reading will highlight case studies of the successful application of physics biological problems.

INTENDED-AUDIENCE: 3rd year B.Sc, 1-2 year M.Sc. students in Biology and Physics

Prerequisites: BSc/BE/BTech 2nd year; BSc level knowledge of Classical mechanics; MSc level knowledge of Cell and molecular biology; MSc level knowledge of Biochemistry; Basic python programmingINDUSTRY-SUPPORT: Microscopy companies, Centrifuge companies, Spectroscopy companies

Lectures

Week 1

  1. Introduction - Part 01 YouTube
  2. Introduction - Part 02 YouTube
  3. Introduction - Part 03 YouTube
  4. Solids vs Fluids YouTube
  5. Viscosity YouTube
  6. Measuring Viscosity YouTube
  7. Tutorial - Part 01 YouTube
  8. Tutorial - Part 02 YouTube
  9. Tutorial - Part 03 YouTube

Week 2

  1. Water: Macromolecular Nature & Hydrophobicity, Structure of Ice, Pauling-Bernal-Fowler Model of Water YouTube
  2. Entropy and Probability of Water Conformations, Boltzmann Law of Entropy YouTube
  3. Reynolds Number YouTube
  4. Tutorial - Part 01 YouTube
  5. Tutorial - Part 02 YouTube
  6. Tutorial - Part 03 YouTube
  7. Hagen-Poisuielle Equation YouTube
  8. Tutorial - Part 04 YouTube

Week 3

  1. Sedimentation and Centrifugation - Part 1 YouTube
  2. Sedimentation and Centrifugation - Part 2 YouTube
  3. Blood Centrifugation YouTube
  4. Review: Paperfuge for Hematology YouTube
  5. Biology by Numbers YouTube
  6. Biology by Numbers: Bomb Yield Solved YouTube
  7. Order of Magnitude Estimates and Approximations YouTube
  8. Physical Basis of Life YouTube
  9. Approximating Cellular and Molecular Size Scales YouTube

Week 4

  1. Quantifying DNA and Chromatin YouTube
  2. Protein Abundance and Spacing YouTube
  3. Model Gene YouTube
  4. Cell-Biology by Numbers YouTube
  5. Experimental Techniques to Quantify Cells YouTube
  6. Time-Scales in Cells YouTube
  7. Energy Scale YouTube
  8. Energy and Thermodynamics of Life - Part: 01 YouTube

Week 5

  1. Energy and Thermodynamics of Life - Part: 02 YouTube
  2. Energy and Life- Osmotic Engine YouTube
  3. Energy and Life- Interconversion of Energy YouTube
  4. Random Walk Statistics, Stoke-Einstein - Part 01 YouTube
  5. Random Walk Statistics, Stoke-Einstein - Part 02 YouTube
  6. Demonstration of Diffusion of Micron Sized Particles YouTube

Week 6

  1. Macromolecular Crowding - Part 01 YouTube
  2. Macromolecular Crowding - Part 02 YouTube
  3. Cytoskeleton YouTube
  4. Beam Theory Applied to Biopolymer YouTube
  5. Understanding Chromosomes as Statistical Polymers - Part 01 YouTube
  6. Understanding Chromosomes as Statistical Polymers - Part 02 YouTube

Week 7

  1. Brownian Ratchets and Molecular Motors YouTube
  2. Polymerization Dynamics - Part 1 YouTube
  3. Polymerization Dynamics - Part 2 YouTube
  4. Polymerization Dynamics - Part 3 YouTube
  5. Python Programming - Part 1 YouTube
  6. Python Programming - Part 2 YouTube
  7. Python Programming - Part 3 YouTube

Week 8

  1. Introduction to Membrane Mechanics YouTube
  2. Membrane Deformation YouTube
  3. Developmental Pattern Formation YouTube
  4. Turing Model YouTube
  5. Phyllotaxis - Part 1 YouTube
  6. Phyllotaxis - Part 2 YouTube
  7. Phyllotaxis - Part 3 YouTube

Syllabus and materials

At NPTEL, as the course publishes them.

Credits and licence

Institution
IISER Pune
Department
Biotechnology
Teacher
Prof. Chaitanya A.Athale
Level
Graduate
Language
English
Subjects
Biology
Source
NPTEL
Licence
CC BY-NC-SA, as NPTEL states it. Non-commercial use only. NPTEL's terms
Attribution
NPTEL states: "Distributed under Creative Commons Attribution-ShareAlike / CC BY - NC - SA", beside a BY-NC-SA badge. Coordinated by IIT Madras.
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