Publications: Athale Lab

S. no.	Course code	Course name	Period taught	Objectives	Topics	Assesment Criteria	Pre-requisites	Suggested Reading
1	Bi3144/Bi6134	Cellular Biophysics 1	2025/08 to 2025/12	1) Scaling relations of cellular size, time and energy 2) Springs, rods and pendula applied to cell biology: simple models and their limits 3)Random walk polymers: DNA, proteins and cytoskeleton 4) Mechanics of biological membranes 5) Boltzmann statistics to connect energetics with the bulk-biochemistry. 6) Python programming to reconcile models and theory	Order of magnitude estimates and the value of quantification Mechanical forces and energetics: equilibrium approach to cells Mass, stiffness and the damping of proteins Thermal energy and relative energy scales Polymer mechanics Molecular motor stepping Membrane mechanics: bending and undulations Simplest models of cell shape Force spectroscopy of proteins and nucleic acids Cytoskeleton: Actin and microtubules Motor proteins Protein diffusion, ligand-receptor binding and effect of crowding Biomembrane mechanics Cell adhesion and migration Tutorials of computational exercises that complement theoretical concepts	40% End-Sem Examination 20% Mid-Sem Examination 40% Assignments, quizzes, paper reading and programming	Introductory Cell biology, Introductory Physics: both 1st year level	Nelson Philip: Biological Physics by Philip Nelson. [Edn 1 copies available in the library] Philips, Kondev, Theriot: Physical Biology of the Cell [Hard copies available in the library] Dill & Bromberg. Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics and Nanosceince. Garland Press. 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
2	Bi4233	Cellular Biophysics 2	2025/01 to 2025/05			40% End-Sem Examination 40 20% Mid-Sem Examination 40% Assignments, quizzes, paper reading and programming	Cellular biophysics 1 (Bi3144/6134)	Nelson Philip: Biological Physics by Philip Nelson. [Edn 1 copies available in the library] Philips, Kondev, Theriot: Physical Biology of the Cell [Hard copies available in the library] Dill & Bromberg. Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics and Nanosceince. Garland Press. 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

S. no.

Course code

Course name

Period taught

Objectives

Topics

Assesment Criteria

Pre-requisites

Suggested Reading

Bi3144/Bi6134

Cellular Biophysics 1

2025/08 to 2025/12

1) Scaling relations of cellular size, time and energy
2) Springs, rods and pendula applied to cell biology: simple models and their limits
3)Random walk polymers: DNA, proteins and cytoskeleton
4) Mechanics of biological membranes
5) Boltzmann statistics to connect energetics with the bulk-biochemistry.
6) Python programming to reconcile models and theory

Order of magnitude estimates and the value of quantification
Mechanical forces and energetics: equilibrium approach to cells
Mass, stiffness and the damping of proteins
Thermal energy and relative energy scales
Polymer mechanics
Molecular motor stepping
Membrane mechanics: bending and undulations
Simplest models of cell shape
Force spectroscopy of proteins and nucleic acids
Cytoskeleton: Actin and microtubules
Motor proteins
Protein diffusion, ligand-receptor binding and effect of crowding
Biomembrane mechanics
Cell adhesion and migration
Tutorials of computational exercises that complement theoretical concepts

40% End-Sem Examination
20% Mid-Sem Examination
40% Assignments, quizzes, paper reading and programming

Introductory Cell biology, Introductory Physics: both 1st year level

Nelson Philip: Biological Physics by Philip Nelson. [Edn 1 copies available in the library]
Philips, Kondev, Theriot: Physical Biology of the Cell [Hard copies available in the library]
Dill & Bromberg. Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics and Nanosceince. Garland Press.
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

Bi4233

Cellular Biophysics 2

2025/01 to 2025/05

40% End-Sem Examination 40
20% Mid-Sem Examination
40% Assignments, quizzes, paper reading and programming

Cellular biophysics 1 (Bi3144/6134)

Nelson Philip: Biological Physics by Philip Nelson. [Edn 1 copies available in the library]
Philips, Kondev, Theriot: Physical Biology of the Cell [Hard copies available in the library]
Dill & Bromberg. Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics and Nanosceince. Garland Press.
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

Cytoskeleton and Cell Shape (CyCelS) Lab

Teaching