CyCels Lab logo

CyCelS Lab

Teaching

BS-MS theory courses BS-MS lab courses Workshops

BS-MS theory courses

Year Semester Course code Course title Instructor, Guest lecturers, Teaching Assts. Learning goals Reading list Link
2025 August (Monsoon) Bi3144/6134 Cellular Biophysics 1 Instructor: Prof. Chaitanya A. Athale, Guest lect: NIL, TA: Prachi Negi
  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
  • Phillips et al. Physical Biology of the cell, Publ.: Garland Sciences
  • Nelson, P. Biological Physics
 [TBA] Most material is posted on the google classroom
2025 July to September BT60 (NPTEL) NOC: Cellular Biophysics: A Framework for Quantitative Biology, IISER Pune Instructor: Prof. Chaitanya A. Athale, Guest lect: NIL, TA: Kajal Singh, Prachi Negi 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 to problems.
  • Phillips et al. Physical Biology of the cell, Publ.: Garland Sciences
  • Nelson, P. Biological Physics
 https://nptel.ac.in/courses/102106093 (registration free, proctored exams and certificate on payment).
2025 January (Vasant) Bi4233 Cellular Biophysics 2 Instructor: Prof. Chaitanya A. Athale, Guest lect: NIL, TA: NIL
  • Phillips, Kondev, Theriot. Physical Biology of the Cell. 2nd Edition, Garland Press
  • Philip Nelson Biological Physics: Energy Information, Life, Chiliagon Science
  • Howard Berg Random Walks in Biology, Princeton Universities Press
  • Jonathon Howard Mechanics of Motor Proteins and the Cytoskeleton, Oxford Universities Press
  • Vogel Life in Moving Fluids, Princeton Universities Press
  • Physical Models of Living System by Philip Nelson, WH Freeman
 [TBA] Most material is posted on the google classroom
2024 July to September NOC24-BT43 (NPTEL) Cellular Biophysics: A Framework for Quantitative Biology, IISER Pune Instructor: Prof. Chaitanya A. Athale, Guest lect: NIL, TA: Kajal Singh, Prachi Negi 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 to problems.
  • Phillips et al. Physical Biology of the cell, Publ.: Garland Sciences
  • Nelson, P. Biological Physics
 BT43 (registration free, proctored exams and certificate on payment).
2024 August (Monsoon) Bi3144/6134 Cellular Biophysics 1 Instructor: Prof. Chaitanya A. Athale, Guest lect: NIL, TA: NIL
  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
  • Phillips et al. Physical Biology of the cell, Publ.: Garland Sciences
  • Nelson, P. Biological Physics
 [TBA] Most material is posted on the google classroom
2023 Jul to Oct noc23_bt39 Biophysics: A Framework For Quantitative Biology Instructor: Prof. Chaitanya A. Athale, Guest lect: NIL, TA: Mahima Gautam 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 to problems.
  • Phillips et al. Physical Biology of the cell, Publ.: Garland Sciences
  • Nelson, P. Biological Physics
 Registration free, proctored exams and certificate on payment (NPTEL online certificate- NOC)
2023 Aug (Monsoon) Bi3144/6134 Cellular Biophysics 1 Instructor: Prof. Chaitanya A. Athale, Guest lect: NIL, TA: NIL
  1. Dimensions, measurements, orders of magnitude and biophysics at the beach
  2. Thermodynamics: Life, energy, viruses and cells
  3. Elasticity, minimisation and equilibrium
  4. Beam mechanics applied to the cytoskeleton
  5. Elasticity applied to DNA, proteins and chromatin
  6. Newtons law of fluids and viscosity
  7. Viscoelasticity
  8. Membrane mechanics
  9. Random walk theory of biopolymers
  10. Statistical mechanics, entropy and how viruses highjack cells
  11. Integrated mechanical properties of a cell
  12. Experimental techniques
  • Philip Nelson: Biological Physics (3 library copies)
  • Rob Phillips, Jane Kondev, Julie Theriot: Physical Biology of the Cell (~10 library copies)
  • Biology by Numbers http://book.bionumbers.org/
  • Thomas M. Nordlund: An Introduction to Biophysics
  • Howard Berg: Random Walks in Biology (3 library copies)
  • Ethier & Simmons: Introductory Biomechanics
 [TBA] Most material is posted on the google classroom
2023 Jan (Vasant) Bi4233/6623 Cellular Biophysics 2 Instructor: Prof. Chaitanya A. Athale, Guest lect: NIL, TA: NIL
  1. Concepts in fluid dynamics, cell mechanics and cell motility (6)
  2. Diffusion and Macromolecular crowding (5)
  3. Dynamics of macromolecules: Cytoskeleton (6)
  4. Molecular motors and Brownian Ratchets: Rate equation paradigm (2)
  5. Embryogenesis and the role of reaction diffusion patterns (3)
  6. Mechanics and development (2)
  7. Labs and paper reading (6)
  • Phillips, Kondev, Theriot. Physical Biology of the Cell. 2nd Edition, Garland Press
  • Philip Nelson Biological Physics: Energy Information, Life, Chiliagon Science
  • Howard Berg Random Walks in Biology, Princeton Universities Press
  • Jonathon Howard Mechanics of Motor Proteins and the Cytoskeleton, Oxford Universities Press
  • Vogel Life in Moving Fluids, Princeton Universities Press
  • Physical Models of Living System by Philip Nelson, WH Freeman
 [TBA] Most material is posted on the google classroom
2022 Aug (Monsoon) Bi3144/6134 Cellular Biophysics 1 Instructor: Prof. Chaitanya A. Athale, Guest lect: NIL, TA: NIL
  1. Order of magnitude estimates and the value of quantification (2)
  2. Mechanical forces and energetics: equilibrium approach to cells (2)
  3. Mass, stiffness and the damping of proteins (1)
  4. Thermal energy and relative energy scales (3)
  5. Polymer mechanics (7)
  6. Molecular motor stepping (2)
  7. Membrane mechanics: bending and undulations (3)
  8. Simplest models of cell shape (3)
  9. Force spectroscopy of proteins and nucleic acids (2) Cytoskeleton: Actin and microtubules (3)
  10. Motor proteins (2)
  11. Protein diffusion, ligand-receptor binding and effect of crowding (3)
  12. Biomembrane mechanics (3) Cell adhesion and migration (2)
  13. Tutorials of computational exercises that complement theoretical concepts (4)
  • Philip Nelson: Biological Physics (3 library copies)
  • Rob Phillips, Jane Kondev, Julie Theriot: Physical Biology of the Cell (~10 library copies)
  • Biology by Numbers http://book.bionumbers.org/
  • Thomas M. Nordlund: An Introduction to Biophysics
  • Howard Berg: Random Walks in Biology (3 library copies)
  • Ethier & Simmons: Introductory Biomechanics
 [TBA] Most material is posted on the google classroom
2021 Aug (Monsoon) Bi3144/6134 Cellular Biophysics 1 Instructor: Prof. Chaitanya A. Athale, Guest lect: NIL, TA: NIL
  1. Order of magnitude estimates and the value of quantification (2)
  2. Mechanical forces and energetics: equilibrium approach to cells (2)
  3. Mass, stiffness and the damping of proteins (1)
  4. Thermal energy and relative energy scales (3)
  5. Polymer mechanics (7)
  6. Molecular motor stepping (2)
  7. Membrane mechanics: bending and undulations (3)
  8. Simplest models of cell shape (3)
  9. Force spectroscopy of proteins and nucleic acids (2) Cytoskeleton: Actin and microtubules (3)
  10. Motor proteins (2)
  11. Protein diffusion, ligand-receptor binding and effect of crowding (3)
  12. Biomembrane mechanics (3) Cell adhesion and migration (2)
  13. Tutorials of computational exercises that complement theoretical concepts (4)
  • Philip Nelson: Biological Physics (3 library copies)
  • Rob Phillips, Jane Kondev, Julie Theriot: Physical Biology of the Cell (~10 library copies)
  • Biology by Numbers http://book.bionumbers.org/
  • Thomas M. Nordlund: An Introduction to Biophysics
  • Howard Berg: Random Walks in Biology (3 library copies)
  • Ethier & Simmons: Introductory Biomechanics
 [TBA] Most material is posted on the google classroom
2021 Jan (Vasant) Bio435 Cellular Biophysics 2: Out of equilibrium systems Instructor: Prof. Chaitanya A. Athale, Guest lect: Dr. Anita Jannasch, Uni Tuebingen, Germany, TA: NIL
  1. Concepts in fluid dynamics, cell mechanics and cell motility (6)
  2. Diffusion & Macromolecular crowding (5)
  3. Dynamics of macromolecules: Cytoskeleton (6)
  4. Molecular motors and Brownian Ratchets: Rate equation paradigm (2)
  5. Embryogenesis and the role of reaction diffusion patterns (3)
  6. Mechanics and development (2)
  7. Labs and paper reading (6)
  • Phillips, Kondev, Theriot. Physical Biology of the Cell. 2nd Edition, Garland Press
  • Philip Nelson Biological Physics: Energy Information, Life, Chiliagon Science
  • Howard Berg Random Walks in Biology, Princeton Universities Press
  • Jonathon Howard Mechanics of Motor Proteins and the Cytoskeleton, Oxford Universities Press
  • Vogel Life in Moving Fluids, Princeton Universities Press
  • Physical Models of Living System by Philip Nelson, WH Freeman
 [TBA] Most material is posted on the google classroom
    {lockdown}
2020 Aug (Monsoon) Bi315/606 Cellular Biophysics 1 Instructor: Prof. Chaitanya A. Athale, Guest lect: Dr. Aadish Dani, TIFR, TA: NIL
  1. Order of magnitude estimates and the value of quantification (2)
  2. Mechanical forces and energetics: equilibrium approach to cells (2)
  3. Mass, stiffness and the damping of proteins (1)
  4. Thermal energy and relative energy scales (3)
  5. Polymer mechanics (7)
  6. Molecular motor stepping (2)
  7. Membrane mechanics: bending and undulations (3)
  8. Simplest models of cell shape (3)
  9. Force spectroscopy of proteins and nucleic acids (2) Cytoskeleton: Actin and microtubules (3)
  10. Motor proteins (2)
  11. Protein diffusion, ligand-receptor binding and effect of crowding (3)
  12. Biomembrane mechanics (3) Cell adhesion and migration (2)
  13. Tutorials of computational exercises that complement theoretical concepts (4)
  • Philip Nelson: Biological Physics (3 library copies)
  • Rob Phillips, Jane Kondev, Julie Theriot: Physical Biology of the Cell (~10 library copies)
  • Biology by Numbers http://book.bionumbers.org/
  • Thomas M. Nordlund: An Introduction to Biophysics
  • Howard Berg: Random Walks in Biology (3 library copies)
  • Ethier & Simmons: Introductory Biomechanics
 WebPage
2020 Aug IBB, Pune University Biophysics (guest lect) Guest lectures
  1. Cytoskeletal mechanics
  2. Cytoskeletal dynamics and polymerization
  • Lee A. Segel and Leah Edelstein-Keshet (2013) A Primer on Mathematical Models in Biology Author(s):
  • Rob Phillips, Jane Kondev, Julie Theriot: Physical Biology of the Cell (~10 library copies)
 [TBA]
    {lockdown}
2019 Aug (Monsoon)
    {lockdown}
 Bio315 Cellular Biophysics 2: Out of equilibrium systems Instructor: Prof. Chaitanya A. Athale, Guest lect: Dr. Anita Jannasch, Uni Tuebingen, Germany, TA: NIL
  1. Concepts in fluid dynamics, cell mechanics and cell motility (6)
  2. Diffusion & Macromolecular crowding (5)
  3. Dynamics of macromolecules: Cytoskeleton (6)
  4. Molecular motors and Brownian Ratchets: Rate equation paradigm (2)
  5. Embryogenesis and the role of reaction diffusion patterns (3)
  6. Mechanics and development (2)
  7. Labs and paper reading (6)
  • Phillips, Kondev, Theriot. Physical Biology of the Cell. 2nd Edition, Garland Press
  • Philip Nelson Biological Physics: Energy Information, Life, Chiliagon Science
  • Howard Berg Random Walks in Biology, Princeton Universities Press
  • Jonathon Howard Mechanics of Motor Proteins and the Cytoskeleton, Oxford Universities Press
  • Vogel Life in Moving Fluids, Princeton Universities Press
  • Physical Models of Living System by Philip Nelson, WH Freeman
 [TBA] Most material is posted on the google classroom
    {lockdown}
2018 Aug (Monsoon) Bio315 Cellular Biophysics 2: Out of equilibrium systems Instructor: Prof. Chaitanya A. Athale, Guest lect: Dr. Anita Jannasch, Uni Tuebingen, Germany, TA: NIL
  1. Concepts in fluid dynamics, cell mechanics and cell motility (6)
  2. Diffusion & Macromolecular crowding (5)
  3. Dynamics of macromolecules: Cytoskeleton (6)
  4. Molecular motors and Brownian Ratchets: Rate equation paradigm (2)
  5. Embryogenesis and the role of reaction diffusion patterns (3)
  6. Mechanics and development (2)
  7. Labs and paper reading (6)
  • Phillips, Kondev, Theriot. Physical Biology of the Cell. 2nd Edition, Garland Press
  • Philip Nelson Biological Physics: Energy Information, Life, Chiliagon Science
  • Howard Berg Random Walks in Biology, Princeton Universities Press
  • Jonathon Howard Mechanics of Motor Proteins and the Cytoskeleton, Oxford Universities Press
  • Vogel Life in Moving Fluids, Princeton Universities Press
  • Physical Models of Living System by Philip Nelson, WH Freeman
 [TBA]
2010-2018: Every year Bio315 in Aug-Semester and alternate years Bio435 in the Jan-Semester.

Labs/Practical courses

Year Semester Course code Course title Instructor, Guest lecturers, Teaching Assts. Learning goals Reading list Link
2019 Jan (Vasant) Bio122 Designing a Gene for Expression using Modular Components Instructor: Chaitanya A. Athale
  1. Practical understanding of the concept of a gene
  2. To use sequence editing software
  3. Understand the role of the regulatory steps in gene expression
  4. Simulate the first step in recombinant protein expression
  5. Design a test at the level of the construct to know if the construct is successful
  6. Represent the result of the design
  • Kuldell, Natalie., Bernstein, Rachel., Ingram, Karen., Hart, Kathryn M (2015) BioBuilder: Synthetic Biology in the Lab. United States: O'Reilly Media, Incorporated, 
 [TBA]

Workshops

Year Workshop theme Module Instructor Outline Materials
Last updated: 14-Oct-2025