Teaching

Semester
Course name
Description
Course content
2024 Fall (Monsoon) Aug-Nov Cellular Biophysics 1: Most of the material will be shared through GoogleClassrooms. In addition a web page with content can also be referred to. This is a course for 3-4yr BS-MS students, iPhD and PhD students. Those wishing to audit or listen in should speak to me in advance.

Office Hours: WED 15-1600h, Room 316, 2nd floor Biology Wing, Research Block
  1. Growth, form and size: Galileo, Dárcy Thompson and living systems
  2. Applying classical mechanics to cellular components: linear elasticity
  3. Fluid drag: life in water
  4. Cells as material: viscoelasticity
  5. Membrane biophysics: shape, size and flexibility
  6. Ligand-Receptor systems: Boltzmann formalism
  7. Random walk model: polymer physics of DNA and proteins
  8. Embryogenesis and pattern formation
2024 July onwards (8 weeks) MOOC: Cellular Biophysics: a framework for quantitative biology [ONLINE] An online, free course as part of SWAYAM (स्वयं) hosted by the Ministry of Education (MHRD) Govt of India, NPTEL (National Programme on Technology Enhanced Learning) and IIT Madras. Week-wise schedule:

  1. Week 1: Fluid dynamics of cellular scale life
  2. Week 2: Diffusion and crowding
  3. Week 3: Cytoskeletal dynamics
  4. Week 4: Molecular motors and Brownian Ratchets
  5. Week 5: Rate equations in cells: gene interactions
  6. Week 6: Noise
  7. Week 7: Models of embryogenesis
  8. Week 8: Mechanics in embryogenesis
2023 Fall (Monsoon) Aug-Dec Cellular Biophysics 1 This is a course for 3-4yr BS-MS students, iPhD and PhD students. Those wishing to audit or listen in should speak to me in advance.

Office Hours: FRIDAY 15-1600h, Room 316, 2nd floor Biology Wing, Research Block
  1. Why are things they size they are? from allometry to mechanics
  2. Elasticity and Beam bending
  3. Viscoelasticity
  4. Membrane biophysics
  5. Boltzmann statistics of cells and molecules
  6. Random walk model polymer models of DNA and proteins
  7. Biophysics of embryogenesis and pattern formation
2023 July onwards (8 weeks) MOOC: Cellular Biophysics: a framework for quantitative biology An online, free course as part of SWAYAM (स्वयं) hosted by the Ministry of Education (MHRD) Govt of India, NPTEL (National Programme on Technology Enhanced Learning) and IIT Madras. Platform hosting is through Google Inc. USA and Persistent Systems Ltd. India Week-wise schedule:

  1. Week 1: Concepts in fluid dynamics as they apply to cellular scale life
  2. Week 2: Diffusion & Macromolecular crowding
  3. Week 3: Dynamics of macromolecules: Cytoskeleton
  4. Week 4: Molecular motors and Brownian Ratchets
  5. Week 5: The rate equation paradigm and genetic networks
  6. Week 6: Noise in biological systems
  7. Week 7: Turing patterns in embryogenesis
  8. Week 8: Mechanics in embryogenesis and Future directions
2023 Spring (Winter) Jan-May Cellular Biophysics 2 We will touch upon some of the most recent theoretical and experimental approaches to understand the out of equilibrium aspects of biophysics. The integration of the hierarchies of molecules and cells that appear to work so flawlessly in our macroscopic world will be addressed from a biophysics perspective. Research paper reading will highlight case studies.
  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)
2022 Fall (Monsoon) Cellular Biophysics 1 (BI3144/6134) This is a course for 3rd and 4th year BS-MS students, intPhD and PhD students. Pre-requisites for BS-MS students are the existing coursework of years 1&2. For PhD/intPhD students, a 12th standard level Maths, interest in learning programming (no prior experience required) and 1st year B.Sc. level physics.
Evaluation: continuous (50%) and exam formats (50%). Lectures, assignments (incl. programming assignments), in class tasks and quizzes.
  1. The role of scale in biology,
  2. mechanics of cells,
  3. statistical properties of cellular material,
  4. random walk model of diffusion,
  5. polymer model of biomolecules,
  6. cell mechanics

    7. and

  7. developmental pattern formation
2022 Fall (Monsoon) NPTEL course NOC22_BT32: Cellular Biophysics: a framework for quantitative biology Bsc, MSc students studying Physics or Biochem, Cell-MolBio, Biotechnology
  1. Size- and time-scales
  2. Classical mechanics: springs and beams
  3. Statistical mechanics: stochasticity and randomness, Boltzmann statistics
  4. Polymer mechanics and DNA
  5. Membrane mechanics
  6. Developmental biophysics: pattern formation, phyllotaxy and morphogen gradients
2021 Fall (Monsoon) BI3144/6134: Cellular Biophysics 1: This is a course for 3-4 year BS-MS students, iPhD and PhD students. No pre-requisites. Biology level 2-3 year B.S./B.Sc., Physics level 1st year BS/B.Sc. and interest in programming (prior experience is not required). Lectures, assignments (incl. programming assignments), in class tasks and quizzes. Evaluation: continuous (60%) and exam formats (40%).
Due to the continued pandemic and closure of in-person teaching, all classes will be virtual. I will meet you once a week via google classroom, while the remaining 2 lectures per week will be recorded. Email, messageboards and phone-ins are all being used to make up for the reduced means of communication.		 Contents in brief: The role of scale in biology, mechanics of cells, statistical properties of cellular material, random walk model of diffusion, polymer model of biomolecules, cell mechanics and migration. Material will be posted on the course website and GoogleClassroom
2021 Spring (Vasant) IBB Biophysics of the Cytoskeleton A five-lecture series on the mechanics and dynamics of the cytoskeleton and motor proteins.
2020 Monsoon Bio315: Cellular Biophysics 1 Lectures, assignments (incl. programming assignments), in class tasks and quizzes. Evaluation: continuous and exam formats.
Due to the pandemic teaching will be virtual. All material will be online and shared via the web, google classroom, virtual class discussions and emails.		 Contents in brief: The role of scale in biology, mechanics of cells, statistical properties of cellular material, random walk model of diffusion, polymer model of biomolecules, cell mechanics and migration
Material will be posted on the course website and GoogleClassroom
2020 Spring/Summer Cytoskeletal dynamics and mechanics, IBB Pune University Lectures and reading material Mechanics and Dynamics of the cytoskeleton. Experimental techniques and mathematical models used to understand them. [LECTURE NOTES]
2019 Monsoon Bio315: Cellular Biophysics 1 Lectures, assignments (incl. programming assignments), in class tasks and quizzes. Evaluation: continuous and exam formats. Contents in brief: The role of scale in biology, mechanics of cells, statistical properties of cellular material, random walk model of diffusion, polymer model of biomolecules, cell mechanics and migration
Material will be posted on the course website and GoogleClassroom
2019 Winter (25 Feb to 2 Mar 2019) BIO122: Introduction to Synthetic Biology The Module on SynthBio BIO122 [materials and method and outcomes] Location: LHC303, Time: 0900-1200h This is an introduction to synthetic biology through a computers-only lab.
2019 Winter (02 Jan to 30 Apr 2019) BIO435: Cellular Biophysics 2 The course website of BIO435 [course-outline, announcements, assignments and reading material] This course will deal with the approaches taken to deal with out of equilibrium and active processes at a cellular scale. In that sense, it continues from where BIO322 cellular biophysics 1 left off, at equilibrium systems. More information on the course can be seen on the course website.
2018 Monsoon (18-22 Sept 2018) Blood smear and RBC count lab Slides and other information about the lab- including a form to post your statistics The additional statistics are being collected as a long-term study in the variability observed. This 2 part laboratory is based on (a) a gold-standard technique of used in pathology labs for cell-identification on the basis of morphology and (b) on a fundamental statistical property of cell counting (or counting any discrete event that is probabilistic)
2018 Monsoon (Aug-Dec) Bio315: Cellular Biophysics Lectures, assignments (incl. programming assignments), in class tasks and quizzes. Performance in class, on assignments and in exams will be used to evaluate your performance continuously and in the conventional exam format.
[Course Website + Google Classroom]		 We will start by understanding the role of scale and proceed with Applying the classical and statistical mechanics to biological systems at the cellular scale. We will demonstrate the utility of applying the reasoning of physics to cellular scale phenomena through models, data analysis and some programming tasks.
The course will follow content based on a few textbooks and more up-to date research papers where necessary.

  1. Phillips, Kondev, Theriot: PBOC
  2. Nelson, P. Biological Physics
  3. Berg Random Walks in Biology

Material will be posted on the course website and GoogleClassroom
2017 Fall/Monsoon Bio322: Biophysics 1: Introduction to physical biology of the cell. Lectures, assignments (incl. programming assignments), in class tasks and quizzes. Performance in class, on assignments and in exams will be used to evaluate your performance continuously and in the conventional exam format.
[Course Website + Google Classroom]		 We will start by understanding the role of scale and proceed with Applying the classical and statistical mechanics to biological systems at the cellular scale. We will demonstrate the utility of applying the reasoning of physics to cellular scale phenomena through models, data analysis and some programming tasks.
The course will follow content based on a few textbooks and more up-to date research papers where necessary.

  • Phillips, Kondev, Theriot: PBOC
  • Nelson, P. Biological Physics
  • Berg Random Walks in Biology

Material will be posted on the Course Website and GoogleClassroom
2017 Fall/Monsoon First year biology lab: Blood smear and RBC count Lab Introduction to the think smear preparation of blood smear and RBC counting
thinsmear protocol
2017 Summer Indian Society of Developmental Biology (InSDB) Biennial Meeting 2017, IISER Pune– Workshop Details of 2017 wintlab here.
Image analysis of time-series data: C. Athale. & A. Chaphalkar. TA’s: N. Khetan and Y. Jawale.		 Ref.: Data: Mark Terasaki (1998) Imaging of Echinoderm Fertilization. Mol Biol Cell. 1998 Jul; 9(7): 1609–1612.
Algorithms: ImageJ macro language guide
2017 Winter (Spring) BIO413/MTH427 On the kinetics approach to polymerization, multimerization and biochemical and gene regulation. Ref: “A primer on mathematical models in biology” by Lee Segel and Leah Edelstein-Keshet.
Further reading:

  1. A. E. Carlsson (2005) The Effect of Branching on the Critical Concentration and Average Filament Length of Actin. Biophys J. 89(1): 130–140.
  2. A. E. Carlsson, M. A. Wear, and J. A. Cooper (2004) End versus Side Branching by Arp2/3 Complex. Biophys J. 86(2): 1074–1081.
2017 Winter (Spring) Cloning a gene and expressing it virtually BIO122: Expressing a gene virtually We will use the BioBricks standard method for simulating the cloning of a gene and taking care that the regulatory sequences are intact. The materials (plasmid sequences) for the exercise are here. Protocol can be had here.
2016 Monsoon (Fall) Thin smear and RBC count Lab121- first year labs Preparing a sample of your own blood and using morphological and staining (colour) reactions, to distinguish between WBC cell types is the first aim of the experiment. Additionally, to understand the basic quantification of cells, you will perform an RBC count on a sample.
2016 Monsoon (Fall) Bio322: Biophysics 1 (Introd. to Physical Biology) Biophysics 1 course [Introduction to Physical Biology] Using the power of physics to unravel simple problems in Biology- at the cellular scale. Topics covered include order of magnitude estimates (‘Street Fighting Mathematics’ a la Mahajan), classical mechanics (springs, rods, pendula etc.) and introductory statistical mechanics. All used to understand biological complexity.
Summer School 2016 Physics of Biological Patterns: Reading material Short lecture and movie screening “Cherche Toujour” Physical Principles of Biological Patterns: A brief walk through some human-made and naturally ocurring patterns, ending with a discussion of some mathematical and physical laws that constrain biological pattern formation.
2016 Vasant (Spring) Bio435: Biophysics 2 (Introd. to Physical Biology) Biophysics 2 course [ Physical Biology of dynamical living systems] Out of equilibrium biophysics.
2015 Monsoon (Fall) Bio322: Biophysics 1 (Introd. to Physical Biology) Biophysics 1 course [Introduction to Physical Biology] Using the power of physics to unravel simple problems in Biology- at the cellular scale. We develop on standard results in classical mechanics (springs, rods, pendula etc.) for biological insight, and introduce statistical mechanics as a means of dealing with biological complexity. We intersperse this with a constant discussion of the number-scales and experimental techniques used to test these theoretical pradigms.
2015 Monsoon (Fall) Bio121- Lab 3 Blood smear and RBC count You will perform the ‘gold standard’ in blood tests- the blood smear. Together with Dr. K. Karmodiya (working on malarial molecular genetics) we will discuss how to interpret these smears and take an RBC count of a blood sample. We will end with calculations, that reveal an aspect of measurement error in quantitative biology.
2014 Fall/Monsoon Bio322: Biophysics 1 (Introd. to Physical Biology) Biophysics 1 course [Introduction to Physical Biology] Introducing methods from classical and statistical mechanics to address biological problems, mostly at the cellular scale. The approaches are based on equilibrium assumptions. The course will also involve addressing biophysical techniques and their principles.
2014 Fall/Monsoon 1st year Bio-Lab Blood smear [First year biology lab5] Learning how to make a blood smear, identify multiple white blood cell (WBC) types and perform a red blood cell (RBC) count.
2014 Spring/Vasant Bio491: Literature review in the biosciences Literature review course [Searching and reviewing the literature] Reading and writing a literature review. The methods, pitfalls and care to be taken while reviewing biological literature.
2013 Fall/Monsoon Bio322: Biophysics I Biophysics [Physical Biology of the Cell I] Equilibrium Physics applied to biology of molecules, cells and tissues. Biophysical techniques- hands on and theory. This course is a pre-requisite for the Biophysics II (Bio435) conducted in the Spring/Vasant (Jan-May) semester.
2013 Fall/Monsoon 1st year Bio-Lab Blood smear [First year biology lab3] Learning how to make a blood smear, identify multiple white blood cell (WBC) types and perform a red blood cell (RBC) count.
2013 Spring/Vasant Bio435: Biophysics II Biophysics II Classical and statistical mechanics of molecular motors, cells and development.
2012 Fall/Monsoon Bio322: Biophysics I Biophysics [Physical Biology of the Cell I] Physical biology of molecules, cells and tissues. Biophysical techniques- hands on and theory. This course is a pre-requisite for the Biophysics II (Physical Biology of the Cell II) conducted in the Spring (Jan-May) semester.
2012 Spring/Vasant Bio435: Biophysics II Biophysics II Classical and statistical mechanics of molecular motors, cells and development.
2011 Monsoon/Winter Bio322: Biophysics I Biophysics I Physical biology of molecules, cells and tissues.
2011 Spring/Vasant Reaction diffusion gradients in morphogenesis Reaction diffusion models in morphogenesis An overview of models and quantitative experiments
2011 Spring/Vasant Idc102: Scientific computing 2011-Jan to Apr Random numbers, RNGs and tests for randomness 2011-Jan to Apr
2011 Spring/Vasant Bio435: BiophysicsII 2011-Jan to Apr Molecular, cellular and tissue scale biophysics, experimental techniques, practical demonstrations, computer-practicals, out of equilibrium statistical mechanics and biology Link
2010 Monsoon/Winter Bio322: Biophysics Bio 322 2010-Aug to Nov Physical biology from molecular to cellular scale, experimental techniques, practicals Link
2010 Spring Bio202: Introduction to Systems Biology 2010-04-23 Modeling in systems biology
2010 Spring 2010-04-16: Models in development
2010 Spring 2010-04-15: Theories of signal transduction
2010 Spring 2010-04-12: Chaos and self organization
2010 Spring Bio490/Mth470 (IDC) Mathematical Modelling in the Sciences 2010-04-12 modelling diffusion in cells Examples and case-studies of methods
2010 Spring 2010-04-06
2010 Spring 2010-04-05
2010 Spring Bio491 Modern topics in biology Zipped file of all papers Literature survey of current topics in modern biological research
2009 Fall (Monsoon) Bio311 Adv. Cell Biology 2009-10-29: [PDF] Introduction to cytoskeleton
2009 Fall (Monsoon) 2009-11-02: [PDF] Cytoskeleton-Cytoskeletal dynamics
2009-11-03: [PDF] Cytoskeleton-Cytoskeletal motors
2009-11-05: Paper on contractile actin network and its role in mitosis [Lenart2005] and and a paper on the physics of contractile actin networks [bathe2008].
2009 Fall (Monsoon) Bio311 Adv. Cell Biology 2009-10-04 [PDF] Diffusion in cells
2009 Fall (Monsoon) 2009-10-05 [PDF] Role of diffusion in cells

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