Teaching
January7
| Semester | Course | Lectures/Labs | Description |
|---|---|---|---|
| 2023 Spring (Vasant) | Bi4233 (formerly Bio435): Biophysics 2 | Biophysics 2 course website [ Physical Biology of dynamical living systems] | Fluid dynamics and cell-swimming, Random walks and diffusion, LAB: Measuring diffusion, Macromolecular crowding, Rate equations and polymerization, LAB: Enzyme kinetics in crowded environments, Brownian ratchets and molecular motors, Cell migration & Developmental Mechanics. You will also be reading & reviewing 5 papers. |
| 2022 Fall (Monsoon) | BI3144/6134: Cellular Biophysics 1 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. | Lectures, assignments (incl. programming assignments), in class tasks and quizzes. Evaluation: continuous (60%) and exam formats (40%). I will use Google-Classroom to post assignments. Unless otherwise stated all assignments are to be electronically submitted. |
Course contents:
and |
| 2022 Fall (Monsoon) | NOC22_BT32: Cellular Biophysics: a framework for quantitative biology This is an NPTEL course for physics students in undergraduate (BSc) and 1st year MSc courses interested in topics at the interface AND BSc and MSc students in BIOLOGY/BIOTECHNOLOGY/BIOCHEMISTRY interested in learning about the insights that can be obtaned from this inter-disciplinary subject. | All material is posted on the NPTEL website and you need to register (FREE) to follow the course. It is an 8 week long course. | Course contents:
|
| 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. | 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.
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.
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. |
| 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:
|
| 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 |
| 2010-04-22 | |||
| 2010-04-16: Models in development | |||
| 2010-04-15: Theories of signal transduction | |||
| 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 |
| 2010-04-06 | |||
| 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 Winter | Bio311 Adv. Cell Biology | 2009-10-29: [PDF] | Introduction to cytoskeleton |
| 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 Winter | Bio311 Adv. Cell Biology | 2009-10-04 [PDF] | Diffusion in cells |
| 2009-10-05 [PDF] | Role of diffusion in cells |
