[IISER-p] [Instructor's webpage]

# [ver.2.o]

0=online; 2021-Aug to Dec

Physical biology of molecules, cells and tissues.

### News

• EVERY THURDAY 1700-1800h: Office hours by previous appointment in Google Classroom or over the phone (scroll down for more details)
• Assessment to include 40% weightage for end-semester exams and 20% mid semester and remaining 40% for continuous assessment
• Programming assignments via Google Collaboratory https://colab.research.google.com/ which runs Jupyter notebook style python.
• If you face problems accessing it (we haven't started yet, please email the course email ... bio315 ... @ ... students ...
• Make use of the discussion forum (google group). Your individual comments could help the others too.
• In case a few of you have issues with GoogleClassroom based notes and slides, please email me. A list of lectures is being maintained on the LECTURE NOTES PAGE.

### General observations

• Given the pandemic, all classes will be online. We will use a mix of GoogleClassroom, Overleaf for LaTex Hypothes.is and online real time polling as quizzes in class. Details will be discussed in the introductory class.
• The course will be conducted in synchronous (real-time) and asynchronous modes. With 3 scheduled lectures per week, 2 lectures will be pre-recorded and 1 will be post-recorded.
• With some previously announced exceptions, live instructor presence will be on MON. TUE & WED will be recorded.
• Anybody with connectivity issues should write to me, or call me in my office to find another way to virtually attend classes. We will make every attempt to ensure nobody loses out.
• Most importantly in the absence of classroom interactions I will be experimenting with many methods of interaction. Your active involvement will make this course more enjoyable and a better learning experience.

 Applying the very successful methods of thinking from classical and statistical-mechanics in physics to unravel problems in biology at the cellular scale. We use standard results from classical mechanics (springs, rods, pendula etc.) and examine how far we can use them for biological systems. We spend some time with Random Walk models and Boltzmann Statistics, and use these to derive theoretical results that connect energetics with the bulk-biochemistry. We intersperse this with a constant discussion of the following two aspects: the number-scales experimental techniques Since most of our discussions will revolve around theory or standard models, the discussion will allow us to understand how one can seek to employ these theories as usable theoretical models by experimental validation or just reasoning through. The phenomena that will be examined are: Force spectroscopy of proteins and nucleic acids Cytoskeleton: Actin and microtubules Motor proteins Protein diffusion, ligand-receptor binding and crowding effects Biomembrane mechanics Red blood cells Cell adhesion and migration The models that will be invoked will build upon concepts from classical and statistical mechanics. At the end of the course the student will be expected to understand the following models in their application to cellular biophysics: Mechanical forces Mass, stiffness and the damping of proteins Thermal forces Polymer mechanics Molecular motor stepping Membrane bending and vesicle formation Simplest models of cell shape Tutorials will involve a few computational and experimental exercises to complement theoretical concepts. Paper reading of biophysical techniques will be evaluated in class. Additional problem based assignments will intersperse the course. Regular quizzes will be conducted after the conclusion of substantial material. They will be announced and surprise, open- and closed-book. Continuous assessment will constitute half the assessment, the other half being traditional exams. At the end of the course you should be able to understand and evaluate sensible theoretical models of cell-biological systems from a biophysics perspective. The course will be complementary to Cell Biology (based on the book by B. Alberts et al. Mol. Biol. Cell). Intructors: Primary instructor: Dr. Chaitanya Athale (Div. of Biology @iiserpune) Guest lectures: TBA Assessment: Internal assesment includes evaluation of assignments, paper-reading, technique-presentations and quizzes. Exam based assesment is currently uncertain but sometime in December 2020. In the introductory lectures you will be provided an opportunity to choose what form of assessment you will be willing to accept. Course-Coordinator email: bio322 at the rat e student s dot ii serpune do t a c d o t in You can also in case of urgent issues email me at cathale at the rate of iiser pune dot academia dot in.

## Course Contents

1. Introduction: aims of the course. Using order of magnitude estimates to develop a feeling for the numbers
2. E. coli as the idealized cell
3. Life, energy, minimization and optimality
4. Mechanics: elasticity, viscosity and springs in cellular systems
5. Rods, cantilevers and the basis for elasticity & cytoskeleton
6. Membrane mechanics
7. Statistical mechanics and entropy
8. Polymer mechanics
9. Simple cells and their mechanobiology

Lecture notes (on google classrooms): Those having issues accessing them please email me or call me

I am maintaining a parallel lecture-notes page here.

### Assignments

The assignments page [link] contains all the assignmnts and their solutions as the deadline passes.

Scores will be scaled as ${y=e}^{-x/3}$, (i.e. y= exp(-x/3)), where x=delay in days after date of submission, and y=score.

 Policy on originality and plagiarism [pdf]: A document of what is acceptable usage of existing resources. It particularly deals with what IS and IS NOT acceptable use of information, figures, graphs and words from peer-reviewed, published, online, wikipedia, journal-article and other sources.

## Meeting times for the instructor

Weekly meetings: Monday every week in class hours 1200-1300h. Online or if you face connection issues call my office number which reads as (pune prefix) zero twenty (IISER prefix) twentyfive nine ty and the extension five eighty fifty.

. At the pre-determined time I will make myself avaiable in my personal web-chat room. For any meeting outside this time, please take an appointment to pre-arrange such a meeting to be sure to meet me. This will be the office hour. Using google-classroom discssions or emails to my @students iiserpune address, you can seek such an appointment.

For course and assignment related queries contact bio322 at the rate students stop iiserpune stop ac dot indiain

• Nelson Philip: Biological Physics by Philip Nelson. [copies available in the library and with the Publisher/amzn etc.]
• Philips, Kondev, Theriot: Physical Biology of the Cell [link]
• Dill & Bromberg. Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics and Nanosceince. Garland Press. [link to publisher]
• 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 [website]

## Schedule

• Quiz1: TBA
• Quiz2: TBA
• Mid-sem Exams: 4-Oct-2021 to 14-Oct-2021
• Quiz3: TBA
• Quiz4: TBA
• End-sem Exams: 7-Dec-2021 to 17-Dec-2021

### Order of magnitude estimates & numbers in cell biology

Book: John Tyler Bonner "Why size matters"

### Statistical mechanics formalism applied to multi-molecular systems

Systems as diverse as ligand-receptor binding (e.g. Hemoglobin and O2), ion channels and protein dynamics and genetic evolution are reviewed in some of these following papers:

Historical accounts of Linus Pauling's work in biology

### Mechanics in Biology

1. David Boal (2002) Mechanics of the Cell. Cambrdige Univ. Press
2. Pennycuick C..J. (1992) Newton Rules Biology: Physical Approach to Biological Problems

### Viscoelasticity

1. Lakes R. (2010) Viscoelastic Materials. Cambridge Univ. Press.

## Course calendar

Last updated: 03-Aug-2021