[IISER-p] [Instructor's webpage]

# [ver. 2016]

Physical biology of molecules, cells and tissues at equilibrium. Biophysical techniques.

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
1. the number-scales
2. experimental techniques
to test these validity of these theoretical pradigms. The emphasis is on usable theoretical models.

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.

Intructors:

Primary instructor: Dr. Chaitanya Athale (bio@iiserpune)

Guest lectures by: Dr. Shiva Patil (physics@iiserpune)

Assessment: Internal assesment (50%) includes evaluation of assignments, paper-reading and quizzes. Exam based assesment carries the remaining 50% of the score.

Course-Coordinator email: bio322 at the rat e student s dot ii serpune do t a c d o t in

### News

• Class on 29-Sep-2016 at 0900h LOCATION: Computer Lab in LHC303 (2nd floor)
• MID SEMESTER EXAM has been scheduled (as announced) for 23-Sep-2016 3:00-5:00 pm. The examination room has been changed to LHC203 (not LHC101 as announced in the dean's email)
• The assignment 3 submission deadline has been futher extended to 13-Sept-2016 @1400h
• The assignment page has been updated
• he class on 25-Aug-2016 will be conducted in LHC303 (computer teaching lab)
• The lecture notes for the first few modules (introduction, energetics, dimensions and order of magnitude estimates) have been uploaded and can be accessed on the lecture notes page.

## Course Contents

1. Introduction
2. Energy of life
3. Dimensional analysis and a feel for numbers
4. Random walks and biopolymers
5. Classical mechanics of beams and springs applied to DNA, proteins and membranes
6. Statistical mechanics and entropy: understanding molecular configuration
7. Cell mechanics and tissue shape
8. Biophysical techniques (together with the relevant topics: reading)
• Light
• Measuring forces
• Movement of cells and analysis
• Bio-molecular kinetics
9. Assignments: calculations, (python) computations and reading

Lecture notes

### 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 plagiarism [pdf]: A document of what is acceptable usage of existing resources. It particularly deals with what IS and IS NOT acceptable use of published, online, wikipedia, journal-article and other sources of information, figures, graphs and words. It is mandatory for all course attendees to have read it. A quiz will be conducted on your understanding.

Lecture notes (TBA)

## Meeting times for the instructor

Wed 1600-1630h, Main Building, Biology Block, 2nd floor

Any other slot must be pre-arranged by appointment if you want to be sure to meet me.

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

• Nelson Philip: Biological Physics [free pdf] by Philip Nelson.
• 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.

## Schedule

• Quiz1
• Quiz2
• Mid-sem Exams
• Quiz3
• Quiz4
• End-sem Exams