[IISER-p]

# [ver. 2015]

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

This course will focus on developing concepts to leverage the power of physics to unravel problems in biology at the cellular scale. We build on standard results in classical mechanics (springs, rods, pendula etc.) for biological insight. From this we introduce statistical mechanics as a means of dealing with biological complexity at the molecular and cellular scale. We intersperse this with a constant discussion of the number-scales and experimental techniques used to test these theoretical pradigms.

Intructors:

Primary instructor: Dr. Chaitanya Athale (bio)

Guest lectures by: Dr. Apratim Chatterjee (phy) and Dr. Shiva Patil (phy)

Coordinator in IISER-Tvm: Dr. Satish Khurana (bio)

Teaching assistants: 2 Pune, 1 Trivandrum

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

### News

• Marks distributions for Pune and Trivandrum are uploaded on the Scores and Answer Key Page.
• IISER Pune students can coordinate with the Teaching Assistants to see their end-semester answer papers. Kindly make either an appointment or find a common time.
• The end-semester exam will cover all material taught in the course. This includes the KD measurement techniques covered by students in IISER Pune. Kindly refer to the original references that have been uploaded on these topics.

## 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. Biophysical techniques
• Light
• Measuring forces
• Movement of cells and analysis
• Bio-molecular kinetics

### Assignments

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 [password protected]. A mixture of lecture-slides and summaries of the material covered. Please do not treat these as a replacement for (a) attending the class and (b) reading on your own.

The extranet (outside iiserpune domain) site for the course can be accessed here.

## Meeting times for the instructor

Wed 1200-1300h, 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

## Reference books

• Nelson Philip: Biological Physics [free pdf] by Philip Nelson.
• Philips, Kondev, Theriot: Physical Biology of the Cell [link]
• 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

• 4-Aug 2015: First class
• 21 to 29-Sep 2015: Mid-semester exams
• 22-25 Oct 2015: Mid-sem break
• 19-Nov 2015: Last lecture
• 22 to 30-Nov 2015: End-semester exams:

## Course calendar

Last updated: 9-Dec-2015 @1730h