[IISER-p]

Bio322: Biophysics (Introduction to Physical Biology)

[ver. 2014]

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

Biology has progressed tremendously since the discovery of the chemistry underlying it in terms of DNA, RNA, proteins and lipids. How these interact with one another is however governed by physico-chemical laws. This course will introduce these physical principles, key experiments and models of the physical principles that govern the unit of life- a cell and its components. It will also introduce means to measure these aspects.

News

  • TVM score distribution [plot]
  • PUN score distribution [plot]
  • Answer key [END-SEM]
  • IISER Pune students can see their answer papers from 10-Nov onwards in the TA's lab (Neha Khetan, Main Block, 2nd floor, Biology Wing, Bio-Computing Lab 01 (athale-lab)
  • End-sem exam [26-Nov-2014, time: 15-1700h (3-5pm)]. Due to numerous emails about the portion: All semester material with emphasis on the 2nd quarter (post-midsem), technique presentation topics based on whatever is available (link to original paper/report if any), presentations (if any) and video talks (if any) together with those talks that were "live". Principle of technique and link to rest of the course will be emphasized.
  • Bring calculators to the end-sem exam. Paper will consist of multiple choice questions (MCQ)
  • Revision session class video can be accessed from the lectures page
  • Mid-sem exam answer key
  • In class hands-on session (assignment): Persistence length [optional and NOT MARKED]
  • The Minisymposium on biophysics technique for iiser-TVM students concludes with the last session on 15-Nov (Sat, Time: 1600-1830h) (video recorded)- PLEASE NOTE: We will begin at 4pm.
  • 15-Nov @4pm: The new TA Ramesh Bondada will coordinate with you to put ALL slides on one computer before the start to reduce delays and technical glitches.
  • iiserTvm: The video of the lecture on 3-Nov video can be accessed from the lecture-notes page.
  • iiserPune: Technique presentations by TVM students from 1st and 10th Nov are also linked to the lecture notes page.
  • The assignment for RG has bee updated. The problem with upload access has been fixed. Please upload ONE PDF file here. This should include the script you wrote to calculate R G
  • The atom-movie: ibm-research used the scanning tunneling microscope to make a movie out of CO atoms and stop-motion [video]
Random walk models, AFM images of molecules and cells and cytokinesis

Course Contents

  1. Introduction:

    1.1. What, where, how, why biophysics?

    1.2. Searching for information, citation, plagiarism and originality

  2. Order of magnitude physics, Energy and Life

    2.1. Physical principles in biology; Energetics and order in living systems

    2,2. Dimensional analysis

    2.3. Molecular scales and biology by numbers

  3. Cellular architecture
    4. 3.1 Nucleic acids 3.2 Construction plans for cells and organisms 3.4 Rate equations (differential equations) and dynamics of the cell 3.5 Biopolymers and cytoskeletal dynamics 3.6 Network organization in space and time 3.7 Lipids, membranes and biophysics
    • Biophysical techniques
      • Light in biology, microscopy techniques
      • Measuring forces in bio-molecules
      • Movement of cells and analysis
      • Measuring energetics of bio-molecular reactions.
      • List of technique presentation topics These are presentations you students will make. This includes a signup form and a list of summarized topics with dates.

Policy on plagiarism [pdf]: A document of what is acceptable usage of existing (online, wikipedia, journal-article and other) sources.

Lecture slides and additional material from the lecture.

Assignments Late submission policy: 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.

Teaching assistant (TA)

Name: Neha Khetan (Pun), Kunalika Jain (Pun), Ramesh Bondada Sreejith Alipra (Tvm)
Location: C301, HR4, E-classroom, 2nd floor, IISER Pune Campus

Meeting times for the instructor

Thurday 1100-1230h, 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.

Exam schedule

  • Mid-semester exams: 22 to 27-Sep
  • End-semester exams: 24 to 29-Nov

Course calendar

Last update: 9-Dec-2014