Biophysics

 

Lecturer:              Reza Ejtehadi

Time:                   Sundays and Tuesdays, 12:00 – 1:30

Room:                 Talar 3

Office time:         Saturdays, 10:30 – 12:00     

 

Text: Biological Physics: Energy, Information, Life

By Philip Nelson  

 

Have a look at the  table of Contents

 

 

 

 

 

Tutorial:   

TA:             Nima Hamedani Radja nima@mehr.sharif.ac.ir

Time:           Saturdays, 12:00 – 1:30 and  Sunday 1:30 – 3:00

Room:         Ask Nima

 

First lecture:       Tue. Feb. 1st (13 Bahman)

Last lecture:        Tue.  May 30th (10 Khordad)

Midterm Exam:   Tue. Apr. 12th (23 Farvardin)

Final Exam:        TBA

 

Marking:

Homework and Quizzes            20%

Midterm                                   30%

Final Exam                               50%

Bonus problems                       10%

 

To the students:

This course hopefully will help us to figure out how much physics is involving on biological life, among them thermodynamics, entropic forces, low Reynold’s number hydrodynamics, phase transition,  chemical forces, molecular motors,  charged systems. The text book also serves to introduce much of the conceptual material underlying the young fields of nanotechnology and soft materials. Definitely, I am not going to teach Biology in this course, as I don’t know that myself! This is very much a physics course, and will emphasize the quantitative aspects of biological phenomena. I strongly recommend all students to read this and this before taking the course.

 

Some homework problems require some computational work. A basic knowledge of computing (Mathematica, C or FORTRAN) would likely come in handy.

 

Even though I will briefly review some thermodynamic concepts, some basic knowledge of statistical mechanics and thermodynamics are necessary.

 

Useful links:

·   RasMol (a free pdb viewer) is available here.

·   Xmol (another freeware pdb viewer) is available here.

·   pdb files for proteins available at the Protein Database.

·   pdb files for nucleic acids are available at the Nucleic Acid Database.

·   Some educational resources are listed here and also here.

·   A rich selection of web resources for computational biology.

Lecture 1:

·       Some basic concepts of thermodynamics

·       Home work: Problems of the chapter 1 of the text book

Lecture 2:

·       Some terminology and overview on biological systems

·       Cell (structure and function)

·       Cell division movie can be download from this site.

·       The movie of the neutrophil chasing a bacterium can be found here.

·       This site help you to imagine protein structure.

Lecture 3:

·       Review and continue of lecture 2

·       Structural objects inside cell

·       Genetics and heredity

·       Some basic educational resources are available here.

·       Home works: Do yourself problem of chapter 2

Lecture 4:

·       Some introduction about probability density function

·       Moments and cumulants

·       Central limit theorem

·       Velocity distribution of gas molecules

Lecture 5:

·       A excursion on genetic and heredity

·       Home works: chapter 3

Lecture 6:

·       Random walk, friction and diffusion

·       Einstein’s fluctuation-dissipation relation

·       Boltzmann’s constant and Avogadro number

Lecture 7:

·       Other examples for random walk

·       Diffusion equation

Lecture 8:

·       How diffusion is important in life

·       Home works: chapter 4

·       To see more examples of influence of Brownian motion in the life, read this very recent review article by Frey and Kroy.

Lecture 9:

·       Fluid dynamics at low Reynolds number

·       See this very nice presentation about the life at low Reynolds number by Purcell.

Lecture 10:

·       How one can swim in viscose media?

·       See this very simple swimmer by Ali Najafi and Ramin Golestanian.

·       Information about Cilia and Flagella movement with some very interesting movies of microscopic creatures movements are available in these websites:

o      http://jcs.biologists.org/cgi/content/full/117/9/1641/DC1

o      http://saints.css.edu/bio/schroeder/cytoskeleton.html

o      http://www.cytochemistry.net/Cell-biology/cilia.htm

o      http://www.ncbi.nlm.nih.gov/books/bv.fcgi

o      http://www.jochemnet.de/fiu/bot4404/BOT4404_14.html

o      http://www.rowland.org/labs/bacteria/movies_ecoli.html

·       Homework: chapter 5

Lecture 11:

·       Entropy, Temperature and Free Energy

·       Entropic force

Lecture 12:

·       Entropy, Temperature and Free Energy

·       Systems in equilibrium

·       Two state systems: Small Proteins and RNA

·       Homework: Chapter 6

Lecture 13:

·       Osmotic pressure, force and flow

·       Depletion force

Lecture 14:

·       Electrostatic interactions in water environment

·       Screening effect

Lecture 15:

·       Unusual properties of water

·       Hydrogen-bonds

·       Hydrophobic interaction

·       See following pages for more special properties of water:

o      http://www.lsbu.ac.uk/water/anmlies.html

o      http://www.pdhcenter.com/courses/c104/c104.htm

o      http://www.chemguide.co.uk/atoms/bonding/hbond.html

o      http://www.elmhurst.edu/~chm/vchembook/161Ahydrogenbond.html

·       Homework: Chapter 7

Lecture 16:

·       Midterm exam

·       Midterm exam solution 

·       Results

Lecture 17:

·       Chemical potential

·       Equilibrium constant and reaction quotient

·       Acids and Bases

Lecture 18:

·       Self assembly of amphiphiles

·       Emulation, micelles and membranes

·       Cell membranes elasticity

·       Homework: Chapter 8

Lecture 19:

·       Protein folding problem

·       Driving forces

·       Elasticity of rubber

Lecture 20:

·       Elasticity models of polymers

o      Freely Joined Chain (FJC) model

o      Self Avoiding Random Walk (SARW)

o      Worm like chain (rod like chain) model

o       

·       Final Results

 

 

Text Box: Note: The course powerpoints and some other materials are available here.