BioPhysics | Physics Department, Sharif University of Technology

Midterm Exam:
27 FEB 2013
(7 اردیبهشت 1392)

Final Exam:
TBA

Welcome

This course hopefully will help us to figure out how much physics is involving on the life, among them thermodynamics, statistical mechanics, low Reynolds’s number hydrodynamics, phase transition, molecular motors, and charged systems. The text book is a very interesting book which 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

or MATLAB) would likely come in handy.

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

Textbook:
Biological Physics: Energy, Information, Life
updated first edition (2008)
By Philip Nelson

Have a look at the  table of Contents

Further Readings:

Physical Biology of the cell (2009)
By Phillips/Kondev/Theriot
Don’t miss interesting materials (powerpoints, videos, ….) in the book home page.

Quantitative Understanding of Biosystems: An Introduction to Biophysics (2010)
By Thomas M. Nordlund

Lecturer:	Reza Ejtehadi
Time:	Saturdays and Mondays, 13:30 - 15:00
Room:	Physics 412
Office time:	Weekdays before 9:00 and Sundays, 11:00 – 12:00

TA:	Hamid Seyyed-Alaei
Time:	?
Room:	?
Homeworks page:	?

Scores:

Homework and Quizzes (TA)	20%
Midterm	30%
Final Exam	50%
Bonus problems/Class Quizzes	5%

Useful links:

• The free encyclopedia of Wikipedia.
• RasMol (a free 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.
• American biophysical society http://www.biophysics.org
• You can find lots of educational/informative movies on youtube.
• And here also http://www.allthingsscience.com.
• And finally you can learn a lot by searching in Google.

Lecture 1:

• Some basic concepts of thermodynamics
• Home work: Problems of the chapter 1 of the text book
• Stand on the shoulders of giants
• Benjamin Franklin (1706 – 1790)
• Sir Benjamin Thompson, Count Rumford (1753 – 1814)

Lecture 2:

• Some terminology and overview on biological systems
• Cell (structure and function)
• Cell division movie can be downloaded from this site.
• The movie of the neutrophil chasing a bacterium can be found here.
• This site helps you to imagine protein structure.
• Home work: Exercises of the chapter 2 of the text book

Lecture 3:

• Some introduction about probability density function
• Moments and cumulants
• Central limit theorem
• Velocity distribution of gas molecules
• Stand on the shoulders of giants
• Ludwig Eduard Boltzmann (February 20, 1844 – September 5, 1906)

Lecture 4:

• An excursion on genetic and heredity
• Home works: Problems of the chapter 3 of the text book
• Stand on the shoulders of giants
• Charles Robert Darwin (12 February 1809 – 19 April 1882)
• Gregor Johann Mendel (July 20[1], 1822 – January 6, 1884)
• Thomas Hunt Morgan (September 25, 1866 – December 4, 1945)
• Erwin Rudolf Josef Alexander Schrödinger (August 12, 1887 – January 4, 1961)
• Max Delbrück (September 4, 1906 – March 9, 1981)

Lecture 5:

• Random walk, friction and diffusion
• Einstein's fluctuation-dissipation relation
• Boltzmann's constant and Avogadro number
• Stand on the shoulders of giants
• Count Lorenzo Romano Amedeo Carlo Avogadro di Quaregna e Cerreto (August 9, 1776–July 9, 1856)
• Albert Einstein (March 14, 1879 – April 18, 1955)

Lecture 6:

• Other examples for random walk
• Polymer structures
• Stand on the shoulders of giants
• Paul John Flory (June 19, 1910 – September 9, 1985)
• Pierre-Gilles de Gennes (October 24, 1932 – May 18, 2007)

Lecture 7:

• Fick's and Diffusion equation.
• How is diffusion important in life?
• Stand on the shoulders of giants
• Adolf Eugen Fick (3 September, 1829 – 21 August, 1901)

Lectures 8:

• Nernst - Planck formula.
• Stand on the shoulders of giants
• Walther Hermann Nernst (June 25, 1864 – November 18, 1941)
• Max Karl Ernst Ludwig Planck (April 23, 1858 – October 4, 1947)
• To see more examples of influence of Brownian motion in the life, read this recent review article by Frey and Kroy.

· Home works: Problems of the chapter 4 of the text book