Biophysics          

Text: Biological Physics: Energy, Information, Life
By Philip Nelson  

Have a look at the  table of Contents

Tutorial:

TA:	Farnoosh Farahpoor
Time:	TBA
Room:	TBA

First lecture:       Tues. Jan. 31^st (11 Bahman)
Last lecture:        Sun.  June. 3^rd (13 Khordad)

Midterm Exam:   TBA
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 Reynolds 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, basic knowledge of statistical mechanics and thermodynamics are necessary.

Useful links:

·   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 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:

• Structural objects inside cell
• Genetics and heredity
• Some basic educational resources are available here.
• A very interesting documentary introduction on Human evolution.
• Home works: Do yourself problem of chapter 2.

Lecture 4:

• Some introduction about probability density function
• Moments and cumulants
• Central limit theorem

Lecture 5:

• Velocity distribution of gas molecules
• An excursion on genetic and heredity
• Home works: chapter 3
• 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 6:

• Random walk, friction and diffusion
• Einstein's fluctuation-dissipation relation
• Boltzmann's constant and Avogadro number
• Stand on the shoulders of giants
  • Ludwig Eduard Boltzmann (February 20, 1844 – September 5, 1906)
  • 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 7:

• 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 (born October 24, 1932) . His personal homepage.

Lecture 8:

• Fick's and Diffusion equation.
• How is diffusion important in life?
• Home works: chapter 4, problems 1- 6.
• Stand on the shoulders of giants
  • Adolf Eugen Fick (3 September, 1829 – 21 August, 1901)

Lectures 9:

• 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: chapter 4, problems 7- 10.