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Physics 452: Biophysics, Spring 2008

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Homework Assignments

Homework is due at the beginning of class on the due date. No late homework accepted.

Homework Number Assignment, Due Date Links
HW #1 Due: Feb 11: Create an OWW Account and list yourself on our People Page. Read Nelson Chapter 1-4. Homework Problem Nelson #4.3.
HW #2 Due: Feb 20:

(1) Read Nelson Chapter 5-6

(2) Ask or Answer a question related to our recent class content on the wiki page.

(3) Nelson 5.5

(4) You have two microcentrifuge tubes (a cylinder R=0.5cm, L=3cm), one with a solution of bacteria (R=1 micron) and one with a solution of eukaryotic cells (R=10 micron). You want to exchange the buffer they are in, so you want to force all cells to a small pellet at the bottom of the tube using a centrifuge. You also don't want it to take more than 5 minutes. If the centrifuge radius is 10 cm, how fast do you have to spin? What is the acceleration in g?

(5) Relate the last section of this paper: Multiple Association States between Glycine Receptors and Gephyrin Identified by SPT Analysis "Properties of the equilibrium of GlyR traveling into and out of gephyrin clusters" with the ideas in Nelson 6.6.4. Make an argument that they calculated the potential energy in a cluster correctly (or incorrectly).

(6) Physics Grads only: Derive the Hagen-Poiseuille relation from the Navier-Stokes equation.

HW #3 Due: March 3:

(1) Read Nelson Chapter 7-8

(2) Nelson 7.3, 7.4, 8.3

(3) Imagine you are building a pH sensor based on a molecule that weakly binds H. The molecule with a bound H has a different Raman scattering signature than the unbound molecule. Each "sensor" is a 100 nm bead with 1000 such molecules. If 50% of molecules are occupied at pH 6, show (a) the percent occupied vs pH, (b) the sensitivity vs pH given by dS/d(pH) where S=Nunbound/(Nunbound + Nbound).

(4) Numerical warmup: Compute numerically a 30 second trajectory of a membrane protein diffusing with D=0.05 micron^2/s. Use 1000 time steps to generate the trajectory. Use the computer program of your choice (but MATLAB is recommended). Give the code, and the trajectory with properly labeled axes.

(5) Physics Grads Only: Nelson 6.9