PHYC452Biophysics:Assignments
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HW #1  HW #1  
 '''Due: Feb 11''': Create an OWW Account and list yourself on our [[PHYC452Biophysics:PeoplePeople Page]]. Read Nelson Chapter 14. Homework Problem Nelson #4.3.   '''Due: Feb 11''': Create an OWW Account and list yourself on our [[PHYC452Biophysics:PeoplePeople Page]]. Read Nelson Chapter 14. Homework Problem Nelson #4.3.  
    +   [http://panda3.phys.unm.edu/~klidke/452sp2008/HW1.pdf Solutions] 
    
+  HW #2  
+   '''Due: Feb 20''':  
+  (1) Read Nelson Chapter 56  
+  (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: [http://www.biophysj.org/cgi/content/abstract/92/10/3706 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 HagenPoiseuille relation from the NavierStokes equation.  
+   [http://panda3.phys.unm.edu/~klidke/452sp2008/HW2.pdf Solutions]  
+    
+  HW #3  
+   '''Due: March 3''':  
+  
+  (1) Read Nelson Chapter 78  
+  
+  (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  
+   [http://panda3.phys.unm.edu/~klidke/452sp2008/HW3.pdf Solutions]  
+  
+  [[/HW3_4 Solution for (4)]]  
+    
+  HW #4  
+   '''Due: March 14, Extended: March 28''':  
+  
+  (1) Read Nelson Chapter 9  
+  
+  (2) Compare the force extension curves of simulated Worm Like Chains (WLCs) to the approximate functional form given by Nelson eq. 9.42. Assume a link size of 1 nm, persistence length of 50 nm and that the applied force is along the z axis.  
+  
+  (a) Given a link with direction r(θ,φ), where θ is polar angle from the zaxis, find the probability of the next link r'(θ,φ,θ',φ').  
+  
+  (b) Show how to make a random selection of θ',φ' from the probability distribution in (a) when given random numbers uniformly distributed from 0 to 1.  
+  
+  (c) Use (a) and (b) to construct a 1000 link chain for a certain force.  
+  
+  (d) Repeat (c) as many times as necessary for the same force to obtain a well defined <z>.  
+  
+  (e) Repeat (d) for several different forces between 0 and the force that gives <z>~Lo where Lo is the T=0 K length.  
+  
+  (f) Plot <z> vs f of your simulation with errors given by standard error of the mean. On the same plot also show eq. 9.42. Be sure to include correct units.  
+  
+  (g) Comment on your result.  
+  
+  
+    
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Current revision
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 14. Homework Problem Nelson #4.3.  Solutions 
HW #2  Due: Feb 20:
(1) Read Nelson Chapter 56 (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 HagenPoiseuille relation from the NavierStokes equation.  Solutions 
HW #3  Due: March 3:
(1) Read Nelson Chapter 78 (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  Solutions 
HW #4  Due: March 14, Extended: March 28:
(1) Read Nelson Chapter 9 (2) Compare the force extension curves of simulated Worm Like Chains (WLCs) to the approximate functional form given by Nelson eq. 9.42. Assume a link size of 1 nm, persistence length of 50 nm and that the applied force is along the z axis. (a) Given a link with direction r(θ,φ), where θ is polar angle from the zaxis, find the probability of the next link r'(θ,φ,θ',φ'). (b) Show how to make a random selection of θ',φ' from the probability distribution in (a) when given random numbers uniformly distributed from 0 to 1. (c) Use (a) and (b) to construct a 1000 link chain for a certain force. (d) Repeat (c) as many times as necessary for the same force to obtain a well defined <z>. (e) Repeat (d) for several different forces between 0 and the force that gives <z>~Lo where Lo is the T=0 K length. (f) Plot <z> vs f of your simulation with errors given by standard error of the mean. On the same plot also show eq. 9.42. Be sure to include correct units. (g) Comment on your result.
