Problem Set 2, Problem 2

a.	Start the Nernst Potential Simulator, and load the file Problem3A.init (note that due to a recent renumbering of the problem set, this file name does not match the problem number!). Predict the final membrane potential using the GHK equation. Show your work. Note that, as in Problem 1, because of small differences in temperature and concentration, your calculation may differ slightly from the value predicted by the simulator.
b.	Now start the simulation briefly, immediately pause it, and click on a potassium (red), sodium (blue) and chloride (green) ion to track them. Describe the movements of the selected ions and the graph of the membrane potential relative to the predicted potential (red line). Predict what will happen over time. Run the simulation for 10,000 iterations to see if your prediction is correct. Take a screenshot for your lab notebook, including the plot of the Membrane Potential. From the actual measured intracellular and extracellular ion concentrations (found in the table on the right) and the GHK equation, what should the final membrane potential be? What has happened to account for the change in the initial predicted membrane potential, and that which you observe after 10,000 iterations?
c.	In this problem, you will design your own neuron with a unique set of ionic parameters. You must first create a table in your lab notebook by clicking this link and copying the table template into your notebook. Devise a set of concentrations and permeabilities to represent a nerve cell at rest with a negative resting potential. In your imaginary neuron, movement of chloride ions should be primarily responsible for the resting potential (this implies that neither sodium nor potassium ions contribute significantly to the resting potential). Report the concentration and permeabilities in the table in your lab notebook. Next, using the same concentrations, devise a different set of permeabilities to represent a neuron at the peak of the action potential (i.e., at a positive membrane potential in the range of +10 mV to +50 mV, approximately; the action potential is a temporary depolarization of the membrane that neurons use to send signals across long distances; you will learn much more about this in the coming units). Movement of potassium ions should be primarily responsible for the depolarization at the peak (this implies that neither sodium nor chloride ions contribute significantly to peak of the action potential). Record these permeabilities in the table in your lab notebook. Using the GHK equation, calculate the membrane potential of the neuron you have designed for both sets of permeabilities. Show your work and your answers in your lab notebook. If necessary, revise your parameters until the membrane potential meets the criteria stated above for both when the neuron is resting and when it is at the peak of the action potential. Now test your values in the simulator (both the "Selective Permeability" and "Electrostatics" boxes should be checked). Enter the concentrations and permeabilities for the cell at rest, run the simulation for a few thousand iterations, and take a screenshot. Next, pause the simulation and change the permeabilities to those you chose for a cell during the action potential. Run the simulation again to see what happens, and take another screenshot. You can imagine that if you had such a cell with a membrane capable of selectively changing its permeability under certain conditions, you would have a cell capable of very interesting behavior!