Problem Set 1, Problem 1

a.	If you have not already done so, download the Nernst Potential Simulator using the links in the section A Simulation Program for Understanding Electrochemistry.
b.	Double click the program icon to open the simulator. Under the File menu, choose Load Initial Conditions, and then select Problem1.init. This file should be in the same folder as the one in which you found the Nernst Potential Simulator program. Note that the permeability, which is a measure of the number of channels that will allow a particular kind of ion to cross the membrane, has been set to zero for all of the ions. When the permeability is set to 1, the maximum number of channels are available to those ions. Also note that the Electrostatics box is unchecked. This means that the ions will be treated as uncharged particles. Consequently, ignore the Membrane Potential plot on the right side of the window. It is only applicable when Electrostatics is turned on, which will only happen during part (f) of this problem.
c.	Start the simulation (press Start). Click on one of the red ions, which will enlarge it. Describe what you observe about the motion of the single ion, as well as the movements of all of the ions in the intracellular compartment. Predict the long term behavior of the system, record your prediction, and observe the system for at least 2,000 iterations to see if your long term prediction is likely to be correct (the iteration number is updated on the lower left-hand corner of the window).
d.	Pause the simulation (press Pause). Change the permeability for the $\text{K}^+$ ions from 0 to 1 (either by moving the slider, or typing 1 into the box). Also change the permeability of the $\text{Na}^+$ and $\text{Cl}^-$ ions to 1. Note that the Selective Permeability box is unchecked. Thus, increasing the permeability to $\text{Na}^+$ and $\text{Cl}^-$ under these conditions will provide many opportunities for potassium ions to move through the membrane. You can see the many channels shown in the zoom window at the bottom middle of the simulation. Before continuing, take a screenshot of the simulation for your lab notebook. Now continue the simulation (press Continue). Observe what happens to the individual ion that you have selected, and to all of the ions over time. Also observe the change in the intracellular and extracellular concentrations of $\text{K}^+$ listed in the table under the graph to the right. Predict the final intracellular and extracellular concentrations of $\text{K}^+$ ions. Note that in this exercise the "ions" in the simulation have no charge (the Electrostatics setting is disabled), and so they will behave like electrically-neutral particles, such as glucose. Run the system for up to another 5,000 iterations to see if your long term prediction is likely to be correct. Take another screenshot of the simulation for your lab notebook.
e.	Take the simulation back to the initial conditions loaded from the file by pressing the "Reset with Loaded Initial Conditions" button. Now switch the intracellular concentration of $\text{K}^+$ from 2000 to 0, and the extracellular concentration of $\text{K}^+$ from 0 to 2000, so that the $\text{K}^+$ ions are all in the extracellular compartment. Change the permeability of all the ions from 0 to 1. Before starting the simulation, take another screenshot for your lab notebook. Start the simulation, and again click on one of the red ions. Predict the long term intracellular and extracellular concentrations of $\text{K}^+$ ions, and observe the system for about 5,000 iterations to see if your long term prediction is correct. Note to the careful student: the extracellular and intracellular compartments have slightly different volumes in this simulation, but you may treat them as identical volumes for these questions. Take another screenshot of the simulation after at least 5,000 iterations have passed.
f.	Use these results to describe the long term behavior of any system in which a single particle species has different concentrations in the intracellular and extracellular spaces, and is allowed to freely diffuse across a permeable membrane. First answer this assuming that the particle is uncharged (as in the exercises above). Then, discuss what will happen if the particle has a charge (e.g., is an ion) and is associated with a second ion of opposite and equal charge (e.g., sodium and chloride ions, or potassium and chloride ions); assume the second ion has the same initial concentrations as the first on the same side of the membrane and is equally permeable. Test your prediction by running the simulation and see what happens. You can give the particles charge in the simulation by checking the Electrostatics box. Take screenshots before and after allowing the two ionic species to diffuse and include these in your lab notebook.