UTF-8Template for Final ExamEffects of Hypertonic and Hypotonic Extracellular Environments upon Cell Volume
Your Name:{John Gary DeMuth}
1. State the Question you are investigating:
{Examining the effects of increased (or lowered) pressure--due to surrounding environment--upon the internal volume of a given cell.}
2. Explain why this quesion is interesting:
{When discussions of planet colonization occur (with regards to leaving our planet and the Milky Way galaxy because the sun will eventually "die"), scientists often talk about (after discussions of if there's any water on a given planet because water is essential for metabolic processes, i.e., life) introducing bacteria to begin life-sustaining processes, e.g., oxygen production, nitrogen fixation, etc.. But what about the effects of pressure upon these bacteria? Are bacteria capable of being manufactured to have the structural integrity to withstand stronger pressures in a different enviros?}
3. Explain why this quesion is specific enough to be testable with simulation so as to give a definite answer.
{It is specific enough because we will be looking at the effect of a given extracellular environment upon the cell volume at the atomic level. Of course, to make better "guesstimates" about the structural integrity of a given constructed bacteria's cell wall one would have to try to make a MW simulation comprised of the actual bacterial wall components, e.g., peptidoglycan, n-acetylglucosamine, etc. (vs. the simplistic level used here), as well as consider & employ the specific environmental conditions (temperature, pressure, chemical composition, etc.) that would be encountered upon a given planet.}
4. Describe your reasoning in building the simulation the way you did, the testing you did, and changes you
had to make to make it work.
{To try to simulate/study the effects of pressure upon cell volume, due to a cell's surrounding environment, I had to first delineate the cell's interior from the exterior (i.e., make a cell membrane), replicate the ionic conditions normally found within a given cell, and finally, to vary the extracellular environment's ionic conditions so as to be able to compare and contrast the effects of such upon the cell's volume. NOTE: I did not choose to examine an isotonic environment, which would have served as a control for the hypertonic and hypotonic environments, knowing that little to nothing should happen in terms of the cell's volume (plus, Dr. Leontis noted that inserting a third container can make the MW program run a little whacky) . Here's how I attempted this:
#1 To separate the cell from its surrounding environment, I inserted a barrier (yellowish coloration, in the middle of the container) which would serve as the cell membrane; and to further simulate a cell membrane, I chose to make it semi-permeable (permeable to the white, neutral ions which were to represent water, and impermeable to the negatively and positively charged ions, respectively). I also tried to center the barrier as accurately as possible by eye (not sure where to look upon MW to see if was set dead-center and to adjust accordingly if need be) so as to make any observed barrier movement due to the movement of the water vs. because of a smaller vs. larger starting volumes on either side of the barrier.
CHANGES: I found I had to make the barrier wide enough so that there wasn't a clustering/clumping--from both the interior and exterior sides--of the white, water molecules across the cell membrane. I also changed its density from 100,000 down to 250 so as to have any movement of the barrier, which is the manifestation of changes in cell volume due to pressure, able to be discerned.
#2 To simulate a hypertonic extracellular environment, I introduced more (but an equal number, 15 each) of positively and negatively charged ions to the exterior of the cell membrane (in this case, on the left), relative to the interior of the cell (in this case, on the right), which had 5 each of the positively and negatively charged ions. Also introduced 50 neutral ions, which are to represent water, on both sides of the barrier; kept the number equal on both sides of the cell membrane so that their net movement was due solely to the differences in ionic content of the cell's interior and extracellular environment.
CHANGES: initially, I had chosen to only use negative ions, knowing that the cell interior is more electronegative than the extracellular environment is.
#3 To simulate a hypotonic extracellular environment, I used the same conditions as above for the hypertonic extracellular environment, EXCEPT I now removed all charged ions from the extracellular side.
CHANGES: initially, I had chosen to only use negative ions, knowing that the cell interior is more electronegative than the extracellular environment is.
#4 As for the intially randomly distributed white, neutral, "supposed to be water" ions: I gave them a mass of 50, an atomic radius of 3 (because a water molecule is larger than an ion of Na+ or Cl- for instance), and intermolecular attractions (to the ions) of 1 so that they were somewhat attracted to the ions (& thus, the phenomenon of excluded volume avoided).
#5 As for the initially randomly distributed blue, +1 charged ions: I gave them a mass of 50, an atomic radius of 1 (to keep excluded volume from dominating) , and kept the intermolecular attractions at 0.1.
#6 As for the initially randomly distributed green, -1 charged ions: I gave them as mass of 50, an atomic radius of 1 (to keep excluded volume from dominating), and kept the intermolecular attractions at 0.1.
#7 Water bath: introduced and used the temperature of 300 degrees K, though, I could have obvioulsy used various temperature levels to mimic what might be found upon a given planet of interest}
5. What variables will stay fixed for the experiment and how did you choose the values for those variables?
{See #4}
6. What variable will you change to answer the question? Over what range of values will you test the effect of the variable?
{See #4}
7. What variables will you monitor or measure? How will you output or measure them? Examples of variables we
have output include the volume, the temperature (or average KE), the total energy, the potential energy, the arrangements of
particles, etc.
{I will be watching the movement of the water molecules, and ultimately, for shifting of the yellow barrier (i.e., the cell membrane) whose movement (to the left = increased internal cellular volume, to the right = decreased internal cellular volume) will indicate the effects of the surrounding extracellular environmental conditions upon a given cell's volume.}
8. Usually you need to equilibrate your simulation before running to measure results. Will you equilibrate your simulation with the heat bath on (Isothermally) or without the heat bath -- i.e. Adiabatically? Explain.
{No.}
9. When you actually run the simulation -- will you do it with the heat bath on or off? Explain.
{Yes.}
10. Provide directions for someone else to run your simulations to reproduce the experiments you got, and describe the results you obtained:
{For the former, see #4. As for the hypertonic extracellular environment, its effect upon cell volume was to decrease it due to . As for the hypotonic extracellular environment, its effect upon the cell volume was to increase it due to .}
11. State the answer to your question and intepret the results in terms of relevant fundamental concepts (for example, Conservation of momentum, conservation of energy, conservation of charge, Coulomb's Law, Entropy, etc.). Any surprises?
{
}
Build simulations Here: truetrue14true14true14true14true14true255 0 014true255 0 014true14255 0 014true255 0 014true14255 0 014true255 0 014true14255 0 014true14true14true14255 0 014255 0 014255 0 014255 0 014true255 0 014255 0 014255 0 014255 0 014255 0 014true255 0 014255 0 014255 0 014255 0 014true255 0 014255 0 014255 0 014true255 0 014255 0 014255 0 014255 0 014255 0 014255 0 014255 0 014255 0 014255 0 014255 0 014true255 0 014true14true14255 0 014true255 0 014true14255 0 014true14true14true14true14255 0 014255 0 014true14255 0 014255 0 014true255 0 014true14255 0 014true14true14255 0 014true14true14255 0 014255 0 014255 0 014true14true14true14true14org.concord.mw2d.activity.AtomContainerDeMuth_FINAL_EXAM$0.mmlorg.concord.mw2d.activity.AtomContainerDeMuth_FINAL_EXAM$1.mmltrue14true14