UTF-8SAM E1 Model 1Modeling Atoms
How does the Molecular Workbench work?
The Molecular Workbench uses Newton's Third Law to model how atoms move.
The software computes the following:
It calculates the forces on each atom.
MW computes the forces from a potential energy called the Lennard-Jones potential.
Then the software uses F=ma to determine the acceleration.
The acceleration is used to compute how much the velocity changes.
This gives the velocity of each atom, which is used to move the atom forward a tiny time step.
This whole process is repeated thousands of times each second.
MW uses time steps measured in femtoseconds. This is one-millionth of one-billionth of a second.
You should know:
The atoms are fee to move.
Do this:
Use the pointer tool to move the atoms around. Note how each atom affects every other one.
Use the "Start from Rest" button to run the model with three atoms. Note how complex the motion is.
Take a snapshot of the graph of the motion of three atoms.
Show on the snapshot where on the graph the KE, PE, and total energies are greatest.
Red: KE per atom
Blue: PE per atom
Green: Total energy per atom.
Do this:
Use the third tool to add more atoms.
Run the model a few times starting with eight atoms. What do you observe?
Think about
Why are there peaks on the KE graph and valleys on the PE graphs?
What about the results shows that the total energy never changes unless you add or remove KE?
1true16true20.0org.concord.modeler.text.BulletIcon$SquareBulletIcontrue20.0org.concord.modeler.text.BulletIcon$SquareBulletIcon20.0org.concord.modeler.text.BulletIcon$SquareBulletIcon20.0org.concord.modeler.text.BulletIcon$SquareBulletIcon20.0org.concord.modeler.text.BulletIcon$SquareBulletIconorg.concord.modeler.PageButtonChange the Lennard-Jones potentialShow the interactive L-J potential graph.org.concord.mw2d.models.MolecularModel0Change the van der Waals parameters20.0org.concord.modeler.text.BulletIcon$SquareBulletIcon20.020.0org.concord.modeler.text.BulletIcon$SquareBulletIcon20.0org.concord.modeler.text.BulletIcon$SquareBulletIcon20.0org.concord.modeler.text.BulletIcon$SquareBulletIcon20.0org.concord.modeler.text.BulletIcon$SquareBulletIcon20.020.01org.concord.mw2d.activity.AtomContainerPage8$0.mmlorg.concord.modeler.PageXYGraph0Time (fs)Kinetic Energy/ParticlePotential Energy/ParticleTotal Energy/Particle400350Time (fs)Energy (eV)true320450-333301-1falseorg.concord.modeler.PageButton<html><b><font size=3>Reset</html>Restart the model and graph7028org.concord.mw2d.models.MolecularModel0Execute MW scriptorg.concord.modeler.PageButton<html><b><font size=3>Start from Rest</html>13028org.concord.mw2d.models.MolecularModel0Execute MW scriptorg.concord.modeler.PageButton<html><b><font size=3>Add KE</html>Add kinetic energy to all atoms9028org.concord.mw2d.models.MolecularModel0trueExecute MW scriptorg.concord.modeler.PageSliderorg.concord.mw2d.models.MolecularModel00.097999999970197680.100000001490116125.050Time step30060falsetrue{value="0.9799999997019767", label="1"}{value="2.057999999374151", label="2"}{value="1.9599999994039534", label="2"}{value="3.037999999076128", label="3"}{value="4.997999998480082", label="5"}{value="0.48999999985098835", label=".5"}{value="0.09799999997019768", label=".1"}Execute MW script20.040.0org.concord.modeler.text.BulletIcon$SquareBulletIcon40.0org.concord.modeler.text.BulletIcon$SquareBulletIcon20.020.040.0org.concord.modeler.text.BulletIcon$SquareBulletIcon40.0org.concord.modeler.text.BulletIcon$SquareBulletIconorg.concord.modeler.ImageQuestion400300Lowered Etched<html><font face="Verdana" size="2">Insert here a snapshot of a graph for a system with eight atoms that has <b>negative</b> total energy. In the caption, explain how this is possible. </font></html>org.concord.modeler.ActivityButtonHint 1Hint about how to get negative PEThink about the separation of two atoms that gives negative PE.Hintorg.concord.modeler.ActivityButtonHint 2Hint about how to position atoms for negative PE.If atoms are close but the force is small, their PE is negative. Start the model with many atoms positioned so that they are close and the force on each is small. Hintorg.concord.modeler.ImageQuestion400300Lowered Etched<html><font face="Verdana" size="2">Insert here a snapshot of a graph for a system with eight atoms that has <b>positive</b> total energy. In the caption, explain how you created this model. </font></html>org.concord.modeler.ActivityButtonHint 1Hint about how to start the modelYou cannot get a positive energy if you start the atoms at rest. PE is never positive and at rest KE is zero, so their sum will always be zero or negative. Hintorg.concord.modeler.ActivityButtonHint 2Hint about how to start the modelStart the model and use the button that adds KE. Hint