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Simulating Diffusion of Proteins in Water
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Highlights: This exercise uses vPython to computationally model a protein diffusing in water.
Abstract: This exercise puts the first two exercises in the sequence together and uses a list to create many particles interacting in the same way two particles did in Modeling the Exchange of Momentum Between a Ligand and an Enzyme. The coding in this exercise primarily relies on changing initial conditions to allow the code to model the situation of a single protein diffusing in water. Students are asked to consider the appropriate numerical values of this simulation, and then asked to play with parameters to make the water invisible to the eye. Lastly students compare this simulation to a video of a protein folding in water.
Resource Types: In-class activity, Lab
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Copyright:   2021 Abhilash Nair, Vashti Sawtelle, Lisa Lapidus

License:   CC: BY-NC-SA - Attribution, No Commercial uses and Share Alike. Derivative works must have the same license

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