Living Physics Portal: Simulating Diffusion of Proteins in Water

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Simulating Diffusion of Proteins in Water

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Part of Diffusion Model through Conservation of Momentum and Energy

Part 3 of 3

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

Authors:

Abhilash Nair

Michigan State University

Vashti Sawtelle

Michigan State University

Lisa Lapidus

Michigan State University

BLiSS Physics

Living Physics Portal Team

TOPICS

Physics Topics:

Classical Mechanics > Linear Momentum > Collisions in One Dimension, Conservation of Linear Momentum

Classical Mechanics > Motion in One Dimension > Velocity

Thermo & Stat Mech > Kinetic and Diffusive Processes > Brownian Motion, Diffusion

Thermo & Stat Mech > Second and Third Law > Entropy

Life Sciences Topics:

Biochemistry > Proteins

Molecular and Cellular Biology > Cellular Dynamics, Cellular Interactions

Chemistry Topics:

Macromolecules > Proteins

Spontaneity > Entropy

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Diffusion Model through Conservation of Momentum and Energy > Simulating Diffusion of Proteins in Water

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

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