How to simulate a protein diffusing into a charged cage

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As part of the verification process for my engineering capstone, I need to simulate the movement of a protein into a cage. The protein is 15 nm tall, and the cage needs to be large enough to contain the protein in its centre (~30 nm^3).

Both the protein and the cage are negatively charged: the protein is 2x the charge of an electron, the cage is 2180x the charge of an electron, and it has a diagonal in its centre with a charge of 42e- which is where the protein will bind to.

The fluid has an electrolyte salt concentration of 150 mmol/L.

I have set up all of the above parameters in COMSOL's electrostatic interface and am unsure of how to proceed and would appreciate any help!

I have two goals for my simulation: (1) Optimize the size of the cage opening to allow for the protein to enter. A smaller size will be cheaper to produce. (2) Test at different distances to see if there are any electrostatic effects between the cage and the protein.

Do you have any suggestions of what type of physics to use and how to define the domains and boundaries in order to study the movement and meet my two goals?



1 Reply Last Post 2022年12月1日 GMT-5 04:11
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Hello Hannah Bernstein

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Posted: 2 months ago 2022年12月1日 GMT-5 04:11

In the nanometer scale diffusion is irrelevant. A macroscopic approach, i.e. a transport equation does not make much sense. The issue is that how a protein molecule approaches the cage. Sounds like a problem of molecular dynamics.

In the nanometer scale diffusion is irrelevant. A macroscopic approach, i.e. a transport equation does not make much sense. The issue is that how a protein molecule approaches the cage. Sounds like a problem of molecular dynamics.

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