Simulations

These simulations illustrate how specific cellular functions are controlled by proteins, or how proteins move and function. What is the difference between a simulation and an animation? Read more here.

Molecular Scale

All-Atom Molecular Dynamics simulations

are linked from the Theoretical and Computational Biophysics Group (TCBG) at UIUC.

Water through a protein channel.

By TCBG at UIUC.

 

 

 

Protein folding

By TCBG at UIUC

 

Coarse-grained Molecular Dynamics simulations

were generated by undergraduates taking “Modeling the Living Cell” in 2017 at JHU, using their own MATLAB code.

Simplified H-P model protein

By: Nicole Pagane, Tiffany Hu, and Melissa Mai

 

 

 

Simplified H-P model, with more complex energy function

By: Melissa Mai, Nicole Pagane, and Tiffany Hu.

 

Cell Scale

Structure-resolved Reaction-diffusion Simulations

Clathrin proteins assembling into cages in solution

By: The Johnson Lab

 

 

Clathrin assembly nucleated by membrane localization

By: The Johnson Lab

 

 

 

Clathrin assembly (!) in solution

By: The Johnson Lab

 

 

Continuum PDE Reaction-diffusion simulation

using The Virtual Cell software

 

Min proteins controlling bacterial cell division site

By: Athena Chen and Mekhi Closson

 

MATLAB animation of the protein concentrations

 

 

 

Visit the bacterial cell division page!