Two data visualizations I did in 2010 using the output of folding simulations of protein molecules. These renderings were created by combining thousands of protein models generated by the computer across several simulations for the protein ubiquitin. The simulated folding process progresses from the initial, unfolded, random coil ensamble of the molecule, ultimately converging into a more localized set of conformations that resemble the biologically functional state of the protein.
.
.
.
.
The simulations were carried out using algorithms and models I contributed to develop as a postdoctoral researcher at the University of Chicago (see this page for more details about the research). In each one of these simulations, the computer starts off the process with an extended or unfolded chain of the protein in consideration. By minimizing a potential energy function using a simulated annealing algorithm, the molecule folds into more compact structures that bring down the potential energy. Due to the probabilistically nature of the algorithm, each simulation instance generates a slightly different result. By combining all these results into a single representation, it is possible to see the converging nature of the process.
The first rendering is called “Convergence” for the reasons just explained, and it was created upon a request from Professor Karl Freed, as a print for permanent display at the James Frank Institute. The image also shows part of the code from the simulated annealing loop used to compute the simulations.
A second rendering using the same dataset is called “Divergence”, as the vantage point was placed precisely around the converged structures, and looking towards the unfolding direction. The gallery below contains low-resolution images of these visualizations. For high-resolution versions (4096×4096 pixels), please download the following zip packages containing the images in tiff format: convergence, divergence.
These visualizations were generated with the Processing programming language in combination with the GLGraphics and Proscene libraries.
