Subunits Size Distribution

This page illustrates potential uses of DESSA by presenting data one can derive from a simulation. Note that the visualizations here are not produced directly by DESSA but were made with Matlab from DESSA output data.

Mass fractions of intermediates versus time for sample trajectories of a capsid systems. The figures shows total mass vs. time for all possible assembly sizes from a single trajectory of a simulation model of cowpea chlorotic mottle virus (CCMV). Data for CCMV systems was gathered from prior work of [1]. Such single-trajectory data is useful for identifying features of the overall assembly process. In this case, the data suggests a nucleation-limited assembly in which a pool of pentameric intermediates appears to play an important role.

Capsid Structure

Computer model of a completed CCMV capsid. It provides the structure of the final assembly of a simulation of a single capsid, which can be plotted in MATLAB. In this case, we see the complete icosahedral structure that was used to define the local rules for CCMV. Such visualizations can also, however, allow one to analyze partially built structures and gain insight into key steps in the assembly of a system.

Bond Frequency

Table of bond frequencies for the simplified CCMV model at 12.75 uM concentration. Each plot is organized into a set of rows and columns such that the shading of the box in row i and column j denotes the fraction of oligomers of size i produced by a binding reaction involving an oligomer of size j. Lighter colors denote higher frequencies and darker colors lower frequencies, with black representing a reaction unobserved in the course of the simulations. This kind of analysis, generated by aggregating results from many simulations, provides one a picture of the overall ensemble of frequent assembly trajectories for a system.


[1] G. L. Casini, D. Graham, D. Heine, R. L. Garcea, and D. T. Wu. In vitro papillomavirus capsid assembly analyzed by light scattering. Virology, 325(2):320-327, 2004.