Schaeffer MPP 2011

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Visualizing Stochastic Simulations of Nucleic Acid Folding

  • Joseph Schaeffer, Caltech


The Multistrand program simulates nucleic acid kinetics at the secondary structure level with single base-pair steps. A single kinetic trajectory can contain thousands of steps (or more), and understanding that data requires tools to condense that information into something useful. At the standard exchange rate of a picture being worth a thousand words, a movie of a kinetic trajectory has the possibility of conveying the information in a single trajectory in an understandable way. To create a good movie, we have to answer many questions: How do we visualize a secondary structure? How do we visualize a kinetic step between two secondary structures? Can we display every single step contained in a trajectory? Is that even useful? How do we handle systems with many distinct complexes?