“Multiscale Biomolecular Modeling in 4-D”
Willy Wriggers, Department of Mechanical and Aerospace Engineering,
Old Dominion University
As observed in computer simulations or in multi-scale structures, the behavior of “biological machines” that emerges on temporal and spatial scales in not only more than the sum of the parts, but quite different and unexpected. Examaples include: (1) A novel “fast mutual information” analytics, which can transform time domain data into spatial images through a hand-shaking between fast and slow degrees of freedom. The statistical data mining takes advantage of the detailed time series of computer simulations and it yields spatial heat maps that can be visualized on molecular structures or in the form of interaction networks. (2) The hierarchical structures revealed by electron microscopy or tomography imaging of molecular systems. Fitting and segmentation in the spatial anda temporal domain reveal the complex arrangement of the molecular building blocks of living organisms. (3) Computer graphics. There is currently a paradigm shift under way towards the use of more realistic global illumination models. We adapted the “screen-space ambient occlusion” approach that originated in the video game industry to our open-source multi-scale modeling program, Sculptor. Our approach has been uniquely customized with shading that is tuned for pockets and cavities of a user-defined size, making it useful for visualizing molecular features at multiple spatial scales of interest. The three examples demonstrate that it is often useful to employ a “systems” perspective in computational modeling of 4-D biological structures whenever complex phenomena arise that cannot be predicted from isolated degrees of freedom.