SCI: Multiscale Modeling To Develop A Cyberinfrastructure For The Dynamics Of Flexible And Stiff Entangled Macromolecules

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A combined theoretical and experimental project is used to predict the dynamics and mobility of flexible, and semi-flexible macromolecular chains in a concentrated environment. The dynamics of polymers cover a large range of length and timescales, so they are not directly amenable to molecular dynamics studies. Instead, we implement a multiscale, coarse-graining approach utilizing slip-links to model entanglements on the mesoscopic level. The approach is robust, allowing consideration of lightly crosslinked elastic networks, semi-flexible mobility in gels, linear viscoelasticity of entangled chains, or nonlinear rheology of linear and star-shaped macromolecules. Mesoscopic-level parameters for the model may be determined by Monte Carlo (MC) and Molecular Dynamics (MD) simulations, although the smallest characteristic time scale (_e) is more easily treated phenomenologically. The approach allows modeling of time scales from the atomic up to hundreds of seconds. The resulting computational tools represent a major advance in soft-condensed matter physics, in particular for biological materials, and significantly enhances the shared cyberinfrastructure necessary to study, model and exploit such systems.The experimental component of the study takes advantage of recently acquired knowledge about the biosynthesis of branched proteins to generate a systematic collection of star-shaped proteins of defined architecture and molecular weight. The behavior of these proteins at various levels of entanglement with an immobile matrix are explored by characterizing their mobility during electrophoresis. The biological properties of branched polypeptides are the subject of intense interest but their analysis has been hampered by their anomalous behavior in most analytical techniques.