Coarse-Graining of Complex Liquids: Structure and Dynamics

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Marina Guenza at the University of Oregon Eugene is supported by an award from the Chemical Theory, Models and Computational Methods program focusing on understanding the relation between molecular structure and macroscopic properties of synthetic polymeric materials and large biological molecules. Computer simulations are useful to provide information about the microscopic molecular structure of a liquid, but describing the macroscopic properties that are measured experimentally exceeds the computational capabilities of traditional simulations. New computational strategies are being developed here to accelerate simulations and connect the molecular structure to the macroscopic properties for different temperatures and other thermodynamic conditions. This provides an important tool to study the properties of novel materials and biological molecules such as proteins, DNAs, and RNAs.This project uses a coarse-graining theory with the desirable property that structural and thermodynamic consistency are maintained throughout coarse-graining. Novel applications include the search for macromolecular structures that self-assmble in a soft crystal lattice of desired geometry. An original approach is used for the coarse-grained dynamics of biological macromolecules, specifically protein, DNA, and RNA, that is based on the Langevin equation for the dynamics of macromolecules in solution. This method also accounts for the presence of local conformational barriers and for internal hydrophobic regions. Theoretical predictions are compared to experimental data from collaborators at the University of Oregon.