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Design of New Materials: Navigating Molecular Worms Inside Chemical Labyrinths

Access of a molecule to a particular site or place in a chemical system is important in chemistry and material science. For example, a substrate has to have access to an active site of an enzyme (catalyst) before the enzymatic (catalytic) reaction can take place. The “accessible volume” which is available to a penetrating molecule is useful in discussing physical properties such as diffusion, viscosity, and electrical conductivity in glasses, polymers and porous materials. Predicting if a molecule can traverse chemical labyrinths of channels usually requires performing computationally intensive molecular dynamics simulations. Since it is impractical to test each molecule/labyrinth pair using computationally expensive methods, we have built sophisticated algorithms to explore geometric configurations and prune possibilities, using a moving “molecular worm” assembled from solid blocks connected by flexible structures, and which can then compute accessible regions using a variant of Fast Marching Methods. Joint with the LBNL EFRC (Energy Frontier Research Center), we are using these techniques to prune detailed zeolite databases for potential materials for carbon sequestration.