This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. In order to extend molecular dynamics simulations to large polysaccharides as well as to study their motions on the micro- to millisecond timescale, we have begun to develop a low-resolution (molecular resolution rather than atomic) model for carbohydrate residues. This model uses a single spherical particle to model an individual glycosyl residue. The particles are hinged together through a vertex equivalent to the glycosidic oxygen atom. Electrostatic interactions are modeled as point centered multipole expansions, while steric and torsional terms are modeled as van der Waals surfaces and Fourier expansions respectively. Solvent effects will be incorporated using approaches based on the Poisson-Boltzmann approximation.
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