A Reduced Basis Method for Molecular Dynamics Simulation

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dc.contributor.authorVincent-Finley, Rachel Elisabethen_US
dc.date.accessioned2018-06-18T17:56:58Zen_US
dc.date.available2018-06-18T17:56:58Zen_US
dc.date.issued2005-12en_US
dc.date.noteDecember 2005en_US
dc.descriptionThis work was also published as a Rice University thesis/dissertation: http://hdl.handle.net/1911/18830en_US
dc.description.abstractIn this dissertation, we develop a method for molecular simulation based on principal component analysis (PCA) of a molecular dynamics trajectory and least squares approximation of a potential energy function. Molecular dynamics (MD) simulation is a computational tool used to study molecular systems as they evolve through time. With respect to protein dynamics, local motions, such as bond stretching, occur within femtoseconds, while rigid body and large-scale motions, occur within a range of nanoseconds to seconds. To capture motion at all levels, time steps on the order of a femtosecond are employed when solving the equations of motion and simulations must continue long enough to capture the desired large-scale motion. To date, simulations of solvated proteins on the order of nanoseconds have been reported. It is typically the case that simulations of a few nanoseconds do not provide adequate information for the study of large-scale motions. Thus, the development of techniques that allow longer simulation times can advance the study of protein function and dynamics. In this dissertation we use principal component analysis (PCA) to identify the dominant characteristics of an MD trajectory and to represent the coordinates with respect to these characteristics. We augment PCA with an updating scheme based on a reduced representation of a molecule and consider equations of motion with respect to the reduced representation. We apply our method to butane and BPTI and compare the results to standard MD simulations of these molecules. Our results indicate that the molecular activity with respect to our simulation method is analogous to that observed in the standard MD simulation with simulations on the order of picoseconds.en_US
dc.format.extent141 ppen_US
dc.identifier.citationVincent-Finley, Rachel Elisabeth. "A Reduced Basis Method for Molecular Dynamics Simulation." (2005) <a href="https://hdl.handle.net/1911/102046">https://hdl.handle.net/1911/102046</a>.en_US
dc.identifier.digitalTR05-15en_US
dc.identifier.urihttps://hdl.handle.net/1911/102046en_US
dc.language.isoengen_US
dc.titleA Reduced Basis Method for Molecular Dynamics Simulationen_US
dc.typeTechnical reporten_US
dc.type.dcmiTexten_US
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