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UBC Theses and Dissertations

Bottom-up coarse-graining : theory, implementation, application Tran, Hoang


Molecular dynamics simulations at the atomic scale are a powerful tool to study the structure and dynamics of biological systems. However, important processes, such as protein folding, are still too computationally expensive to be investigated with atomistic simulations. In these situations, different coarse-grained force fields have been developed to appropriately reproduce the static structure of the systems. These strategies can range from specially designed, ad hoc approaches to transferrable, bottom-up plans. Nevertheless, because of the reduction in number of degrees of freedom, the obtained dynamics typically suffer from inaccuracies, which may be not adjustable using trivial scaling. To correctly reintroduce these properties, one can apply the Mori-Zwanzig formalism, essentially injecting the memory effects into these coarse-graining schemes. In practice, because of the difficulty in algorithm designing and the limit on computing power, the memory is often assumed to be short-term, and therefore can be approximated as a delta function. Recently, some investigations have been done successfully on simple models with significantly long memory. This work aims to extend these successes on systems with more complex topology. In particular, we applied the Mori-Zwanzig formalism to the system of polyethylene chains. Using GROMACS united atom model, molecular dynamics simulation was performed to obtain the coarse-grained force field and the memory kernel of the nonbonded interaction. These elements allowed for a successful coarse-grained simulation, which captured both static and dynamical structures of the reference system.

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