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Title: Monte Carlo Simulation of Molecules and Ions In Liquid Water
Keywords: Molecular simulation, Monte Carlo, distributed multipoles, force fields, amino acids, neuraminidase inhibitors
Issue Date: 2-Jun-2011
Citation: MICHAEL YUDISTIRA (2011-06-02). Monte Carlo Simulation of Molecules and Ions In Liquid Water. ScholarBank@NUS Repository.
Abstract: Derivation of reaction free energy of chemical processes in aqueous environments can be aided by the knowledge of hydration free energy. Monte Carlo simulation can be done in conjunction with the thermodynamic perturbation method, by means of Bennett's acceptance ratio, in order to obtain the free energy. The solute molecule was 'morphed' from a non-interacting 'ghost' molecule inside a box containing TIP3P/TIP4P water molecules under the periodic boundary conditions to its full potential functions, by subjecting the two endpoint systems and intermediate systems with soft-core solute-solvent interaction potentials to separate MC simulations. All MC simulations were performed using a homegrown Fortran90 program that allowed choice of solvent models and custom interaction functions, and was well-tailored for morphing oriented works. A good deal of attention was put on the potential functions used for solute-solvent interaction. While empirical functions were used, they are largely consistent with established theoretical arguments and constructs.
Appears in Collections:Ph.D Theses (Open)

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