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dc.titleMolecular simulations of transport and separation in Protein crystals
dc.contributor.authorHU ZHONGQIAO
dc.identifier.citationHU ZHONGQIAO (2009-09-07). Molecular simulations of transport and separation in Protein crystals. ScholarBank@NUS Repository.
dc.description.abstractAs novel bionanoporous materials, protein crystals have demonstrated increasing potentials in a wide variety of applications such as bioseparation, biocatalysis and biosensing. Deep insight into the transport properties and separation mechanisms in protein crystals is crucial to better exploring their emerging applications. Toward this end, molecular dynamics (MD) simulations were employed in this thesis to investigate transport and separation in different protein crystals. First the structural and dynamic properties of water and ions were studied. Diffusivities in protein crystals are reduced by one ~ two orders of magnitude than in bulk phase. The mobility in the crystals is enhanced with increasing porosity. Anisotropic diffusion is found preferentially along the pore axis. Upon exposure to electric field, the stability of protein reduces slightly. The water dipole moment along the pore axis rises linearly with increasing field strength. Equilibrium and non-equilibrium MD simulations give consistent electrical conductivity in the crystal. Subsequently achiral and chiral separation processes were examined for amino acids. Three amino acids (Arg, Phe and Trp) have the elution order Arg > Phe > Trp in glucose isomerase crystal. In thermolysin crystal, D-phenylglycine transports slower than L-phenylglycine. The separation mechanisms were elucidated from energetic and structural analysis. Finally, three biomolecular force fields (OPLS-AA, AMBER03 and GROMOS96) in conjunction with three water models (SPC, SPC/E and TIP3P) were assessed for the transport of water and ions in a lysozyme crystal. Water diffusivities from OPLS-AA and AMBER03 along with SPC/E model match fairly well with experimental data. A combination of OPLS-AA for lysozyme and Kirkwood-Buff model for NaCl is superior to others in predicting ion mobility.
dc.subjectsimulations; transport; separation; protein crystals
dc.contributor.supervisorJIANG JIANWEN
dc.description.degreeconferredDOCTOR OF PHILOSOPHY
Appears in Collections:Ph.D Theses (Open)

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