Browsing by Author "Gamieldien, Mogamat Riedaa"

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    Open Access
    Investigations of the solution properties of both unmodified and modified cyclodextrins
    (2008) Gamieldien, Mogamat Riedaa; Naidoo, Kevin J
    The major part of this focuses on investigating the anomalous solubility of β-cyclodextrin using time correlation functions as the main tool for analysis. The primary focus is on the conformational metrics which govern the internal motions of the three main, unmodified cyclodextrins (namely a, β and y). The conformational space and dynamics of the interglycosidic dihedral angles, individual glucose tilting and verticallibrations of each glucose unit is investigated. Also the hydrogen bonding across the glycosidic linkage is examined. We then investigate the solution properties of cyclodextrin solutions using both ultrasonic interferometry and molecular dynamics.
  • Thumbnail Image
    Item
    Open Access
    Parameterization of the Gay-Berne coarse-grained potential from atomistically detailed anisotropic free energy volumes
    (2012) Gamieldien, Mogamat Riedaa; Naidoo, Kevin J
    Simulating a system of 300,000+ atoms, such as an explicitly solvated protein using all atom molecular dynamics on the microsecond time-scale, would require an enormous amount of computing power and specialized software, even with which would still require months of computing time. However, if the atomic degrees of freedom of the system can be reduced (or averaged) in some physically intuitive manner, while still retaining a connection with the underlying atomistic detail, microsecond simulations could be achieved within weeks or days. Coarse-graining, a sub-class of mesoscale modelling, is used to represent molecules in a reduced form as either regular spheroids (ellipsoids) or as continuum models, using specialized interaction potentials. The Gay-Berne is a one such coarse-grain potential, which has been particularly successful in that it has been used in modelling of liquid crystals, protein dynamics and lipid membrane and micelle formation...