Large-scale simulations of layered double hydroxide nanocomposite materials.
Doctoral thesis, UCL (University College London).
Layered double hydroxides (LDHs) have generated a large amount of interest in recent years due to their ability to intercalate a multitude of anionic species. Atomistic simulation techniques such as molecular dynamics have provided considerable insight into the behaviour of these materials. The advent of supercomputing grids allows us to explore larger scale models with considerable ease. In this thesis we present our findings from large scale molecular dynamics simulations of Mg_2AI-LDHs intercalated with either chloride ions or a mixture of DNA and chloride ions. The system exhibits emergent properties, which are suppressed in smaller scale simulations. Undulatory modes are caused by the collective thermal motion of atoms in the LDH layers. Thermal undulations provide information about the materials properties of the system. In this way, we obtain values for elastic properties of the system including the bending modulus, Young's moduli and Poisson's ratios. The intercalation of DNA into LDHs has various applications, including drug delivery for gene therapy and origins of life studies. The nanoscale dimensions of the interlayer region make the exact conformation of the intercalated DNA difficult to elucidate experimentally. We use molecular dynamics techniques to perform simulations of double stranded, linear and plasmid DNA up to 480 base pairs in length intercalated within LDHs. Currently only limited experimental data has been reported for these systems. Our models are found to be in agreement with experimental observations, according to which hydration is a crucial factor in determining the structural stability of DNA. Phosphate backbone groups are found to align with aluminium lattice positions. At elevated temperatures and pressures, relevant to origins of life studies which maintain that the earliest life forms originated around deep ocean hydrothermal vents, the structural stability of LDH-intercalated DNA is substantially enhanced as compared to DNA in bulk water. We also discuss how the materials properties of the LDH are modified due to DNA intercalation. Recent experimental studies of LDHs have shown that these minerals can form staged intermediate structures during intercalation. However, the mechanism which produces staged structures remains undetermined. Our studies show that LDHs are flexible enough to deform around bulky intercalants such as DNA. The flexibility of layered materials has been shown to affect the pathway by which staging occurs. Even though the structures under study are all energetically very similar, overall there is greater diffusion of DNA strands in a Daumas-Hérold configuration compared to a Rüdorff model and a stage-1 structure.
|Title:||Large-scale simulations of layered double hydroxide nanocomposite materials|
|Additional information:||Authorisation for digitisation not received. Abstract contains LATEX text. Please see thesis for rendered formulae and equations|
|UCL classification:||UCL > School of BEAMS > Faculty of Maths and Physical Sciences > Chemistry|
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