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Atomistic Insights Into Photoprotein Formation: Computational Prediction Of The Properties Of Coelenterazine And Oxygen Binding In Obelin, Thomas M. Griffiths

University of Wollongong Thesis Collection 2017+

Bioluminescence in marine systems is dominated by the use of one ligand for light production, coelenterazine. The bioluminescent reaction of coelenterazine is an enzyme catalysed, oxidative decarboxylation. During the reaction coelenterazine reacts with molecular oxygen to form carbon dioxide, coelenteramide and light. One such class of bioluminescent systems is the Ca[sup]2+-regulated photoproteins. These proteins, rather than continuously processing substrate, bind 2-hydroperoxycoelenterazine as an intermediate along the reaction pathway. The reaction is halted here until an external stimulus triggers the continuation of the bioluminescent reaction. There are currently no reported experimental, atomistic descriptions of the states that lead to this ternary …

Mathematical Modelling For Graphitic Nanostructures, Thomas Dyer

University of Wollongong Thesis Collection 2017+

Graphitic nanomaterials have been some of the most widely studied materials of the last decade. The isolation of monolayer graphene in 2004 sparked attention from numerous researchers due to the sheer breadth of its exceptional properties. Thus, it is important that theoretical models keep up with the pace of experimental discovery.

Remarkably, macroscale modelling techniques translate well to nanoscale application. Treating graphitic structures as continuous surfaces allows the application of continuum mechanics and variational calculus amongst others. This thesis involves the formulation and subsequent analysis of three mathematical models relating to the conformation of graphitic structures.

Firstly, we study the …

Molecular Dynamics Simulation Of Adsorption And Lubrication Of Hydrocarbons And Aqueous Copolymer Lubricants On Iron And Iron Oxide Surfaces, Thi Dinh Ta

University of Wollongong Thesis Collection 1954-2016

A classical molecular dynamics (MD) simulation has been used to investigate the adsorption and tribological performance of hydrocarbon lubricant between different iron and iron oxide surfaces. A realistic all-atom model of alkane was employed using the COMPASS force field (FF) while the relaxed surfaces and an effective force field for interactions between surface and lubricant were obtained from ab-initio calculations. A comparative analysis of adsorption of six n-alkanes (C_nH_2n+2, n = 4, 6, 8, 10, 12, 16) on Fe(110), FeO(110), and Fe₂O₃(0001) and thin film lubrication of hexadecane between Fe(100), Fe(110), Fe(111), …

Dnag As An Antibacterial Target, Zorik Chilingaryan

University of Wollongong Thesis Collection 1954-2016

The rise of “superbugs” – antibiotic resistant infection-causing bacteria - poses a catastrophic threat to public health, and prompts the investigation of new drug targets. In this work, the inhibition of specific proteins in bacterial DNA replication machinery – a rich source of new targets - was investigated.

The single stranded DNA-binding protein, SSB, is an interaction hub that engages in vital interactions with several partner proteins through a flexible C-terminal peptide motif (DDDIPF; SSB-Ct). Based on available crystal structures of SSB-Ct with partner proteins, molecular dynamics simulations were used to identify mobile elements of SSB-Ct and important interactions in …

Molecular Dynamics Simulation Of Fracture Behaviour In Nanocrystalline Fcc Structures, Linqing Pei

University of Wollongong Thesis Collection 1954-2016

The study of material failure has always been very important for human beings. Previous studies were mostly conducted at the macroscopic and microscopic scale based on continuum mechanics. However, the effect of nanostructural features on fracture has not been fully understood. Therefore, it is necessary to investigate the fracture mechanics at the atomic scale. Computational modelling, particularly atomistic (or molecular) simulation is becoming an increasingly important technology with which to analyse fracture. In this thesis, molecular dynamics (MD) simulations were carried out to investigate the fracture behaviours in Face Centred Cubic (fcc) nanocrystals.

Nanotwinned Copper (Cu) has an unusual combination …

Atomistic Simulation Of Plasticity Mediated By Grain Boundary And Stacking Fault Tetrahedron In Fcc Metals, Liang Zhang

University of Wollongong Thesis Collection 1954-2016

Nanocrystalline material has been the subject of widespread research over the past couple of decades. When the grain sizes of crystals are down to nanoscale, the so-called nanocrystalline material can exhibit distinct physical properties, unlike their conventional counterparts. The strength and plastic deformation of nanocrystalline material were among the most broadly investigated properties from the mechanical and material perspective. But since the rapid increases in computational power, atomistic simulation has been used extensively to study the mechanical properties of nanocrystalline material from which enormous progress has been made in computational simulation to understand the deformation mechanisms at an atomic scale. …

Deformation Mechanisms In Nanotwinned Materials By Molecular Dynamics Simulations, Xing Zhao

University of Wollongong Thesis Collection 1954-2016

Molecular dynamics simulations are performed to investigate the deformation mechanisms of nanotwinned materials. The simulations oftextured polycrystalline Cu under tensile loading parallel to the twin boundary (TB) reveal that the transmissions of dislocations dominate the plastic deformation. The majority of the TBs retain their initial coherency even after a considerable deformation. The tensile strength monotonically increases as the twin spacing decreases. The main strengthening effect in nanotwinned Cu results from TB restricting the dislocation transmission across TB. Dislocation processes involved in the slip-twin interactions are identified at atomic level, including the direct and indirect transmissions. The direct transmission involves either …

Molecular Dynamics Simulation Of Crack Propagation On Different Slip Planes Of Bcc Iron, Y. Gao, C. Lu, A. K. Tieu, H. T. Zhu

Faculty of Engineering - Papers (Archive)

In this paper, molecular dynamic simulations of crack propagation in body centre cubic (bcc) single crystal have been performed. The crack propagation behaviors on two different slip planes ({1 1 0} and {2 1 1}) have been investigated. A self-adaptive time step algorithm has been proposed to increase the stability of the simulations. It has been found that the slip plane significantly affects the propagation speed of the crack.