Thesis (Ph. D.)--State University of New York at Binghamton, Department of Mathematical Sciences, 2008. / Includes bibliographical references.

Thesis (Ph. D.)--Duke University, 2007. / Includes bibliographical references.

Submitted in fulfilment of the requirements of Master's Degree in Chemistry, Durban University of Technology, 2017. / DNA damage plays a pivotal role in the pathogenesis of Alzheimer’s disease (AD) therefore, an innovative ss-DNA/dopamine/TiO2/FTO electrode strategy was developed to detect the genotoxicity upon photocatalytic reactions. This study involves a computational and electrochemical investigation towards the direct measurement of DNA damage. Computational chemistry was useful to resolve the intricate chemistry problems behind electrode constructions. The computational protocols were simultaneously carried out comprising of density functional theory (DFT) calculations, Metropolis Monte Carlo (MC) adsorption studies, and molecular dynamics (MD) simulations. The DFT calculations elucidated the structural, electronics, and vibrational properties of the electrode components resulting in a good agreement with the experimental parameters. The MC simulations carried out using simulated annealing predicted the adsorption process within layer-by-layer electrode as well generating reliable inputs prior to MD simulations. A 100 ns MD simulations were performed using a canonical ensemble provided information on the thermodynamics parameters such as total energy, temperature, and potential energy profiles, including radius of gyrations and atomic density profiles. Binding energies calculated from the MD trajectories revealed increasing interaction energies for the layer-by-layer electrode, in agreement with the electrochemical characterization studies (i.e. gradual decrease of cyclic voltammogram (CV) as well as increasing diameter of electrochemical impedance spectroscopy (EIS) semicircle upon electrode modification). The higher binding energies may lead to smaller changes in the electrochemical polarizability which directly affect to the decreasing of redox peak current and charge transfer resistance enhancement. Instead, HOMO-LUMO DFT levels are also taken into account to explain electron transfer phenomena within layer construction leading to the alteration of CV behaviours. Experimentally, the ss-DNA was electronically linked to TiO2/FTO surface through dopamine as a molecular anchor. Electrochemical measurements using cyclic voltammetry and EIS were employed to characterize the electrode modifications. The square wave voltammetry was subsequently used to measure the DNA damage and the potency of antioxidant treatment using ascorbic acid (AA) due to its ability in protecting the DNA from the damages. The presence of AA significantly protected the DNA from the damage, therefore was able to be used as a potential treatment in AD. Theoretically, guanine residues predicted by DFT as the most reactive sites of the ss-DNA involved in the genotoxic reactions. Overall, the theoretical studies successfully validated the experimental study as well as providing the molecular basis of interaction phenomena towards electrode constructions. Our results highlight the potential application of this methodology to screen the genotoxicity in Alzheimer’s, suggesting the important role of theoretical studies to predict the molecular interaction and validation of the DNA-based sensors and bioelectronics. / M

Thesis (M.S.)--State University of New York at Binghamton, Thomas J. Watson School of Engineering and Applied Science, Department of Electrical and Computer Engineering, 2008. / Includes bibliographical references.

Membrane computing investigates models of computation inspired by certain features of biological cells, especially features arising because of the presence of membranes. Because of their inherent large-scale parallelism, membrane computing models (called P systems) can be fully exploited only through the use of a parallel computing platform. However, it is an open question whether it is feasible to develop an efficient and useful parallel computing platform for membrane computing applications. Such a computing platform would significantly outperform equivalent sequential computing platforms while still achieving acceptable scalability, flexibility and extensibility. To move closer to an answer to this question, I have investigated a novel approach to the development of a parallel computing platform for membrane computing applications that has the potential to deliver a good balance between performance, flexibility, scalability and extensibility. This approach involves the use of reconfigurable hardware and an intelligent software component that is able to configure the hardware to suit the specific properties of the P system to be executed. As part of my investigations, I have created a prototype computing platform called Reconfig-P based on the proposed development approach. Reconfig-P is the only existing computing platform for membrane computing applications able to support both system-level and region-level parallelism. Using an intelligent hardware source code generator called P Builder, Reconfig-P is able to realise an input P system as a hardware circuit in various ways, depending on which aspects of P systems the user wishes to emphasise at the implementation level. For example, Reconfig-P can realise a P system in a rule-oriented manner or in a region-oriented manner. P Builder provides a unified implementation framework within which the various implementation strategies can be supported. The basic principles of this framework conform to a novel design pattern called Content-Form-Strategy. The framework seamlessly integrates the currently supported implementation approaches, and facilitates the inclusion of additional implementation strategies and additional P system features. Theoretical and empirical results regarding the execution time performance and hardware resource consumption of Reconfig-P suggest that the proposed development approach is a viable means of attaining a good balance between performance, scalability, flexibility and extensibility. Most of the existing computing platforms for membrane computing applications fail to support nondeterministic object distribution, a key aspect of P systems that presents several interesting implementation challenges. I have devised an efficient algorithm for nondeterministic object distribution that is suitable for implementation in hardware. Experimental results suggest that this algorithm could be incorporated into Reconfig-P without too significantly reducing its performance or efficiency. / Thesis (PhDInformationTechnology)--University of South Australia, 2010