PARAMETRIC STUDY OF REAXFF SIMULATION PARAMETERS FOR MOLECULAR DYNAMICS MODELING OF REACTIVE CARBON GASES

Abstract The development of innovative carbon-based materials can be greatly facilitated by molecular modeling techniques. Although the Reax Force Field (ReaxFF) can be used to simulate the chemical behavior of carbon-based systems, the simulation settings required for accurate predictions have not been fully explored. Using the ReaxFF, molecular dynamics (MD) simulations are used to simulate the chemical behavior of pure carbon and hydrocarbon reactive gases that are involved in the formation of carbon structures such as graphite, buckyballs, amorphous carbon, and carbon nanotubes. It is determined that the maximum simulation time step that can be used in MD simulations with the ReaxFF is dependent on the simulated temperature and selected parameter set, as are the predicted reaction rates. It is also determined that different carbon-based reactive gases react at different rates, and that the predicted equilibrium structures are generally the same for the different ReaxFF parameter sets, except in the case of the predicted formation of large graphitic structures with the Chenoweth parameter set under specific conditions.

Experimental and theoretical study of microstructure effect on piezoelectric property of one dimensional ZnO nanostructures

Emerging nanogenerators have attracted the attention of the research community, focusing on energy generation using piezoelectric nanomaterials. Nanogenerators can be utilized for powering NEMS/MEMS devices. Understanding the piezoelectric properties of ZnO one-dimensional materials such as ZnO nanobelts (NBs) and Nanowires (NWs) can have a significant impact on the design of new devices. The goal of this dissertation is to study the piezoelectric properties of one-dimensional ZnO nanostructures both experimentally and theoretically. First, the experimental procedure for producing the ZnO nanostructures is discussed. The produced ZnO nanostructures were characterized using an in-situ atomic force microscope and a piezoelectric force microscope. It is shown that the electrical conductivity of ZnO NBs is a function of applied mechanical force and its crystalline structure. This phenomenon was described in the context of formation of an electric field due to the piezoelectric property of ZnO NBs. In the PFM studies, it was shown that the piezoelectric response of the ZnO NBs depends on their production method and presence of defects in the NB. Second, a model was proposed for making nanocomposite electrical generators based on ZnO nanowires. The proposed model has advantages over the original configuration of nanogenerators which uses an AFM tip for bending the ZnO NWs. Higher stability of the electric source, capability for producing larger electric fields, and lower production costs are advantages of this configuration. Finally, piezoelectric properties of ZnO NBs were simulated using the molecular dynamics (MD) technique. The size-scale effect on piezoelectric properties of ZnO NBs was captured, and it is shown that the piezoelectric coefficient of ZnO NBs decreases by increasing their lateral dimensions. This phenomenon is attributed to the surface charge redistribution and compression of unit cells that are placed on the outer shell of ZnO NBs.

A THEORETICAL STUDY OF INTERACTION OF NANOPARTICLES WITH BIOMOLECULE

Many types of materials at nanoscale are currently being used in everyday life. The production and use of such products based on engineered nanomaterials have raised concerns of the possible risks and hazards associated with these nanomaterials. In order to evaluate and gain a better understanding of their effects on living organisms, we have performed first-principles quantum mechanical calculations and molecular dynamics simulations. Specifically, we will investigate the interaction of nanomaterials including semiconducting quantum dots and metallic nanoparticles with various biological molecules, such as dopamine, DNA nucleobases and lipid membranes. Firstly, interactions of semiconducting CdSe/CdS quantum dots (QDs) with the dopamine and the DNA nucleobase molecules are investigated using similar quantum mechanical approach to the one used for the metallic nanoparticles. A variety of interaction sites are explored. Our results show that small-sized Cd4Se4 and Cd4S4 QDs interact strongly with the DNA nucleobase if a DNA nucleobase has the amide or hydroxyl chemical group. These results indicate that these QDs are suitable for detecting subcellular structures, as also reported by experiments. The next two chapters describe a preparation required for the simulation of nanoparticles interacting with membranes leading to accurate structure models for the membranes. We develop a method for the molecular crystalline structure prediction of 1,2-Dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC), 1,2-Dimyristoyl-sn-glycero-3-phosphorylethanolamine (DMPE) and cyclic di-amino acid peptide using first-principles methods. Since an accurate determination of the structure of an organic crystal is usually an extremely difficult task due to availability of the large number of its conformers, we propose a new computational scheme by applying knowledge of symmetry, structural chemistry and chemical bonding to reduce the sampling size of the conformation space. The interaction of metal nanoparticles with cell membranes is finally carried out by molecular dynamics simulations, and the results are reported in the last chapter. A new force field is developed which accurately describes the interaction forces between the clusters representing small-sized metal nanoparticles and the lipid bilayer molecules. The permeation of nanoparticles into the cell membrane is analyzed together with the RMSD values of the membrane modeled by a lipid bilayer. The simulation results suggest that the AgNPs could cause the same amount of deformation as the AuNPs for the dysfunction of the membrane.

WATER USE AND SYSTEM RELIABILITY UNDER DIESELGENERATOR AND SOLAR PHOTOVOLTAIC POWERED PUMPING SYSTEMS: A CASE STUDY OF SOLLA TOGO

Access to improved potable water sources is recognized as one of the key factors in improving health and alleviating global poverty. In recently years, substantial investments have been made internationally in potable water infrastructure projects, allowing 2.3 billion people to gain access to potable water from 1990-2012. One such project was planned and installed in Solla, Togo, a rural village in the northern part of the country, from 2010-2012. Ethnographic studies revealed that, while the community has access to potable water, an estimated 45% of the village’s 1500 residents still rely on unprotected sources for drinking and cooking. Additionally, inequality in system use based on income level was revealed, with the higher income groups accessing the system more regularly than lower income groups. Cost, as well as the availability of cheaper sources, was identified as the main deterrent from using the new water distribution system. A new water-pricing scheme is investigated here with the intention of making the system accessible to a greater percentage of the population. Since 2012, a village-level water committee has been responsible for operations and maintenance (O&M), fulfilling the community management model that is recommended by many development theorists in order to create sustainable projects. The water committee received post-construction support, mostly in the form of technical support during system breakdowns, from the Togolese Ministry of Water and Sanitation (MWSVH). While this support has been valuable in maintaining a functional water supply system in Solla, the water committee still has managerial challenges, particularly with billing and fee collection. As a result, the water committee has only received 2% - 25% of the fees owed at each private connection and public tap stand, making their finances vulnerable when future repairs and capital replacements are necessary. A new management structure is proposed by the MWSVH that will pay utilities workers a wage and will hire an accountant in order to improve the local management and increase revenue. This proposal is analyzed under the new water pricing schemes that are presented. Initially, the rural water supply system was powered by a diesel-generator, but in 2013, a solar photo-voltaic power supply was installed. The new system proved a fiscal improvement for the village water committee, since it drastically reduced their annual O&M costs. However, the new system pumps a smaller volume of water on a daily basis and did not meet the community’s water needs during the dry season of 2014. A hydraulic network model was developed to investigate the system’s reliability under diesel-generator (DGPS) and solar photovoltaic (PVPS) power supplies. Additionally, a new system layout is proposed for the PVPS that allows pumping directly into the distribution line, circumventing the high head associated with pumping solely to the storage tank. It was determined that this new layout would allow for a greater volume of water to be provided to the demand points over the course of a day, meeting a greater fraction of the demand than with the current layout.