Indiana University-Purdue University Indianapolis (IUPUI) / Nanoscale materials have become an active area of research due to the enhanced mechanical properties of the nanomaterials in comparison to their respective bulk materials. The effect that the size and shape of a nanomaterial has on its mechanical properties is important to understand if these materials are to be used in engineering applications. This thesis presents the results of molecular dynamics (MD) simulations on copper, gold, nickel, palladium, platinum, and silver nanowires of three cross-sectional shapes and four diameters. The cross-sectional shapes investigated were square, circular, and octagonal while the diameters varied from one to eight nanometers. Due to a high surface area to volume ratio, nanowires do not have the same atomic spacing as bulk materials. To account for this difference, prior to tensile loading, a minimization procedure was applied to find the equilibrium strain for each structure size and shape. Through visualization of the atomic energy before and after minimization, it was found that there are more than two energetically distinct areas within the nanowires. In addition, a correlation between the anisotropy of a material and its equilibrium strain was found. The wires were then subjected to a uniaxial tensile load in the [100] direction at a strain rate of 108 s-1 with a simulation temperature of 300 K. The embedded-atom method (EAM) was employed using the Foiles potential to simulate the stretching of the wires. The wires were stretched to failure, and the corresponding stress-strain curves were produced. From these curves, mechanical properties including the elastic modulus, yield stress and strain, and ultimate strain were calculated. In addition to the MD approach, an energy method was applied to calculate the elastic modulus of each nanowire through exponential fitting of an energy function. Both methods used to calculate Young’s modulus qualitatively gave similar results indicating that as diameter decreases, Young’s modulus decreases. The MD simulations were also visualized to investigate the deformation and yield behavior of each nanowire. Through the visualization, most nanowires were found to yield and fail through partial dislocation nucleation and propagation leading to {111} slip. However, the 5 nm diameter octagonal platinum nanowire was found to yield through reconstruction of the {011} surfaces into the more energetically favorable {021} surfaces.

Thesis (M.Tech.: Chemistry)-Dept. of Chemistry, Durban Institute of Technology, 2003 ix, 70 leaves + 1 computer laser optical disc / The purpose of this study is to utilize computational techniques in the determination of the mechanistic pathways for the one-pot conversion of a pentacyclo-undecane (PCU) dione 1.1 to a pentacyclo-undecane cage lactam 1.2.

Aquesta tesi tracta de la creació d'un nou programari de codi obert i d'una interfície de programació (API) per realitzar simulacions (bio) moleculars, així com de a la seva aplicació posterior a problemes biològics. El nou programa, Adun, es focalitza en les àrees clau del càlcul d'energies lliures, el desenvolupament ràpid de programari i la productivitat d'alt rendiment. Mètodes com SCAAS, EVB i Born generalitzat han estat implementats per tal d'assolir el primer objectiu. La presencia d'aquestes tècniques, a m´es d'altres, mostra la velocitat de desenvolupament d'Adun. Totes les característiques s´on accessibles mitjanant una interfície gràfica d'usuari avançada que proveeix de noves capacitats, com el tractament de dades integrat o la compartició de dades i de càlculs distribuïts. La capacitat d'Adun de tractar problemes biològics és il·lustrada amb la investigació de la dinàmica de la proteïna Ras i el desenvolupament, implementació i demostració d'un nou mètode per a la determinació de camins de transició. A més, per tal de demostrar el potencial del programa Adun, aquests estudis també proporcionen una visió avançada sobre l'ús de la informació dinàmica en determinar la unció de les proteïnes. L'estat actual del programa i els resultats dels dos estudis és, doncs, discutit, i es donen indicacions dels objectius i direccions futurs. Finalment s'examina el paper dels científics computacionals com desenvolupadors d'eines, per a ells mateixos o per a tota la comunitat científica. / This thesis deals with the creation of a new open-source program and API for biomolecular simulation and its subsequent application to biological problems. The program, Adun, focuses on the key areas of biological free-energy calculations, rapid development and highperformance productivity. Methods such as SCAAS, EVB and switched Generalised-Born have been implemented to realise the first aim. The presence of these techniques, along with a multitude of others, verifies Adun's rapid development potential. All these features are united by an advanced graphical user interface which provides novel capabilities such as inbuilt data management, and distributed datasharing and computation. Adun's ability to tackle biological problems is illustrated with an investigation of Ras dynamics and the development, implementation and testing of a novel method for determining transition paths. In addition to concretely demonstrating Adun's potential these studies also provide insight into the use of dynamic information in elucidating protein function. The current state of the program and the results of the two studies is discussed and indications of future aims and directions given. In addition the role of computational scientists as developers of tools, for themselves and the wider scientific community, is examined.

Thesis (M.Tech.: Chemistry)-Dept. of Chemistry, Durban Institute of Technology, 2003 ix, 70 leaves + 1 computer laser optical disc / The purpose of this study is to utilize computational techniques in the determination of the mechanistic pathways for the one-pot conversion of a pentacyclo-undecane (PCU) dione 1.1 to a pentacyclo-undecane cage lactam 1.2.