<p> Traditionally, Molecular Dynamics combined with pair potential functions or the Embedded Atom Method (EAM) is applied to simulate the motion of atoms. When a defect is generated in the crystalline lattice, the equilibrium of atoms around it is destroyed. The atoms move to find a new place where the potential energy in the system is minimum, which could result in a change of the local atomic structure. This thesis introduces a new Dynamic Relaxation algorithm, which is based on explicit Finite Element Analysis, and pair or EAM potential function, to find equilibrium positions of the block of atoms containing different structural defects.</p> <p> The internal force and stiffness at the atoms (nodes) are obtained by the first and second derivatives of the potential energy functions. The convergence criterion is based on the Euclidean norm of internal force being close to zero when the potential energy is minimum. The damping ratio affects the solution path so that different damping ratios could lead to different minimum potential energy and equilibrium shapes. The choice of scaled mass of atoms, proper time step, boundary conditions and damping appropriate for the efficient and stable simulation is studied.</p> <p> A small block of atoms is used to obtain the numerical responses from a hybrid algorithm of potential energy functions and Dynamic Relaxation techniques such as repulsion and attraction in pair potential, minimum configuration, damping effects and different boundary conditions.</p> <p> The simulation using modified Dynamic Relaxation techniques is performed to the real material model with dislocation defect. The results after relaxation are in agreement with the prediction and current Molecular Dynamics simulation. Therefore, Dynamic Relaxation could be an alternative tool for atomistic simulation.</p> / Thesis / Master of Applied Science (MASc)

No description available.

Nitric oxide (NO), despite being a minor species, influences the chemistry, composition and energy balance of the earth's atmosphere above 90 kilometers. Variations in its density have been shown to strongly correlate with solar x-ray irradiance at lower latitudes and precipitating energetic particles at higher latitudes. Though the broad variations in NO densities with altitude and latitude are well known, there are still uncertainties associated with its chemistry. It is important to accurately model NO and its associated chemistry in an atmospheric model in order to obtain an accurate representation of the thermosphere. The NCAR Thermosphere-Ionosphere-Electrodynamics General Circulation Model (TIEGCM) is a three dimensional first principles based model which includes a self consistent aeronomic scheme that solves for winds, temperatures and densities of various neutral and charged species in the earth's upper atmosphere. Using a combination of the solar irradiance spectrum and solar indices as inputs, the model computes these outputs at every time step. The ability of the TIEGCM to predict NO densities in the thermosphere is examined by comparing results from the model with data obtained from the Student Nitric Oxide Explorer (SNOE). The comparisons are made for the year 1999 at 110 km and 150 km at the equator. Changes are made to the NO chemistry present in the model to reflect recent results obtained from laboratory data. Paricularly, the reaction of atomic oxygen with the first excited electronic state of nitrogen, N ₂(A) has been shown to play an important role in the production of NO. These changes are introduced to the model and their effect on NO densities is studied. Overall, it is seen that the updated chemistry scheme reduces the model agreement with the SNOE data at 110 km while slightly improving the agreement at a 150 km. The loss of agreement at 110 km is attributed to the fact that the neutral temperatures and atomic oxygen densities calculated by the TIEGCM are in sharp disagreement to the temperatures predicted by the NRL-MSIS at a 110 km, on which the new chemistry scheme is based. While the chemistry scheme used in this thesis is a step in the right direction for modelling NO using the TIEGCM, the parameters used were determined from the best fit obtained from the 1-D NO model. In the light of the differences between the NRL-MSIS and TIEGCM, it is necessary to return to the laboratory data and modify the parameters used here to achieve a better agreement with the data. / Master of Science

This dissertation describes computational and experimental studies of synthetic complexes that model the active site of the iron-iron hydrogenase [FeFe]H2ase enzyme. Simple dinuclear iron dithiolate complexes act as functional models of the ironiron hydrogenase enzyme by catalyzing isotopic exchange in D2/H2O mixtures. Density Functional Theory (DFT) calculations and new experiments have been performed that suggest reasonable mechanistic explanations for this reactivity. Evidence for the existence of an acetone derivative of the di-iron complex, as suggested by theory, is presented. Bis-phosphine substituted dinuclear iron dithiolate complexes react with the electrophilic species, H+ and Et+ (Et+ = CH3CH2 +) with differing regioselectivity; H+ reacts to form a 3c-2eâ Fe-H-Fe bond, while Et+ reacts to form a new C-S bond. The instability of a bridging ethyl complex is attributed to the inability of the ethyl group, in contrast to a hydride, to form a stable 3c-2eâ bond with the two iron centers. Gas-phase density functional theory calculations are used to predict the solutionphase infrared spectra for a series of CO and CN-containing dinuclear iron complexes dithiolate. It is shown that simple linear scaling of the computed C-O and C-N stretching frequencies yields accurate predictions of the experimentally determined ν(CO) and ν(CN) values. An N-heterocyclic carbene containing [FeFe]H2ase model complex, whose X-ray structure displays an apical carbene, is shown to undergo an unexpected simultaneous two-electron reduction. DFT shows, in addition to a one-electron Fe-Fe reduction, that the aryl-substituted N-heterocyclic carbene can accept a second electron more readily than the Fe-Fe manifold. The juxtaposition of these two one-electron reductions resembles the [FeFe]H2ase active site with an FeFe di-iron unit joined to the electroactive 4Fe4S cluster. Simple synthetic di-iron dithiolate complexes synthesized to date fail to reproduce the precise orientation of the diatomic ligands about the iron centers that is observed in the molecular structure of the reduced form of the enzyme active site. Herein, DFT computations are used for the rational design of synthetic complexes as accurate structural models of the reduced form of the enzyme active site.

<p>This master's thesis investigates if it is possible to increase the size of the simulations running on NETSim, Network Element Test Simulator, on a specific hardware and operating system. NETSim is a simulator for operation and maintenance of telecommunication network s.</p><p>The conclusions are that the disk usage is not critical and that it is needless to spend time optimizing disk and file system parameters. The amount of memory used by the simulations increased approximately linear with the size of the simulation. The size of the swap disk space is not a limiting factor.</p> / <p>Detta exsamensarbete undersöker om det är möjligt att öka storleken på simuleringskörningar av NETSim, Network Element Test Simulator, på en specifik hårdvaru- och operativsystemsplattform. NETSim är en simulator för styr och övervakning av telekomnätverk.</p><p>Slutsatserna är att diskanvändandet inte är kritiskt och att det är onödigt att ägna tid åt att optimera disk- och filsystemsparametrar. Minnesutnyttjandet ökar approximativt linjärt med storleken på simuleringarna. Storleken på swapdisken är inte någon begränsande faktor.</p>

3D seismic reflection data were acquired by the R/V Langseth and used to extract heat flow information using bottom-simulating reflector (BSR) depths across the southern Costa Rica convergent margin. These data are part of the CRISP Project, which will seismically image the Middle America subduction zone in 3D. The survey was conducted in an area approximately 55x11 km, northwest of the Osa Peninsula, Costa Rica. For the analysis presented here, seismic data were processed using a post-stack time migration. The BSR—a reverse polarity seismic reflection indicating the base of the gas hydrate phase boundary—is imaged clearly within the slope-cover sediments of the margin wedge. If pressure is taken into account, in deep water environments the BSR acts as a temperature gauge revealing subsurface temperatures across the margin. Two heat flow models were used in this analysis. In the Hornbach model BSR depth is predicted using a true 3D diffusive heat flow model combined with Integrated Ocean Drilling Program (IODP) thermal conductivity data and results are compared with actual BSR depth observations to constrain where heat flow anomalies exist. In the second model heat flow values are estimated using the heat flow equation. Uniform heat flow in the region should result in a deeper BSR downslope toward the trench due to higher pressure; however results indicate the BSR is deepest at over 325 meters below the seafloor (mbsf) further landward and shoals near the trench to less than 100 mbsf, suggesting elevated heat flow towards the toe of the accretionary prism. Heat flow values also reflect this relation. In addition to this survey-wide trend, local heat flow anomalies appear in the form of both circular patterns and linear trends extending across the survey, which can be related to mounds, thrust faults, folds, double BSRs, and seafloor erosion imaged in the seismic data. I suggest that these areas of higher local heat flow represent sites where advection of heat from deep, upward-migrating, thermogenically-sourced fluids and/or gases may be taking place. These heat flow trends have implications for not only earthquake nucleation, but also methane hydrate reserve stability. / text

Many places where natural gas hydrate occurs have a regionally extensive, bottom-simulating seismic reflector (BSR) at the base of the gas hydrate stability zone (GHSZ). This reflection marks the top of an underlying free-gas zone (FGZ). Usually, hydrate recycling (that produces gas as the stability field moves upward relative to sediments) is invoked to explain the presence and properties of the sub-BSR FGZ. However, this explanation is not always adequate: FGZs are often thicker in passive-margin environments where hydrate recycling is relatively slow, than in convergent-margin environments where hydrate recycling is relatively fast (e.g. Blake Ridge compared with Cascadia). Furthermore, some areas with thick FGZs and extensive BSRs (e.g. west Svalbard) have similar rates of hydrate recycling to northern Gulf or Mexico, yet the latter has no regional BSR. Here we discuss a gas-forming mechanism that operates in addition to hydrate recycling, and which produces a widespread, regional, BSR when gas is transported upward through the liquid phase; this mechanism is dominant in tectonically passive margins. If the gas-water solubility decreases downward beneath the GHSZ (this occurs where the geothermal gradient and the pressure are relatively high), low rates of upward fluid flow enable pore water to become saturated in a thick layer beneath the GHSZ. The FGZ that this produces achieves a steady-state thickness that is primarily sensitive to the rate of upward fluid flow. Consequently, geophysical observations that constrain the thickness of sub-BSR FGZs can be used to estimate the regional, diffuse, upward fluid flux through natural gas-hydrate systems.

In this thesis we describe the development of a real-space implementation of the Bethe-Salpeter equation (BSE) and use it in conjunction with a semi-empirical tight-binding model to investigate the optoelectronic properties of colloidal quantum- confined nanostructures. This novel implementation exploits the limited radial extent and small size of the atomic orbital basis to treat finite systems containing up to &Tilde;4000 atoms in a fully many-body framework. In the first part of this thesis our tight-binding model is initially benchmarked on zincblende CdSe nanocrystals, before subsequently being used to investigate the electronic states of zincblende CdSe nanoplatelets as a function of thickness. The band-edge electronic states are found to show minimal variation for a range of thicknesses and the results of our tight-binding model show good agreement with those predicted using a 14-band k·p model for a nanoplatelet of 4 monolayers (ML) in thickness. Optical absorption spectra were also computed in the independent-particle approximation. While the results of the tight-binding model show good agreement with those of the 14-band k·p model in the low-energy region of the spectrum, agreement with experiment was poor. This reflects the need for a many-body treatment of optical absorption in nanoplatelet systems. In the second part of this thesis we apply our tight-binding plus BSE model to study the excitonic properties of CdSe nanocrystals and nanoplatelets. Simulations performed on CdSe nanocrystals examined an approximation of the BSE equivalent to configuration interaction singles (CIS), and found that both the optical gap and the low-energy spectral features were unaffected by the approximation. A comparison of exciton binding energies with those predicted by CIS demonstrates the sensitivity of results to the exact treatment of dielectric screening and the decision of whether or not to screen exchange. Our model predicts optical gaps that are in strong agreement with average experimental data for all but the smallest diameters, but was not able to reproduce low-energy spectral features that were fully consistent with experiment. This was attributed to the absence of the spin-orbit interaction in the model. Simulations performed on CdSe nanoplatelets investigate the optical gaps and exciton binding energies as a function of thickness. Exciton binding energies were found to reach &Tilde;200 meV for the thinnest system, however, optical gaps were slightly overestimated in comparison to experiment. This is attributed to the reduced lateral dimensions used in our simulations and our bulk treatment of dielectric screening. A two-dimensional treatment of dielectric screening is expected to further increase binding energies. Calculations of the excitonic absorption spectrum reproduce the characteristic spectral features observed in experiment, and show strong agreement with the spectra of nanoplatelets, with thicknesses ranging from 3 ML to 5 ML.

The objective of this thesis was to create a network emulator, suitable for evaluatingsolutions in a small-cell wireless mesh SDN backhaul network environment, by integratingexisting software. The most important efforts in this process have been a transparentintegration of Mininet and ns-3 at both the data and the control plane, with ns-3 servingas the front-end. The goal has been to design the system such that solutions revolvingaround fast failover, resilient routing, and energy efficient small cell management may beevaluated. The constituent components include an augmented ns-3 WiFi module withmillimeter wave communication capabilities; a socket API suitable for remote-controllermanagement, as well as the network emulator Mininet. Mininet in turn integrates OpenvSwitch, virtual hosts in the form of Linux network namespaces, and OpenFlow controllers.The work has also included a brief evaluation of the system, which revealed that the designhas a fundamental flaw. / SOCRA

This master's thesis investigates if it is possible to increase the size of the simulations running on NETSim, Network Element Test Simulator, on a specific hardware and operating system. NETSim is a simulator for operation and maintenance of telecommunication networks. The conclusions are that the disk usage is not critical and that it is needless to spend time optimizing disk and file system parameters. The amount of memory used by the simulations increased approximately linear with the size of the simulation. The size of the swap disk space is not a limiting factor. / Detta exsamensarbete undersöker om det är möjligt att öka storleken på simuleringskörningar av NETSim, Network Element Test Simulator, på en specifik hårdvaru- och operativsystemsplattform. NETSim är en simulator för styr och övervakning av telekomnätverk. Slutsatserna är att diskanvändandet inte är kritiskt och att det är onödigt att ägna tid åt att optimera disk- och filsystemsparametrar. Minnesutnyttjandet ökar approximativt linjärt med storleken på simuleringarna. Storleken på swapdisken är inte någon begränsande faktor.