Computer simulation of radio-frequency methane/hydrogen plasmas and their interaction with GaAs Surfaces

The following thesis describes the computer modelling of radio frequency capacitively coupled methane/hydrogen plasmas and the consequences for the reactive ion etching of (100) GaAs surfaces. In addition a range of etching experiments was undertaken over a matrix of pressure, power and methane concentration. The resulting surfaces were investigated using X-ray photoelectron spectroscopy and the results were discussed in terms of physical and chemical models of particle/surface interactions in addition to the predictions for energies, angles and relative fluxes to the substrate of the various plasma species. The model consisted of a Monte Carlo code which followed electrons and ions through the plasma and sheath potentials whilst taking account of collisions with background neutral gas molecules. The ionisation profile output from the electron module was used as input for the ionic module. Momentum scattering interactions of ions with gas molecules were investigated via different models and compared against results given by quantum mechanical code. The interactions were treated as central potential scattering events and the resulting neutral cascades were followed. The resulting predictions for ion energies at the cathode compared well to experimental ion energy distributions and this verified the particular form of the electrical potentials used and their applicability in the particular geometry plasma cell used in the etching experiments. The final code was used to investigate the effect of external plasma parameters on the mass distribution, energy and angles of all species impingent on the electrodes. Comparisons of electron energies in the plasma also agreed favourably with measurements made using a Langmuir electric probe. The surface analysis showed the surfaces all to be depleted in arsenic due to its preferential removal and the resultant Ga:As ratio in the surface was found to be directly linked to the etch rate. The etch rate was determined by the methane flux which was predicted by the code.

Computer simulation of liquid flow patterns on distillation trays

This thesis describes work carried out to improve the fundamental modelling of liquid flows on distillation trays. A mathematical model is presented based on the principles of computerised fluid dynamics. It models the liquid flow in the horizontal directions allowing for the effects of the vapour through the use of an increased liquid turbulence, modelled by an eddy viscosity, and a resistance to liquid flow caused by the vapour being accelerated horizontally by the liquid. The resultant equations are similar to the Navier-Stokes equations with the addition of a resistance term.A mass-transfer model is used to calculate liquid concentration profiles and tray efficiencies. A heat and mass transfer analogy is used to compare theoretical concentration profiles to experimental water-cooling data obtained from a 2.44 metre diameter air-water distillation simulation rig. The ratios of air to water flow rates are varied in order to simulate three pressures: vacuum, atmospheric pressure and moderate pressure.For simulated atmospheric and moderate pressure distillation, the fluid mechanical model constantly over-predicts tray efficiencies with an accuracy of between +1.7% and +11.3%. This compares to -1.8% to -10.9% for the stagnant regions model (Porter et al. 1972) and +12.8% to +34.7% for the plug flow plus back-mixing model (Gerster et al. 1958). The model fails to predict the flow patterns and tray efficiencies for vacuum simulation due to the change in the mechanism of liquid transport, from a liquid continuous layer to a spray as the liquid flow-rate is reduced. This spray is not taken into account in the development of the fluid mechanical model. A sensitivity analysis carried out has shown that the fluid mechanical model is relatively insensitive to the prediction of the average height of clear liquid, and a reduction in the resistance term results in a slight loss of tray efficiency. But these effects are not great. The model is quite sensitive to the prediction of the eddy viscosity term. Variations can produce up to a 15% decrease in tray efficiency. The fluid mechanical model has been incorporated into a column model so that statistical optimisation techniques can be employed to fit a theoretical column concentration profile to experimental data. Through the use of this work mass-transfer data can be obtained.

Computer simulation of form-roll design

Changes in modern structural design have created a demand for products which are light but possess high strength. The objective is a reduction in fuel consumption and weight of materials to satisfy both economic and environmental criteria. Cold roll forming has the potential to fulfil this requirement. The bending process is controlled by the shape of the profile machined on the periphery of the rolls. A CNC lathe can machine complicated profiles to a high standard of precision, but the expertise of a numerical control programmer is required. A computer program was developed during this project, using the expert system concept, to calculate tool paths and consequently to expedite the procurement of the machine control tapes whilst removing the need for a skilled programmer. Codifying the expertise of a human and the encapsulation of knowledge within a computer memory, destroys the dependency on highly trained people whose services can be costly, inconsistent and unreliable. A successful cold roll forming operation, where the product is geometrically correct and free from visual defects, is not easy to attain. The geometry of the sheet after travelling through the rolling mill depends on the residual strains generated by the elastic-plastic deformation. Accurate evaluation of the residual strains can provide the basis for predicting the geometry of the section. A study of geometric and material non-linearity, yield criteria, material hardening and stress-strain relationships was undertaken in this research project. The finite element method was chosen to provide a mathematical model of the bending process and, to ensure an efficient manipulation of the large stiffness matrices, the frontal solution was applied. A series of experimental investigations provided data to compare with corresponding values obtained from the theoretical modelling. A computer simulation, capable of predicting that a design will be satisfactory prior to the manufacture of the rolls, would allow effort to be concentrated into devising an optimum design where costs are minimised.

Computer simulation of moist agglomerate collisions

This thesis considers the computer simulation of moist agglomerate collisions using the discrete element method (DEM). The study is confined to pendular state moist agglomerates, at which liquid is presented as either absorbed immobile films or pendular liquid bridges and the interparticle force is modelled as the adhesive contact force and interstitial liquid bridge force. Algorithms used to model the contact force due to surface adhesion, tangential friction and particle deformation have been derived by other researchers and are briefly described in the thesis. A theoretical study of the pendular liquid bridge force between spherical particles has been made and the algorithms for the modelling of the pendular liquid bridge force between spherical particles have been developed and incorporated into the Aston version of the DEM program TRUBAL. It has been found that, for static liquid bridges, the more explicit criterion for specifying the stable solution and critical separation is provided by the total free energy. The critical separation is given by the cube root of liquid bridge volume to a good approximation and the 'gorge method' of evaluation based on the toroidal approximation leads to errors in the calculated force of less than 10%. Three dimensional computer simulations of an agglomerate impacting orthogonally with a wall are reported. The results demonstrate the effectiveness of adding viscous binder to prevent attrition, a common practice in process engineering. Results of simulated agglomerate-agglomerate collisions show that, for colinear agglomerate impacts, there is an optimum velocity which results in a near spherical shape of the coalesced agglomerate and, hence, minimises attrition due to subsequent collisions. The relationship between the optimum impact velocity and the liquid viscosity and surface tension is illustrated. The effect of varying the angle of impact on the coalescence/attrition behaviour is also reported. (DX 187, 340).

Computer simulation for tube-making by the cold roll-forming process

The conventional design of forming rolls depends heavily on the individual skill of roll designers which is based on intuition and knowledge gained from previous work. Roll design is normally a trial an error procedure, however with the progress of computer technology, CAD/CAM systems for the cold roll-forming industry have been developed. Generally, however, these CAD systems can only provide a flower pattern based on the knowledge obtained from previously successful flower patterns. In the production of ERW (Electric Resistance Welded) tube and pipe, the need for a theoretical simulation of the roll-forming process, which can not only predict the occurrence of the edge buckling but also obtain the optimum forming condition, has been recognised. A new simulation system named "CADFORM" has been devised that can carry out the consistent forming simulation for this tube-making process. The CADFORM system applied an elastic-plastic stress-strain analysis and evaluate edge buckling by using a simplified model of the forming process. The results can also be visualised graphically. The calculated longitudinal strain is obtained by considering the deformation of lateral elements and takes into account the reduction in strains due to the fin-pass roll. These calculated strains correspond quite well with the experimental results. Using the calculated strains, the stresses in the strip can be estimated. The addition of the fin-pass roll reduction significantly reduces the longitudinal compressive stress and therefore effectively suppresses edge buckling. If the calculated longitudinal stress is controlled, by altering the forming flower pattern so it does not exceed the buckling stress within the material, then the occurrence of edge buckling can be avoided. CADFORM predicts the occurrence of edge buckling of the strip in tube-making and uses this information to suggest an appropriate flower pattern and forming conditions which will suppress the occurrence of the edge buckling.

Computer simulation of the Cont-Bouchaud percolation model of financial markets

DUE TO COPYRIGHT RESTRICTIONS ONLY AVAILABLE FOR CONSULTATION AT ASTON UNIVERSITY LIBRARY AND INFORMATION SERVICES WITH PRIOR ARRANGEMENT

The development of a computer simulation model of the interaction between the supply and usage of major components in car assembly you use in stock control

DUE TO COPYRIGHT RESTRICTIONS ONLY AVAILABLE FOR CONSULTATION AT ASTON UNIVERSITY LIBRARY AND INFORMATION SERVICES WITH PRIOR ARRANGEMENT

The analogue computer simulation of integrated chemical plant and controller systems

DUE TO COPYRIGHT RESTRICTIONS ONLY AVAILABLE FOR CONSULTATION AT ASTON UNIVERSITY LIBRARY SERVICES WITH PRIOR ARRANGEMENT

Exploration by Means of Computer Simulation of Nonlinear Hierarchical Structure of Neuronal Memory on the Model of Olfactory Bulb

Results of numerical experiments are introduced. Experiments were carried out by means of computer simulation on olfactory bulb for the purpose of checking of thinking mechanisms conceptual model, introduced in [2]. Key role of quasisymbol neurons in processes of pattern identification, existence of mental view, functions of cyclic connections between symbol and quasisymbol neurons as short-term memory, important role of synaptic plasticity in learning processes are confirmed numerically. Correctness of fundamental ideas put in base of conceptual model is confirmed on olfactory bulb at quantitative level.

A computer simulation model for single -lane roundabouts

During the past three decades, the use of roundabouts has increased throughout the world due to their greater benefits in comparison with intersections controlled by traditional means. Roundabouts are often chosen because they are widely associated with low accident rates, lower construction and operating costs, and reasonable capacities and delay. ^ In the planning and design of roundabouts, special attention should be given to the movement of pedestrians and bicycles. As a result, there are several guidelines for the design of pedestrian and bicycle treatments at roundabouts that increase the safety of both pedestrians and bicyclists at existing and proposed roundabout locations. Different design guidelines have differing criteria for handling pedestrians and bicyclists at roundabout locations. Although all of the investigated guidelines provide better safety (depending on the traffic conditions at a specific location), their effects on the performance of the roundabout have not been examined yet. ^ Existing roundabout analysis software packages provide estimates of capacity and performance characteristics. This includes characteristics such as delay, queue lengths, stop rates, effects of heavy vehicles, crash frequencies, and geometric delays, as well as fuel consumption, pollutant emissions and operating costs for roundabouts. None of these software packages, however, are capable of determining the effects of various pedestrian crossing locations, nor the effect of different bicycle treatments on the performance of roundabouts. ^ The objective of this research is to develop simulation models capable of determining the effect of various pedestrian and bicycle treatments at single-lane roundabouts. To achieve this, four models were developed. The first model simulates a single-lane roundabout without bicycle and pedestrian traffic. The second model simulates a single-lane roundabout with a pedestrian crossing and mixed flow bicyclists. The third model simulates a single-lane roundabout with a combined pedestrian and bicycle crossing, while the fourth model simulates a single-lane roundabout with a pedestrian crossing and a bicycle lane at the outer perimeter of the roundabout for the bicycles. Traffic data was collected at a modern roundabout in Boca Raton, Florida. ^ The results of this effort show that installing a pedestrian crossing on the roundabout approach will have a negative impact on the entry flow, while the downstream approach will benefit from the newly created gaps by pedestrians. Also, it was concluded that a bicycle lane configuration is more beneficial for all users of the roundabout instead of the mixed flow or combined crossing. Installing the pedestrian crossing at one-car length is more beneficial for pedestrians than two- and three-car lengths. Finally, it was concluded that the effect of the pedestrian crossing on the vehicle queues diminishes as the distance between the crossing and the roundabout increases. ^

The (Un)Folding of Multidomain Proteins Through the Lens of Single-molecule Force-spectroscopy and Computer Simulation

Proteins are specialized molecules that catalyze most of the reactions that can sustain life, and they become functional by folding into a specific 3D structure. Despite their importance, the question, "how do proteins fold?" - first pondered in in the 1930's - is still listed as one of the top unanswered scientific questions as of 2005, according to the journal Science. Answering this question would provide a foundation for understanding protein function and would enable improved drug targeting, efficient biofuel production, and stronger biomaterials. Much of what we currently know about protein folding comes from studies on small, single-domain proteins, which may be quite different from the folding of large, multidomain proteins that predominate the proteomes of all organisms.

In this thesis I will discuss my work to fill this gap in understanding by studying the unfolding and refolding of large, multidomain proteins using the powerful combination of single-molecule force-spectroscopy experiments and molecular dynamic simulations.

The three model proteins studied - Luciferase, Protein S, and Streptavidin - lend insight into the inter-domain dependence for unfolding and the subdomain stabilization of binding ligands, and ultimately provide new insight into atomistic details of the intermediate states along the folding pathway.

A parametric study of flip-chip reliability via computer simulation

Abstract not available

Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 µm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

Predicting the performance of passenger ships using computer simulation

When designing a new passenger ship or naval vessel or modifying an existing design, how do we ensure that the proposed design is safe from an evacuation point of view? In the wake of major maritime disasters such as the Herald of Free Enterprise and the Estonia and in light of the growth in the numbers of high density, high-speed ferries and large capacity cruise ships, issues concerned with the evacuation of passengers and crew at sea are receiving renewed interest. In the maritime industry, ship evacuation models are now recognised by IMO through the publication of the Interim Guidelines for Evacuation Analysis of New and Existing Passenger Ships including Ro-Ro. This approach offers the promise to quickly and efficiently bring evacuation considerations into the design phase, while the ship is "on the drawing board" as well as reviewing and optimising the evacuation provision of the existing fleet. Other applications of this technology include the optimisation of operating procedures for civil and naval vessels such as determining the optimal location of a feature such as a casino, organising major passenger movement events such as boarding/disembarkation or restaurant/theatre changes, determining lean manning requirements, location and number of damage control parties, etc. This paper describes the development of the maritimeEXODUS evacuation model which is fully compliant with IMO requirements and briefly presents an example application to a large passenger ferry.