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1
Rowley, Adrian. "Computer simulation of oxides." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.298405.
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Henson, Neil Jon. "Computer simulation of zeolites." Thesis, University of Oxford, 1996. http://ora.ox.ac.uk/objects/uuid:bd348db7-259a-42e2-952c-0e4723978b63.
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The application of a wide range of computational methods to several problems in zeolite chemistry is explored in this thesis. Symmetry-constrained lattice energy minimisations have been performed on a series of pure silica polymorphs using the shell model for silicates and quantitative agreement is found between the experimental and calculated structures. The computed lattice energies of the silicas are found to be between 8 and 20 kJmol-1 less stable than quartz. The energies are found to be directly dependent on the densities of the structures and show good agreement with a recent calorimetric study. A new forcefield for aluminophosphates based on the shell model has been obtained by fitting to the structure and properties of berlinite and lattice energy minimisation calculations have been carried out on a series of aluminium phosphate polymorphs. The experimental structures are reproduced to a reasonable accuracy, especially in cases where high quality crystallographic data are available on calcined structures. In cases where experimental methods give conflicting results regarding the space group symmetry, calculated structures having lower symmetry than those observed in the crystallographic studies are suggested. An approximately linear dependence of lattice energy on density is again observed; the computed lattice energies are found to span a range of 11.7 kJmol-1 higher than berlinite, which compares to an experimentally determined range of 9.7 kJmol-1. Proton binding calculations have been performed on the structure of H-SAPO-37 to determine the most favourable binding proton sites. The calculations correctly reproduce the sites which have the highest fractional occupancies in a crystallographic study. Molecular dynamics simulation has been used to study the diffusion of xenon in ferrierite and zeolite-L. It was found that at 298K and a loading level of 1.33 atoms per unit cell, diffusion down the tenring channel in ferrierite is a more facile process than down the wider twelve-ring channel in zeolite-L (D=8.90xl0-9 m2s-1 for ferrierite versus 1.78xl0-9 for zeolite-L). This effect can be rationalised by consideration of the effect of channel shape on the diffusion pathway. Under the same conditions, the interaction energy was calculated to be more favourable for ferrierite (ΔU=-25.7 kJmol-1 versus -20.0 kJmol-1). A new forcefield for the interaction of hydrocarbons and aromatics with siliceous zeolites was fitted to thermochemical and crystallographic data. The forcefield successfully reproduced the crystallographically determined positions of pyridine and propylamine in siliceous ferrierite and dodecasil-3C. In addition, quantum mechanical calculations were used to fit a forcefield for the interaction of benzene with cation-containing zeolites. Molecular dynamics calculations were used to study the transport of benzene in siliceous faujasite. The coupling of lattice vibrations to the benzene molecule was found to enhance the mobility (for example, at 298K, D=0.11xl0-9m2s-1 with a fixed lattice compared to D=0.31xl0-9m2s-1 with aflexible lattice). Two diffusion regimes were observed corresponding to intra- and inter-cage benzene mobility which correlate well with hypothetical hopping pathways. Analogous pathways for benzene in cation-containing zeolites have shown that cation sites act as traps for the benzene in Na-X and Na-Y, which reduce the mobility compared to the siliceous case. In Na-X, the pathways are further modified by the addition of extra cation sites that act to reduce the hopping activation energy and therefore enhance the diffusion. This behaviour is consistent with observed trends in experimentally determined diffusivities.
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Drew, Philip Morton. "Computer simulation of dendrimers." Thesis, University of Leeds, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.418245.
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Hawkins, James David. "Computer simulation of trachoma." Thesis, University of Southampton, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.255761.
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Moskalenko, A. M. "Nature of computer simulation." Thesis, Київський національний університет технологій та дизайну, 2019. https://er.knutd.edu.ua/handle/123456789/14368.
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Růžička, Štěpán. "Computer simulation of mesocrystals." Thesis, University of Warwick, 2014. http://wrap.warwick.ac.uk/63807/.
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The mesoscale is a thousand times larger than the atomistic scale with colloidal particles, rather than atoms or molecules, forming the constituent building blocks for organized structures. Nanotechnology has recently started interpreting colloidal units as colloidal molecules, and a lot of interest emerged in their assembly into self-organized structures called colloidal crystals. A mesocrystal is a special type of colloidal crystal, where constituent colloidal units are crystallographically registered nanocrystals. Computer simulation of colloidal self-assembly requires coarse-graining, where short-range attraction is usually the dominant force on the colloidal scale. In this thesis, moderately deep quenches of short-range attractive spherical colloids at low packing fractions are performed, because strong clustering into liquid drops preceding crystallization is known to follow quenching and is reminiscent of mesocrystallization. Moreover, variation of simulation parameters in those models allows an easy investigation of the competition between the fundamental processes of multiscale assembly such as coarsening, crystallization, gelation, and phase separation interfering with the dynamical slowing down. Since colloidal building blocks are usually characterized by complex anisotropic interactions we use Monte Carlo rather than dynamical simulations. The thesis is focused on the development of the Virtual Move Monte Carlo which is a Monte Carlo cluster algorithm selecting the moving clusters according to the local energy gradients. The algorithm allows one to control the rates of local crystal evolution and a larger scale cluster aggregation. The thesis investigates the conditions at which the crystallization precedes the aggregation and vice versa. It is confirmed by the Monte Carlo simulations that the properties of kinetically slowed down structures are independent of the microscopic dynamics, and that three different linear growth regimes, correlated to the local order, are present in systems where structure evolves mainly via single particle exchange. It is also shown that long-range repulsions are necessary to stabilize the phase separated aggregates, and that a renormalization of the repulsion leads to a significant decrease of polydispersity of the liquid or recrystallized drops. The efficiency of rotational cluster moves simulating the alignment into crystallographic register is enhanced by several orders of magnitude in this thesis. The results are discussed in the language of recent colloidal physics and related to a wider range of coarsening and self-assembly phenomena observed during the nonclassical crystallization or mesocrystallization processes.
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Melheim, Jens Andreas. "Computer simulation of turbulent electrocoalescence." Doctoral thesis, Norwegian University of Science and Technology, Department of Energy and Process Engineering, 2007. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-1514.
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Offshore wells produce some water, and the ratio of water increases during the lifetime of a well, in particular when water is injected to increase the extraction rate. Hence, oil companies demand techniques that enhance the separation of oil and water. A speed-up of the separation process is achieved by applying electric fields to turbulent-flow water-in-oil emulsions. The electric field gives rise to attractive forces between close droplets and increases the probability of coalescence at contact, while the turbulence enhances the frequency of droplet collisions.
To improve the understanding of the mutual interaction between the turbulence and the electric field, this thesis presents a framework for computer simulation of turbulent electrocoalescence. The framework is based on the Eulerian-Lagrangian approach where each droplet is tracked and the electric and the hydrodynamic interactions between the droplets are handled.
The forces working between two droplets in stagnant oil are modelled and compared with experimental data. It was found that the electric dipole-dipole forces and the filmthinning forces dominate at small droplet spacings.
The turbulence felt by the droplets is modelled by a stochastic differential-equation model. A new model is proposed to correlate the fluid velocities seen by close droplets, and this is important for the prediction of the collision velocity, the collision frequency, and the clustering of droplets.
Two algorithmic improvements are made: An adaptive cell structure and the cluster integration method. The proposed adaptive cell structure adapts to the number density of droplets and ensures an efficient computation without any input from the user regarding the cell structure. The cluster integration method assembles clusters of droplets that interact and integrates each cluster separately using a variable step-size Runge-Kutta method. A significant speed-up compared to traditional approaches is reported.
Finally, the results obtained by computer simulations of turbulent electrocoalescence agree qualitatively with experimental observations in the literature.
Paper III reprinted with kind permission of Elsevier, Sciencedirect.com
8
Alam, Sadaf. "Simulation of the UKQCD computer." Thesis, University of Edinburgh, 2004. http://hdl.handle.net/1842/24120.
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HASE, the Hierarchical computer Architecture design and Simulation Environment, allows for parameterised prototyping of computing systems at multiple abstraction levels encompassing system hardware and application software components. The UKQCD computer simulation research aims to explore the design space and to investigate the performance restricting features of a recent, application-specific supercomputer called QCDOC — Quantum Chromodynamics On-Chip. QCD is a particle physics theory and a 'grand challenge' application. The QCDOC computer employs IBM System-On-Chip technology for a Teraflop-scale supercomputer design. An application-driven simulation approach is introduced for application-specific supercomputer modelling in HASE. Parameterised hardware-software co-simulation models of the QCDOC machine have been created. Advantages of the application-driven co-simulation include a wider design space exploration of hardware components - not restricted by static workload configurations - and simulation metamodelling. Workload scalability and load balancing experiments have been conducted along with performance evaluation of QCDOC's custom-designed features. Moreover, together with HASE features, simulation metamodelling allows efficient generation of alternate simulation models with maximum component reuse and minimum design overhead. Experiments with HASE QCDOC and its successor Bluegene/L simulation models confirm that QCDOC on-chip memory configurations are optimised for QCD code.
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Steiner, Stefan. "Grace Hospital computer simulation model." Thesis, University of British Columbia, 1989. http://hdl.handle.net/2429/27638.
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A simulation model, written in GPSS/H, was created to study utilization of Grace Hospital, a special-purpose maternity hospital. The model assumes that a patient's transfers and length of stay depend only on her present location and classification, and not on any past history. The model includes a sophisticated overflow policy, and allows the factors used to govern a patient's transfers and length of stay to depend on her treatment stage. Also, to more accurately simulate the mid-morning peak load in the hospital, the length of stay in Postpartum depends on a patient's arrival time in Postpartum. The average census, and the number of patient-days spent in inappropriate units or lost due to overcrowding are determined for several future scenarios. It was concluded that Grace is running very close to capacity, and must continue to limit the number of admissions allowed. In addition, an early discharge program was shown to be very effective in alleviating the overcrowding.Science, Faculty of
Mathematics, Department of
Graduate
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Eldridge, Matthew David. "Computer simulation of colloidal suspensions." Thesis, University of Oxford, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.359410.
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Xiao, Cheng. "Computer simulation of fluid systems." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.386636.
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Mulholland, Adrian John. "Computer simulation of enzyme mechanisms." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.260722.
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Castiglione, Michael. "Computer simulation of superionic fluorides." Thesis, University of Oxford, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.365812.
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Cotin, Stéphane. "Computer Based Interactive Medical Simulation ." Habilitation à diriger des recherches, Université des Sciences et Technologie de Lille - Lille I, 2008. http://tel.archives-ouvertes.fr/tel-00839511.
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La simulation médicale interactive sur ordinateur est une technologie révolutionnaire pour améliorer l'efficacité de nombreuses interventions médicales tout en réduisant le niveau de risque pour les patients. Bien que visant essentiellement l'apprentissage, ces simulations pourraient être utilisées, dans un futur proche, pour la planification d'interventions complexes ou même pour assister le praticien / clinicien dans la salle d'opération. Ce manuscrit présente une revue détaillée du domaine multi-disciplinaire de la simulation médicale, et illustre nos différentes contributions dans ce domaine. Après une vue d'ensemble, au Chapitre I, de nombreuses applications en simulation médicale, le Chapitre II décrit nos contributions sur les modèles, depuis la modélisation anatomique (afin de créer des représentations réalistes, et potentiellement adaptées au patient, de l'anatomie humaine) jusqu'à la modélisation biomécanique (pour déterminer les caractéristiques des tissus mous et définir des modèles mathématiques décrivant leur comportement). Les problématiques liées à la modélisation de matériel médical (instruments flexibles ou systèmes d'imagerie) ou encore la modélisation physiologique (pour le calcul d'écoulement sanguin par exemple) sont également abordées. Le Chapitre III s'attache à la modélisation des interactions entre instruments et tissus mous, qui occupent une part très importante dans toute intervention médicale. Les différentes techniques à mettre en oeuvre pour modéliser de telles interactions (détection de collision, modélisation des contacts et rendu haptique) sont décrites dans ce chapitre. Au Chapitre IV sont présentées plusieurs contributions liées à la validation, que ce soit pour comparer des modèles déformables ou pour l'évaluation de systèmes d'apprentissage. Le Chapitre V est dédié à la description de divers prototypes de simulateurs développés au cours de ces travaux de recherche, et le Chapitre VI présente nos récents travaux visant au développement d'une plate-forme Open Source dédiée à la simulation médicale. Cette plate-forme, appelée SOFA, est le fruit d'un travail collaboratif international à travers lequel nous espérons fédérer de nombreuses équipes de recherche. Finalement, le Chapitre VII résume nos différentes contributions et présente un ensemble de perspectives et de défis, en particulier dans les domaine de la simulation et de la planification sur des données spécifiques à des patients.
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Grieve, David G. "Computer simulation of rotary forging." Thesis, University of Nottingham, 1991. http://eprints.nottingham.ac.uk/14392/.
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This thesis presents two computer packages to simulate the rotary forging process, by means of a mathematical model. The results are displayed in a graphical and numerical manner, showing the tool movement and the tool / workpiece interaction. The first package, PATH, is shown to be capable of simulating the motions of all known rotary forging systems. Its results show the rotary forging tool path throughout a chosen process. The motions of any rotary forging system can be programed by a simple set of instructions displayed on the screen, and the results displayed quickly and graphically. The widely used motions of rocking - die rotary forging machines were investigated. From these investigations, formulae were put forward, which were shown to be capable of predicting the tool motion of any rocking - die rotary forging situation. The second package, PROFS, presents a meshed representation of the tools and workpieces used in rotary forging systems. The rotary forging tool is represented as a conic wire frame mesh, on which no forces or loads are considered to act. The workpiece is represented as a cylinder constructed from a number of hexahedral elements. The elements are treated in either a non - constant volume or a constant volume manner. The non - constant volume model workpiece is one which is simply cut away by the action of the tool on it. This model is similar to a process of 'rotary cutting'. Using the model, a technique of investigation into the progression of the contact geometries created during a real rotary forging, was developed. It enabled the progression and size of the contact geometry to be followed from start to finish of the forging cycle. No consideration of the loads or forces occurring during the process was taken into account. The constant model workpiece requires that its volume remains fixed during the simulation. This is achieved by a radial expansion of the elements of the workpiece as it is being 'deformed' by the tool. Again no consideration of the loads or forces occurring in rotary forging was taken into account. Investigations, using the model, enabled the instantaneous contact geometries, contact areas, and displaced volumes of material to be predicted during two real rotary forging processes. Results revealed the potential of PROFS, to determine areas of workpiece instability in the early stages of forging, and reveal ares of insufficient die fill. The potential of data from the simulations, to control a rotary forging machine, is discussed, and is seen as the first step towards the design and manufacture of rotary forging parts and dies by a C.A.D. - C.A.M. route. Contact areas produced during the rotary forging process are essential for any calculations of the forces and stresses occurring in the die and workpiece. The possibility of PROFS to be used as a die / design tool and in pre production trials for new parts is discussed. A physical simulation of a non - constant volume model workpiece was carried out using a 'short lead milling' technique to cut away a solid workpiece. This revealed the instantaneous contact geometries and areas of the workpiece, which were shown to be accurately predicted by PROFS using the non - constant volume. The results confirmed the accuracy and validity of the simulated instantaneous geometries, allowing a large degree of confidence to be assumed in the accuracy of the package. A data base of radial, circumferential, and custom die profiles has been built up and incorporated into PROFS. From the data base a chosen profile can be used to generate a conic meshed representation of a rotary forging die. Investigations, using a die generated from a custom profile, revealed areas of possible workpiece instability. The two packages put forward in this thesis have been shown to be capable of simulating the motions and contact geometries of the rotary forging process, and confirmed using physical and real rotary forging comparisons.
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McBride, Carl. "Computer simulation of liquid crystals." Thesis, Durham University, 1999. http://etheses.dur.ac.uk/4588/.
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Molecular dynamics simulation performed on modern computer workstations provides a powerful tool for the investigation of the static and dynamic characteristics of liquid crystal phases. In this thesis molecular dynamics computer simulations have been performed for two model systems. Simulations of 4,4'-di-n-pentyl-bibicyclo[2.2.2]octane demonstrate the growth of a structurally ordered phase directly from an isotropic fluid. This is the first time that this has been achieved for an atomistic model. The results demonstrate a strong coupling between orientational ordering and molecular shape, but indicate that the coupling between molecular conformational changes and molecular reorientation is relatively weak. Simulations have also been performed for a hybrid Gay-Berne/Lennard-Jones model resulting in thermodynamically stable nematic and smectic phases. Frank elastic constants have been calculated for the nematic phase formed by the hybrid model through analysis of the fluctuations of the nematic director, giving results comparable with those found experimentally. Work presented in this thesis also describes the parameterisation of the torsional potential of a fragment of a dimethyl siloxane polymer chain, disiloxane diol (HOMe(_2)Si)(_2)O, using ab initio quantum mechanical calculations.
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Wang, Xuanmin. "Computer simulation of rotational moulding." Thesis, Queen's University Belfast, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282352.
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Cicek, H. "Computer simulation of melt spinning." Thesis, University of Leeds, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.235356.
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Oganov, Artem Romaevich. "Computer simulation studies of minerals." Thesis, University College London (University of London), 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.271656.
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Higgins, Steven Paul. "Computer simulation of optoelectronic devices." Thesis, University of Essex, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.413634.
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Bates, Martin Alexander. "Computer simulation of liquid crystals." Thesis, University of Southampton, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.243183.
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Chapman, Andrew Barry. "Computer simulation of bilayer membranes." Thesis, University of Bristol, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.335378.
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Goldbeck-Wood, E. Gerhard. "Computer simulation of polymer crystallization." Thesis, University of Bristol, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.317157.
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Baskaran, Preetisri. "Computer simulation of protein superabsorbents." Thesis, Högskolan i Borås, Institutionen Ingenjörshögskolan, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:hb:diva-20927.
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The aim of this project is to develop superabsorbents from proteins in our case it is azygomycetes fungus, where the process of this fungus is studied experimentally in Universityof Borås. As a result of this experiment by-products of protein are produced and this project isabout the study to make use of such proteins as superabsorbing materials.The water absorbing capacity is computationally studied using Gibbs ensemble Monte Carlo(GEMC) simulations to determine the absorbing properties and to effectively improve theabsorbing capacity by using specific treatments, where this project focuses in using mesoscaleforce fields such as the MARTINI force field instead of atomistic force fields which wereused in studying the structure of the superabsorbents.For this purpose, the program code GEMMS is modified to make it read the desirable fileformats in order to perform the simulations. C++ is used here to code the program to read theGROMACS topology file (.top) for MARTINI force field instead of, as currently reading theatom type file (.atp) and the residue type file (.rtp) for the AMBER99 atomistic force field.
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McDonald, Andrew John. "Computer simulation of liquid crystals." Thesis, University of Bristol, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.247893.
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Weehuizen, Hermanis Frans. "Simulation of distributed computer networks." Doctoral thesis, University of Cape Town, 1987. http://hdl.handle.net/11427/21869.
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Bibliography: pages 77-80.This is a study of the simulated performance of two local area networks, Ethernet and the MAP network, respectively based on the IEEE standards 802.3 and 802.4. The simulation language chosen is of the discrete event type rather than the more usual analytical model. This is done in order to observe the interaction between the various entities of a network in order to gain a better understanding of the method of operation of such a system. The performance demanded of a node entity by the networks is determined. The performance of some commercially available hardware is derived from manufacturer's specifications and compared with that required by the network. It is found that there is a significant disparity, with the network requirements far exceeding that of the hardware capabilities. The simulation models developed are used to determine the performance of the networks both with and without the limitations imposed by currently available hardware. While the inclusion of the hardware performance causes little ·loss in performance for the Ethernet network, it has a highly detrimental effect on that of the MAP network. A possible solution is found to this limitation which requires minimal change to the existing protocol. The conclusions reached are that with currently available hardware a group of nodes are able to fully utilise the performance of the Ethernet LAN although a single pair of nodes is unable to do so. With regard to the MAP network, the network performance is limited by that of the node performance although this can be offset to a certain extent by careful choice of one of the protocol parameters, or modification of the hardware design.
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Falkingham, Peter Lewis. "Computer simulation of dinosaur tracks." Thesis, University of Manchester, 2010. https://www.research.manchester.ac.uk/portal/en/theses/computer-simulation-of-dinosaur-tracks(3b3b150d-c05e-4667-96b5-3c17405856e5).html.
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Fossil tracks represent the only direct record of behaviour and locomotion of extinct animals. A computer model using finite element analysis (FEA) has been developed to simulate vertebrate track formation in cohesive substrates. This model has been designed for, and successfully run on, high performance computing (HPC) resources. A number of individual studies were carried out using the computer model to simulate both abstract indenters and virtual dinosaur autopodia. In addition to the simulation studies, two fossil tracks were described, including the first report of bird tracks at the Mammoth Site of Hot Springs, South Dakota (USA) and a re-description of a 'dinosaur tail drag' as the trace of a crocodilian. Using the computer model, it has been shown that in a wet, soft mud the indentation of a non-webbed virtual tridactyl foot created a resultant track with features analogous to 'webbing' between digits. This 'webbing' was a function of sediment deformation and subsequent failure in 3D, specific to rheology. Apparent webbing impressions were clearly developed only within a limited range of sediment conditions and pedal geometry. Indenter (pedal) geometry and morphology affect track depth independently of substrate and loading parameters. More complex morphologies interact with the cohesive substrate creating a lower effective load than that applied. In non-cohesive substrates such as sand, this effect is reversed, and it is the more compact morphologies that indent to a lesser degree. Virtual sauropod tracks were modelled, based on published soft tissue reconstructions of autopodia anatomy, and published mass/centre of mass estimates. It was shown that foot morphology and differential loading between fore- and hind- limbs leads to a range of substrates in which only the manus or pes are able to generate tracks. This offers a new mechanism for the formation of manus-only sauropod trackways, previously interpreted as having been made by swimming dinosaurs. A series of tracks were simulated using input data (loads, pedal morphologies) from four different dinosaurs (Brachiosaurus, Tyrannosaurus, Struthiomimus, and Edmontosaurus). The cohesive substrates used displayed a 'Goldilocks' effect, allowing the formation for tracks only for a very limited range of loads for any given foot. In addition, there was a strong bias toward larger animals, both in homogeneous and theoretically heterogeneous substrates. These findings imply that interpretations from track assemblages must consider that only a small proportion of the total fauna present may be recorded as a track assemblage due to substrate properties. The use of FEA to simulate dinosaur track formation has been shown to be successful, and offers a number of advantages over physical modelling including; consistency between experiments, specific control over input variables, rapid undertaking of repeatable experiments, and the ability to view subsurface deformation non-destructively. It is hoped that this work will lead to an increased interest in modelling tracks, and offer a quantitative method for studying fossil tracks.
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Eger, Steffen. "Computer simulation of language evolution." [S.l. : s.n.], 2007. http://nbn-resolving.de/urn:nbn:de:bsz:16-opus-72552.
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Battisti, Anna. "Computer Simulation of Biological Systems." Doctoral thesis, Università degli studi di Trento, 2012. https://hdl.handle.net/11572/368453.
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This thesis investigates two biological systems using atomistic modelling and molecular dynamics simulation.
The work is focused on: (a) the study of the interaction between a segment of a DNA molecule and a functionalized surface; (b) the dynamical modelling of protein tau, an intrinsically disordered protein.
We briefly describe here the two problems; for their detailed introduction we refer respectively to chapter DNA and chapter TAU.
The interest in the study of the adsorption of DNA on functionalized surfaces is related to the considerable effort that in recent years has been devoted in developing technologies for faster and cheaper genome sequencing.
In order to sequence a DNA molecule, it has to be extracted from the cell where it is stored (e.g. the blood cells). As a consequence any genomic analysis requires a purification process in order to remove from the DNA molecule proteins,
lipids and any other contaminants. The extraction and purification of DNA from biological samples is hence the first step towards an efficient and cheap genome sequencing.
Using the chemical and physical properties of DNA it is possible to generate an attractive interaction between this macromolecule and a properly treated surface. Once positioned on the surface, the DNA can be more easily purified.
In this work we set up a detailed molecular model of DNA interacting with a surface functionalized with amino silanes. The intent is to investigate the free energy of adsorption of small DNA oligomers as a function of the pH and ionic strength of the solution.
The tau protein belongs to the category of Intrinsically Disordered Proteins (IDP), which in their native state do not have an average stable structure and fluctuate between many conformations.
In its physiological state, tau protein helps nucleating and stabilizing the microtubules in the axons of the neurons. On the other hand, the same tau - in a pathological aggregation - is involved in
the development of the Alzheimer disease.
IDPs do not have a definite 3D structure, therefore their dynamical simulation cannot start from a known list of atomistic positions, like a protein data bank file.
We first introduce a procedure to find an initial dynamical state for a generic IDP, and we apply it to the tau protein.
We then analyze the dynamical properties of tau, like the propensity of residues to form temporary secondary structures like beta-sheets or alpha-helices.
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Battisti, Anna. "Computer Simulation of Biological Systems." Doctoral thesis, University of Trento, 2012. http://eprints-phd.biblio.unitn.it/689/1/Tesi-PhD.pdf.
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This thesis investigates two biological systems using atomistic modelling and molecular dynamics simulation.
The work is focused on: (a) the study of the interaction between a segment of a DNA molecule and a functionalized surface; (b) the dynamical modelling of protein tau, an intrinsically disordered protein.
We briefly describe here the two problems; for their detailed introduction we refer respectively to chapter DNA and chapter TAU.
The interest in the study of the adsorption of DNA on functionalized surfaces is related to the considerable effort that in recent years has been devoted in developing technologies for faster and cheaper genome sequencing.
In order to sequence a DNA molecule, it has to be extracted from the cell where it is stored (e.g. the blood cells). As a consequence any genomic analysis requires a purification process in order to remove from the DNA molecule proteins,
lipids and any other contaminants. The extraction and purification of DNA from biological samples is hence the first step towards an efficient and cheap genome sequencing.
Using the chemical and physical properties of DNA it is possible to generate an attractive interaction between this macromolecule and a properly treated surface. Once positioned on the surface, the DNA can be more easily purified.
In this work we set up a detailed molecular model of DNA interacting with a surface functionalized with amino silanes. The intent is to investigate the free energy of adsorption of small DNA oligomers as a function of the pH and ionic strength of the solution.
The tau protein belongs to the category of Intrinsically Disordered Proteins (IDP), which in their native state do not have an average stable structure and fluctuate between many conformations.
In its physiological state, tau protein helps nucleating and stabilizing the microtubules in the axons of the neurons. On the other hand, the same tau - in a pathological aggregation - is involved in
the development of the Alzheimer disease.
IDPs do not have a definite 3D structure, therefore their dynamical simulation cannot start from a known list of atomistic positions, like a protein data bank file.
We first introduce a procedure to find an initial dynamical state for a generic IDP, and we apply it to the tau protein.
We then analyze the dynamical properties of tau, like the propensity of residues to form temporary secondary structures like beta-sheets or alpha-helices.
31
Aryal, Babu Ram. "Developing the computer simulation model of buzz electronics simulation." Online version, 2009. http://www.uwstout.edu/lib/thesis/2009/2009aryalb.pdf.
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Singh, Harpreet. "Computer simulations of realistic microstructures implications for simulation-based materials design/." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/22564.
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Thesis (Ph. D.)--Materials Science and Engineering, Georgia Institute of Technology, 2008.Committee Chair: Dr. Arun Gokhale; Committee Member: Dr. Hamid Garmestani; Committee Member: Dr. Karl Jacob; Committee Member: Dr. Meilin Liu; Committee Member: Dr. Steve Johnson.
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Naumann, Steve E. (Steve Eugene). "Computer Simulation Placements in a Unit of Instruction." Thesis, University of North Texas, 1994. https://digital.library.unt.edu/ark:/67531/metadc278685/.
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Educators considering implementing a computer simulation must decide on the optimum placement of the simulation in the unit of instruction to maximize student learning. This study examined student achievement using two different placements for the computer simulation, The Civil War, in a unit of instruction of 8th grade American History students in a suburban middle school.
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Bose, Sonia Manjusri. "Computer simulation modelling of polymer ageing." Thesis, University of Surrey, 2002. http://epubs.surrey.ac.uk/843495/.
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Detailed information of the underlying mechanisms of macromolecular disintegration processes is not always fully available from lab-based experiments and GPC. A powerful computer simulation technique was thus indispensable in this respect whilst saving time, labour and expense. This project aims to develop an interactive computer program to capture the behaviour of a complex reactor and offer the following functionality: mathematical calculations, graph/chart generation, processing simulation-experiment pertaining to user-given scission and environmental characteristics, data saving and re-loading etc, Windows-style menu-driven interfaces provide templates for easy implementation of complex mathematical algorithms -a new simulation technique (Slider interfaces) presented in the thesis, based on cellulose-ageing study in electrical transformers (Heywood, 2000). A novel statistical concept was introduced to significantly improve real-tune performance of mathematical calculations to simulate polymer chain fragmentation phenomena, enabling transformation of the simple iterative to a semi-iterative and instant calculation algorithm. Three new mathematical functions were constructed - (a) Monte Carlo Dynamic (Slider), (b) Algebraic Exact, (c) Markov Statistical models, initially using an arbitrary time scale for degradation. Real-time simulation was developed using three time model variants that included the interpretation of deviations in the order reaction rate from linearity to an exponential type function. The above transformation enhanced reproducibility and accuracy of degraded MWD curve sampling whilst then- graphical display & clarity via 'Cubic B-Spline' smoothing-algorithm. Complex models were created from a ranking ensemble of single scission mechanisms, structured with levels of probability constructs to effectively simulate GPC-like curve-deformities and side-shifts. The simulation results provided new information in the following key areas: the temporal shift patterns of MWD/PCLD under different ageing conditions graphical comparisons between simulated and observed Idnetic and scission parameters. the dominant types of scission strategy at different reactor conditions, the dependence of reaction behaviour on the polymer structural order. An alternative way of predicting life expectancy of an ageing polymer via relating time- temperature to the magnitude of intermediate MWD curve shifts that is independent on DP. The latter is an average value and subjected to errors. An equation was derived for this. Introduction of a binary tree "death time" algorithm for calculation of the life expectancy of different categories of polymer chain species. Non-iterative techniques developed here opens up new avenues of further research. The developed algorithms and computer program may provide ample scope for investigating the ageing of other industrially important polymers and can be utilised in other areas of polymer research with little modification where probability distribution is sought.
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Ruhweza, Moses. "Computer simulation of Dinitrotoluene Nitration Process." Thesis, Karlstads universitet, Avdelningen för kemiteknik, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kau:diva-66259.
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p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 11.5px Garamond} This paper presents an approach for modelling a commercial dinitrotoluene (DNT) production process using the CHEMCAD simulation software. A validation of the model was performed based on results of an experimental study carried out at Chematur Engineering AB, Sweden. Important parameters such as fluid properties, temperature profile and other operating conditions for CHEMCAD steady state model were selected so as to obtain the crude DNT yield as well as the acid –and organic phase compositions within the same range as the reference values from the experimental study. The results showed that the assumption of the steady state model was correct, and that acid –and organic phase compositions were in good agreement, although with a slightly lower sulphuric acid concentration than that observed in the experimental study. Also, a detailed study was carried out to analyse the effects of physicochemical conditions on the desired product yield. Both the results from the experimental study and the simulated model agree that the effects of mixed acids or heats of mixing acids contribute significantly to the energy balance. For the appropriateness of the thermodynamics, a NRTL model was chosen and the reactor system was optimized by an equilibrium based approach, producing MNT in 99.8% yield and crude DNT in 99.9% yield. An 80.1/19.9 DNT isomer ratio of the main isomers was achieved and a reduction of by-products in the crude DNT shows a good agreement between the model and the experimental study.p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 11.5px Garamond} I denna rapport presenteras en metod för att modellera en kommersiell nitreringsprocess för tillverkning av dinitrotoluen (DNT) med simuleringsprogrammet CHEMCAD. En validering av modellen gjordes baserat på resultat från en experimentell studie utförd hos Chimärer Engineering AB, Sverige. CHEMCAD-modellen utgår från ”steady-state” drift av anläggningen. Viktiga parametrar såsom fluidegenskaper, temperaturprofil och andra driftsbetingelser i CHEMCAD-modellen valdes för att erhålla ett utbyte av DNT samt sammansättningar av såväl syrafas som organisk fas i god överensstämmelse med referensvärdena från den experimentella studien. Resultaten visade att antagandena i modellen var korrekta och sammansättningarna för syrafasen och den organiska fasen överensstämde med data från den experimentella studien. Det genomfördes också en detaljerad studie för att analysera effekterna av fysikalisk-kemiska betingelser på det önskade produktutbytet. Både resultaten från den experimentella studien och data från anläggning i drift överensstämde med den simulerade modellen avseende utspädningsvärmens bidrag till energibalansen. För att erhålla en lämplig beskrivning av reaktionssystemets termodynamik valdes en NRTL-modell och reaktorsystemet optimerades, vilket gav 99,8 % utbyte av MNT och 99,9 % DNT utbyte. Ett förhållande på 80,1 / 19,9 mellan de två huvudisomererna av DNT uppnåddes och en minskning av biprodukter i DNT produktblandningen. Detta är två exempel på en bra överensstämmelse mellan modellen och experimentstudien.
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Hoyles, Matthew, and Matthew Hoyles@anu edu au. "Computer Simulation of Biological Ion Channels." The Australian National University. Theoretical Physics, 2000. http://thesis.anu.edu.au./public/adt-ANU20010702.135814.
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This thesis describes a project in which algorithms are developed for the rapid and accurate solution of Poisson's equation in the presence of a dielectric boundary and multiple point charges. These algorithms are then used to perform Brownian dynamics simulations on realistic models of biological ion channels. An iterative method of solution, in which the dielectric boundary is tiled with variable sized surface charge sectors, provides the flexibility to deal with arbitrarily shaped boundaries, but is too slow to perform Brownian dynamics. An analytical solution is derived, which is faster and more accurate, but only works for a toroidal boundary. Finally, a method is developed of pre-calculating solutions to Poisson's equation and storing them in tables. The solution for a particular configuration of ions in the channel can then be assembled by interpolation from the tables and application of the principle of superposition. This algorithm combines the flexibility of the iterative method with greater speed even than the analytical method, and is fast enough that channel conductance can be predicted. The results of simulations for a model single-ion channel, based on the acetylcholine receptor channel, show that the narrow pore through the low dielectric strength medium of the protein creates an energy barrier which restricts the permeation of ions. They further show that this barrier can be removed by dipoles in the neck of the channel, but that the barrier is not removed by shielding by counter-ions. The results of simulations for a model multi-ion channel, based on a bacterial potassium channel, show that the model channel has conductance characteristics similar to those of real potassium channels. Ions appear to move through the model multi-ion channel via rapid transitions between a series of semi-stable states. This observation suggests a possible physical basis for the reaction rate theory of channel conductance, and opens up an avenue for future research.
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Muzaffar, Towhid Bin. "Computer simulation of Shawnee historical phonology." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/mq25868.pdf.
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Gerritsen, Karin Gerarda Maria. "Computer simulation of FES-assisted locomotion." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp03/NQ31026.pdf.
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Ball, Jonathan Andrew. "Computer simulation of disorder in ceramics." Thesis, Imperial College London, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.439087.
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Woods, Gary B. "Computer simulation of fluids in zeolites." Thesis, University of Oxford, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.237831.
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Adcock, Stewart Alan. "Computer simulation of membrane bound molecules." Thesis, University of Oxford, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.249194.
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Jessop, David. "Computer simulation of the sprint start." Thesis, Loughborough University, 2011. https://dspace.lboro.ac.uk/2134/8360.
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The aim of this project was to investigate the mechanics of the sprint start through the use of computer simulation. Experimental data was collected on one male athlete in accordance with a procedure agreed by Loughborough University Ethical Advisory Committee. The data provided subject specific data for the creation of a four and fourteen segment, angle and torque driven models of the sprint start. The models simulated the start from the moment of onset of force production until takeoff from the starting block. The four segment model comprised a head and trunk, thigh, shank and foot whilst the fourteen segment model also included a lower spine and pelvis, upper arms, forearms and hands, as well as the other leg including two segment feet. Subject specific torque data was combined with EMG data to provide input to the torque models Results from the four segment angle driven model demonstrated that the participant will benefit from using smaller joint angles than usual in the set position as this resulted in increased velocity on takeoff with minimal increase in movement time. The model also showed large joint torques during such starts and so suggested that this is likely to limit start performance. The four segment torque driven model also revealed that optimal joint angles exist for the hip and knee but such a result was not clear for the ankle. For this model the optimum angle at the hip was 73 (the smallest tested) and 108 at the knee which was the athlete's usual angle. Increasing the athlete's strength parameters resulted in a small increase in horizontal velocity on takeoff for some simulations and all simulations had enhanced acceleration. Increasing initial muscle activations didn't increase horizontal takeoff velocity but did also increase horizontal acceleration. The fourteen segment angle driven model was used to optimise spring parameters for input into a torque driven model. The fourteen segment torque driven model simulated movements and forces realistically but an adequate match was not found to the sprint start performance of the participant due to long simulation times and lack of computing power.
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Eid, Hussein M. H. "Computer simulation of crawl arm stroke." Thesis, Loughborough University, 1988. https://dspace.lboro.ac.uk/2134/10323.
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A four segment model of the crawl arm stroke is developed and validated. The construction of a theoretical model is discussed in a number of progressive stages. First, discussion is focussed on a basic two segment model; second, on a linearly configured simple three segment model; third, on the same model extended by introducing hand angle changes: then fourth, on modification of the forearm-hand configuration and on the effects of progressive lateral displacements changing as a functionofnormalised cycle time. Validation is sought from the start in a step-by-step process in which a physical model of the arm, first as a one and then a two segment system, is designed. built and tested in parallel. Thus, during the early stages of development, the behaviour of the physical model can be used to check the computer simulation of the theoretical model. Subsequently, as the theoretical model is extended to a four segment system, its validation is achieved by comparison with a series of experimental observations of five highly skilled competitive crawl-stroke swimmers. Film analysis procedures are developed to establish the velocities, lift, drag and total propulsive forces acting on, or generated from the arm and body segments. These parameters are obtained from an analysis of the digitized coordinates of eight body landmarks from two camera views. The two cameras are used with the aid of specially designed open plan periscopes for underwater filming. The initial values of the measured parameters from film are then incorporated into the model and the output values of the simulation are compared with the swimmers actual performances to establish the accuracy of the theoretical model. The comparison use of the theoretical model and the physical model results in a range of error between 6% and 30% for the total force and 6% and 11% for the body velocity. The comparison of the theoretical model and film analysis results in maximum error of 12% for the body velocity and 18% for the total propulsive force. Simulations of the crawl arm stroke during the underwater phase provide examples of the procedure. The examples illustrate the value of such simulations in that quantitative results are obtained which can be used to alter and improve performance. Considerable changes in the total force occur when the force acting on the hand is related to the angle of attack and to the rate at which the angle is altered. A maximum increase of 18% in the total force is obtained when the hand isorientated at 20 degrees to the horizontal on entry compared with an increase of only 14% at 40 degrees. During mid-stroke an entty angle of 10 degrees inaeases total force by 16%. The difference between maximum and minimum peak velocity is 19% when angles increase from 10 to 40 degrees on entry. The body velocity is found to increase by 25% if the input power is increased by 30%. The hand is able to deliver about 46% to 63% of the total propulsive force, the forearm is found to contribute by 28%. and the upper arm by about 2O%. Within limits a 5% change in hand size results in about a 1.6% change in velocity. A maximumin increase of 0.15% in body velocity is obtained as a result of a gradual increase followed by a gradual decreases of the hand angle of pitch, 0.72% as a result of modifying the forearm lateral movement and 2.6% as a result of combined modification.
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Stern, Abraham C. "Computer Simulation of Metal-Organic Materials." Scholar Commons, 2010. http://scholarcommons.usf.edu/etd/3584.
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Computer simulations of metal-organic frameworks are conducted to both
investigate the mechanism of hydrogen sorption and to elucidate a detailed,
molecular-level understanding of the physical interactions that can lead to successful
material design strategies. To this end, important intermolecular interactions are
identified and individually parameterized to yield a highly accurate representation
of the potential energy landscape. Polarization, one such interaction found to play a
significant role in H 2 sorption, is included explicitly for the first time in simulations
of metal-organic frameworks. Permanent electrostatics are usually accounted for by
means of an approximate fit to model compounds. The application of this method
to simulations involving metal-organic frameworks introduces several substantial
problems that are characterized in this work. To circumvent this, a method is
developed and tested in which atomic point partial charges are computed more
directly, fit to the fully periodic electrostatic potential. In this manner, long-range
electrostatics are explicitly accounted for via Ewald summation. Grand canonical
Monte Carlo simulations are conducted employing the force field parameterization
developed here. Several of the major findings of this work are: Polarization is found
to play a critical role in determining the overall structure of H 2 sorbed in
metal-organic frameworks, although not always the determining factor in uptake.
The parameterization of atomic point charges by means of a fit to the periodic
electrostatic potential is a robust, efficient method and consistently results in a
reliable description of Coulombic interactions without introducing ambiguity
associated with other procedures. After careful development of both hydrogen and
framework potential energy functions, quantitatively accurate results have been
obtained. Such predictive accuracy will aid greatly in the rational, iterative design
cycle between experimental and theoretical groups that are attempting to design
metal-organic frameworks for a variety of purposes, including H 2 sorption and CO2
sequestration.
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Colley, B. A. "Computer simulation of marine traffic systems." Thesis, University of Plymouth, 1985. http://hdl.handle.net/10026.1/2223.
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A computer model was constructed that allowed two vessels involved in a possible collision situation to take collision avoidance action following the "International Regulations for Preventing Collisions at Sea". The mariners’ actions were modelled by the concepts of the domain and the RDRR (Range to Domain/Range-rate). The domain was used to determine if a vessel was threatening and the RDRR to determine the time at which a vessel should give-way to a threatening target. Each vessel in the simulation had four domains corresponding to the type of encounter in which the vessel was involved. Values for the time at which a vessel manoeuvres and the domain radii were determined from an analysis of high quality cine films of the radar at H.M. Coastguard at St. Margaret's Bay, Dover. Information was also taken from simulator exercises set up on the Polytechnic radar simulator. The two ship encounter was then developed to become the multi-ship encounter and eventually was able to model over 400 vessels over a two day period through a computer representation of the Dover Strait. A further development included a computer graphical representation of a radar simulator running in real-time, and which allowed a mariner to navigate one of the vessels using computer control. A validation of the computer model was undertaken by comparing the simulated results with those observed from the cine films. Following the validation several examples of the computer model being used as a decision support system were included.
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Deering, P. R. "Computer simulation of the mine environment." Thesis, University of Nottingham, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.371276.
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Tadayon, M. "Computer simulation of signalized highway intersections." Thesis, University of Bradford, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.372165.
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Fowler, R. F. "Computer simulation of microscopic liquid drops." Thesis, University of Kent, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.371212.
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Lindstrom, Per G. "Computer simulation of hybrid cross-correlators." Thesis, University of Manchester, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.234894.
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Russell, L. W. "Computer simulation of process plant availability." Thesis, Teesside University, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.328836.
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