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

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.

Langevin equations with multiplicative noise: Application to domain growth

Langevin Equations of Ginzburg-Landau form, with multiplicative noise, are proposed to study the effects of fluctuations in domain growth. These equations are derived from a coarse-grained methodology. The Cahn-Hiliard-Cook linear stability analysis predicts some effects in the transitory regime. We also derive numerical algorithms for the computer simulation of these equations. The numerical results corroborate the analytical predictions of the linear analysis. We also present simulation results for spinodal decomposition at large times.

Evolutionary synthesis of stochastic gene network models using feature-based search spaces

A feature-based fitness function is applied in a genetic programming system to synthesize stochastic gene regulatory network models whose behaviour is defined by a time course of protein expression levels. Typically, when targeting time series data, the fitness function is based on a sum-of-errors involving the values of the fluctuating signal. While this approach is successful in many instances, its performance can deteriorate in the presence of noise. This thesis explores a fitness measure determined from a set of statistical features characterizing the time series' sequence of values, rather than the actual values themselves. Through a series of experiments involving symbolic regression with added noise and gene regulatory network models based on the stochastic 'if-calculus, it is shown to successfully target oscillating and non-oscillating signals. This practical and versatile fitness function offers an alternate approach, worthy of consideration for use in algorithms that evaluate noisy or stochastic behaviour.

Real time manufacturing systems simulator

A área da simulação computacional teve um rápido crescimento desde o seu apareciment, sendo actualmente uma das ciências de gestão e de investigação operacional mais utilizadas. O seu princípio baseia-se na replicação da operação de processos ou sistemas ao longo de períodos de tempo, tornando-se assim uma metodologia indispensável para a resolução de variados problemas do mundo real, independentemente da sua complexidade. Das inúmeras áreas de aplicação, nos mais diversos campos, a que mais se destaca é a utilização em sistemas de produção, onde o leque de aplicações disponível é muito vasto. A sua aplicação tem vindo a ser utilizada para solucionar problemas em sistemas de produção, uma vez que permite às empresas ajustar e planear de uma maneira rápida, eficaz e ponderada as suas operações e os seus sistemas, permitindo assim uma rápida adaptação das mesmas às constantes mudanças das necessidades da economia global. As aplicações e packages de simulação têm seguindo as tendências tecnológicas pelo que é notório o recurso a tecnologias orientadas a objectos para o desenvolvimento das mesmas. Este estudo baseou-se, numa primeira fase, na recolha de informação de suporte aos conceitos de modelação e simulação, bem como a respectiva aplicação a sistemas de produção em tempo real. Posteriormente centralizou-se no desenvolvimento de um protótipo de uma aplicação de simulação de ambientes de fabrico em tempo real. O desenvolvimento desta ferramenta teve em vista eventuais fins pedagógicos e uma utilização a nível académico, sendo esta capaz de simular um modelo de um sistema de produção, estando também dotada de animação. Sem deixar de parte a possibilidade de integração de outros módulos ou, até mesmo, em outras plataformas, houve ainda a preocupação acrescida de que a sua implementação recorresse a metodologias de desenvolvimento orientadas a objectos.

Are We Sims? How Computer Simulations Represent and What this Means for the Simulation Argument

N. Bostrom’s simulation argument and two additional assumptions imply that we are likely to live in a computer simulation. The argument is based upon the following assumption about the workings of realistic brain simulations: The hardware of a computer on which a brain simulation is run bears a close analogy to the brain itself. To inquire whether this is so, I analyze how computer simulations trace processes in their targets. I describe simulations as fictional, mathematical, pictorial, and material models. Even though the computer hardware does provide a material model of the target, this does not suffice to underwrite the simulation argument because the ways in which parts of the computer hardware interact during simulations do not resemble the ways in which neurons interact in the brain. Further, there are computer simulations of all kinds of systems, and it would be unreasonable to infer that some computers display consciousness just because they simulate brains rather than, say, galaxies.

The design of a support department simulator for use in the design of manufacturing systems

Manufacturing firms are driven by competitive pressures to continually improve the effectiveness and efficiency of their organisations. For this reason, manufacturing engineers often implement changes to existing processes, or design new production facilities, with the expectation of making further gains in manufacturing system performance. This thesis relates to how the likely outcome of this type of decision should be predicted prior to its implementation. The thesis argues that since manufacturing systems must also interact with many other parts of an organisation, the expected performance improvements can often be significantly hampered by constraints that arise elsewhere in the business. As a result, decision-makers should attempt to predict just how well a proposed design will perform when these other factors, or 'support departments', are taken into consideration. However, the thesis also demonstrates that, in practice, where quantitative analysis is used to evaluate design decisions, the analysis model invariably ignores the potential impact of support functions on a system's overall performance. A more comprehensive modelling approach is therefore required. A study of how various business functions interact establishes that to properly represent the kind of delays that give rise to support department constraints, a model should actually portray the dynamic and stochastic behaviour of entities in both the manufacturing and non-manufacturing aspects of a business. This implies that computer simulation be used to model design decisions but current simulation software does not provide a sufficient range of functionality to enable the behaviour of all of these entities to be represented in this way. The main objective of the research has therefore been the development of a new simulator that will overcome limitations of existing software and so enable decision-makers to conduct a more holistic evaluation of design decisions. It is argued that the application of object-oriented techniques offers a potentially better way of fulfilling both the functional and ease-of-use issues relating to development of the new simulator. An object-oriented analysis and design of the system, called WBS/Office, are therefore presented that extends to modelling a firm's administrative and other support activities in the context of the manufacturing system design process. A particularly novel feature of the design is the ability for decision-makers to model how a firm's specific information and document processing requirements might hamper shop-floor performance. The simulator is primarily intended for modelling make-to-order batch manufacturing systems and the thesis presents example models created using a working version of WBS/Office that demonstrate the feasibility of using the system to analyse manufacturing system designs in this way.

A simulation of an ERP implementation with informal processes

This paper presents a discrete event simulation study to examine tenancy service performance in a shopping centre. The study aims to provide an understanding of how informal management mechanisms could enhance existing ERP systems. The research shows the potential benefits of combining the traditional strengths of ERP in providing better performance in terms of efficiency with the ability to react with flexibility to customer's requests. © 2012 SIMULATION COUNCILS, INC.

Simulation of photoinduced processes in organic chromophores: mapping photochemically relevant states for accurate dynamics

The simulation of ultrafast photoinduced processes is a fundamental step towards the understanding of the underlying molecular mechanism and interpretation/prediction of experimental data. Performing a computer simulation of a complex photoinduced process is only possible introducing some approximations but, in order to obtain reliable results, the need to reduce the complexity must balance with the accuracy of the model, which should include all the relevant degrees of freedom and a quantitatively correct description of the electronic states involved in the process. This work presents new computational protocols and strategies for the parameterisation of accurate models for photochemical/photophysical processes based on state-of-the-art multiconfigurational wavefunction-based methods. The required ingredients for a dynamics simulation include potential energy surfaces (PESs) as well as electronic state couplings, which must be mapped across the wide range of geometries visited during the wavepacket/trajectory propagation. The developed procedures allow to obtain solid and extended databases reducing as much as possible the computational cost, thanks to, e.g., specific tuning of the level of theory for different PES regions and/or direct calculation of only the needed components of vectorial quantities (like gradients or nonadiabatic couplings). The presented approaches were applied to three case studies (azobenzene, pyrene, visual rhodopsin), all requiring an accurate parameterisation but for different reasons. The resulting models and simulations allowed to elucidate the mechanism and time scale of the internal conversion, reproducing or even predicting new transient experiments. The general applicability of the developed protocols to systems with different peculiarities and the possibility to parameterise different types of dynamics on an equal footing (classical vs purely quantum) prove that the developed procedures are flexible enough to be tailored for each specific system, and pave the way for exact quantum dynamics with multiple degrees of freedom.