In this thesis, a systematic study of the structural characterization of the capsular polysaccharides of Streptococcus pneumoniae is conducted using Molecular Modelling methods. S.pneumoniae causes invasive pneumococcal disease (IPD), a leading cause of death in children under five. The serotypes in group 6 are amongst the most common of IPD causing serotypes. We performed structural characterization of serogroup 6 to understand the structural relationships between serotypes 6A, 6B, 6C and 6D in an attempt to understand the cross protection seen within the group. The 6B saccharide has been included in the early conjugate vaccine (PCV-7), and has shown to elicit protection against the 6B as well as offer some cross-protection against 6A. 6A has since been included in the latter conjugate vaccines in the hopes of eliciting stronger protection against 6A and 6C. Molecular Dynamics simulations were used to investigate the conformations of oligosaccharides with the aim of elucidating a conformational rationale for why small changes in the carbohydrate primary structure result in variable efficacy. We began by examining the Potential of Mean Force (PMF) plots of the disaccharide subunits which make up the Serogroup 6 oligosaccharides. The PMFs showed the free energy proles along the torsional angles space of the disaccharides. This conformational information was then used to build the four oligosaccharides on which simulations were conducted. These simulations showed that serotype pairs 6A/6C and 6B/6D have similar structures.

Modern Molecular Dynamics force fields, such as the CHARMM36 and GLYCAM06 carbohydrate force fields, are parametrised to reproduce behaviours for specific molecules under specific conditions in order to be able to predict the behaviour of similar molecular systems, where there is often no experimental data. Coupled with the sheer number available, this makes choosing the appropriate force field a formidable task. For this reason it is important that modern force fields be regularly compared. Streptococcus pneumoniae is a cause of invasive pneumococcal disease (IPD) such as pneumonia and meningitis in children under five. While there are over 90 pneumococcal serotypes only a handful of these are responsible for disease. Immunisation with the conjugate vaccine PCV7, has markedly decreased invasive pneumoccocal disease. Following PCV7 immunisation, incidences of non-vaccine serotypes, especially serotype 19A, have increased. Serotype 19F's capsular polysaccharide differs from 19A's at a single linkage position. Where 19A possesses an a-D-Glcp-(1->3)-a-L-Rhap (G13R), 19F possesses an a-D-Glcp-(1->2)-a-L-Rhap (G12R) linkage. For this reason it was thought that a 19F conjugate would cross protect against 19A. Unfortunately PCV7 vaccination appears to have been largely ineffective against 19A disease. The lack of conformational information for the G12R and G13R disaccharides provided a good opportunity to compare the CHARMM and GLYCAM force fields. The dynamics of the G12R and G13R disaccharides were investigated under both CHARMM and GLYCAM.While we did identify some discrepancies, overall the force fields were in agreement in predicting a more flexible G12R than the more restricted G13R. While it is possible that these differences account for the lack of 19F to 19A cross protectionprotection, further research is required.

The aim of the thesis is to rationalize the water heaters welding area in Tatramat company - ohrievače s.r.o. The rationalization consists of three parts. The first part deals with the arrangement of the workplaces, the second part re-evaluates the monthly production planning. The third part describes in detail the production of one type, which based on simulations created in the simulation software Witness, compares the recorded time in company informartion system Orfert to the real production time in the operation. Each individual part offers optimization proposals and merging them into one unit, will create an efficient, transparent and economically value adding rationalization of the water heaters welding area.

This thesis compares the results of two of the more popular flexible aircraft modeling formulations, the mean-axes method and the fixed-axes method, for application in real-time motion simulators. First, the time-domain equations of motion for an elastic body using the fixed-axes are derived. Subsequently, the mean-axes equations are derived by making a few assumptions from the fixed-axis equations. The two formulations are then implemented for a scaled-up beam model of a Cessna Citation aircraft, with the deformations represented by the modal expansion of the whole aircraft from their respective constrained and free-free finite element solutions. Time-domain results, consisting of the acceleration, velocity, and attitude of a point on the aircraft body, are obtained in both models at two beam-stiffness configurations using a quasi-steady aerodynamic model for a single maneuver at one flight condition. The two methods produced similar results with the fixed-axes formulation producing slightly more accurate results.

This thesis compares the results of two of the more popular flexible aircraft modeling formulations, the mean-axes method and the fixed-axes method, for application in real-time motion simulators. First, the time-domain equations of motion for an elastic body using the fixed-axes are derived. Subsequently, the mean-axes equations are derived by making a few assumptions from the fixed-axis equations. The two formulations are then implemented for a scaled-up beam model of a Cessna Citation aircraft, with the deformations represented by the modal expansion of the whole aircraft from their respective constrained and free-free finite element solutions. Time-domain results, consisting of the acceleration, velocity, and attitude of a point on the aircraft body, are obtained in both models at two beam-stiffness configurations using a quasi-steady aerodynamic model for a single maneuver at one flight condition. The two methods produced similar results with the fixed-axes formulation producing slightly more accurate results.

International Telemetering Conference Proceedings / October 30-November 02, 1989 / Town & Country Hotel & Convention Center, San Diego, California / The telemetry group has begun a new program in conjunction with Goddard Space Flight Center to investigate the possibilities of using parallel processing configurations for the real-time processing of Space Station data. In order to evaluate the potential configurations, a program based on using discrete-event simulation models is being used. This modeling software allows for generic configurations to be modeled and the relevant parameters to be modified to see the effects on performance. This paper represents a description of the work we will be undertaking over the next 18 months and the environment to be used in creating the simulation models at NMSU.

Cosmological simulations are used by astronomers to investigate large scale structure formation and galaxy evolution. Structure nding, that is, the discovery of gravitationally-bound objects such as dark matter halos, is a crucial step in many such simulations. During recent years, advancing computational capacity has lead to halo-nders needing to manage increasingly larger simulations. As a result, many multi-core solutions have arisen in an attempt to process these simulations more eciently. However, a many-core approach to the problem using graphics processing units (GPUs) appears largely unexplored. Since these simulations are inherently n-body problems, they contain a high degree of parallelism, which makes them very well suited to a GPU architecture. Therefore, it makes sense to determine the potential for further research in halo-nding algorithms on a GPU. We present a number of modified algorithms, for accelerating the identication of halos and sub-structures, using entry-level graphics hardware. The algorithms are based on an adaptive hierarchical renement of the friends-of-friends (FoF) method using six phase-space dimensions: This allows for robust tracking of sub-structures. These methods are highly amenable to parallel implementation and run on GPUs. We implemented four separate systems; two on GPUs and two on CPUs. The first system for both CPU and GPU was implemented as a proof of concept exercise to familiarise us with the problem: These utilised minimum spanning trees (MSTs) and brute force methods. Our second implementation, for the CPU and GPU, capitalised on knowledge gained from the proof of concept applications, leading us to use kd-trees to efficiently solve the problem. The CPU implementations were intended to serve as benchmarks for our GPU applications. In order to verify the efficacy of the implemented systems, we applied our halo finders to cosmological simulations of varying size and compared the results obtained to those given by a widely used FoF commercial halo-finder. To conduct a fair comparison, CPU benchmarks were implemented using well-known libraries optimised for these calculations. The best performing implementation, with minimal optimisation, used kd-trees on the GPU. This achieved a 12x speed-up over our CPU implementation, which used similar methods. The same GPU implementation was compared with a current, widely-used commercial halo finder FoF system, and achieved a 2x speed-up for up to 5 million particles. Results suggest a scalable solution, where speed-up increases with the size of dataset used. We conclude that there is great potential for future research into an optimised kd-tree implementation on graphics hardware for the problem of structure finding in cosmological simulations.

Multiprotein complexes are responsible for many vital cellular functions, and understanding their formation has many applications in medical research. Computer simulation has become a valuable tool in the study of biochemical processes, but simulation of large molecular structures such as proteins on a useful scale is computationally expensive. A compromise must be made between the level of detail at which a simulation can be performed, the size of the structures which can be modelled and the time scale of the simulation. Techniques which can be used to reduce the cost of such simulations include the use of coarse-grained models and parallelisation of the code. Parallelisation has recently been made more accessible by the advent of Graphics Processing Units (GPUs), a consumer technology which has become an affordable alternative to more specialised parallel hardware. We extend an existing implementation of a Monte Carlo protein-protein docking simulation using the Kim and Hummer coarse-grained protein model [1] on a heterogeneous GPU-CPU architecture [2]. This implementation has achieved a significant speed-up over previous serial implementations as a result of the efficient parallelisation of its expensive non-bonded potential energy calculation on the GPU. Our contribution is the addition of the optional capability for modelling flexible linkers between rigid domains of a single protein. We implement additional Monte Carlo mutations to allow for movement of residues within linkers, and for movement of domains connected by a linker with respect to each other. We also add potential terms for pseudo-bonds, pseudo-angles and pseudo-torsions between residues to the potential calculation, and include additional residue pairs in the non-bonded potential sum. Our flexible linker code has been tested, validated and benchmarked. We find that the implementation is correct, and that the addition of the linkers does not significantly impact the performance of the simulation. This modification may be used to enable fast simulation of the interaction between component proteins in a multiprotein complex, in configurations which are constrained to preserve particular linkages between the proteins. We demonstrate this utility with a series of simulations of diubiquitin chains, comparing the structure of chains formed through all known linkages between two ubiquitin monomers. We find reasonable agreement between our simulated structures and experimental data on the characteristics of diubiquitin chains in solution.

The Cooperative Co-Evolution model has been used in Evolutionary Computation to optimize the training of artificial neural networks (ANNs). This architecture has proven to be a useful extension to domains such as Neuro-Evolution (NE), which is the training of ANNs using concepts of natural evolution. However, there is a need for real-time systems and the ability to solve more complex tasks which has prompted a further need to optimize these Cooperative Co-Evolution methods. Cooperative Co-Evolution methods consist of a number of phases, however the evaluation phase is still the most compute intensive phase, for some complex tasks taking as long as weeks to complete. This study uses NE as a test case study and we design a parallel Cooperative Co-Evolution processing framework and implement the optimized serial and parallel versions using the Golang (Go) programming language. Go is a multi-core programming language with first-class constructs, channels and goroutines, that make it well suited to parallel programming. Our study focuses on Enforced Subpopulations (ESP) for single-agent systems and Multi-Agent ESP for multi-agent systems. We evaluate the parallel versions in the benchmark tasks; double pole balancing and prey-capture, for single and multi-agent systems respectively, in tasks of increasing complexity. We observe a maximum speed-up of 20x for the parallel Multi-Agent ESP implementation over our single core optimized version in the prey-capture task and a maximum speedup of 16x for ESP in the harder version of double pole balancing task. We also observe linear speed-ups for the difficult versions of the tasks for a certain range of cores, indicating that the Go implementations are efficient and that the parallel speed-ups are better for more complex tasks. We find that in complex tasks, the Cooperative Co-Evolution Neuro-Evolution (CCNE) methods are amenable to multi-core acceleration, which provides a basis for the study of even more complex Cooperative Co-Evolution methods in a wider range of domains.

The main objective of this research is to compare the performance of cyclic steam injection using horizontal wells based on the analytical model developed by Gunadi against that based on numerical simulation. For comparison, a common reservoir model was used. The reservoir model measured 330 ft long by 330 ft wide by 120 ft thick, representing half of a 5-acre drainage area, and contained oil based on the properties of the Bachaquero-01 reservoir (Venezuela). Three steam injection cycles were assumed, consisting of a 20-day injection period at 1500 BPDCWE (half-well), followed by a 10-day soak period, and a 180-day production period. Comparisons were made for two cases of the position of the horizontal well located on one side of the reservoir model: at mid-reservoir height and at reservoir base. The analytical model of Gunadi had to be modified before a reasonable agreement with simulation results could be obtained. Main modifications were as follows. First, the cold horizontal well productivity index was modified to that based on the Economides-Joshi model instead of that for a vertical well. Second, in calculating the growth of the steam zone, the end-point relative permeability??s of steam and oil were taken into consideration, instead of assuming them to be the same (as in the original model of Gunadi). Main results of the comparative analysis for both cases of horizontal well positions are as follows. First, the water production rates are in very close agreement with results obtained from simulation. Second, the oil production rates based on the analytical model (averaging 46,000 STB), however, are lower than values obtained from simulation (64,000 STB). This discrepancy is most likely due to the fact that the analytical model assumes residual oil saturation in the steam zone, while there is moveable oil based on the simulation model. Nevertheless, the analytical model may be used to give a first-pass estimate of the performance of cyclic steam injection in horizontal wells, prior to conducting more detailed thermal reservoir simulation.