Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-06-06T13:42:32Z No. of bitstreams: 1 camillodelellisfalcaodasilva.pdf: 1420414 bytes, checksum: f38c14f74131ea594b1e105fbfdb1619 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-06-06T14:07:56Z (GMT) No. of bitstreams: 1 camillodelellisfalcaodasilva.pdf: 1420414 bytes, checksum: f38c14f74131ea594b1e105fbfdb1619 (MD5) / Made available in DSpace on 2017-06-06T14:07:56Z (GMT). No. of bitstreams: 1 camillodelellisfalcaodasilva.pdf: 1420414 bytes, checksum: f38c14f74131ea594b1e105fbfdb1619 (MD5) Previous issue date: 2014-05-22 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Atualmente, a eficiência dos algoritmos de simulação estocástica para a simulação de redes de regulação gênica (RRG) tem motivado diversos trabalhos científicos. O interesse por tais algoritmos deve-se ao fato de as novas tecnologias em biologia celular — às vezes chamadas de tecnologias de alto rendimento (high throughput technology cell biology) — te-rem mostrado que a expressão gênica é um processo estocástico. Em RRG com atrasos, os algoritmos para simulação estocástica existentes possuem problemas — como crescimento linear da complexidade assintótica, descarte excessivo de números aleatórios durante a si-mulação e grande complexidade de codificação em linguagens de programação — que podem resultar em um baixo desempenho em relação ao tempo de processamento de simulação de uma RRG. Este trabalho apresenta um algoritmo para simulação estocástica que foi chamado de método da próxima reação simplificado (SNRM). Esse algoritmo mostrou-se mais eficiente que as outras abordagens existentes para simulações estocásticas realizadas com as RRGs com atrasos. Além do SNRM, um novo grafo de dependências para reações com atrasos também é apresentado. A utilização desse novo grafo, que foi nomeado de delayed dependency graph (DDG), aumentou consideravelmente a eficiência de todas as versões dos algoritmos de simulação estocástica com atrasos apresentados nesse trabalho. Finalmente, uma estrutura de dados que recebeu o nome de lista ordenada por hashing é utilizada para tratar a lista de produtos em espera em simulações de RRGs com atrasos. Essa estrutura de dados também se mostrou mais eficiente que uma heap em todas as simulações testadas. Com todas as melhorias mencionadas, este trabalho apresenta um conjunto de estratégias que contribui de forma efetiva para o desempenho dos algoritmos de simulação estocástica com atrasos de redes de regulação gênica. / Recently, the time efficiency of stochastic simulation algorithms for gene regulatory networks (GRN) has motivated several scientific works. Interest in such algorithms is because the new technologies in cell biology — called high-throughput technologies cell biology — have shown that gene expression is a stochastic process. In GRN with delays, the existing algorithms for stochastic simulation have some drawbacks — such as linear growth of complexity, excessive discard of random numbers, and the coding in a programming language can be hard — that result in poor performance during the simulation of very large GRN. This work presents an algorithm for stochastic simulation of GRN. We called it simplified next reaction method (SNRM). This algorithm was more efficient than other existing algorithms for stochastically simulation of GRN with delays. Besides SNRM, a new dependency graph for delayed reactions is also presented. The use of this new graph, which we named it delayed dependency graph (DDG), greatly increased the efficiency of all versions of the algorithms for stochastic simulation with delays presented in this work. Finally, a data structure that we named hashing sorted list is used to handle the waiting list of products in simulations of GRN with delays. This data structure was also more efficient than a heap in all tested simulations. With all the improvements mentioned, this work presents a set of strategies that contribute effectively to increasing performance of stochastic simulation algorithms with delays for gene regulatory networks.

Master of Science / Department of Agronomy / Scott A. Staggenborg / With the increase in bio-energy production there is also an increase in by-products. Without proper disposal, these by-products might cause future economic and/or ecological problems. Land application has potential as a disposal and/or nutrient cycling method if these by-products have nutritive value for agricultural crops. The purpose of the study was to compare the use of two by-products of bio-energy production, dry distillers grains (ethanol) and charcoal(pyrolysis), as fertilizer with urea in corn (Zea mays L.). The experiment consisted of four location-years in Kansas. Treatments were dry distiller’s grains (DDG) no-till and tilled for four location-years and char no-till and tilled for three location-years. No-till urea was used as a baseline for comparison at all location-years. The Nitrogen rates ranged from 45 to 180 kg N ha-1. All source material was spring applied before tillage and planting. The corn yields for DDGs and urea were the almost the same across tillage treatments and locations. For DDG no-till, DDG tilled, and urea, the rates at which to achieve the same yields were 97, 111, 78 kg N ha-1, respectively. Corn yields for char at all rates and tillage treatments were the same as no fertilizer. The char, because of immobilization or lack of decomposition, did not contribute to the nitrogen needs of the corn. Neither material showed any inhibitory or otherwise negative effects on the corn in terms of grain yield compared with the control. But both DDGs and char had to have large amounts of material applied to achieve the same amount of nitrogen as urea. Land application of DDGs and char has potential merit for disposal/nitrogen cycling with DDGs being preferred for its nitrogen contribution.

The need for a reduced dependence on fossil fuels is motivated by a wide range of factors: from increasing fuel costs, to national security implications of supply, to rising concern for environmental impact. Although much focus is given to terrestrial systems, over 90% of the world's freight is transported by ship. Likewise, naval warfighting systems are critical in supporting U.S. national interests abroad. Yet the vast majority of these vessels rely on fossil fuels for operation. The results of this thesis illustrate a common theme that hybrid mechanical-electrical marine propulsion systems produce substantially better fuel efficiency than other technologies that are typically emphasized to reduce fuel consumption. Naval and commercial powertrains in the 60-70 MW range are shown to benefit substantially from the utilization of mechanical drive for high speed propulsion; complemented by an efficient electric drive system for low speed operations. This hybrid architecture proves to be able to best meet the wide range of performance requirements for each of these systems, while also being the most easily integrated technology option. Naval analyses evaluate powertrain options for the DDG-51 Flight III. Simulation results using actual operational profile data show a CODLAG system produces a net fuel savings of up to 12% more than a comparable all-electric system, corresponding to a savings of 37% relative the existing DDG-51 powertrain. These results prove that a mechanical linkage for the main propulsion engine greatly reduces fuel consumption and that for power generation systems requiring redundancy, diesel generators represent a vastly superior option to gas turbines. For the commercial application it is shown that an augmented PTO/PTI hybrid system can better reduce cruise fuel consumption than modern sail systems, while also producing significant benefit with regard to CO2 emissions. In addition, using such a shaft mounted hybrid system for low speed electric drive in ports reduces NOx emissions by 29-43%, while CO is reduced 57-66% and PM may be reduced up to 25%, depending on the specific operating mode. As an added benefit, fuel consumption rates under these conditions are reduced 20-29%. / text

Approved for public release; distribution is unlimited / In 2001 the USS WINSTON CHURCHILL (DDG-81) was subjected to three underwater explosions as part of a ship shock trial. Using the actual trial data from experiment and three-dimensional dynamic models of the ship and surrounding fluid very successful comparisons of the vertical motion have been achieved. On average, the magnitude of the vertical motion is three to four times the magnitude of athwartship motion. Previous simulations of this athwartship motion have been less accurate than the vertical motion simulations. This thesis examines recent efforts attempted to improve the simulation results of the athwartship motion including shock spectra analysis, and the reasons behind the disparities that exist between the simulated values and the actual trial data. / Lieutenant, United States Coast Guard

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Approved for public release, distribution is unlimited / Evaluations, otherwise known as ship shock trials, have been conducted in order to determine the seaworthiness of each new class of ship commissioned in the U.S. Fleet. While beneficial in determining the overall survivability of a ship and its mission essential equipment in a severe shock environment, these Navy-mandated tests pose serious danger to the crew, ship and environment. As an alternative to these labor intensive, costly and time consuming at-sea tests, the recent advances in computer processing power have made it possible to employ finite element methods involving complex geometries in the modeling and simulation of shock response for the ship and surrounding fluid. This thesis examines the accuracy of shock simulation predictions as compared to the ship shock trials conducted on USS WINSTON S. CHURCHILL (DDG-81). An investigation of the effects of sensor location, damping and shot geometry is presented as validation of the Naval Postgraduate School modeling and simulation methodology. / Lieutenant, United States Navy