Numerical simulation methods have become an important tool in the study of chemical reaction networks in living cells. Many systems can, with high accuracy, be modeled by deterministic ordinary differential equations, but other systems require a more detailed level of modeling. Stochastic models at either the mesoscopic level or the microscopic level can be used for cases when molecules are present in low copy numbers. In this thesis we develop efficient and flexible algorithms for simulating systems at the microscopic level. We propose an improvement to the Green's function reaction dynamics algorithm, an efficient microscale method. Furthermore, we describe how to simulate interactions with complex internal structures such as membranes and dynamic fibers. The mesoscopic level is related to the microscopic level through the reaction rates at the respective scale. We derive that relation in both two dimensions and three dimensions and show that the mesoscopic model breaks down if the discretization of space becomes too fine. For a simple model problem we can show exactly when this breakdown occurs. We show how to couple the microscopic scale with the mesoscopic scale in a hybrid method. Using the fact that some systems only display microscale behaviour in parts of the system, we can gain computational time by restricting the fine-grained microscopic simulations to only a part of the system. Finally, we have developed a mesoscopic method that couples simulations in three dimensions with simulations on general embedded lines. The accuracy of the method has been verified by comparing the results with purely microscopic simulations as well as with theoretical predictions. / eSSENCE

In mesoscale manufacturing desired dimensional and surface characteristics are defined, but edge conditions are not specified in design. The final edge conditions that exist in mesoscale objects are created not only by the manufacturing process but, because of their size, also by part handling procedures. In these parts, the concern is not only with burrs, which can be formed by some mesoscale manufacturing processes, but also with the shape and size of the edge. These properties are critically important as the edge can constitute a large percentage of the smallest features of mesoscale objects. Undefined edge geometry can result in measurement, assembly, and operational difficulties. Due to the potential problems caused by edge conditions, it is desirable to have the ability to measure and characterize the edge conditions of parts. This thesis considers mesoscale measurement tools to provide an edge measurement tool recommendation based on edge size and properties. A set of analysis techniques is developed to determine the size and shape of the measured edge, locate any local inconsistencies such as burrs or dents, and track trends in calculated parameters as a function of edge position. Additionally, a standard method for communicating design requirements is suggested in order to differentiate between acceptable and unacceptable edges.

In this study, it is hypothesized that the mesoscale environment can indirectly control the cloud-to-ground (CG) lightning polarity of severe storms by directly affecting their structural, dynamical, and microphysical properties, which in turn directly control cloud electrification and CG flash polarity. A more specific hypothesis, which has been supported by past observational and laboratory charging studies, suggests that broad, strong updrafts and associated large liquid water contents in severe storms lead to enhanced positive charging of graupel and hail via the noninductive charging mechanism, the generation of an inverted charge structure, and increased positive CG lightning production. The corollary is that environmental conditions favoring these kinematic and microphysical characteristics should support severe storms generating an anomalously high (> 25%) percentage of positive CG lightning (i.e., positive storms), while environmental conditions relatively less favorable should sustain storms characterized by a typical (≤ 25%) percentage of positive CG lightning (i.e., negative storms). Forty-eight inflow proximity soundings were analyzed to characterize the environments of nine distinct mesoscale regions of severe storms (four positive and five negative) on six days during May – June 2002 over the central United States. This analysis clearly demonstrated significant and systematic differences in the mesoscale environments of positive and negative storms, which were consistent with the stated hypothesis. When compared to negative storms, positive storms occurred in environments associated with a drier low to midtroposphere, higher cloud base height, smaller warm cloud depth, stronger conditional instability, larger 0-3 km AGL wind shear, stronger 0-2 km AGL storm-relative wind speed, and larger buoyancy in the mixed-phase zone, at a statistically significant level. Differences in the warm cloud depth of positive and negative storms were by far the most dramatic, suggesting an important role for this parameter in controlling CG lightning polarity. Subjective visual inspection of radar imagery revealed no strong relationship between convective mode and CG lightning polarity, and also illustrated that positive and negative severe storms can be equally intense.

In this study, it is hypothesized that the mesoscale environment can indirectly control the cloud-to-ground (CG) lightning polarity of severe storms by directly affecting their structural, dynamical, and microphysical properties, which in turn directly control cloud electrification and CG flash polarity. A more specific hypothesis, which has been supported by past observational and laboratory charging studies, suggests that broad, strong updrafts and associated large liquid water contents in severe storms lead to enhanced positive charging of graupel and hail via the noninductive charging mechanism, the generation of an inverted charge structure, and increased positive CG lightning production. The corollary is that environmental conditions favoring these kinematic and microphysical characteristics should support severe storms generating an anomalously high (> 25%) percentage of positive CG lightning (i.e., positive storms), while environmental conditions relatively less favorable should sustain storms characterized by a typical (≤ 25%) percentage of positive CG lightning (i.e., negative storms). Forty-eight inflow proximity soundings were analyzed to characterize the environments of nine distinct mesoscale regions of severe storms (four positive and five negative) on six days during May - June 2002 over the central United States. This analysis clearly demonstrated significant and systematic differences in the mesoscale environments of positive and negative storms, which were consistent with the stated hypothesis. When compared to negative storms, positive storms occurred in environments associated with a drier low to midtroposphere, higher cloud base height, smaller warm cloud depth, stronger conditional instability, larger 0-3 km AGL wind shear, stronger 0-2 km AGL storm-relative wind speed, and larger buoyancy in the mixed-phase zone, at a statistically significant level. Differences in the warm cloud depth of positive and negative storms were by far the most dramatic, suggesting an important role for this parameter in controlling CG lightning polarity. Subjective visual inspection of radar imagery revealed no strong relationship between convective mode and CG lightning polarity, and also illustrated that positive and negative severe storms can be equally intense.

In this study, a month-long simulation of gravity waves over North America and North Atlantic Ocean is performed using the mesoscale model MM5 for January 2003, verified with Advanced Microwave Sounding Unit-A (AMSU-A) radiance observations in the upper troposphere and lower stratosphere. According to the monthly mean statistics, four regions of strong gravity wave activities are found both in the simulation and the AMSU-A observations: northwestern Atlantic, Appalachian Mountains, Rocky Mountains and Greenland, respectively. Those over the northwestern Atlantic Ocean are strongly associated with the midlatitude baroclinic jet-front systems, while the other three regions are apparently collocated with high topography. Imbalance diagnosis and numerical sensitivity experiments of a strong gravity wave event during January 18-22 show that the gravity waves are strongly linked to the unbalanced flow in the baroclinic jet-front system. The gravity waves are usually radiated from the upper tropospheric jet exit region with maximum nonlinear balance equation residual ( Δ NBE; key indicator of flow imbalance), distinctly different from other surface sources. Flow imbalance related strongly to tropopause folding and frontogenesis of the large-scale background flow. Similar wave characteristics are simulated in experiments with different microphysics and grid resolutions. The Δ NBE is again shown to be a good predictor for jet-front related gravity waves, suggesting its potential application to gravity wave parameterizations for global and climate models.

This dissertation establishes a precipitation climatology for common storm types and structures in southeast Texas, investigating diurnal, seasonal, and interannual rainfall variations in addition to climatological differences in raindrop size distributions and storm divergence profiles. Divergence profiles observed by an S-band, Doppler radar are compared to ensemble simulations of ten precipitating systems occurring in warm season, weakly baroclinic, and strongly baroclinic environments. Eight triply-nested mesoscale model simulations are conducted for each case using single- and double- moment microphysics with four convective treatments (i.e., two convective parameterizations and explicit vs. parameterized convection at 9 km). Observed and simulated radar reflectivities are objectively separated into convective, stratiform, and non-precipitating anvil columns and comparisons are made between ensemble mean echo coverages and levels of non-divergence (LNDs). In both the model and observations, storms occurring in less baroclinic environments have more convective rain area, less stratiform rain area, and more elevated divergence profiles. The model and observations agree best for well-organized, leading-line trailing stratiform systems. Excessive convective rain area and elevated LNDs are simulated for several less organized cases. Simulations parameterizing convection on the intermediate grid produced less elevated divergence profiles with smaller magnitudes compared to their explicit counterparts. In one warm season case, double-moment microphysics generated lower LNDs associated with variations in convective intensity and depth, detraining less ice to anvil and stratiform regions at midlevels relative to a single-moment scheme. Similarly, mesoscale convective vortex simulations employing an ensemble-based versus a single-closure convective parameterization produced the least elevated heating structures (closer to observed) resulting in the weakest midlevel vortices. Finally, this dissertation is unique in that some of the data collection and a portion of the analysis involved 95 undergraduates in a five-year research and education program, the Student Operational ADRAD Project (SOAP). In addition to documenting the program's structure and implementation, student-reported experiences, confidence, and interest in performing SOAP tasks are also analyzed. Students participating in SOAP for multiple years were significantly more confident in performing SOAP tasks, more likely to obtain science or meteorology-related employment upon graduation, and more likely to matriculate to graduate programs, suggesting programs like SOAP have a strong influence on students' career outcomes and self-efficacy.

Cement-based composite materials are widely used in engineering applications. The strength and damage patterns of such materials depend upon the properties of the constituent components as well as the microstructure. Three scale levels are generally recognized in the analysis of the mechanical behaviour of composites, namely, macro-scale, meso-scale, and nano- or atomistic scale. Modelling of the mechanical properties at the meso-level provides a powerful means for the understanding of the physical processes underlying the macroscopic strength and failure behaviour of the composite materials under various loading conditions. This thesis endeavours to develop effective and efficient mesoscale models for cement-based composites, especially concrete, with a focus on dynamic analysis applications and in a three-dimensional stress-strain environment. These models are subsequently applied to investigate the intrinsic microscopic mechanisms governing the behaviour of such material under complex and high rate loadings, such as those due to shock, impact and blast. To cater to the needs of dynamic analysis under complex stress conditions, a general 2-dimensinal (2D) mesoscale modelling framework is further developed with the incorporation of the 3-D effect. This framework integrates the capabilities of MATLAB programming for the generation of the mesoscale geometric structure, ANSYS-CAE for finite element mesh generation, and the hydrocode LS-DYNA for solving the dynamic response of the model. The 3D effect is incorporated via a novel pseudo-3D modelling scheme such that the crucial lateral confinement effect during the transient dynamic response can be realistically represented. With the above mesoscale model a comprehensive investigation is conducted on the dynamic increase factor (DIF) in the concrete strength under compression, with particular focus on the variation trend at different strain rate regimes, and the key influencing factors. The wave propagation effect under high strain rate is scrutinised from a strip-by-strip perspective, and the correlation between the externally measured stress-strain quantities and the actual processes within the specimen is examined. The contribution of the material heterogeneity, as well as the structural effect (inertia), in the dynamic strength enhancement is evaluated. The classical Brazilian (splitting) test for the dynamic tensile behaviour of concrete is also investigated with the aid of the mesoscale model. Of particular interest here is the validity of such an indirect setup in reproducing the tensile behaviour of the specimen under high strain rates, as well as the effect of the heterogeneity in the dynamic tensile strength. Complications are found to arise as the loading rate increases. The change of the damage patterns with increase of the loading rate and the implications on the interpretation of the results are discussed. As an ideal solution to modelling of the 3-D effects, a methodology for the creation of a complex real 3-dimensional mesoscale model is put forward in the last part of the thesis. A geometric concept, called convex hull, is adopted for the representation of aggregates, and this makes it possible to utilize the relevant algorithms in computational geometry for the present purpose of generation of random 3-D aggregates. A take-and-place procedure is employed to facilitate the generation of the complete 3-D meso-structure. Associated techniques are developed for fast detection of particle inclusion-intersection. An example 3D mesoscale model is presented and representative numerical simulations are carried out to demonstrate the performance of the 3-D mesoscale modelling scheme.

<p>This study examines whether and how land-atmosphere interactions can have an impact on the nocturnal convection over the Southern Great Plains (SGP) through numerical simulations of an intense nocturnal mesoscale convective system (MCS) on 19-20 June 2007 with the Weather Research and Forecasting (WRF V3.3) model. High-resolution nested simulations were conducted using realistic and idealized land-surfaces and two different planetary boundary layer parameterizations: Yonsei University (YSU) and Mellor-Yamada-Janjic (MYJ). All simulations show a persistent dry layer around 2 km during daytime and, despite ample instability in the boundary layer, the lack of a mesoscale lifting mechanism prevents precipitating convection in the daytime and in the evening ahead of the MCS passage after local midnight. Integral differences in timing and amount of MCS precipitation among observations and model results were examined in the light of daytime land-atmosphere interactions, nocturnal pre-storm environment, cold pool strength, squall line morphology and propagation speed, and storm rainfall. At the meso-gamma scale, differences in land-cover and soil type have as much of an effect on the simulated pre-storm environment as the choice of PBL parameterization: MYJ simulations exhibit strong sensitivity to changes in the land-surface in contrast to negligible impact in the case of YSU. A comparison of one-way and two-way nested MYJ results demonstrates that daytime land-atmosphere interactions modify the pre-storm environment remotely through advection of low-level thermodynamic features, which strongly impact the development phases of the MCS. At the end of the afternoon, as the boundary layer collapses, a more homogenous and deeper PBL (and stronger low level shear) is evident in the case of YSU as compared to MYJ when initial land-surface conditions are the same. For different land-surface conditions, propagation speed is generally faster, and organization (bow echo morphology) and cold pool strength enhanced when nocturnal PBL heights are higher and there is stronger low level shear in the pre-storm environment independently of the boundary layer parameterization. To elucidate the distinct roles of mesoscale transport and redistribution of low level instability (daytime remote feedbacks) and low level shear in the downwind pre-storm environment (nighttime local feedbacks), which is to separate the nonlinear land-atmosphere physical processes from PBL parameterization-specific effects on simulated storm dynamics, requires addressing the phase delay in storm development and propagation between the observed and the simulated MCS.</p><p>Another research objective was to examine the contribution of the land surface at short time scales. A second set of experiments was performed in which the land surface properties were homogenized every 5 minutes. The results show that surface effects are most pronounced during periods of insolation and, for the Yonsei University PBL parameterization, effects on the PBL height are most pronounced at the time of PBL collapse. Image processing techniques were found to be a useful measure of the spatial variation within fields. The results of this study show that, for this case, the integrated effect of the land surface can have a noticeable effect on convection, but such effects are not readily discernible at the 5-minute scale. While this study focused on the thermodynamic effects, further work should examine sensitivity to grid spacing and surface roughness.</p> / Thesis

The circulation of the Gulf of Mexico is controlled by presence of large mesoscale structures (10-500 km). We investigate its variability and predictability from interannual to intraseasonal time scales, and the dynamical interactions between physical circulation and biological productivity. We do so by analyzing an ensemble of numerical integrations using the Regional Ocean Modeling System and hydrographic and biogeochemistry observations collected during summer field campaigns in 2010, 2011, and 2012. First, we explore the potential relationships and linkages between Mississippi-Atchafalaya River runoff, nutrient loads, and ocean dynamics from our field data. A negative correlation between nutrient concentration and salinity was confirmed at the surface and in the upper 60m of the water column for nitrite, nitrate, phosphate and silicate. No major changes in the nutrient concentrations were found between our data and previous measurements from twenty years ago. The biological activity in the stations sampled (northern Gulf) is nitrogen limited in 79% of them and phosphorus limited in 8%. Besides the direct input of nutrients from river discharges, the distribution of nutrients in intermediate and high salinity waters in the euphotic layer is influenced by dynamical processes at the ocean mesoscales such as eddies, coastal upwelling events and Loop Current (LC) intrusions. Then, using an ensemble of four model integrations we investigate how mesoscale motions dominate the variability of the Gulf of Mexico circulation both at the surface and in deep waters on intraseasonal time scales. We focus on its predictability by exploring the impact of small variations in the initial conditions and the role of the boundary conditions in the circulation evolution. In all runs, the model provides a good representation of the mean circulation features. However, the shedding of the Loop Current Eddies (LCE) differs in each run considered, and our analysis shows that the detachment of the LCE is a stochastic process. We show that the interannual variability at the model boundaries affects the representation of the LC strength and of the Yucatan Channel transport. On the other hand, the circulation in the LATEX Shelf, TAVE Shelf, and Bay of Campeche is insensitive to the details of the model boundaries, is not affected by the LC, but depends only on the wind variability, and it is therefore predictable if the atmospheric conditions are known. On the contrary, the circulation in the central basin is affected by the LC extension and by the Rings, and dominated by mesoscale features. In most of the basin, mesoscale features are coherent in the top ~ 1000 m of the water column, and below it, but not correlated between the surface and the deep layer. Coherency throughout the whole water column is attributed to particular topographic features such as the south-west corner of the Sigsbee Deep. The chaotic behavior associated with the propagation of the LCE and the elevated mesoscale activity restricts the predictability of the system at intra-seasonal scales to the coastal areas. In consequence, assimilation of continuous in-situ measurements is necessary to insure good hindcasts and forecasts at surface and below 1000 m depth. Finally, since mesoscale activity is key to understand the horizontal and vertical dynamics in the Gulf, we further analyze the model representation of mesoscale circulation under low (monthly) and high (6 hourly) frequency atmospheric forcing. The temporal scale variation from monthly to 6-hourly in the wind forcing impacts the timing of horizontal dynamics, but not the strength. However, high frequency winds impact the model representation of vertical transport that increases as the temporal resolution of the forcing increases. Vertical velocities in the simulation forced by 6-hourly winds are ten times greater than the one obtained using monthly averaged winds. The energy injected by the winds into the ocean is transported in the water column by mesoscale eddies and near-inertial oscillations. If the forcing used by the model does not resolve the inertial frequency (1.4 days in the Gulf), then vertical transport processes are underestimated. Those processes are particularly important for the model representation of biological activity in the ocean upper layers, since they contribute to the input of nutrients into the euphotic zone.

A Zona de Convergência do Atlântico Sul (ZCAS) é um fenômeno meteorológico que exerce um papel preponderante no regime de chuvas na região onde atua, acarretando altos índices pluviométricos na América do Sul. Este estudo mostra que, em uma análise de mesoescala, um Vórtice Ciclônico de Mesoescala (VCM) está associado à ZCAS através de um processo de retroalimentação. Este sistema é gerado dentro de um ambiente estratiforme na região da ZCAS, suga a umidade, acelera os ventos na vertical provocando intensa precipitação e, como conseqüência, pode afetar drasticamente as regiões atingidas provocando sérios danos sócio-econômicos. Este trabalho enfoca a atuação destes VCMs que se formam associados à ZCAS, identificando as propriedades termodinâmicas durante os diversos estágios de seu ciclo de vida. O trabalho é desenvolvido em três fases: (a) documentação da representação da precipitação e do transporte de umidade para a região da ZCAS através de conjuntos de reanálises de nova geração; (b) avaliação da importância da atuação dos VCMs embebidos na ZCAS, através do desenvolvimento de um sistema de detecção para determinação de estatística de ocorrência e (c) realização de simulações com o modelo de mesoescala BRAMS (Brazilian Regional Atmospheric Modeling System) para compreensão do comportamento de episódios específicos destes sistemas de mesoescala e sua relação com a ZCAS. A primeira parte do trabalho evidencia o avanço das novas reanálises da tentativa de representar de forma mais adequada à variável precipitação acumulada na região da ZCAS. A documentação é baseada em seis conjuntos de reanálises atmosféricas (MERRA, ERA-Interim, ERA-40, NCEP 1, NCEP 2 e NCEP CFSR) e cinco conjuntos de produtos observados de precipitação (SALDAS, CPC, CMAP, GPCP e GLDAS). Através das reanálises também foi avaliado o transporte de umidade sobre a região da ZCAS, para os anos de 1979 a 2007. Os diagramas de Taylor mostram que os produtos de precipitação estão bem correlacionados com o ponto de referência (CPC), com coeficientes entre 0,6 e 0,9. Somente a reanálise do NCEP CFSR possui correlações próximas as dos produtos de precipitação. Os VCMs, embebidos na banda de nebulosidade da ZCAS, são selecionados através de um critério objetivo de detecção, baseado na vorticidade e circulação do sistema, aplicado ao período de 2000 a 2009. Um total de 300 VCMs úmidos foram detectados na baixa troposfera, enquanto que na média e alta troposfera foram detectados 277 VCMs. Na baixa troposfera a maioria dos VCMs úmidos se localiza mais para SW na região continental costeira (ZCC) da ZCAS. Verifica-se também uma concordância entre os vórtices destas regiões de máxima vorticidade ciclônica e os extremos de precipitação. O estudo de dois casos específicos nas regiões da Continental Amazônica (ZCA) e ZOC, simulados através do modelo BRAMS, enfoca a relação entre a formação de mesovórtices e a atividade convectiva presente próximo à região de formação. Em ambas as regiões, os VCMs apresentam características similares, que podem ser consideradas como uma assinatura do sistema. Nos dois casos simulados estes sistemas apresentam o ciclo de vida inferior a 24 horas, escala espacial de aproximadamente 200 x 200 km2, intensa precipitação, deslocamento no mesmo sentido do escoamento na baixa troposfera, vorticidade relativa da mesma ordem de magnitude do parâmetro de Coriolis (10-4 s-1), núcleo quente acima do nível de máxima intensidade e um rápido crescimento do centro de vorticidade ciclônica principalmente nos baixos níveis. O balanço de vorticidade e o ciclo de energia desses sistemas são analisados. Pela comparação da chuva simulada com o produto Hidroestimador, sugere-se que o modelo BRAMS, com uma alta resolução espacial e temporal, melhora a representação do VCM, comparado com os dados da reanálise CFSR do NCEP. / The South Atlantic Convergence Zone (SACZ) is a meteorological phenomena that plays an important role in the precipitation regime over the region it covers, resulting in a high pluviometric indices in South America. This study shows, from the mesoscale analysis prospective that Mesoscale Cyclonic Vortex (MCV) is associated to the SACZ through a feedback process. This system is generated embedded in a stratiform environment within the SACZ region, taking moisture up, increasing vertical winds resulting in intense precipitation and consequently can affect drastically susceptible regions prone to natural disasters causing serious social and economic problems. This study highlights the MCVs associated to the SACZ, identifying the thermodynamic properties of the various stages during its lifetime cycle. This study is separated in 3 distinct parts as follows: (a) document the representation of the precipitation and moisture transport into the SACZ new generation reanalysis; (b) develop a detection system to compute the frequency statistics to assess the importance of the embedded MCVs to the SACZ and (c) use of the BRAMS (Brazilian Regional Atmospheric Modeling System) mesoscale model to understand specific MCVs episodes and its relationship with SACZ. In its first part, this work clearly shows the progresses made by the new reanalysis on the correct representation of the accumulated precipitation over the SACZ region. The documentation is based upon six atmospheric reanalysis datasets namely MERRA, ERA-Interim, ERA-40, NCEP 1, NCEP 2 and NCEP CFSR in addition to five precipitation products namely SALDAS, CPC, CMAP, GPCP and GLDAS. The reanalysis were also used to assess the moisture transport over the SACZ region from 1979 through 2007. Taylor plots show that the precipitation products are well associated to the reference dataset (CPC) with correlation coefficients varying between 0,6 and 0,9. Furthermore, only the NCEP CFSR reanalysis present precipitation correlation close to the abovementioned products. The MCVs embedded within the SACZ cloud bands are selected through an objective detection criteria based on the vorticity and circulation of the system, performed from 2000 to 2009. A total of 300 moist MCVs were detected in the lower troposphere whereas in the medium and high troposphere 277 were detected. Most of the MCVs in the lower troposphere were located in the Southwestern region of the continental coastal line of the SACZ and are possibly associated to topographic effects and local instability caused by incursion of transient systems into the SACZ region. Moreover, the vortices in this region match very well the regions of maximum cyclonic vorticity and maximum precipitation intensity. Two case studies were conducted over the Continental Amazonia Zone, simulated using the BRAMS model, showing the relationship between the mesovortices formation and the convective activity near its formation region. In both regions the MCVs present similar characteristics which could be considered as a \"signature\" for such systems. The case studies also present a lifetime shorter than 24 hours and spatial scale of approximately 200 km2 in addition to intense precipitation, shifting in the flow direction in the lower troposphere, relative vorticity of the same order as the Coriolis parameter (10-4 s-1), warm core above the level of maximum intensity and rapid growth of the cyclonic vorticity center mostly in the lower levels. The vorticity balance and the energy cycle of these systems is then analyzed. The simulated precipitation is compared against the Hidroestimador precipitation product. The results suggest that the BRAMS model, configured with high spatial and temporal resolutions improves the representation of the MCVs when compared to the NCEP CFSR reanalysis.