Multiscale Modeling and Simulation of Stepped Crystal Surfaces

A primary goal of this dissertation is to understand the links between mathematical models that describe crystal surfaces at three fundamental length scales: The scale of individual atoms, the scale of collections of atoms forming crystal defects, and macroscopic scale. Characterizing connections between different classes of models is a critical task for gaining insight into the physics they describe, a long-standing objective in applied analysis, and also highly relevant in engineering applications. The key concept I use in each problem addressed in this thesis is coarse graining, which is a strategy for connecting fine representations or models with coarser representations. Often this idea is invoked to reduce a large discrete system to an appropriate continuum description, e.g. individual particles are represented by a continuous density. While there is no general theory of coarse graining, one closely related mathematical approach is asymptotic analysis, i.e. the description of limiting behavior as some parameter becomes very large or very small. In the case of crystalline solids, it is natural to consider cases where the number of particles is large or where the lattice spacing is small. Limits such as these often make explicit the nature of links between models capturing different scales, and, once established, provide a means of improving our understanding, or the models themselves. Finding appropriate variables whose limits illustrate the important connections between models is no easy task, however. This is one area where computer simulation is extremely helpful, as it allows us to see the results of complex dynamics and gather clues regarding the roles of different physical quantities. On the other hand, connections between models enable the development of novel multiscale computational schemes, so understanding can assist computation and vice versa. Some of these ideas are demonstrated in this thesis. The important outcomes of this thesis include: (1) a systematic derivation of the step-flow model of Burton, Cabrera, and Frank, with corrections, from an atomistic solid-on-solid-type models in 1+1 dimensions; (2) the inclusion of an atomistically motivated transport mechanism in an island dynamics model allowing for a more detailed account of mound evolution; and (3) the development of a hybrid discrete-continuum scheme for simulating the relaxation of a faceted crystal mound. Central to all of these modeling and simulation efforts is the presence of steps composed of individual layers of atoms on vicinal crystal surfaces. Consequently, a recurring theme in this research is the observation that mesoscale defects play a crucial role in crystal morphological evolution.

Smoking, depression, and suicide risk in the nursing staff of a Third-Level Hospital

Objective: To determine the association between smoking, depression and suicide risk in the Nursing Staff of a University Hospital. Materials and method: this was a non-experimental, correlational cross-range study with observational analysis carried out between May 2012 and May 2013. We studied 232 nurses of the “Dr. José Eleuterio gonzález” University Hospital. two self-administered scales were applied, one for depression and one for suicide risk. Another hetero-applied scale of nicotine dependency was also used, and the subjects’ socio-demographic records were reviewed. Results: A total of 527,232 nurses were studied. A smoking prevalence of 22.8% (53 subjects), an operational depression prevalence of 15.1% (35 subjects), and a suicide risk of 5.1% (12 subjects) were found. Gender and age, speciically being male and young (mean age 29.2 years) were found to increase the risk of smoking. We also found that those nurses who had a partner and had a higher level of education smoked less compared to those who did not have a partner or had a lower degree of education. there were hospital departments where there was a higher prevalence of smoking, such as Internal Medicine and Shock trauma. No association between smoking and the presence of depression was found. Regarding depression, we found that those nurses who worked in the Department of Pensioners were more likely to develop operational depression than those working in any other department. We also found that the risk of presenting operational depression decreases as age increases. About suicide risk, a statistically signiicant association between smoking and suicide risk was found. We also found an association between operational depression and suicide risk.Conclusions: It is recommended to consider nicotine dependence as a fundamental part of psychopathology assessment because of its strong association with suicide risk. this study emphasizes the complexity of the issue of the comorbidity of smoking and psychopathology and the need to continue research lines.

Impact of a fall prevention program in the Internal Medicine wards of a tertiary care university hospital

Objective: To determine whether a falls prevention program reduces the incidence of falls within a hospital. Materials and methods: Each patient admitted to the Internal Medicine ward was classiied into a risk category (high, medium, low) according to the scale of J.H. Downton, and then various general and speciic measures were applied by risk group. Interventions included appointments, teaching materials, and training of medical staff and family. Furthermore, a registration system was developed that allowed adverse event fe edback to the program and identiicat ion of the causes of the fall. The SPSS version 20.0 was used for the data analysis. Descriptive analysis was used for quantitative variables, and qualitative variables were expressed as proportions. To compare the rate of pre- and post-program implementation falls, x 2 was used, with a  = 0.05 determining a signiicant statistical value. Results: Since the implementation of the program, the rate of falls per 1000 days/patient decreased from 1.9 in 2007 to 0.67 in the period 2008-2013, representing a decrease of the rate of falls of up to 70%, with a statistically signiicant difference (P=.02). Conclusions: The implementation of a falls prevention program is an effective tool and reduces the rate and complications associated with them.

Transient scaling and resurgence of chimera states in networks of Boolean phase oscillators.

We study networks of nonlocally coupled electronic oscillators that can be described approximately by a Kuramoto-like model. The experimental networks show long complex transients from random initial conditions on the route to network synchronization. The transients display complex behaviors, including resurgence of chimera states, which are network dynamics where order and disorder coexists. The spatial domain of the chimera state moves around the network and alternates with desynchronized dynamics. The fast time scale of our oscillators (on the order of 100ns) allows us to study the scaling of the transient time of large networks of more than a hundred nodes, which has not yet been confirmed previously in an experiment and could potentially be important in many natural networks. We find that the average transient time increases exponentially with the network size and can be modeled as a Poisson process in experiment and simulation. This exponential scaling is a result of a synchronization rate that follows a power law of the phase-space volume.

Landscape metrics as indicators of coastal morphology and its use in ecological niche modelling of seagrass species

Dependence of some species on landscape structure has been proved in numerous studies. So far, however, little progress has been made in the integration of landscape metrics in the prediction of species associated with coastal features. Specific landscape metrics were tested as predictors of coastal shape using three coastal features of the Iberian Peninsula (beaches, capes and gulfs) at different scales. We used the landscape metrics in combination with environmental variables to model the niche and find suitable habitats for a seagrass species (Cymodocea nodosa) throughout its entire range of distribution. Landscape metrics able to capture variation in the coastline enhanced significantly the accuracy of the models, despite the limitations caused by the scale of the study. We provided the first global model of the factors that can be shaping the environmental niche and distribution of C. nodosa throughout its range. Sea surface temperature and salinity were the most relevant variables. We identified areas that seem unsuitable for C. nodosa as well as those suitable habitats not occupied by the species. We also present some preliminary results of testing historical biogeographical hypotheses derived from distribution predictions under Last Glacial Maximum conditions and genetic diversity data.

Effect of Playing Interactive Computer Game on Distress of Insulin Injection Among Type 1 Diabetic Children

Background: Diabetic children and their families experience high level stress because of daily insulin injection. Objectives: This study was conducted to investigate the impact of an interactive computer game on behavioral distress due to insulin injection among diabetic children. Patients and Methods: In this clinical trial, thirty children (3-12 years) with type 1 diabetes who needed daily insulin injection were recruited and allocated randomly into two groups. Children in intervention groups received an interactive computer game and asked to play at home for a week. No special intervention was done for control group. The behavioral distress of groups was assessed before, during and after the intervention by Observational Scale of Behavioral Distress–Revised (OSBD-R). Results: Repeated measure ANOVA test showed no significantly difference of OSBD-R over time for control group (P = 0.08), but this changes is signification in the study group (P = 0.001). Comparison mean score of distress were significantly different between two groups (P = 0.03). Conclusions: According to the findings, playing interactive computer game can decrease behavioral distress induced by insulin injection in type 1 diabetic children. It seems this game can be beneficial to be used alongside other interventions.

Climate change and irrigation water requirement at Jaguaribe river basin, semi-arid northeast of Brazil.

Summary: Climate change has a potential to impact rainfall, temperature and air humidity, which have relation to plant evapotranspiration and crop water requirement. The purpose of this research is to assess climate change impacts on irrigation water demand, based on future scenarios derived from the PRECIS (Providing Regional Climates for Impacts Studies), using boundary conditions of the HadCM3 submitted to a dynamic downscaling nested to the Hadley Centre regional circulation model HadRM3P. Monthly time series for average temperature and rainfall were generated for 1961-90 (baseline) and the future (2040). The reference evapotranspiration was estimated using monthly average temperature. Projected climate change impact on irrigation water demand demonstrated to be a result of evapotranspiration and rainfall trend. Impacts were mapped over the target region by using geostatistical methods. An increase of the average crop water needs was estimated to be 18.7% and 22.2% higher for 2040 A2 and B2 scenarios, respectively. Objective ? To analyze the climate change impacts on irrigation water requirements, using downscaling techniques of a climate change model, at the river basin scale. Method: The study area was delimited between 4º39?30? and 5º40?00? South and 37º35?30? and 38º27?00? West. The crop pattern in the target area was characterized, regarding type of irrigated crops, respective areas and cropping schedules, as well as the area and type of irrigation systems adopted. The PRECIS (Providing Regional Climates for Impacts Studies) system (Jones et al., 2004) was used for generating climate predictions for the target area, using the boundary conditions of the Hadley Centre model HadCM3 (Johns et al., 2003). The considered time scale of interest for climate change impacts evaluation was the year of 2040, representing the period of 2025 to 2055. The output data from the climate model was interpolated, considering latitude/longitude, by applying ordinary kriging tools available at a Geographic Information System, in order to produce thematic maps.

Application of the UK Foresight Obesity Model in Ireland: The Health and Economic Consequences of Projected Obesity Trends in Ireland

Given the scale of the current obesity epidemic and associated health consequences there has been increasing concern about the economic burden placed on society in terms of direct healthcare costs and indirect societal costs. In the Republic of Ireland these costs were estimated at €1.13 billion for 2009. The total direct healthcare costs for six major obesity related conditions (coronary heart disease & stroke, cancer, hypertension, type 2 diabetes and knee osteoarthritis) in the same year were estimated at €2.55 billion. The aim of this research is to project disease burden and direct healthcare costs for these conditions in Ireland to 2030 using the established model developed by the Health Forum (UK) for the Foresight: Tackling Obesities project.

Humanizing the facade of the public commercial building in a contemporary American culture

The projects studied for this thesis show that the more the façades match the values, tastes, and needs of its target individuals, the more frequently the place will be visited. They endow it with a sense of place and uniqueness and create an emotional bond with the individuals. The intent of this research was to derive a framework of principles to be used in the design of façades, and to establish a relationship between the facade, human scale, urban context, and building. The methodology for developing this framework is based on the analysis of building façades from the Renaissance to current examples of New York Times Square. The principles were generated from strategies of the case studies analyzed. Principles of monumentality, symbolism, and iconography were used to perceive façades as essential forms of architecture. The scale of facades emphasizes human dimensions. In turn, the façade is a device of communication to inform individuals, and its impact on retelling culture for a city.

Racialized Sexualities within the Romance Tour Industry: the Influence of Affect and Emotion Upon Transnational Hierarchies of Desire

Online international introduction sites that offer romance tours to American men in search of a foreign bride are an important and rapidly growing component of the internet dating industry; the number of these agencies in the U.S. tripled from two hundred to six hundred in the past 10 years. Previous scholars have examined the so-called ‘mail order bride’ industry in order to demonstrate that the women involved are agents and not victims. Many scholars have also highlighted the importance of race in shaping American men’s desires in one particular region or country. My dissertation provides an important addition to the literature surrounding romance tourism by including participants from all three major regions associated with romance tourism: Eastern Europe, South America, and Southeast Asia. I collected the data for the dissertation by becoming a participant observer of a romance tour in Ukraine, Colombia, and the Philippines. I argue that romance tourism is an important example of the global intimate, and the ways in which globalized processes are created and sustained through everyday intimate emotions and interactions. By examining the ways in which the emotions of desire, disgust, and anxiety influence individual romance tour participant’s constructions of racialized hierarchies, the links between individual emotions and global systems are revealed. The concept of the global intimate challenges the hierarchy of scale that places the body, the home, and the intimate on a much lower level than the scale of the global or the national, and at the same time challenges the binary that divides the individual from the global. Through highlighting the different emotional negotiations that are constantly occurring in the romance tour industry, I highlight the important ways in which individual emotions and affects influence global processes on a large scale and vice versa.

Mixing theory for culture and harvest in bioreactors of human mesenchymal stem cells on microcarriers

The use of human mesenchymal stem cells (hMSCs) in regenerative medicine is a potential major advance for the treatment of many medical conditions, especially with the use of allogeneic therapies where the cells from a single donor can be used to treat ailments in many patients. Such cells must be grown attached to surfaces and for large scale production, it is shown that stirred bioreactors containing ~200 μm particles (microcarriers) can provide such a surface. It is also shown that the just suspended condition, agitator speed NJS, provides a satisfactory condition for cell growth by minimizing the specific energy dissipation rate, εT, in the bioreactor whilst still meeting the oxygen demand of the cells. For the cells to be used for therapeutic purposes, they must be detached from the microcarriers before being cryopreserved. A strategy based on a short period (~7 min) of very high εT, based on theories of secondary nucleation, is effective at removing >99% cells. Once removed, the cells are smaller than the Kolmogorov scale of turbulence and hence not damaged. This approach is shown to be successful for culture and detachment in 4 types of stirred bioreactors from 15 mL to 5 L.

Subfilter-scale Stress Modelling for Large Eddy Simulations

A subfilter-scale (SFS) stress model is developed for large-eddy simulations (LES) and is tested on various benchmark problems in both wall-resolved and wall-modelled LES. The basic ingredients of the proposed model are the model length-scale, and the model parameter. The model length-scale is defined as a fraction of the integral scale of the flow, decoupled from the grid. The portion of the resolved scales (LES resolution) appears as a user-defined model parameter, an advantage that the user decides the LES resolution. The model parameter is determined based on a measure of LES resolution, the SFS activity. The user decides a value for the SFS activity (based on the affordable computational budget and expected accuracy), and the model parameter is calculated dynamically. Depending on how the SFS activity is enforced, two SFS models are proposed. In one approach the user assigns the global (volume averaged) contribution of SFS to the transport (global model), while in the second model (local model), SFS activity is decided locally (locally averaged). The models are tested on isotropic turbulence, channel flow, backward-facing step and separating boundary layer. In wall-resolved LES, both global and local models perform quite accurately. Due to their near-wall behaviour, they result in accurate prediction of the flow on coarse grids. The backward-facing step also highlights the advantage of decoupling the model length-scale from the mesh. Despite the sharply refined grid near the step, the proposed SFS models yield a smooth, while physically consistent filter-width distribution, which minimizes errors when grid discontinuity is present. Finally the model application is extended to wall-modelled LES and is tested on channel flow and separating boundary layer. Given the coarse resolution used in wall-modelled LES, near the wall most of the eddies become SFS and SFS activity is required to be locally increased. The results are in very good agreement with the data for the channel. Errors in the prediction of separation and reattachment are observed in the separated flow, that are somewhat improved with some modifications to the wall-layer model.

Reindeer habitat selection under the risk of brown bear predation during calving season

The depredation of semi-domesticated reindeer by large carnivores reflects an important human-wildlife conflict in Fennoscandia. Recent studies have revealed that brown bears (Ursus arctos) may kill substantial numbers of reindeer calves (Rangifer tarandus tarandus) in forest areas in Sweden. Several authors have suggested that predation risk is an important driver of habitat selection in wild Rangifer populations where predation is a limiting factor, but little is known about these mechanisms in semi-domesticated populations. We examined the habitat selection of female reindeer in relation to spatial and temporal variations in brown bear predation risk on the reindeer calving grounds and evaluated the simultaneous responses of brown bears and reindeer to landscape characteristics. We used GPS data from 110 reindeer years (97 individuals) and 29 brown bear years (19 individuals), from two reindeer herding districts in the forest area of northern Sweden. Our results did not indicate that reindeer alter their behavior in response to spatiotemporal variation in brown bear predation risk, on the scale of the calving range. Instead, we suggest that spatiotemporal behavioral adjustments by brown bears were the main driver of prey-predator interactions in our study system. Contrasting responses by brown bears and reindeer to clear-cuts and young forest indicate that forestry can influence species interactions and possibly yield negative consequences for the reindeer herd. Even if clear-cuts may be beneficial in terms of calf survival, logging activity will eventually cause greater abundance of young regenerating forest, reducing available reindeer habitats and increasing habitat preferred by brown bears. Domestication may have made semi-domesticated reindeer in Fennoscandia less adapted to cope with predators. Areal restrictions, limiting the opportunity for dispersion and escape, possibly make the calves more susceptible to predation. Also, a generally higher population density in semi-domesticated herds compared to wild populations can make dispersion a less efficient strategy and the reindeer calves easier prey. Overall, the lack of ability of the reindeer females to reduce brown bear encounter risk on the scale of the calving range is probably an important reason for the high brown bear predation rates on reindeer calves documented in our study areas. 

Fate of discards from deep water crustacean trawl fishery off the south coast of Portugal

Trawling for crustaceans takes place on the south coast of Portugal at depths between 200 and 800 m. Large amounts of discards are released back to sea, reaching the bottom in the general area where trawling occurs. The objective of this work was to study the time taken for decomposition of the discards, to identify the most important scavenging species involved, and to evaluate the impact on the species targeted by the fishery. We conducted a series of 22 trials, using traps baited with samples of the discards. The time of immersion varied between 1 and 40 h. The amount of tissue removed from the discards was evaluated on a qualitative scale of 1–3, and quantitatively. The species caught in the traps were identified. Considerable consumption of the bait had occurred after 5 h of immersion. After 24 h of immersion only fish bones were left; past 40 h, consumption was complete. The conger eel (Conger conger) was the most common fish species present in the traps. Two species, the amphipod Scopelocheirus hopei and the isopod Natatolana (Cirolana) borealis, were identified as most important for the recycling of organic matter in the system. The stomach contents of a sample of species caught in trawls were analysed for the presence of small scavengers. Preliminary results show that S. hopei and N. (C.) borealis are part of the diet of some of the target species of this fishery, such as the Norway lobster, Nephrops norvegicus and the rose shrimp Parapenaeus longirostris.

Eulerian-Lagrangian definition of coarse bed-load transport: Theory and verification with low-cost inertial measurement units

Fluvial sediment transport is controlled by hydraulics, sediment properties and arrangement, and flow history across a range of time scales. This physical complexity has led to ambiguous definition of the reference frame (Lagrangian or Eulerian) in which sediment transport is analysed. A general Eulerian-Lagrangian approach accounts for inertial characteristics of particles in a Lagrangian (particle fixed) frame, and for the hydrodynamics in an independent Eulerian frame. The necessary Eulerian-Lagrangian transformations are simplified under the assumption of an ideal Inertial Measurement Unit (IMU), rigidly attached at the centre of the mass of a sediment particle. Real, commercially available IMU sensors can provide high frequency data on accelerations and angular velocities (hence forces and energy) experienced by grains during entrainment and motion, if adequately customized. IMUs are subjected to significant error accu- mulation but they can be used for statistical parametrisation of an Eulerian-Lagrangian model, for coarse sediment particles and over the temporal scale of individual entrainment events. In this thesis an Eulerian-Lagrangian model is introduced and evaluated experimentally. Absolute inertial accelerations were recorded at a 4 Hz frequency from a spherical instrumented particle (111 mm diameter and 2383 kg/m3 density) in a series of entrainment threshold experiments on a fixed idealised bed. The grain-top inertial acceleration entrainment threshold was approximated at 44 and 51 mg for slopes 0.026 and 0.037 respectively. The saddle inertial acceleration entrainment threshold was at 32 and 25 mg for slopes 0.044 and 0.057 respectively. For the evaluation of the complete Eulerian-Lagrangian model two prototype sensors are presented: an idealised (spherical) with a diameter of 90 mm and an ellipsoidal with axes 100, 70 and 30 mm. Both are instrumented with a complete IMU, capable of sampling 3D inertial accelerations and 3D angular velocities at 50 Hz. After signal analysis, the results can be used to parametrize sediment movement but they do not contain positional information. The two sensors (spherical and ellipsoidal) were tested in a series of entrainment experiments, similar to the evaluation of the 111 mm prototype, for a slope of 0.02. The spherical sensor entrained at discharges of 24.8 ± 1.8 l/s while the same threshold for the ellipsoidal sensor was 45.2 ± 2.2 l/s. Kinetic energy calculations were used to quantify the particle-bed energy exchange under fluvial (discharge at 30 l/s) and non-fluvial conditions. All the experiments suggest that the effect of the inertial characteristics of coarse sediments on their motion is comparable to the effect hydrodynamic forces. The coupling of IMU sensors with advanced telemetric systems can lead to the tracking of Lagrangian particle trajectories, at a frequency and accuracy that will permit the testing of diffusion/dispersion models across the range of particle diameters.