Programming Molecular Devices using Nucleic Acid Hairpins

Nucleic Acid hairpins have been a subject of study for the last four decades. They are composed of single strand that is

hybridized to itself, and the central section forming an unhybridized loop. In nature, they stabilize single stranded RNA, serve as nucleation

sites for RNA folding, protein recognition signals, mRNA localization and regulation of mRNA degradation. On the other hand,

DNA hairpins in biological contexts have been studied with respect to forming cruciform structures that can regulate gene expression.

The use of DNA hairpins as fuel for synthetic molecular devices, including locomotion, was proposed and experimental demonstrated in 2003. They

were interesting because they bring to the table an on-demand energy/information supply mechanism.

The energy/information is hidden (from hybridization) in the hairpin’s loop, until required.

The energy/information is harnessed by opening the stem region, and exposing the single stranded loop section.

The loop region is now free for possible hybridization and help move the system into a thermodynamically favourable state.

The hidden energy and information coupled with

programmability provides another functionality, of selectively choosing what reactions to hide and

what reactions to allow to proceed, that helps develop a topological sequence of events.

Hairpins have been utilized as a source of fuel for many different DNA devices. In this thesis, we program four different

molecular devices using DNA hairpins, and experimentally validate them in the

laboratory. 1) The first device: A

novel enzyme-free autocatalytic self-replicating system composed entirely of DNA that operates isothermally. 2) The second

device: Time-Responsive Circuits using DNA have two properties: a) asynchronous: the final output is always correct

regardless of differences in the arrival time of different inputs.

b) renewable circuits which can be used multiple times without major degradation of the gate motifs

(so if the inputs change over time, the DNA-based circuit can re-compute the output correctly based on the new inputs).

3) The third device: Activatable tiles are a theoretical extension to the Tile assembly model that enhances

its robustness by protecting the sticky sides of tiles until a tile is partially incorporated into a growing assembly.

4) The fourth device: Controlled Amplification of DNA catalytic system: a device such that the amplification

of the system does not run uncontrollably until the system runs out of fuel, but instead achieves a finite

amount of gain.

Nucleic acid circuits with the ability

to perform complex logic operations have many potential practical applications, for example the ability to achieve point of care diagnostics.

We discuss the designs of our DNA Hairpin molecular devices, the results we have obtained, and the challenges we have overcome

to make these truly functional.

Investigation of factors driving the costs of operating the 2020 Irish power system with large-scale wind generation

The main goal of this work is to determine the true cost incurred by the Republic of Ireland and Northern Ireland in order to meet their EU renewable electricity targets. The primary all-island of Ireland policy goal is that 40% of electricity will come from renewable sources in 2020. From this it is expected that wind generation on the Irish electricity system will be in the region of 32-37% of total generation. This leads to issues resulting from wind energy being a non-synchronous, unpredictable and variable source of energy use on a scale never seen before for a single synchronous system. If changes are not made to traditional operational practices, the efficient running of the electricity system will be directly affected by these issues in the coming years. Using models of the electricity system for the all-island grid of Ireland, the effects of high wind energy penetration expected to be present in 2020 are examined. These models were developed using a unit commitment, economic dispatch tool called PLEXOS which allows for a detailed representation of the electricity system to be achieved down to individual generator level. These models replicate the true running of the electricity system through use of day-ahead scheduling and semi-relaxed use of these schedules that reflects the Transmission System Operator's of real time decision making on dispatch. In addition, it carefully considers other non-wind priority dispatch generation technologies that have an effect on the overall system. In the models developed, three main issues associated with wind energy integration were selected to be examined in detail to determine the sensitivity of assumptions presented in other studies. These three issues include wind energy's non-synchronous nature, its variability and spatial correlation, and its unpredictability. This leads to an examination of the effects in three areas: the need for system operation constraints required for system security; different onshore to offshore ratios of installed wind energy; and the degrees of accuracy in wind energy forecasting. Each of these areas directly impact the way in which the electricity system is run as they address each of the three issues associated with wind energy stated above, respectively. It is shown that assumptions in these three areas have a large effect on the results in terms of total generation costs, wind curtailment and generator technology type dispatch. In particular accounting for these issues has resulted in wind curtailment being predicted in much larger quantities than had been previously reported. This would have a large effect on wind energy companies because it is already a very low profit margin industry. Results from this work have shown that the relaxation of system operation constraints is crucial to the economic running of the electricity system with large improvements shown in the reduction of wind curtailment and system generation costs. There are clear benefits in having a proportion of the wind installed offshore in Ireland which would help to reduce variability of wind energy generation on the system and therefore reduce wind curtailment. With envisaged future improvements in day-ahead wind forecasting from 8% to 4% mean absolute error, there are potential reductions in wind curtailment system costs and open cycle gas turbine usage. This work illustrates the consequences of assumptions in the areas of system operation constraints, onshore/offshore installed wind capacities and accuracy in wind forecasting to better inform the true costs associated with running Ireland's changing electricity system as it continues to decarbonise into the near future. This work also proposes to illustrate, through the use of Ireland as a case study, the effects that will become ever more prevalent in other synchronous systems as they pursue a path of increasing renewable energy generation.

Obesity, Cardiovascular Risk Factors, and Weight Loss in a Population of Adult Mexican Americans

The study of obesity has evolved into one of the most important public health issues in the United States (U.S.), particularly in Hispanic populations. Mexican Americans, the largest Hispanic ethnic subgroup in the U.S., have been significantly impacted by obesity and related cardiovascular diseases. Mexican Americans living in the Lower Rio Grande Valley (the Valley) in the Texas-Mexico border are one of the most disadvantaged and hard-to-reach minority groups. Demographic factors, socioeconomic status, acculturation, and physical activity behavior have been found to be important predictors of health, although research findings are mixed when establishing predictors of obesity in this population. Furthermore, while obesity has long been linked to cardiovascular disease (CVD) risk factors such as hypertension, type 2 diabetes, and dyslipidemia; information on the relationships between obesity and these CVD risk factors have been mostly from non-minority population groups. Overall, research has been mixed in establishing the association between obesity and related CVD risk factors in this population calling attention to the need for further research. Nevertheless, identifying predictors of success for weight loss in this population will be important if health disparities are to be addressed. The overall objective of the findings presented in this dissertation was to attain a more informed profile of obesity and CVD risk factors in this population. In particular, we examined predictors of obesity, measures of obesity and association with cardiovascular disease risk factors in a sample of 975 Mexican Americans participating in a health promotion program in the Valley region. Findings suggest acculturation factors to be one of the most important predictors of obesity in this population. Results also point to the need of identifying other possible risk factors for predicting CVD risk. Finally, initial body mass index is an important predictor of weight loss in this population group. Thus, indicating that this population is not only amenable to change, but that improvements in weight loss are feasible. This finding strengthens the relevance of prevention programs such as Beyond Sabor for Mexican populations at risk, in particular, food bank recipients.

Stable oxygen isotope composition of planktonic foraminifera in the Canary Islands region

Seasonal depth stratified plankton tows, sediment traps and core tops taken from the same stations along a transect at 29°N off NW Africa are used to describe the seasonal succession, the depth habitats and the oxygen isotope ratios (delta18O(shell)) of five planktic foraminiferal species. Both the delta18O(shell) and shell concentration profiles show variations in seasonal depth habitats of individual species. None of the species maintain a specific habitat depth exclusively within the surface mixed layer (SML), within the thermocline, or beneath the thermocline. Globigerinoides ruber (white) and (pink) occur with moderate abundance throughout the year along the transect, with highest abundances in the winter and summer/fall season, respectively. The average delta18O(shell) of G. ruber (w) from surface sediments is similar to the delta18O(shell) values measured from the sediment-trap samples during winter. However, the delta18O(shell) of G. ruber (w) underestimates sea surface temperature (SST) by 2 °C in winter and by 4 °C during summer/fall indicating an extension of the calcification/depth habitat into colder thermocline waters. Globigerinoides ruber (p) continues to calcify below the SML as well, particularly in summer/fall when the chlorophyll maximum is found within the thermocline. Its vertical distribution results in delta18O(shell) values that underestimate SST by 2 °C. Shell fluxes of Globigerina bulloides are highest in summer/fall, where it lives and calcifies in association with the deep chlorophyll maximum found within the thermocline. Pulleniatina obliquiloculata and Globorotalia truncatulinoides, dwelling and calcifying a part of their lives in the winter SML, record winter thermocline (~180 m) and deep surface water (~350 m) temperatures, respectively. Our observations define the seasonal and vertical distribution of multiple species of foraminifera and the acquisition of their delta18O(shell).

Investigation of the effects of flow conditions at rotor inlet on mixed flow turbine performance for automotive applications

Current trends in the automotive industry have placed increased importance on engine downsizing for passenger vehicles. Engine downsizing often results in reduced power output and turbochargers have been relied upon to restore the power output and maintain drivability. As improved power output is required across a wide range of engine operating conditions, it is necessary for the turbocharger to operate effectively at both design and off-design conditions. One off-design condition of considerable importance for turbocharger turbines is low velocity ratio operation, which refers to the combination of high exhaust gas velocity and low turbine rotational speed. Conventional radial flow turbines are constrained to achieve peak efficiency at the relatively high velocity ratio of 0.7, due the requirement to maintain a zero inlet blade angle for structural reasons. Several methods exist to potentially shift turbine peak efficiency to lower velocity ratios. One method is to utilize a mixed flow turbine as an alternative to a radial flow turbine. In addition to radial and circumferential components, the flow entering a mixed flow turbine also has an axial component. This allows the flow to experience a non-zero inlet blade angle, potentially shifting peak efficiency to a lower velocity ratio when compared to an equivalent radial flow turbine.
This study examined the effects of varying the flow conditions at the inlet to a mixed flow turbine and evaluated the subsequent impact on performance. The primary parameters examined were average inlet flow angle, the spanwise distribution of flow angle across the inlet and inlet flow cone angle. The results have indicated that the inlet flow angle significantly influenced the degree of reaction across the rotor and the turbine efficiency. The rotor studied was a custom in-house design based on a state-of-the-art radial flow turbine design. A numerical approach was used as the basis for this investigation and the numerical model has been validated against experimental data obtained from the cold flow turbine test rig at Queen’s University Belfast. The results of the study have provided a useful insight into how the flow conditions at rotor inlet influence the performance of a mixed flow turbine.

Are you ready for a tender project? – Analysis of organisational project management maturity in the Austrian-Hungarian border region

Are you ready for a tender project? – Analysis of organisational project management maturity in the Austrian- Hungarian border region. Since the 1990s the European Union has paid more and more attention to subsidising cross-border development. It is understandable that different funding from proposal sources is particularly important for the border area, especially to those of utmost importance that support co-operation and rural development. Therefore, they could become a driving force for development. The authors’ research analyses the organisational project management maturity of the projects implemented in the frame of the Austria-Hungary Cross-border Cooperation Programme 2007-2013 (AT-HU). Analysing this kind of organisation is an important issue, since the new call for proposals are open in 2016 and the results of this study may provide a self-evaluation opportunity to organisations that need to know if they are ready or mature enough for a new tender project. The aim of this study was twofold. First of all, those indicators that could be used to analyse the project management maturity of implementing organisations in the AT-HU programme were identified. Based on the empirical research these are the project experience accumulated by the organisation, the internal processes operating at the institution and the professional background. Secondly, factors that can affect this project management maturity were explored and we determined five influencing area: the organisational structure, culture, project managers motivation and the typical and important competences.

Optimization models and methods for real-time transportation planning in forestry

Lors du transport du bois de la forêt vers les usines, de nombreux événements imprévus peuvent se produire, événements qui perturbent les trajets prévus (par exemple, en raison des conditions météo, des feux de forêt, de la présence de nouveaux chargements, etc.). Lorsque de tels événements ne sont connus que durant un trajet, le camion qui accomplit ce trajet doit être détourné vers un chemin alternatif. En l’absence d’informations sur un tel chemin, le chauffeur du camion est susceptible de choisir un chemin alternatif inutilement long ou pire, qui est lui-même "fermé" suite à un événement imprévu. Il est donc essentiel de fournir aux chauffeurs des informations en temps réel, en particulier des suggestions de chemins alternatifs lorsqu’une route prévue s’avère impraticable. Les possibilités de recours en cas d’imprévus dépendent des caractéristiques de la chaîne logistique étudiée comme la présence de camions auto-chargeurs et la politique de gestion du transport. Nous présentons trois articles traitant de contextes d’application différents ainsi que des modèles et des méthodes de résolution adaptés à chacun des contextes. Dans le premier article, les chauffeurs de camion disposent de l’ensemble du plan hebdomadaire de la semaine en cours. Dans ce contexte, tous les efforts doivent être faits pour minimiser les changements apportés au plan initial. Bien que la flotte de camions soit homogène, il y a un ordre de priorité des chauffeurs. Les plus prioritaires obtiennent les volumes de travail les plus importants. Minimiser les changements dans leurs plans est également une priorité. Étant donné que les conséquences des événements imprévus sur le plan de transport sont essentiellement des annulations et/ou des retards de certains voyages, l’approche proposée traite d’abord l’annulation et le retard d’un seul voyage, puis elle est généralisée pour traiter des événements plus complexes. Dans cette ap- proche, nous essayons de re-planifier les voyages impactés durant la même semaine de telle sorte qu’une chargeuse soit libre au moment de l’arrivée du camion à la fois au site forestier et à l’usine. De cette façon, les voyages des autres camions ne seront pas mo- difiés. Cette approche fournit aux répartiteurs des plans alternatifs en quelques secondes. De meilleures solutions pourraient être obtenues si le répartiteur était autorisé à apporter plus de modifications au plan initial. Dans le second article, nous considérons un contexte où un seul voyage à la fois est communiqué aux chauffeurs. Le répartiteur attend jusqu’à ce que le chauffeur termine son voyage avant de lui révéler le prochain voyage. Ce contexte est plus souple et offre plus de possibilités de recours en cas d’imprévus. En plus, le problème hebdomadaire peut être divisé en des problèmes quotidiens, puisque la demande est quotidienne et les usines sont ouvertes pendant des périodes limitées durant la journée. Nous utilisons un modèle de programmation mathématique basé sur un réseau espace-temps pour réagir aux perturbations. Bien que ces dernières puissent avoir des effets différents sur le plan de transport initial, une caractéristique clé du modèle proposé est qu’il reste valable pour traiter tous les imprévus, quelle que soit leur nature. En effet, l’impact de ces événements est capturé dans le réseau espace-temps et dans les paramètres d’entrée plutôt que dans le modèle lui-même. Le modèle est résolu pour la journée en cours chaque fois qu’un événement imprévu est révélé. Dans le dernier article, la flotte de camions est hétérogène, comprenant des camions avec des chargeuses à bord. La configuration des routes de ces camions est différente de celle des camions réguliers, car ils ne doivent pas être synchronisés avec les chargeuses. Nous utilisons un modèle mathématique où les colonnes peuvent être facilement et naturellement interprétées comme des itinéraires de camions. Nous résolvons ce modèle en utilisant la génération de colonnes. Dans un premier temps, nous relaxons l’intégralité des variables de décision et nous considérons seulement un sous-ensemble des itinéraires réalisables. Les itinéraires avec un potentiel d’amélioration de la solution courante sont ajoutés au modèle de manière itérative. Un réseau espace-temps est utilisé à la fois pour représenter les impacts des événements imprévus et pour générer ces itinéraires. La solution obtenue est généralement fractionnaire et un algorithme de branch-and-price est utilisé pour trouver des solutions entières. Plusieurs scénarios de perturbation ont été développés pour tester l’approche proposée sur des études de cas provenant de l’industrie forestière canadienne et les résultats numériques sont présentés pour les trois contextes.

Common Environment for Undergraduate Computer Programming

We present an Integrated Environment suitable for learning and teaching computer programming which is designed for both students of specialised Computer Science courses, and also non-specialist students such as those following Liberal Arts. The environment is rich enough to allow exploration of concepts from robotics, artificial intelligence, social science, and philosophy as well as the specialist areas of operating systems and the various computer programming paradigms.

An Integrated Programming Environment for Undergraduate Computing Courses

The Computing Division of the Business School at University College Worcester provides computing and information technology education to a range of undergraduate students. Topics include various approaches to programming, artificial intelligence, operating systems and digital technologies. Each of these has its own potentially conflicting requirements for a pedagogically sound programming environment. This paper describes an endeavor to develop a common programming paradigm across all topics. This involves the combined use of autonomous robots and Java simulations.

Mixed-layer salinity budget in the tropical Indian Ocean: seasonal cycle based only on observations

The mixed-layer salinity (MLS) budget in the tropical Indian Ocean is estimated from a combination of satellite products and in situ observations over the 2004-2012 period, to investigate the mechanisms controlling the seasonal MLS variability. In contrast with previous studies in the tropical Indian Ocean, our results reveal that the coverage, resolution, and quality of available observations are now sufficient to approach a closed monthly climatology seasonal salt budget. In the South-central Arabian Sea and South-western Tropical Indian Ocean (SCAS and STIO, respectively), where seasonal variability of the MLS is pronounced, the monthly MLS tendency terms are well captured by the diagnostic. In the SCAS region, in agreement with previous results, the seasonal cycle of the MLS is mainly due to meridional advection driven by the monsoon winds. In the STIO, contrasting previous results indicating the control of the meridional advection over the seasonal MLS budget, our results reveal the leading role of the freshwater flux due to precipitation.

Quichua-Spanish language contact in Salcedo, Ecuador: revisiting media lengua syncretic language practices

The purpose of the current thesis is to develop a better understanding of the interaction between Spanish and Quichua in the Salcedo region and provide more information for the processes that might have given rise to Media Lengua, a ‘mixed’ language comprised of a Quichua grammar and Spanish lexicon. Muysken attributes the formation of Media Lengua to relexification, ruling out any influence from other bilingual phenomena. I argue that the only characteristic that distinguishes Media Lengua from other language contact varieties in central Ecuador is the quantity of the overall Spanish borrowings and not the type of processes that might have been employed by Quichua speakers during the genesis of Media Lengua. The results from the Salcedo data that I have collected show how processes such as adlexification, code-mixing, and structural convergence produce Media Lengua-type sentences, evidence that supports an alternative analysis to Muysken’s relexification hypothesis. Overall, this dissertation is developed around four main objectives: (1) to describe the variation of Spanish loanwords within a bilingual community in Salcedo; (2) to analyze some of the prominent and recent structural changes in Quichua and Spanish; (3) to determine whether Spanish loanword use can be explained by the relationship consultants have with particular social categories; and (4) to analyze the consultants’ language ideologies toward syncretic uses of Spanish and Quichua. Overall, 58% of the content words, 39% of the basic vocabulary, and 50% of the subject pronouns in the Salcedo corpus were derived from Spanish. When compared to Muysken’s description of highlander Quichua in the 1970’s, Spanish loanwords have more than doubled in each category. The overall level of Spanish loanwords in Salcedo Quichua has grown to a level between highlander Quichua in the 1970’s and Media Lengua. Similar to Spanish’s lexical influence in Media Lengua, the increase of Spanish borrowings in today’s rural Quichua can be seen in non-basic and basic vocabularies as well as the subject pronoun system. Significantly, most of the growth has occurred through forms of adlexification i.e., doublets, well-established borrowings, and cultural borrowings, suggesting that ‘ordinary’ lexical borrowing is also capable of producing Media Lengua-type sentences. I approach the second objective by investigating two separate phenomena related to structural convergence. The first examines the complex verbal constructions that have developed in Quichua through Spanish loan translations while the second describes the type of Quichua particles that are attached to Spanish lexemes while speaking Spanish. The calquing of the complex verbal constructions from Spanish were employed when speaking standard Quichua. Since this standard form is typically used by language purists, I argue that their use of calques is a strategy of exploiting the full range of expression from Spanish without incorporating any of the Spanish lexemes which would give the appearance of ‘contamination’. The use of Quichua particles in local varieties of Spanish is a defining characteristic of Quichuacized Spanish, spoken most frequently by women and young children in the community. Although the use of Quichua particles was probably not the main catalyst engendering Media Lengua, I argue that its contribution as a source language to other ‘mixed’ varieties, such as Media Lengua, needs to be accounted for in descriptions of BML genesis. Contrary to Muysken’s representation of relatively ‘unmixed’ Spanish and Quichua as the two source languages of Media Lengua, I propose that local varieties of Spanish might have already been ‘mixed’ to a large degree before Media Lengua was created. The third objective attempts to draw a relationship between particular social variables and the use of Spanish loanwords. Whisker Boxplots and ANOVAs were used to determine which social group, if any, have been introducing new Spanish borrowings into the bilingual communities in Salcedo. Specifically, I controlled for age, education, native language, urban migration, and gender. The results indicate that none of the groups in each of the five social variables indicate higher or lower loanword use. The implication of these results are twofold: (a) when lexical borrowing occurs, it is immediately adopted as the community-wide norm and spoken by members from different backgrounds and generations, or (b) this level of Spanish borrowing (58%) is not a recent phenomenon. The fourth and final objective draws on my ethnographic research that addresses the attitudes of syncretic language use. I observed that Quichuacized Spanish and Hispanicized Quichua are highly stigmatized varieties spoken by the country’s most marginalized populations and families, yet within the community, syncretic ways of speaking are in fact the norm. It was shown that there exists a range of different linguistic definitions for ‘Chaupi Lengua’ and other syncretic language practices as well as many contrasting connotations, most of which were negative. One theme that emerged from the interviews was that speaking syncretic varieties of Quichua weakened the consultant’s claim to an indigenous identity. The linguistic and social data presented in this dissertation supports an alternative view to Muysken’s relexification hypothesis, one that has the advantage of operating with well-precedented linguistic processes and which is actually observable in the present-day Salcedo area. The results from the study on lexical borrowing are significant because they demonstrate how a dynamic bilingual speech community has gradually diversified their Quichua lexicon under intense pressure to shift toward Spanish. They also show that Hispanicized Quichua (Quichua with heavy lexical borrowing) clearly arose from adlexification and prolonged lexical borrowing, and is one of at least six identifiable speech styles found in Salcedo. These results challenge particular interpretations of language contact outcomes, such as, ones that depict sources languages as discrete and ‘unmixed.’ The bilingual continuum presented in this thesis shows on the one hand, the range of speech styles that are accessible to different speakers, and on the other hand, the overlapping, syncretic features that are shared among the different registers and language varieties. It was observed that syncretic speech styles in Salcedo are employed by different consultants in varied interactional contexts, and in turn, produce different evaluations by other fellow community members. In the current dissertation, I challenge the claim that relexification and Media Lengua-type sentences develop in isolation and without the influence of other bilingual phenomena. Based on Muysken's Media Lengua example sentences and the speech styles from the Salcedo corpus, I argue that Media Lengua may have arisen as an institutionalized variant of the highly mixed "middle ground" within the range of the Salcedo bilingual continuum discussed above. Such syncretic forms of Spanish and Quichua strongly resemble Media Lengua sentences in Muysken’s research, and therefore demonstrate how its development could have occurred through several different language contact processes and not only through relexification.

Mindfulness-Based Cognitive Therapy for older people in a community setting: a mixed methods feasibility study

Rationale: In line with complex intervention development, this research takes a systematic approach to examining the feasibility and acceptability of delivering Mindfulness-Based Cognitive Therapy (MBCT) to older people who experience symptoms of depression. Methods: A mixed methods approach was adopted in line with recommendations made by the MRC Complex Intervention Development framework. Quantitative and qualitative methods were combined by administering questionnaires as well as conducting post intervention interviews. A number of trial feasibility factors were examined such as recruitment and attrition rates. Qualitative data was analysed using Braun and Clarke’s thematic analysis framework. Results: Nine participants started the MBCT intervention and six completed the 8-week programme. The results suggest that MBCT for older people is feasible and acceptable. Participants reported improved mindfulness skills. Participants responded positively to being asked to take part in research and appeared to particularly value the group delivery format of the intervention. Conclusions: MBCT is both feasible and acceptable for older people experiencing symptoms of depression. Further research is required with larger sample sizes to allow for more robust statistical exploration of outcome measures, including mechanisms of change.

Optimization models and methods for real-time transportation planning in forestry

Lors du transport du bois de la forêt vers les usines, de nombreux événements imprévus peuvent se produire, événements qui perturbent les trajets prévus (par exemple, en raison des conditions météo, des feux de forêt, de la présence de nouveaux chargements, etc.). Lorsque de tels événements ne sont connus que durant un trajet, le camion qui accomplit ce trajet doit être détourné vers un chemin alternatif. En l’absence d’informations sur un tel chemin, le chauffeur du camion est susceptible de choisir un chemin alternatif inutilement long ou pire, qui est lui-même "fermé" suite à un événement imprévu. Il est donc essentiel de fournir aux chauffeurs des informations en temps réel, en particulier des suggestions de chemins alternatifs lorsqu’une route prévue s’avère impraticable. Les possibilités de recours en cas d’imprévus dépendent des caractéristiques de la chaîne logistique étudiée comme la présence de camions auto-chargeurs et la politique de gestion du transport. Nous présentons trois articles traitant de contextes d’application différents ainsi que des modèles et des méthodes de résolution adaptés à chacun des contextes. Dans le premier article, les chauffeurs de camion disposent de l’ensemble du plan hebdomadaire de la semaine en cours. Dans ce contexte, tous les efforts doivent être faits pour minimiser les changements apportés au plan initial. Bien que la flotte de camions soit homogène, il y a un ordre de priorité des chauffeurs. Les plus prioritaires obtiennent les volumes de travail les plus importants. Minimiser les changements dans leurs plans est également une priorité. Étant donné que les conséquences des événements imprévus sur le plan de transport sont essentiellement des annulations et/ou des retards de certains voyages, l’approche proposée traite d’abord l’annulation et le retard d’un seul voyage, puis elle est généralisée pour traiter des événements plus complexes. Dans cette ap- proche, nous essayons de re-planifier les voyages impactés durant la même semaine de telle sorte qu’une chargeuse soit libre au moment de l’arrivée du camion à la fois au site forestier et à l’usine. De cette façon, les voyages des autres camions ne seront pas mo- difiés. Cette approche fournit aux répartiteurs des plans alternatifs en quelques secondes. De meilleures solutions pourraient être obtenues si le répartiteur était autorisé à apporter plus de modifications au plan initial. Dans le second article, nous considérons un contexte où un seul voyage à la fois est communiqué aux chauffeurs. Le répartiteur attend jusqu’à ce que le chauffeur termine son voyage avant de lui révéler le prochain voyage. Ce contexte est plus souple et offre plus de possibilités de recours en cas d’imprévus. En plus, le problème hebdomadaire peut être divisé en des problèmes quotidiens, puisque la demande est quotidienne et les usines sont ouvertes pendant des périodes limitées durant la journée. Nous utilisons un modèle de programmation mathématique basé sur un réseau espace-temps pour réagir aux perturbations. Bien que ces dernières puissent avoir des effets différents sur le plan de transport initial, une caractéristique clé du modèle proposé est qu’il reste valable pour traiter tous les imprévus, quelle que soit leur nature. En effet, l’impact de ces événements est capturé dans le réseau espace-temps et dans les paramètres d’entrée plutôt que dans le modèle lui-même. Le modèle est résolu pour la journée en cours chaque fois qu’un événement imprévu est révélé. Dans le dernier article, la flotte de camions est hétérogène, comprenant des camions avec des chargeuses à bord. La configuration des routes de ces camions est différente de celle des camions réguliers, car ils ne doivent pas être synchronisés avec les chargeuses. Nous utilisons un modèle mathématique où les colonnes peuvent être facilement et naturellement interprétées comme des itinéraires de camions. Nous résolvons ce modèle en utilisant la génération de colonnes. Dans un premier temps, nous relaxons l’intégralité des variables de décision et nous considérons seulement un sous-ensemble des itinéraires réalisables. Les itinéraires avec un potentiel d’amélioration de la solution courante sont ajoutés au modèle de manière itérative. Un réseau espace-temps est utilisé à la fois pour représenter les impacts des événements imprévus et pour générer ces itinéraires. La solution obtenue est généralement fractionnaire et un algorithme de branch-and-price est utilisé pour trouver des solutions entières. Plusieurs scénarios de perturbation ont été développés pour tester l’approche proposée sur des études de cas provenant de l’industrie forestière canadienne et les résultats numériques sont présentés pour les trois contextes.

Estudo comparativo de métodos de regionalização hidrológica e desenvolvimento de um aplicativo para o gerenciamento de outorga de águas superficiais

Dissertação (mestrado)—Universidade de Brasília, Instituto de Geociências, 2016.

The scientific rationale, design and implementation plan for a Biogeochemical-Argo float array

Biogeochemical-Argo is the extension of the Argo array of profiling floats to include floats that are equipped with biogeochemical sensors for pH, oxygen, nitrate, chlorophyll, suspended particles, and downwelling irradiance. Argo is a highly regarded, international program that measures the changing ocean temperature (heat content) and salinity with profiling floats distributed throughout the ocean. Newly developed sensors now allow profiling floats to also observe biogeochemical properties with sufficient accuracy for climate studies. This extension of Argo will enable an observing system that can determine the seasonal to decadal-scale variability in biological productivity, the supply of essential plant nutrients from deep-waters to the sunlit surface layer, ocean acidification, hypoxia, and ocean uptake of CO2. Biogeochemical-Argo will drive a transformative shift in our ability to observe and predict the effects of climate change on ocean metabolism, carbon uptake, and living marine resource management. Presently, vast areas of the open ocean are sampled only once per decade or less, with sampling occurring mainly in summer. Our ability to detect changes in biogeochemical processes that may occur due to the warming and acidification driven by increasing atmospheric CO2, as well as by natural climate variability, is greatly hindered by this undersampling. In close synergy with satellite systems (which are effective at detecting global patterns for a few biogeochemical parameters, but only very close to the sea surface and in the absence of clouds), a global array of biogeochemical sensors would revolutionize our understanding of ocean carbon uptake, productivity, and deoxygenation. The array would reveal the biological, chemical, and physical events that control these processes. Such a system would enable a new generation of global ocean prediction systems in support of carbon cycling, acidification, hypoxia and harmful algal blooms studies, as well as the management of living marine resources. In order to prepare for a global Biogeochemical-Argo array, several prototype profiling float arrays have been developed at the regional scale by various countries and are now operating. Examples include regional arrays in the Southern Ocean (SOCCOM ), the North Atlantic Sub-polar Gyre (remOcean ), the Mediterranean Sea (NAOS ), the Kuroshio region of the North Pacific (INBOX ), and the Indian Ocean (IOBioArgo ). For example, the SOCCOM program is deploying 200 profiling floats with biogeochemical sensors throughout the Southern Ocean, including areas covered seasonally with ice. The resulting data, which are publically available in real time, are being linked with computer models to better understand the role of the Southern Ocean in influencing CO2 uptake, biological productivity, and nutrient supply to distant regions of the world ocean. The success of these regional projects has motivated a planning meeting to discuss the requirements for and applications of a global-scale Biogeochemical-Argo program. The meeting was held 11-13 January 2016 in Villefranche-sur-Mer, France with attendees from eight nations now deploying Argo floats with biogeochemical sensors present to discuss this topic. In preparation, computer simulations and a variety of analyses were conducted to assess the resources required for the transition to a global-scale array. Based on these analyses and simulations, it was concluded that an array of about 1000 biogeochemical profiling floats would provide the needed resolution to greatly improve our understanding of biogeochemical processes and to enable significant improvement in ecosystem models. With an endurance of four years for a Biogeochemical-Argo float, this system would require the procurement and deployment of 250 new floats per year to maintain a 1000 float array. The lifetime cost for a Biogeochemical-Argo float, including capital expense, calibration, data management, and data transmission, is about $100,000. A global Biogeochemical-Argo system would thus cost about $25,000,000 annually. In the present Argo paradigm, the US provides half of the profiling floats in the array, while the EU, Austral/Asia, and Canada share most the remaining half. If this approach is adopted, the US cost for the Biogeochemical-Argo system would be ~$12,500,000 annually and ~$6,250,000 each for the EU, and Austral/Asia and Canada. This includes no direct costs for ship time and presumes that float deployments can be carried out from future research cruises of opportunity, including, for example, the international GO-SHIP program (http://www.go-ship.org). The full-scale implementation of a global Biogeochemical-Argo system with 1000 floats is feasible within a decade. The successful, ongoing pilot projects have provided the foundation and start for such a system.