Bio-physical interactions and feedbacks in a global climate model

This PhD thesis addresses the topic of large-scale interactions between climate and marine biogeochemistry. To this end, centennial simulations are performed under present and projected future climate conditions with a coupled ocean-atmosphere model containing a complex marine biogeochemistry model. The role of marine biogeochemistry in the climate system is first investigated. Phytoplankton solar radiation absorption in the upper ocean enhances sea surface temperatures and upper ocean stratification. The associated increase in ocean latent heat losses raises atmospheric temperatures and water vapor. Atmospheric circulation is modified at tropical and extratropical latitudes with impacts on precipitation, incoming solar radiation, and ocean circulation which cause upper-ocean heat content to decrease at tropical latitudes and to increase at middle latitudes. Marine biogeochemistry is tightly related to physical climate variability, which may vary in response to internal natural dynamics or to external forcing such as anthropogenic carbon emissions. Wind changes associated with the North Atlantic Oscillation (NAO), the dominant mode of climate variability in the North Atlantic, affect ocean properties by means of momentum, heat, and freshwater fluxes. Changes in upper ocean temperature and mixing impact the spatial structure and seasonality of North Atlantic phytoplankton through light and nutrient limitations. These changes affect the capability of the North Atlantic Ocean of absorbing atmospheric CO2 and of fixing it inside sinking particulate organic matter. Low-frequency NAO phases determine a delayed response of ocean circulation, temperature and salinity, which in turn affects stratification and marine biogeochemistry. In 20th and 21st century simulations natural wind fluctuations in the North Pacific, related to the two dominant modes of atmospheric variability, affect the spatial structure and the magnitude of the phytoplankton spring bloom through changes in upper-ocean temperature and mixing. The impacts of human-induced emissions in the 21st century are generally larger than natural climate fluctuations, with the phytoplankton spring bloom starting one month earlier than in the 20th century and with ~50% lower magnitude. This PhD thesis advances the knowledge of bio-physical interactions within the global climate, highlighting the intrinsic coupling between physical climate and biosphere, and providing a framework on which future studies of Earth System change can be built on.

Development Aid to Water Management in Mali: The Actors, ‘Global’ Paradigms, and ‘Local’ Translations

Development aid involves a complex network of numerous and extremely heterogeneous actors. Nevertheless, all actors seem to speak the same ‘development jargon’ and to display a congruence that extends from the donor over the professional consultant to the village chief. And although the ideas about what counts as ‘good’ and ‘bad’ aid have constantly changed over time —with new paradigms and policies sprouting every few years— the apparent congruence between actors more or less remains unchanged. How can this be explained? Is it a strategy of all actors to get into the pocket of the donor, or are the social dynamics in development aid more complex? When a new development paradigm appears, where does it come from and how does it gain support? Is this support really homogeneous? To answer the questions, a multi-sited ethnography was conducted in the sector of water-related development aid, with a focus on 3 paradigms that are currently hegemonic in this sector: Integrated Water Resources Management, Capacity Building, and Adaptation to Climate Change. The sites of inquiry were: the headquarters of a multilateral organization, the headquarters of a development NGO, and the Inner Niger Delta in Mali. The research shows that paradigm shifts do not happen overnight but that new paradigms have long lines of descent. Moreover, they require a lot of work from actors in order to become hegemonic; the actors need to create a tight network of support. Each actor, however, interprets the paradigms in a slightly different way, depending on the position in the network. They implant their own interests in their interpretation of the paradigm (the actors ‘translate’ their interests), regardless of whether they constitute the donor, a mediator, or the aid recipient. These translations are necessary to cement and reproduce the network.

Fellow travelers: an ethnographic study of the dynamics of inter-organizational collaboration

The research is a 13-months ethnographic field work on the early operations of a Multi-party alliance active in the global field of indoor positioning. The study aims to understand and investigate empirically the challenges that at the individual and group level influence the organizing principle guiding the alliance operations and evolution. Its contribution rests on the dynamics affecting ecosystems of innovation and collaborative spaces of value co-creation in inter-organizational projects.

Symbolic Dynamics Analysis: a new methodology for foetal heart rate variability analysis

Cardiotocography (CTG) is a widespread foetal diagnostic methods. However, it lacks of objectivity and reproducibility since its dependence on observer's expertise. To overcome these limitations, more objective methods for CTG interpretation have been proposed. In particular, many developed techniques aim to assess the foetal heart rate variability (FHRV). Among them, some methodologies from nonlinear systems theory have been applied to the study of FHRV. All the techniques have proved to be helpful in specific cases. Nevertheless, none of them is more reliable than the others. Therefore, an in-depth study is necessary. The aim of this work is to deepen the FHRV analysis through the Symbolic Dynamics Analysis (SDA), a nonlinear technique already successfully employed for HRV analysis. Thanks to its simplicity of interpretation, it could be a useful tool for clinicians. We performed a literature study involving about 200 references on HRV and FHRV analysis; approximately 100 works were focused on non-linear techniques. Then, in order to compare linear and non-linear methods, we carried out a multiparametric study. 580 antepartum recordings of healthy fetuses were examined. Signals were processed using an updated software for CTG analysis and a new developed software for generating simulated CTG traces. Finally, statistical tests and regression analyses were carried out for estimating relationships among extracted indexes and other clinical information. Results confirm that none of the employed techniques is more reliable than the others. Moreover, in agreement with the literature, each analysis should take into account two relevant parameters, the foetal status and the week of gestation. Regarding the SDA, results show its promising capabilities in FHRV analysis. It allows recognizing foetal status, gestation week and global variability of FHR signals, even better than other methods. Nevertheless, further studies, which should involve even pathological cases, are necessary to establish its reliability.

Dynamics of coastal aquifers: data-driven forecasting and risk analysis

This work is focused on the study of saltwater intrusion in coastal aquifers, and in particular on the realization of conceptual schemes to evaluate the risk associated with it. Saltwater intrusion depends on different natural and anthropic factors, both presenting a strong aleatory behaviour, that should be considered for an optimal management of the territory and water resources. Given the uncertainty of problem parameters, the risk associated with salinization needs to be cast in a probabilistic framework. On the basis of a widely adopted sharp interface formulation, key hydrogeological problem parameters are modeled as random variables, and global sensitivity analysis is used to determine their influence on the position of saltwater interface. The analyses presented in this work rely on an efficient model reduction technique, based on Polynomial Chaos Expansion, able to combine the best description of the model without great computational burden. When the assumptions of classical analytical models are not respected, and this occurs several times in the applications to real cases of study, as in the area analyzed in the present work, one can adopt data-driven techniques, based on the analysis of the data characterizing the system under study. It follows that a model can be defined on the basis of connections between the system state variables, with only a limited number of assumptions about the "physical" behaviour of the system.

Classical and quantum aspects of black hole dynamics

Il contenuto fisico della Relatività Generale è espresso dal Principio di Equivalenza, che sancisce l'equivalenza di geometria e gravitazione. La teoria predice l'esistenza dei buchi neri, i più semplici oggetti macroscopici esistenti in natura: essi sono infatti descritti da pochi parametri, le cui variazioni obbediscono a leggi analoghe a quelle della termodinamica. La termodinamica dei buchi neri è posta su basi solide dalla meccanica quantistica, mediante il fenomeno noto come radiazione di Hawking. Questi risultati gettano una luce su una possibile teoria quantistica della gravitazione, ma ad oggi una simile teoria è ancora lontana. In questa tesi ci proponiamo di studiare i buchi neri nei loro aspetti sia classici che quantistici. I primi due capitoli sono dedicati all'esposizione dei principali risultati raggiunti in ambito teorico: in particolare ci soffermeremo sui singularity theorems, le leggi della meccanica dei buchi neri e la radiazione di Hawking. Il terzo capitolo, che estende la discussione sulle singolarità, espone la teoria dei buchi neri non singolari, pensati come un modello effettivo di rimozione delle singolarità. Infine il quarto capitolo esplora le ulteriori conseguenze della meccanica quantistica sulla dinamica dei buchi neri, mediante l'uso della nozione di entropia di entanglement.

Temporal dynamics of benthic assemblages along a gradient of ocean acidification at a CO2 vent’s system of the Ischia Island

Global warming and ocean acidification, due to rising atmospheric levels of CO2, represent an actual threat to terrestrial and marine environments. Since Industrial Revolution, in less of 250 years, pH of surface seawater decreased on average of 0.1 unit, and is expected to further decreases of approximately 0.3-0.4 units by the end of this century. Naturally acidified marine areas, such as CO2 vent systems at the Ischia Island, allow to study acclimatation and adaptation of individual species as well as the structure of communities, and ecosystems to OA. The main aim of this thesis was to study how hard bottom sublittoral benthic assemblages changed trough time along a pH gradient. For this purpose, the temporal dynamics of mature assemblages established on artificial substrates (volcanic tiles) over a 3 year- period were analysed. Our results revealed how composition and dynamics of the community were altered and highly simplified at different level of seawater acidification. In fact, extreme low values of pH (approximately 6.9), affected strongly the assemblages, reducing diversity both in terms of taxa and functional groups, respect to lower acidification levels (mean pH 7.8) and ambient conditions (8.1 unit). Temporal variation was observed in terms of species composition but not in functional groups. Variability was related to species belonging to the same functional group, suggesting the occurrence of functional redundancy. Therefore, the analysis of functional groups kept information on the structure, but lost information on species diversity and dynamics. Decreasing in ocean pH is only one of many future global changes that will occur at the end of this century (increase of ocean temperature, sea level rise, eutrophication etc.). The interaction between these factors and OA could exacerbate the community and ecosystem effects showed by this thesis.

MODELING THE DYNAMICS OF AIRWAY CONSTRICTION: EFFECTS OF AGONIST TRANSPORT AND BINDING

Recent advances have revealed that during exogenous airway challenge, airway diameters can not be adequately predicted by their initial diameters. Furthermore, airway diameters can also vary greatly in time on scales shorter than a breath. In order to better understand these phenomena, we developed a multiscale model which allows us to simulate aerosol challenge in the airways during ventilation. The model incorporates agonist-receptor binding kinetics to govern the temporal response of airway smooth muscle (ASM) contraction on individual airway segments, which together with airway wall mechanics, determines local airway caliber. Global agonist transport and deposition is coupled with pressure-driven flow, linking local airway constrictions with global flow dynamics. During the course of challenge, airway constriction alters the flow pattern, redistributing agonist to less constricted regions. This results in a negative feedback which may be a protective property of the normal lung. As a consequence, repetitive challenge can cause spatial constriction patterns to evolve in time, resulting in a loss of predictability of airway diameters. Additionally, the model offers new insight into several phenomena including the intra- and inter-breath dynamics of airway constriction throughout the tree structure.

Accessibility as a determinant of environmental dynamics in socio-economic disparities in mainland Southeast Asia

Access and accessibility are important determinants of people’s ability to utilise natural resources, and have a strong impact on household welfare. Physical accessibility of natural resources, on the other hand, has generally been regarded as one of the most important drivers of land-use and land-cover changes. Based on two case studies, this article discusses evidence of the impact of access to services and access to natural resources on household poverty and on the environment. We show that socio-cultural distances are a key limiting factor for gaining access to services, and thereby for improved household welfare. We also discuss the impact of socio-cultural distances on access to natural resources, and show that large-scale commercial exploitation of natural resources tends to occur beyond the spatial reach of socio-culturally and economically marginalised population segments. We conclude that it is essential to pay more attention to improving the structural environment that presently leaves social minority groups marginalised. Innovative approaches that use natural resource management to induce poverty reduction – for example, through compensation of local farmers for environmental services – appear to be promising avenues that can lead to integration of the objectives of poverty reduction and sustainable environmental stewardship.

Structure and thermodynamics of H3O+(H2O)8 clusters: A combined molecular dynamics and quantum mechanics approach

We have studied the structure and stability of (H3O+)(H2O)8 clusters using a combination of molecular dynamics sampling and high-level ab initio calculations. 20 distinct oxygen frameworks are found within 2 kcal/mol of the electronic or standard Gibbs free energy minimum. The impact of quantum zero-point vibrational corrections on the relative stability of these isomers is quite significant. The box-like isomers are favored in terms of electronic energy, but with the inclusion of zero-point vibrational corrections and entropic effects tree-like isomers are favored at higher temperatures. Under conditions from 0 to 298.15 K, the global minimum is predicted to be a tree-like structure with one dangling singly coordinated water molecule. Above 298.15 K, higher entropy tree-like isomers with two or more singly coordinated water molecules are favored. These assignments are generally consistent with experimental IR spectra of (H3O+)(H2O)8 obtained at 150 K.

A global ”imaging” view on systems approaches in immunology

The immune system exhibits an enormous complexity. High throughput methods such as the "-omic'' technologies generate vast amounts of data that facilitate dissection of immunological processes at ever finer resolution. Using high-resolution data-driven systems analysis, causal relationships between complex molecular processes and particular immunological phenotypes can be constructed. However, processes in tissues, organs, and the organism itself (so-called higher level processes) also control and regulate the molecular (lower level) processes. Reverse systems engineering approaches, which focus on the examination of the structure, dynamics and control of the immune system, can help to understand the construction principles of the immune system. Such integrative mechanistic models can properly describe, explain, and predict the behavior of the immune system in health and disease by combining both higher and lower level processes. Moving from molecular and cellular levels to a multiscale systems understanding requires the development of methodologies that integrate data from different biological levels into multiscale mechanistic models. In particular, 3D imaging techniques and 4D modeling of the spatiotemporal dynamics of immune processes within lymphoid tissues are central for such integrative approaches. Both dynamic and global organ imaging technologies will be instrumental in facilitating comprehensive multiscale systems immunology analyses as discussed in this review.

Dynamics of Spatial Game Theory Networks with Novel Modifications

Introduction: Advances in biotechnology have shed light on many biological processes. In biological networks, nodes are used to represent the function of individual entities within a system and have historically been studied in isolation. Network structure adds edges that enable communication between nodes. An emerging fieldis to combine node function and network structure to yield network function. One of the most complex networks known in biology is the neural network within the brain. Modeling neural function will require an understanding of networks, dynamics, andneurophysiology. It is with this work that modeling techniques will be developed to work at this complex intersection. Methods: Spatial game theory was developed by Nowak in the context of modeling evolutionary dynamics, or the way in which species evolve over time. Spatial game theory offers a two dimensional view of analyzingthe state of neighbors and updating based on the surroundings. Our work builds upon this foundation by studying evolutionary game theory networks with respect to neural networks. This novel concept is that neurons may adopt a particular strategy that will allow propagation of information. The strategy may therefore act as the mechanism for gating. Furthermore, the strategy of a neuron, as in a real brain, isimpacted by the strategy of its neighbors. The techniques of spatial game theory already established by Nowak are repeated to explain two basic cases and validate the implementation of code. Two novel modifications are introduced in Chapters 3 and 4 that build on this network and may reflect neural networks. Results: The introduction of two novel modifications, mutation and rewiring, in large parametricstudies resulted in dynamics that had an intermediate amount of nodes firing at any given time. Further, even small mutation rates result in different dynamics more representative of the ideal state hypothesized. Conclusions: In both modificationsto Nowak's model, the results demonstrate the network does not become locked into a particular global state of passing all information or blocking all information. It is hypothesized that normal brain function occurs within this intermediate range and that a number of diseases are the result of moving outside of this range.