Operational research applied to regional healthcare system

In this thesis we focus on optimization and simulation techniques applied to solve strategic, tactical and operational problems rising in the healthcare sector. At first we present three applications to Emilia-Romagna Public Health System (SSR) developed in collaboration with Agenzia Sanitaria e Sociale dell'Emilia-Romagna (ASSR), a regional center for innovation and improvement in health. Agenzia launched a strategic campaign aimed at introducing Operations Research techniques as decision making tools to support technological and organizational innovations. The three applications focus on forecast and fund allocation of medical specialty positions, breast screening program extension and operating theater planning. The case studies exploit the potential of combinatorial optimization, discrete event simulation and system dynamics techniques to solve resource constrained problem arising within Emilia-Romagna territory. We then present an application in collaboration with Dipartimento di Epidemiologia del Lazio that focuses on population demand of service allocation to regional emergency departments. Finally, a simulation-optimization approach, developed in collaboration with INESC TECH center of Porto, to evaluate matching policies for the kidney exchange problem is discussed.

Modelling coupled physical-biogeochemical processes in ice-covered oceans

The last decades have seen a large effort of the scientific community to study and understand the physics of sea ice. We currently have a wide - even though still not exhaustive - knowledge of the sea ice dynamics and thermodynamics and of their temporal and spatial variability. Sea ice biogeochemistry is instead largely unknown. Sea ice algae production may account for up to 25% of overall primary production in ice-covered waters of the Southern Ocean. However, the influence of physical factors, such as the location of ice formation, the role of snow cover and light availability on sea ice primary production is poorly understood. There are only sparse localized observations and little knowledge of the functioning of sea ice biogeochemistry at larger scales. Modelling becomes then an auxiliary tool to help qualifying and quantifying the role of sea ice biogeochemistry in the ocean dynamics. In this thesis, a novel approach is used for the modelling and coupling of sea ice biogeochemistry - and in particular its primary production - to sea ice physics. Previous attempts were based on the coupling of rather complex sea ice physical models to empirical or relatively simple biological or biogeochemical models. The focus is moved here to a more biologically-oriented point of view. A simple, however comprehensive, physical model of the sea ice thermodynamics (ESIM) was developed and coupled to a novel sea ice implementation (BFM-SI) of the Biogeochemical Flux Model (BFM). The BFM is a comprehensive model, largely used and validated in the open ocean environment and in regional seas. The physical model has been developed having in mind the biogeochemical properties of sea ice and the physical inputs required to model sea ice biogeochemistry. The central concept of the coupling is the modelling of the Biologically-Active-Layer (BAL), which is the time-varying fraction of sea ice that is continuously connected to the ocean via brines pockets and channels and it acts as rich habitat for many microorganisms. The physical model provides the key physical properties of the BAL (e.g., brines volume, temperature and salinity), and the BFM-SI simulates the physiological and ecological response of the biological community to the physical enviroment. The new biogeochemical model is also coupled to the pelagic BFM through the exchange of organic and inorganic matter at the boundaries between the two systems . This is done by computing the entrapment of matter and gases when sea ice grows and release to the ocean when sea ice melts to ensure mass conservation. The model was tested in different ice-covered regions of the world ocean to test the generality of the parameterizations. The focus was particularly on the regions of landfast ice, where primary production is generally large. The implementation of the BFM in sea ice and the coupling structure in General Circulation Models will add a new component to the latters (and in general to Earth System Models), which will be able to provide adequate estimate of the role and importance of sea ice biogeochemistry in the global carbon cycle.

Multi-level models and infrastructures for simulating biological system development

The hierarchical organisation of biological systems plays a crucial role in the pattern formation of gene expression resulting from the morphogenetic processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful for studying such a complex phenomenon of self-organisation. The idea is to model the phenomenon in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events determines the emergent behaviour resulting in the formation of spatial patterns. According to these premises the thesis proposes a review of the different approaches already developed in modelling developmental biology problems, as well as the main models and infrastructures available in literature for modelling biological systems, analysing their capabilities in tackling multi-compartment / multi-level models. The thesis then introduces a practical framework, MS-BioNET, for modelling and simulating these scenarios exploiting the potential of multi-level dynamics. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie’s direct method. The thesis finally proposes the adoption of the agent-based model as an approach capable of capture multi-level dynamics. To overcome the problem of parameter tuning in the model, the simulators are supplied with a module for parameter optimisation. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. The problem is tackled with a metaheuristic algorithm. As an example of application of the MS-BioNET framework and of the agent-based model, a model of the first stages of Drosophila Melanogaster development is realised. The model goal is to generate the early spatial pattern of gap gene expression. The correctness of the models is shown comparing the simulation results with real data of gene expression with spatial and temporal resolution, acquired in free on-line sources.

Soil application of Meliaceae derivatives: effect on carbon and nitrogen dynamics in the soil-plant system

The effect of soil incorporation of 7 Meliaceae derivatives (6 commercial neem cakes and leaves of Melia azedarach L.) on C and N dynamics and on nutrient availability to micropropagated GF677 rootstock was investigated. In a first laboratory incubation experiment the derivatives showed different N mineralization dynamics, generally well predicted by their C:N ratio and only partly by their initial N concentration. All derivatives increased microbial biomass C, thus representing a source of C for the soil microbial population. Soil addition of all neem cakes (8 g kg-1) and melia leaves (16 g kg-1) had a positive effect on plant growth and increased root N uptake and leaf green colour of micropropagated plants of GF677. In addition, the neem cakes characterized by higher nutrient concentration increased P and K concentration in shoot and leaves 68 days after the amendment. In another experiment, soil incorporation of 15N labeled melia leaves (16 g kg-1) had no effect on the total amount of plant N, however the percentage of melia derived-N of treated plants ranged between 0.8% and 34% during the experiment. At the end of the growing season, about 7% of N added as melia leaves was recovered in plant, while 70% of it was still present in soil. Real C mineralization and the priming effect induced by the addition of the derivatives were quantified by a natural 13C abundance method. The real C mineralization of the derivatives ranged between 22% and 40% of added-C. All the derivatives studied induced a positive priming effect and, 144 days after the amendment, the amount of C primed corresponded to 26% of added-C, for all the derivatives. Despite this substantial priming effect, the C balance of the soil, 144 days after the amendment, always resulted positive.

Model reduction techniques in flexible multibody dynamics with application to engine cranktrain simulation

The development of a multibody model of a motorbike engine cranktrain is presented in this work, with an emphasis on flexible component model reduction. A modelling methodology based upon the adoption of non-ideal joints at interface locations, and the inclusion of component flexibility, is developed: both are necessary tasks if one wants to capture dynamic effects which arise in lightweight, high-speed applications. With regard to the first topic, both a ball bearing model and a journal bearing model are implemented, in order to properly capture the dynamic effects of the main connections in the system: angular contact ball bearings are modelled according to a five-DOF nonlinear scheme in order to grasp the crankshaft main bearings behaviour, while an impedance-based hydrodynamic bearing model is implemented providing an enhanced operation prediction at the conrod big end locations. Concerning the second matter, flexible models of the crankshaft and the connecting rod are produced. The well-established Craig-Bampton reduction technique is adopted as a general framework to obtain reduced model representations which are suitable for the subsequent multibody analyses. A particular component mode selection procedure is implemented, based on the concept of Effective Interface Mass, allowing an assessment of the accuracy of the reduced models prior to the nonlinear simulation phase. In addition, a procedure to alleviate the effects of modal truncation, based on the Modal Truncation Augmentation approach, is developed. In order to assess the performances of the proposed modal reduction schemes, numerical tests are performed onto the crankshaft and the conrod models in both frequency and modal domains. A multibody model of the cranktrain is eventually assembled and simulated using a commercial software. Numerical results are presented, demonstrating the effectiveness of the implemented flexible model reduction techniques. The advantages over the conventional frequency-based truncation approach are discussed.

Modelling UV response of biomolecules: from electronic structure to ab-initio dynamics.

The interaction of organic chromophores with light initiates ultrafast processes in the timescale of femtoseconds. An atomistic understanding of the mechanism driving such photoinduced reactions opens up the door to exploit them for our benefit. This thesis studies the interactions of ultraviolet light with the DNA/RNA molecules and the amino-acid tryptophan. Using some of the most accurate electronic structure methods and sophisticated environmental modelling, the works documented herein enable quantitative comparisons with cutting-edge experimental data. The relaxation pathways undertaken by the excited molecule are revealed through static and dynamical investigations of the excited-state potential energy surface. The profound role played by the dynamic response of the environment to guide the excitation in these timescales is addressed thoroughly.

Coastal modelling studies for forecasting and remediation solutions

The coastal area along the Emilia-Romagna (ER), in the Italian side of the northern Adriatic Sea, is considered to implement an unstructured numerical ocean model with the aim to develop innovative tools for the coastal management and a forecasting system for the storm surge risk reduction. The Adriatic Sea has been the focus of several studies because of its peculiar dynamics driven by many forcings acting at basin and local scales. The ER coast is particularly exposed to storm surge events. In particular conditions, winds, tides and seicehs may combine and contribute to the flooding of the coastal area. The global sea level rise expected in the next decades will increase even more the hazard along the ER and Adriatic coast. Reliable Adriatic and Mediterranean scale numerical ocean models are now available to allow the dynamical downscaling of very high-resolution models in limited coastal areas. In this work the numerical ocean model SHYFEM is implemented in the Goro lagoon (named GOLFEM) and along the ER coast (ShyfER) to test innovative solutions against sea related coastal hazards. GOLFEM was succesfully applied to analyze the Goro lagoon dynamics and to assess the dynamical effects of human interventions through the analysis of what-if scenarios. The assessment of storm surge hazard in the Goro lagoon was carried out through the development of an ensemble storm surge forecasting system with GOLFEM using forcing from different operational meteorological and ocean models showing the fundamental importance of the boundary conditions. The ShyfER domain is used to investigate innovative solutions against storm surge related hazard along the ER coast. The seagrass is assessed as a nature-based solution (NBS) for coastal protection under present and future climate conditions. The results show negligible effects on sea level but sensible effects in reducing bottom current velocity.

Molecular modelling of organic functional materials

The investigation of the mechanisms lying behind the (photo-)chemical processes is fundamental to address and improve the design of new organic functional materials. In many cases, dynamics simulations represent the only tool to capture the system properties emerging from complex interactions between many molecules. Despite the outstanding progresses in calculation power, the only way to carry out such computational studies is to introduce several approximations with respect to a fully quantum mechanical (QM) description. This thesis presents an approach that combines QM calculations with a classical Molecular Dynamics (MD) approach by means of accurate QM-derived force fields. It is based on a careful selection of the most relevant molecular degrees of freedom, whose potential energy surface is calculated at QM level and reproduced by the analytic functions of the force field, as well as by an accurate tuning of the approximations introduced in the model of the process to be simulated. This is made possible by some tools developed purposely, that allow to obtain and test the FF parameters through comparison with the QM frequencies and normal modes. These tools were applied in the modelling of three processes: the npi* photoisomerisation of azobenzene, where the FF description was extended to the excited state too and the non-adiabatic events were treated stochastically with Tully fewest switching algorithm; the charge separation in donors-acceptors bulk heterojunction organic solar cells, where a tight-binding Hamiltonian was carefully parametrised and solved by means of a code, also written specifically; the effect of the protonation state on the photoisomerisation quantum yield of the aryl-azoimidazolium unit of the axle molecule of a rotaxane molecular shuttle. In each case, the QM-based MD models that were specifically developed gave noteworthy information about the investigated phenomena, proving to be a fundamental key for a deeper comprehension of several experimental evidences.

Modelling, simulation and control of rotary-wing aircraft in multi-agent scenario

The topic of this thesis is the design and the implementation of mathematical models and control system algorithms for rotary-wing unmanned aerial vehicles to be used in cooperative scenarios. The use of rotorcrafts has many attractive advantages, since these vehicles have the capability to take-off and land vertically, to hover and to move backward and laterally. Rotary-wing aircraft missions require precise control characteristics due to their unstable and heavy coupling aspects. As a matter of fact, flight test is the most accurate way to evaluate flying qualities and to test control systems. However, it may be very expensive and/or not feasible in case of early stage design and prototyping. A good compromise is made by a preliminary assessment performed by means of simulations and a reduced flight testing campaign. Consequently, having an analytical framework represents an important stage for simulations and control algorithm design. In this work mathematical models for various helicopter configurations are implemented. Different flight control techniques for helicopters are presented with theoretical background and tested via simulations and experimental flight tests on a small-scale unmanned helicopter. The same platform is used also in a cooperative scenario with a rover. Control strategies, algorithms and their implementation to perform missions are presented for two main scenarios. One of the main contributions of this thesis is to propose a suitable control system made by a classical PID baseline controller augmented with L1 adaptive contribution. In addition a complete analytical framework and the study of the dynamics and the stability of a synch-rotor are provided. At last, the implementation of cooperative control strategies for two main scenarios that include a small-scale unmanned helicopter and a rover.

Advanced representation of the ocean/sea ice dynamics at high latitudes

Sea ice is a fundamental element of global climate system, with numerous impacts on the polar environment. The ongoing drastic changes in the Earth’s sea ice cover highlight the necessity of monitoring the polar regions and systematically evaluating the quality of different numerical products. The main objective of this thesis is to improve our knowledge of the representation of Arctic and Antarctic sea ice using comprehensive global ocean reanalyses and coupled climate models. The dissertation will explore (i) the Antarctic marginal ice zone (MIZ) and pack ice area in the ensemble mean of four global ocean reanalyses called GREP; (ii) historical representation of the Arctic and Antarctic sea ice state in HighResMIP models; (iii) the future evolution of Arctic sea ice in HighResMIP models. Global ocean reanalyses and GREP are found to adequately capture interannual and seasonal variability in both pack ice and MIZ areas at hemispheric and regional scales. The advantage of the ensemble-mean approach is proved as GREP smooths the strengths and weaknesses of single systems and provides the most consistent and reliable estimates. This work is intended to encourage the use of GREP in a wide range of applications. The analysis of sea ice representation in the coupled climate models shows no systematic impact of the increased horizontal resolution. We argue that a few minor improvements in sea ice representation with the enhanced horizontal resolution are presumably not worth the major effort of costly computations. The thesis highlights the critical importance to distinguish the MIZ from consolidated pack ice both for investigating changes in sea ice distribution and evaluating the product’s performance. Considering that the MIZ is predicted to dominate the Arctic sea ice cover, the model physics parameterizations and sea ice rheology might require modifications. The results of the work can be useful for modelling community.

Urban air mobility: modelling the future transport system

The advances in the aviation field, particularly the development of electric flying vehicles, as UAV and eVTOL, paved the way for setting Urban Air Mobility (UAM) services. UAM would provide services for passengers, goods and emergencies and could offer faster trips than ground ones. It is expected that early UAM operations will be performed at Very Low-Level airspace as 0-500 m Above Ground Level. The purpose of this research is to both explore the main features of UAM and test an aerial network model, which could be integrated in a multimodal transport system where ground and aerial mobility services are provided. Analyses on UAM transport system involved two sub-systems: the transport demand sub-system, i.e., the mobility requirements, and the transport supply sub-system, i.e., the service and facilities enabling mobility. At first, the UAM demand levels and features for an Airport Shuttle service have been explored through a suitable survey, by combining Revealed and Stated Preference methodologies, and by calibrating some discrete mode choice models. Then, the focus has been on the transport supply model for UAM services, by focusing on both the ground access points (vertiports) and the aerial network model. A suitable three-dimensional urban aerial network (3D-UAN) model that could support fast aerial connections between O/D pairs has been proposed. Some tests have been implemented to verify the feasibility of the proposed model. Some flying vehicles supporting an Airport Shuttle service have been simulated on the aerial network, which has been specified in terms of both topological features and link transport costs. The preliminary results have showed that the proposed 3D-UAN model could be suitable for supporting UAM services. As for transport engineering, the UAM system framework proposed in this thesis paves the way for further research on air-ground multimodality in urban areas.