Evolutionary algorithms for the modeling of bioreactors

This work aims to study the application of Genetic Algorithms in anaerobic digestion modeling, in particular when using dynamical models. Along the work, different types of bioreactors are shown, such as batch, semi-batch and continuous, as well as their mathematical modeling. The work intendeds to estimate the parameter values of two biological reaction model. For that, simulated results, where only one output variable, the produced biogas, is known, are fitted to the model results. For this reason, the problems associated with reverse optimization are studied, using some graphics that provide clues to the sensitivity and identifiability associated with the problem. Particular solutions obtained by the identifiability analysis using GENSSI and DAISY softwares are also presented. Finally, the optimization is performed using genetic algorithms. During this optimization the need to improve the convergence of genetic algorithms was felt. This need has led to the development of an adaptation of the genetic algorithms, which we called Neighbored Genetic Algorithms (NGA1 and NGA2). In order to understand if this new approach overcomes the Basic Genetic Algorithms (BGA) and achieves the proposed goals, a study of 100 full optimization runs for each situation was further developed. Results show that NGA1 and NGA2 are statistically better than BGA. However, because it was not possible to obtain consistent results, the Nealder-Mead method was used, where the initial guesses were the estimated results from GA; Algoritmos Evolucionários para a Modelação de Bioreactores Resumo: Neste trabalho procura-se estudar os algoritmos genéticos com aplicação na modelação da digestão anaeróbia e, em particular, quando se utilizam modelos dinâmicos. Ao longo do mesmo, são apresentados diferentes tipos de bioreactores, como os batch, semi-batch e contínuos, bem como a modelação matemática dos mesmos. Neste trabalho procurou-se estimar o valor dos parâmetros que constam num modelo de digestão anaeróbia para o ajustar a uma situação simulada onde apenas se conhece uma variável de output, o biogas produzido. São ainda estudados os problemas associados à optimização inversa com recurso a alguns gráficos que fornecem pistas sobre a sensibilidade e identifiacabilidade associadas ao problema da modelação da digestão anaeróbia. São ainda apresentadas soluções particulares de idenficabilidade obtidas através dos softwares GENSSI e DAISY. Finalmente é realizada a optimização do modelo com recurso aos algoritmos genéticos. No decorrer dessa optimização sentiu-se a necessidade de melhorar a convergência e, portanto, desenvolveu-se ainda uma adaptação dos algoritmos genéticos a que se deu o nome de Neighboured Genetic Algorithms (NGA1 e NGA2). No sentido de se compreender se as adaptações permitiam superar os algoritmos genéticos básicos e atingir as metas propostas, foi ainda desenvolvido um estudo em que o processo de optimização foi realizado 100 vezes para cada um dos métodos, o que permitiu concluir, estatisticamente, que os BGA foram superados pelos NGA1 e NGA2. Ainda assim, porque não foi possivel obter consistência nos resultados, foi usado o método de Nealder-Mead utilizado como estimativa inicial os resultados obtidos pelos algoritmos genéticos.

Advanced numerical modeling of masonry vaulted structures based on BIM parametric geometry generation

Vaults are an architectural element which during construction history have been built with a great variety of different materials, shapes, and sizes. The shape of these structural elements was often dependent by the necessity to cover complex spaces, by the needed loading capacity, or by architectural aesthetics. Within this complex scenario masonry patterns generates also different effects on loading capacity, load percolation and stiffness of the structure. These effects were been extensively investigated, both with empirical observations and with modern numerical methods. While most of them focus on analyzing the load bearing capacity or the texture effect on vaulted structures, the aim of this analysis is to investigate on the effects of the variation of a single structural characteristic on the load percolation in the vault. Moreover, an additional purpose of the work is related to the coding of a parametrical model aiming at generating different masonry vaulted structures. Nevertheless, proposed script can generate different typology of vaulted structure basing on some structural characteristics, such as the span and the length to cover and the dimensions of the blocks.

HBIM methodology for structural preservation of historical buildings: the semantic modeling of the San Felice sul Panaro fortress

Building Information Modelling is changing the design and construction field ever since it entered the market. It took just some time to show its capabilities, it takes some time to be mastered before it could be used expressing all its best features. Since it was conceived to be adopted from the earliest stage of design to get the maximum from the decisional project, it still struggles to adapt to existing buildings. In fact, there is a branch of this methodology that is dedicated to what has been already made that is called Historic BIM or HBIM. This study aims to make clear what are BIM and HBIM, both from a theoretical point of view and in practice, applying from scratch the state of the art to a case study. It had been chosen the fortress of San Felice sul Panaro, a marvellous building with a thousand years of history in its bricks, that suffered violent earthquakes, but it is still standing. By means of this example, it will be shown which are the limits that could be encountered when applying BIM methodology to existing heritage, moreover will be pointed out all the new features that a simple 2D design could not achieve.

Molecular simulations and modeling of pharmaceutically relevant RNA-processing enzymes

The two-metal-ion architecture is a structural feature found in a variety of RNA processing metalloenzymes or ribozymes (RNA-based enzymes), which control the biogenesis and the metabolism of vital RNAs, including non-coding RNAs (ncRNAs). Notably, such ncRNAs are emerging as key players for the regulation of cellular homeostasis, and their altered expression has been often linked to the development of severe human pathologies, from cancer to mental disorders. Accordingly, understanding the biological processing of ncRNAs is foundational for the development of novel therapeutic strategies and tools. Here, we use state-of the-art molecular simulations, complemented with X-ray crystallography and biochemical experiments, to characterize the RNA processing cycle as catalyzed by two two-metal-ion enzymes: the group II intron ribozymes and the RNase H1. We show that multiple and diverse cations are strategically recruited at and timely released from the enzymes’ active site during catalysis. Such a controlled cations’ trafficking leads to the recursive formation and disruption of an extended two-metal ion architecture that is functional for RNA-hydrolysis – from substrate recruitment to product release. Importantly, we found that these cations’ binding sites are conserved among other RNA-processing machineries, including the human spliceosome and CRISPR-Cas systems, suggesting that an evolutionarily-converged catalytic strategy is adopted by these enzymes to process RNA molecules. Thus, our findings corroborate and sensibly extend the current knowledge of two-metal-ion enzymes, and support the design of novel drugs targeting RNA-processing metalloenzymes or ribozymes as well as the rational engineering of novel programmable gene-therapy tools.

Measurement of CP violation with $B^0_{(s)} \to h^+ h^{\prime-}$ decays, $|V_{cb}|$ with $B^0_{s}\to D^{(*)-}_s \mu^+ \nu_\mu$ decays, and simulation and characterisation of the LHCb Upgrade II ECAL

The time-dependent CP asymmetries of the $B^0\to\pi^+\pi^-$ and $B^0_s\toK^+K^-$ decays and the time-integrated CP asymmetries of the $B^0\toK^+\pi^-$ and $B^0_s\to\pi^+K^-$ decays are measured, using the $p-p$ collision data collected with the LHCb detector and corresponding to the full Run2. The results are compatible with previous determinations of these quantities from LHCb, except for the CP-violation parameters of the $B^0_s\to K^+K^-$ decays, that show a discrepancy exceeding 3 standard deviations between different data-taking periods. The investigations being conducted to understand the discrepancy are documented. The measurement of the CKM matrix element $|V_{cb}|$ using $B^0_{s}\to D^{(*)-}_s\mu^+ \nu_\mu$ is also reported, using the $p-p$ collision data collected with the LHCb detector and corresponding to the full Run1. The measurement leads to $|V_{cb}| = (41.4\pm0.6\pm0.9\pm1.2)\times 10^{-3}$, where the first uncertainty is statistical, the second is systematic, and the third is due to external inputs. This measurement is compatible with the world averages and constitutes the first measurement of $|V_{cb}|$ at a hadron collider and the absolute first one with decays of the $B^0_s$ meson. The analysis also provides the very first measurements of the branching ratio and form factors parameters of the signal decay modes. The study of the characteristics ruling the response of an electromagnetic calorimeter (ECAL) to profitably operate in the high luminosity regime foreseen for the Upgrade2 of LHCb is reported in the final part of this Thesis. A fast and flexible simulation framework is developed to this purpose. Physics performance of different configurations of the ECAL are evaluated using samples of fully simulated $B^0\to \pi^+\pi^-\pi^0$ and $B^0\to K^{*0}e^+e^-$ decays. The results are used to guide the development of the future ECAL and are reported in the Framework Technical Design Report of the LHCb Upgrade2 detector.

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.

Modeling of clear cell sarcoma of the kidney of the pediatric age

Clear cell sarcoma of the kidney (CCSK) is the second most common pediatric renal tumor, characterized in 90% of cases by the presence of internal tandem duplications (ITDs) localized at the last exon of BCOR gene. BCOR protein constitute a core component of the non-canonical Polycomb Repressive Complex1 (PRC1.1), which performs a fundamental silencing activity. ITDs in the last BCOR exon at the level of PUFD domain have been identified in many tumor subtypes and could affect PCGF1 binding and the subsequent PRC1.1 activity, although the exact oncogenic mechanism of ITD remains poorly understood. This project has the objective of investigating the molecular mechanisms underlying the oncogenesis of CCSK, approaching the study with different methodologies. A first model in HEK-293 allowed to obtain important informations about BCOR functionality, suggesting that the presence of ITD generates an altered activity which is very different from a loss-of-function. It has also been observed that BCOR function within the PRC1.1 complex varies with different ITDs. Moreover, it allowed the identification of molecular signatures evoked by the presence of BCOR-ITD, including its role in extracellular matrix interactions and invasiveness promotion. The parallel analysis of WTS data from 8 CCSK cases permitted the identification of a peculiar signature for metastatic CCSKs, highlighting a 20-fold overexpression of FGF3. This factor promoted a significant increase in invasive ability in the cellular model. In order to study BCOR-ITD effects over cell stemness and differentiation, an inducible model is being obtained in H1 cells. This way, it will be possible to study the functionality of BCOR-ITD in a context more similar to the origin of CCSKs, evaluating both the specific interactome and phenotypic consequences caused by the mutation.

Thermal and air quality modeling of an electric vehicle cabin with low-cost sensors and reinforcement learning

The design process of any electric vehicle system has to be oriented towards the best energy efficiency, together with the constraint of maintaining comfort in the vehicle cabin. Main aim of this study is to research the best thermal management solution in terms of HVAC efficiency without compromising occupant’s comfort and internal air quality. An Arduino controlled Low Cost System of Sensors was developed and compared against reference instrumentation (average R-squared of 0.92) and then used to characterise the vehicle cabin in real parking and driving conditions trials. Data on the energy use of the HVAC was retrieved from the car On-Board Diagnostic port. Energy savings using recirculation can reach 30 %, but pollutants concentration in the cabin builds up in this operating mode. Moreover, the temperature profile appeared strongly nonuniform with air temperature differences up to 10° C. Optimisation methods often require a high number of runs to find the optimal configuration of the system. Fast models proved to be beneficial for these task, while CFD-1D model are usually slower despite the higher level of detail provided. In this work, the collected dataset was used to train a fast ML model of both cabin and HVAC using linear regression. Average scaled RMSE over all trials is 0.4 %, while computation time is 0.0077 ms for each second of simulated time on a laptop computer. Finally, a reinforcement learning environment was built in OpenAI and Stable-Baselines3 using the built-in Proximal Policy Optimisation algorithm to update the policy and seek for the best compromise between comfort, air quality and energy reward terms. The learning curves show an oscillating behaviour overall, with only 2 experiments behaving as expected even if too slow. This result leaves large room for improvement, ranging from the reward function engineering to the expansion of the ML model.

Computational modeling of human atrial cardiomyocytes: integration of electro-mechanical & mechano-electric feedback pathways

The cardiomyocytes are very complex consisting of many interlinked non-linear regulatory mechanisms between electrical excitation and mechanical contraction. Thus given a integrated electromechanically coupled system it becomes hard to understand the individual contributor of cardiac electrics and mechanics under both physiological and pathological conditions. Hence, to identify the causal relationship or to predict the responses in a integrated system the use of computational modeling can be beneficial. Computational modeling is a powerful tool that provides complete control of parameters along with the visibility of all the individual components of the integrated system. The advancement of computational power has made it possible to simulate the models in a short timeframe, providing the possibility of increased predictive power of the integrated system. My doctoral thesis is focused on the development of electromechanically integrated human atrial cardiomyocyte model with proper consideration of feedforward and feedback pathways.

Multiscale modeling of light-harvesting systems based on rhodamine B aggregates

Rhodamine B (RB) has been successfully exploited in the synthesis of light harvesting systems, but since RB is prone to form dimers acting as quenchers for the fluorescence, high energy transfer efficiencies can be reached only when using bulky and hydrophobic counterions acting as spacers between RBs. In this PhD thesis, a multiscale theoretical study aimed at providing insights into the structural, photophysical and optical properties of RB and its aggregates is presented. At the macroscopic level (no atomistic details) a phenomenological model describing the fluorescence decay of RB networks in presence of both quenching from dimers and exciton-exciton annihiliation is presented and analysed, showing that the quenching from dimers affects the decay only at long times, a feature that can be exploited in global fitting analysis to determine relevant chemical and photophysical information. At the mesoscopic level (atomistic details but no electronic structure) the RB aggregation in water in presence of different counterions is studied with molecular dynamics (MD) simulations. A new force field has been parametrized for describing the RB flexibility and the RB-RB interaction driving the dimerization. Simulations correctly predict the RB/counterion aggregation only in presence of bulky and hydrophobic counterion and its ability to prevent the dimerization. Finally, at the microscopic level, DFT calculations are performed to demonstrate the spacing action of bulky counterions, but standard TDDFT calculations are showed to fail in correctly describing the excited states of RB and its dimers. Moreover, also standard procedures proposed in literature for obtaining ad hoc functionals are showed to not work properly. A detailed analysis on the effect of the exact exchange shows that its short-range contribution is the crucial quantity for ameliorating results, and a new functional containing a proper amount of such an exchange is proposed and successfully tested.

Analysis and optimisation of books flow among branches through simulation: the case of Trondheim’s Public Library

Il presente lavoro di tesi verte sull’analisi e l’ottimizzazione dei flussi di libri generati tra le diverse sedi della biblioteca pubblica, Trondheim folkebibliotek, situata a Trondheim, città del nord norvegese. La ricerca si inserisce nell’ambito di un progetto pluriennale, SmartLIB, che questa sta intraprendendo con l’università NTNU - Norwegian University of Science and Technology. L’obiettivo di questa tesi è quello di analizzare possibili soluzioni per ottimizzare il flusso di libri generato dagli ordini dei cittadini. Una prima fase di raccolta ed analisi dei dati è servita per avere le informazioni necessarie per procedere nella ricerca. Successivamente è stata analizzata la possibilità di ridurre i flussi andando ad associare ad ogni dipartimento la quantità di copie necessarie per coprire il 90% della domanda, seguendo la distribuzione di Poisson. In seguito, sono state analizzate tre soluzioni per ottimizzare i flussi generati dai libri, il livello di riempimento dei box ed il percorso del camion che giornalmente visita tutte le sedi della libreria. Di supporto per questo secondo studio è stato il Vehicle Routing Problem (VRP). Un modello simulativo è stato creato su Anylogic ed utilizzato per validare le soluzioni proposte. I risultati hanno portato a proporre delle soluzioni per ottimizzare i flussi complessivi, riducendo il delay time di consegna dei libri del 50%, ad una riduzione del 53% del flusso di box e ad una conseguente aumento del 44% del tasso di riempimento di ogni box. Possibili future implementazioni delle soluzioni trovate corrispondono all’installazione di una nuova Sorting Machine nella sede centrale della libreria ed all’implementazione sempre in quest’ultima di un nuovo schedule giornaliero.

Simulation and Implementation of a PMSM Sensorless Control Algorithm for Submarine Applications

In this thesis, the study and the simulation of two advanced sensorless speed control techniques for a surface PMSM are presented. The aim is to implement a sensorless control algorithm for a submarine auxiliary propulsion system. This experimental activity is the result of a project collaboration with L3Harris Calzoni, a leader company in A&D systems for naval handling in military field. A Simulink model of the whole electric drive has been developed. Due to the satisfactory results of the simulations, the sensorless control system has been implemented in C code for STM32 environment. Finally, several tests on a real brushless machine have been carried out while the motor was connected to a mechanical load to simulate the real scenario of the final application. All the experimental results have been recorded through a graphical interface software developed at Calzoni.

Jeans modeling of massive early-type galaxies with observed stellar kinematic profiles up to 2-3 effective radii

A recent integral-field spectroscopic (IFS) survey, the MASSIVE survey (Ma et al. 2014), observed the 116 most massive (MK < −25.3 mag, stellar mass M∗ > 10^11.6 M⊙) early-type galaxies (ETGs) within 108 Mpc, out to radii as large as 40 kpc, that correspond to ∼ 2 − 3 effective radii (Re). One of the major findings of the MASSIVE survey is that the galaxy sample is split nearly equally among three groups showing three different velocity dispersion profiles σ(R) outer of a radius ∼ 5 kpc (falling, flat and rising with radius). The purpose of this thesis is to model the kinematic profiles of six ETGs included in the MASSIVE survey and representative of the three observed σ(R) shapes, with the aim of investigating their dynamical structure. Models for the chosen galaxies are built using the numerical code JASMINE (Posacki, Pellegrini, and Ciotti 2013). The code produces models of axisymmetric galaxies, based on the solution of the Jeans equations for a multicomponent gravitational potential (supermassive black hole, stars and dark matter halo). With the aim of having a good agreement between the kinematics obtained from the Jeans equations, and the observed σ and rotation velocity V of MASSIVE (Veale et al. 2016, 2018), I derived constraints on the dark matter distribution and orbital anisotropy. This work suggests a trend of the dark matter amount and distribution with the shape of the velocity dispersion profiles in the outer regions: the models of galaxies with flat or rising velocity dispersion profiles show higher dark matter fractions fDM both within 1 Re and 5 Re. Orbital anisotropy alone cannot account for the different observed trends of σ(R) and has a minor effect compared to variations of the mass profile. Galaxies with similar stellar mass M∗ that show different velocity dispersion profiles (from falling to rising) are successfully modelled with a variation of the halo mass Mh.

Efeito da adição de microfibras de lã de vidro na tenacidade à ruptura de pastas de cimento para poços de petróleo

Although there are a wide variety of additives that act in fresh state, to adjust the properties of cement, there is also a search by additions that improve the tenacity of the cement in the hardened state. This, in turn, can often be increased by inserting fibers, which act on the deflection of microcracks. This study aimed to use a microfiber glass wool (silica-based) as an additive reinforcing the cement matrix, improving the rupture tenacity, in order to prevent the propagation of microcracks in the cement sheath commonly found in oil wells submitted to high temperatures. The fibers were added at different concentrations, 2 to 5% (BWOC) and varied average sizes, grinding for 90 s, 180 s, 300 s, 600 s. The cement slurries were made with a density of 1,90 g/ cm3 (15,6 lb/gal), using Portland cement CPP- Special Class as the hydraulic binder and 40% silica flour. The characterization of the fiber was made by scanning electron microscopy (SEM), particle size by sieving, X-ray fluorescence (XRF), X-ray diffraction (XRD) and thermogravimetry (TG / DTG). Were performed technological tests set by the API (American Petroleum Institute) by rheology, stability, free water, compressive strength, as well as testing rupture energy, elastic modulus and permeability. The characterization results showed good thermal stability of the microfiber glass wool for application in oil wells submitted to steam injection and, also, that from the particle size data, it was possible to suggest that microfibers milled up to 300 s, are ideal to act as reinforcement to the cement slurries. The rheological parameters, there was committal of plastic viscosity when larger lengths were inserted of microfiber (F90). The values obtained by free water and stability were presented according to API. The mechanical properties, the incorporation of microfiber to the cement slurries gave better rupture tenacity, as compared to reference cement slurries. The values of compressive strength, elastic modulus and permeability have been maintained with respect to the reference cement slurries. Thus, cement slurries reinforced with microfiber glass wool can ensure good application for cementing oil wells submitted to steam injection, which requires control of microcracks, due to the thermal gradients

Beherrschung stark korrelierter Logistik- und Produktions-Prozesse

Bei der Simulation von Logistik- und Produktionssystem werden Zufallszahlengeneratoren verwendet, um stochastische Einflüsse zu modellieren. Ein wichtiges Qualitätsmerkmal dieser Generatoren ist die Er-zeugung möglichst unabhängiger Zufallszahlen. Werden jedoch reale Prozesse betrachtet, so sind die Daten im Allgemeinen nicht unabhängig. Diese Arbeit befasst sich mit der Analyse von Praxisdaten bezüglich des Auftretens von Abhängigkeiten. Dazu werden Korrelationsstrukturen gesucht. Außerdem wird gezeigt, dass unabhängige Zufallszahlen in der Regel ungeeignet sind, um stochastische Prozesse mit ausgeprägten Abhängigkeiten zu modellieren.