Modelling and simulating in systems biology: an approach based on multi-agent systems

Systems Biology is an innovative way of doing biology recently raised in bio-informatics contexts, characterised by the study of biological systems as complex systems with a strong focus on the system level and on the interaction dimension. In other words, the objective is to understand biological systems as a whole, putting on the foreground not only the study of the individual parts as standalone parts, but also of their interaction and of the global properties that emerge at the system level by means of the interaction among the parts. This thesis focuses on the adoption of multi-agent systems (MAS) as a suitable paradigm for Systems Biology, for developing models and simulation of complex biological systems. Multi-agent system have been recently introduced in informatics context as a suitabe paradigm for modelling and engineering complex systems. Roughly speaking, a MAS can be conceived as a set of autonomous and interacting entities, called agents, situated in some kind of nvironment, where they fruitfully interact and coordinate so as to obtain a coherent global system behaviour. The claim of this work is that the general properties of MAS make them an effective approach for modelling and building simulations of complex biological systems, following the methodological principles identified by Systems Biology. In particular, the thesis focuses on cell populations as biological systems. In order to support the claim, the thesis introduces and describes (i) a MAS-based model conceived for modelling the dynamics of systems of cells interacting inside cell environment called niches. (ii) a computational tool, developed for implementing the models and executing the simulations. The tool is meant to work as a kind of virtual laboratory, on top of which kinds of virtual experiments can be performed, characterised by the definition and execution of specific models implemented as MASs, so as to support the validation, falsification and improvement of the models through the observation and analysis of the simulations. A hematopoietic stem cell system is taken as reference case study for formulating a specific model and executing virtual experiments.

Feasibility study and flow scheduling optimization of a multi-product pipeline system

The first goal of this study is to analyse a real-world multiproduct onshore pipeline system in order to verify its hydraulic configuration and operational feasibility by constructing a simulation model step by step from its elementary building blocks that permits to copy the operation of the real system as precisely as possible. The second goal is to develop this simulation model into a user-friendly tool that one could use to find an “optimal” or “best” product batch schedule for a one year time period. Such a batch schedule could change dynamically as perturbations occur during operation that influence the behaviour of the entire system. The result of the simulation, the ‘best’ batch schedule is the one that minimizes the operational costs in the system. The costs involved in the simulation are inventory costs, interface costs, pumping costs, and penalty costs assigned to any unforeseen situations. The key factor to determine the performance of the simulation model is the way time is represented. In our model an event based discrete time representation is selected as most appropriate for our purposes. This means that the time horizon is divided into intervals of unequal lengths based on events that change the state of the system. These events are the arrival/departure of the tanker ships, the openings and closures of loading/unloading valves of storage tanks at both terminals, and the arrivals/departures of trains/trucks at the Delivery Terminal. In the feasibility study we analyse the system’s operational performance with different Head Terminal storage capacity configurations. For these alternative configurations we evaluated the effect of different tanker ship delay magnitudes on the number of critical events and product interfaces generated, on the duration of pipeline stoppages, the satisfaction of the product demand and on the operative costs. Based on the results and the bottlenecks identified, we propose modifications in the original setup.

Modelling, simulation and optimization of maintenance considerations on condition based maintenance

Globalization has increased the pressure on organizations and companies to operate in the most efficient and economic way. This tendency promotes that companies concentrate more and more on their core businesses, outsource less profitable departments and services to reduce costs. By contrast to earlier times, companies are highly specialized and have a low real net output ratio. For being able to provide the consumers with the right products, those companies have to collaborate with other suppliers and form large supply chains. An effect of large supply chains is the deficiency of high stocks and stockholding costs. This fact has lead to the rapid spread of Just-in-Time logistic concepts aimed minimizing stock by simultaneous high availability of products. Those concurring goals, minimizing stock by simultaneous high product availability, claim for high availability of the production systems in the way that an incoming order can immediately processed. Besides of design aspects and the quality of the production system, maintenance has a strong impact on production system availability. In the last decades, there has been many attempts to create maintenance models for availability optimization. Most of them concentrated on the availability aspect only without incorporating further aspects as logistics and profitability of the overall system. However, production system operator’s main intention is to optimize the profitability of the production system and not the availability of the production system. Thus, classic models, limited to represent and optimize maintenance strategies under the light of availability, fail. A novel approach, incorporating all financial impacting processes of and around a production system, is needed. The proposed model is subdivided into three parts, maintenance module, production module and connection module. This subdivision provides easy maintainability and simple extendability. Within those modules, all aspect of production process are modeled. Main part of the work lies in the extended maintenance and failure module that offers a representation of different maintenance strategies but also incorporates the effect of over-maintaining and failed maintenance (maintenance induced failures). Order release and seizing of the production system are modeled in the production part. Due to computational power limitation, it was not possible to run the simulation and the optimization with the fully developed production model. Thus, the production model was reduced to a black-box without higher degree of details.

BDI agents for Real Time Strategy games

While the use of distributed intelligence has been incrementally spreading in the design of a great number of intelligent systems, the field of Artificial Intelligence in Real Time Strategy games has remained mostly a centralized environment. Despite turn-based games have attained AIs of world-class level, the fast paced nature of RTS games has proven to be a significant obstacle to the quality of its AIs. Chapter 1 introduces RTS games describing their characteristics, mechanics and elements. Chapter 2 introduces Multi-Agent Systems and the use of the Beliefs-Desires-Intentions abstraction, analysing the possibilities given by self-computing properties. In Chapter 3 the current state of AI development in RTS games is analyzed highlighting the struggles of the gaming industry to produce valuable. The focus on improving multiplayer experience has impacted gravely on the quality of the AIs thus leaving them with serious flaws that impair their ability to challenge and entertain players. Chapter 4 explores different aspects of AI development for RTS, evaluating the potential strengths and weaknesses of an agent-based approach and analysing which aspects can benefit the most against centralized AIs. Chapter 5 describes a generic agent-based framework for RTS games where every game entity becomes an agent, each of which having its own knowledge and set of goals. Different aspects of the game, like economy, exploration and warfare are also analysed, and some agent-based solutions are outlined. The possible exploitation of self-computing properties to efficiently organize the agents activity is then inspected. Chapter 6 presents the design and implementation of an AI for an existing Open Source game in beta development stage: 0 a.d., an historical RTS game on ancient warfare which features a modern graphical engine and evolved mechanics. The entities in the conceptual framework are implemented in a new agent-based platform seamlessly nested inside the existing game engine, called ABot, widely described in Chapters 7, 8 and 9. Chapter 10 and 11 include the design and realization of a new agent based language useful for defining behavioural modules for the agents in ABot, paving the way for a wider spectrum of contributors. Chapter 12 concludes the work analysing the outcome of tests meant to evaluate strategies, realism and pure performance, finally drawing conclusions and future works in Chapter 13.

Electromagnetic simulation and measurement of diffuse scattering from building walls

Il fenomeno dello scattering diffuso è stato oggetto di numerosi studi nell’arco degli ultimi anni, questo grazie alla sua rilevanza nell’ambito della propagazione elettromagnetica così come in molti altri campi di applicazione (remote sensing, ottica, fisica, etc.), ma la compresione completa di questo effetto è lungi dall’essere raggiunta. Infatti la complessità nello studio e nella caratterizzazione della diffusione deriva dalla miriade di casistiche ed effetti che si possono incontrare in un ambiente di propagazione reale, lasciando intuire la necessità di trattarne probabilisticamente il relativo contributo. Da qui nasce l’esigenza di avere applicazioni efficienti dal punto di vista ingegneristico che coniughino la definizione rigorosa del fenomeno e la conseguente semplificazione per fini pratici. In tale visione possiamo descrivere lo scattering diffuso come la sovrapposizione di tutti quegli effetti che si scostano dalle classiche leggi dell’ottica geometrica (riflessione, rifrazione e diffrazione) che generano contributi del campo anche in punti dello spazio e direzioni in cui teoricamente, per oggetti lisci ed omogenei, non dovrebbe esserci alcun apporto. Dunque l’effetto principale, nel caso di ambiente di propagazione reale, è la diversa distribuzione spaziale del campo rispetto al caso teorico di superficie liscia ed omogenea in congiunzione ad effetti di depolarizzazione e redistribuzione di energia nel bilancio di potenza. Perciò la complessità del fenomeno è evidente e l’obiettivo di tale elaborato è di proporre nuovi risultati che permettano di meglio descrivere lo scattering diffuso ed individuare altresì le tematiche sulle quali concentrare l’attenzione nei lavori futuri. In principio è stato quindi effettuato uno studio bibliografico così da identificare i modelli e le teorie esistenti individuando i punti sui quali riflettere maggiormente; nel contempo si sono analizzate le metodologie di caratterizzazione della permittività elettrica complessa dei materiali, questo per valutare la possibilità di ricavare i parametri da utilizzare nelle simulazioni utilizzando il medesimo setup di misura ideato per lo studio della diffusione. Successivamente si è realizzato un setup di simulazione grazie ad un software di calcolo elettromagnetico (basato sul metodo delle differenze finite nel dominio del tempo) grazie al quale è stato possibile analizzare la dispersione tridimensionale dovuta alle irregolarità del materiale. Infine è stata condotta una campagna di misure in camera anecoica con un banco sperimentale realizzato ad-hoc per effettuare una caratterizzazione del fenomeno di scattering in banda larga.

Reproduction and artificial restocking of Acipenser naccarii (Bonaparte, 1836). Genetic and physiological characterization through microsatellite markers and radioimmunoassay of sexual steroids

The Adriatic sturgeon, Acipenser naccarii (Bonaparte, 1836), is a highly threatened species due to human activities, particularly overfishing and habitat destruction. Its peculiar ecology and biology (restricted areal and anadromy) makes this species particularly vulnerable. In March 2010 the IUCN has identified the Adriatic sturgeon as a critically endangered species according to the Red List of Threatened Species. Due to its rapid decline, starting from the 80s, at present there is no evidence of natural reproduction in wild environment, which makes the Adriatic sturgeon dependenton captive breeding programs that need to be improved in order to be effective for the survival of the species. For this purpose this study aims to characterize artificial restocking population of Adriatic sturgeon, with both genetic and physiological analysis in order to establish an efficient restocking program for future reproductions. The research is structured on two levels: First genetically, by analyzing 9 microsatellite loci. This gives information relatively about parent allocation and kinship between individuals that were sampled for this study. Hence to predict which reproduction events are the most optimal in terms of incrementing genetic diversity, by the estimation of multilocus pairwise band sharing coefficients. Second step, physiological analysis: testosterone (T) concentration levels in each individual were measured for sexing, without sacrificing the lives of the animals with the use of an invasive examination of the gonads. The combination of interdisciplinary analysis is important to obtain an overall picture in order to indicate the main broodstock participating in reproduction events and future optimal potential participants, in order to ensure a valid management for restocking program and their monitoring.

Modelling, simulation and characterization of epithelial cell culture biochip

A microfluidic Organ-on-Chip has been developed for monitoring the epithelial cells monolayer. Equivalent circuit Model was used to determine the electrical properties from the impedance spectra of the epithelial cells monolayer. Black platinum on platinum electrodes was electrochemically deposited onto the surface of electrodes to reduce the influence of the electrical double layer on the impedance measurements. Measurements of impedance with an Impedance Analyzer were done to validate the equivalent circuit model and the decrease of the double layer effect. A Lock-in Amplifier was designed to measure the impedance.

Modeling, simulation, and control of a formation of multirotor aircraft for cooperative transportation of suspended loads

The work presented in this thesis aims to contribute to innovation in the Urban Air Mobility and Delivery sector and represents a solid starting point for air logistics and its future scenarios. The dissertation focuses on modeling, simulation, and control of a formation of multirotor aircraft for cooperative load transportation, with particular attention to environmental sustainability. First, a simulation and test environment is developed to assess technologies for suspended load stabilization. Starting from the mathematical model of two identical multirotors, formation-flight-keeping and collision-avoidance algorithms are analyzed. This approach guarantees both the safety of the vehicles within the formation and that of the payload, which may be made of people in the very near future. Afterwards, a mathematical model for the suspended load is implemented, as well as an active controller for its stabilization. The key focus of this part is represented by both analysis and control of payload oscillatory motion, by thoroughly investigating load kinetic energy decay. At this point, several test cases were introduced, in order to understand which strategy is the most effective and safe in terms of future applications in the field of air logistics.

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.

Mobile TuCSoN: theoretical and technological requirements for TuCSoN's porting over Android mobile devices

Communication and coordination are two key-aspects in open distributed agent system, being both responsible for the system’s behaviour integrity. An infrastructure capable to handling these issues, like TuCSoN, should to be able to exploit modern technologies and tools provided by fast software engineering contexts. Thesis aims to demonstrate TuCSoN infrastructure’s abilities to cope new possibilities, hardware and software, offered by mobile technology. The scenarios are going to configure, are related to the distributed nature of multi-agent systems where an agent should be located and runned just on a mobile device. We deal new mobile technology frontiers concerned with smartphones using Android operating system by Google. Analysis and deployment of a distributed agent-based system so described go first to impact with quality and quantity considerations about available resources. Engineering issue at the base of our research is to use TuCSoN against to reduced memory and computing capability of a smartphone, without the loss of functionality, efficiency and integrity for the infrastructure. Thesis work is organized on two fronts simultaneously: the former is the rationalization process of the available hardware and software resources, the latter, totally orthogonal, is the adaptation and optimization process about TuCSoN architecture for an ad-hoc client side release.

Modeling and simulation of a synthetic genetic circuit that implements a multicelled behavior in a growing microcolony of E. coli

Synthetic Biology is a relatively new discipline, born at the beginning of the New Millennium, that brings the typical engineering approach (abstraction, modularity and standardization) to biotechnology. These principles aim to tame the extreme complexity of the various components and aid the construction of artificial biological systems with specific functions, usually by means of synthetic genetic circuits implemented in bacteria or simple eukaryotes like yeast. The cell becomes a programmable machine and its low-level programming language is made of strings of DNA. This work was performed in collaboration with researchers of the Department of Electrical Engineering of the University of Washington in Seattle and also with a student of the Corso di Laurea Magistrale in Ingegneria Biomedica at the University of Bologna: Marilisa Cortesi. During the collaboration I contributed to a Synthetic Biology project already started in the Klavins Laboratory. In particular, I modeled and subsequently simulated a synthetic genetic circuit that was ideated for the implementation of a multicelled behavior in a growing bacterial microcolony. In the first chapter the foundations of molecular biology are introduced: structure of the nucleic acids, transcription, translation and methods to regulate gene expression. An introduction to Synthetic Biology completes the section. In the second chapter is described the synthetic genetic circuit that was conceived to make spontaneously emerge, from an isogenic microcolony of bacteria, two different groups of cells, termed leaders and followers. The circuit exploits the intrinsic stochasticity of gene expression and intercellular communication via small molecules to break the symmetry in the phenotype of the microcolony. The four modules of the circuit (coin flipper, sender, receiver and follower) and their interactions are then illustrated. In the third chapter is derived the mathematical representation of the various components of the circuit and the several simplifying assumptions are made explicit. Transcription and translation are modeled as a single step and gene expression is function of the intracellular concentration of the various transcription factors that act on the different promoters of the circuit. A list of the various parameters and a justification for their value closes the chapter. In the fourth chapter are described the main characteristics of the gro simulation environment, developed by the Self Organizing Systems Laboratory of the University of Washington. Then, a sensitivity analysis performed to pinpoint the desirable characteristics of the various genetic components is detailed. The sensitivity analysis makes use of a cost function that is based on the fraction of cells in each one of the different possible states at the end of the simulation and the wanted outcome. Thanks to a particular kind of scatter plot, the parameters are ranked. Starting from an initial condition in which all the parameters assume their nominal value, the ranking suggest which parameter to tune in order to reach the goal. Obtaining a microcolony in which almost all the cells are in the follower state and only a few in the leader state seems to be the most difficult task. A small number of leader cells struggle to produce enough signal to turn the rest of the microcolony in the follower state. It is possible to obtain a microcolony in which the majority of cells are followers by increasing as much as possible the production of signal. Reaching the goal of a microcolony that is split in half between leaders and followers is comparatively easy. The best strategy seems to be increasing slightly the production of the enzyme. To end up with a majority of leaders, instead, it is advisable to increase the basal expression of the coin flipper module. At the end of the chapter, a possible future application of the leader election circuit, the spontaneous formation of spatial patterns in a microcolony, is modeled with the finite state machine formalism. The gro simulations provide insights into the genetic components that are needed to implement the behavior. In particular, since both the examples of pattern formation rely on a local version of Leader Election, a short-range communication system is essential. Moreover, new synthetic components that allow to reliably downregulate the growth rate in specific cells without side effects need to be developed. In the appendix are listed the gro code utilized to simulate the model of the circuit, a script in the Python programming language that was used to split the simulations on a Linux cluster and the Matlab code developed to analyze the data.

Extending the 2P-Kt ecosystem: CLP and Labelled LP

The ability to create hybrid systems that blend different paradigms has now become a requirement for complex AI systems usually made of more than a component. In this way, it is possible to exploit the advantages of each paradigm and exploit the potential of different approaches such as symbolic and non-symbolic approaches. In particular, symbolic approaches are often exploited for their efficiency, effectiveness and ability to manage large amounts of data, while symbolic approaches are exploited to ensure aspects related to explainability, fairness, and trustworthiness in general. The thesis lies in this context, in particular in the design and development of symbolic technologies that can be easily integrated and interoperable with other AI technologies. 2P-Kt is a symbolic ecosystem developed for this purpose, it provides a logic-programming (LP) engine which can be easily extended and customized to deal with specific needs. The aim of this thesis is to extend 2P-Kt to support constraint logic programming (CLP) as one of the main paradigms for solving highly combinatorial problems given a declarative problem description and a general constraint-propagation engine. A real case study concerning school timetabling is described to show a practical usage of the CLP(FD) library implemented. Since CLP represents only a particular scenario for extending LP to domain-specific scenarios, in this thesis we present also a more general framework: Labelled Prolog, extending LP with labelled terms and in particular labelled variables. The designed framework shows how it is possible to frame all variations and extensions of LP under a single language reducing the huge amount of existing languages and libraries and focusing more on how to manage different domain needs using labels which can be associated with every kind of term. Mapping of CLP into Labeled Prolog is also discussed as well as the benefits of the provided approach.

Investigation on laser shock peening capability by FE simulation

Laser shock peening is a technique similar to shot peening that imparts compressive residual stresses in materials for improving fatigue resistance. The ability to use a high energy laser pulse to generate shock waves, inducing a compressive residual stress field in metallic materials, has applications in multiple fields such as turbo-machinery, airframe structures, and medical appliances. The transient nature of the LSP phenomenon and the high rate of the laser's dynamic make real time in-situ measurement of laser/material interaction very challenging. For this reason and for the high cost of the experimental tests, reliable analytical methods for predicting detailed effects of LSP are needed to understand the potential of the process. Aim of this work has been the prediction of residual stress field after Laser Peening process by means of Finite Element Modeling. The work has been carried out in the Stress Methods department of Airbus Operations GmbH (Hamburg) and it includes investigation on compressive residual stresses induced by Laser Shock Peening, study on mesh sensitivity, optimization and tuning of the model by using physical and numerical parameters, validation of the model by comparing it with experimental results. The model has been realized with Abaqus/Explicit commercial software starting from considerations done on previous works. FE analyses are “Mesh Sensitive”: by increasing the number of elements and by decreasing their size, the software is able to probe even the details of the real phenomenon. However, these details, could be only an amplification of real phenomenon. For this reason it was necessary to optimize the mesh elements' size and number. A new model has been created with a more fine mesh in the trough thickness direction because it is the most involved in the process deformations. This increment of the global number of elements has been paid with an "in plane" size reduction of the elements far from the peened area in order to avoid too high computational costs. Efficiency and stability of the analyses has been improved by using bulk viscosity coefficients, a merely numerical parameter available in Abaqus/Explicit. A plastic rate sensitivity study has been also carried out and a new set of Johnson Cook's model coefficient has been chosen. These investigations led to a more controllable and reliable model, valid even for more complex geometries. Moreover the study about the material properties highlighted a gap of the model about the simulation of the surface conditions. Modeling of the ablative layer employed during the real process has been used to fill this gap. In the real process ablative layer is a super thin sheet of pure aluminum stuck on the masterpiece. In the simulation it has been simply reproduced as a 100µm layer made by a material with a yield point of 10MPa. All those new settings has been applied to a set of analyses made with different geometry models to verify the robustness of the model. The calibration of the model with the experimental results was based on stress and displacement measurements carried out on the surface and in depth as well. The good correlation between the simulation and experimental tests results proved this model to be reliable.

Influence of advanced load simulation models on fatigue design of jackets for offshore wind turbines.

Constant developments in the field of offshore wind energy have increased the range of water depths at which wind farms are planned to be installed. Therefore, in addition to monopile support structures suitable in shallow waters (up to 30 m), different types of support structures, able to withstand severe sea conditions at the greater water depths, have been developed. For water depths above 30 m, the jacket is one of the preferred support types. Jacket represents a lightweight support structure, which, in combination with complex nature of environmental loads, is prone to highly dynamic behavior. As a consequence, high stresses with great variability in time can be observed in all structural members. The highest concentration of stresses occurs in joints due to their nature (structural discontinuities) and due to the existence of notches along the welds present in the joints. This makes them the weakest elements of the jacket in terms of fatigue. In the numerical modeling of jackets for offshore wind turbines, a reduction of local stresses at the chord-brace joints, and consequently an optimization of the model, can be achieved by implementing joint flexibility in the chord-brace joints. Therefore, in this work, the influence of joint flexibility on the fatigue damage in chord-brace joints of a numerical jacket model, subjected to advanced load simulations, is studied.