Micro-simulation models at neighbourhood scale: the interplay of agents, buildings, activities and transport.

Urban systems consist of several interlinked sub-systems - social, economic, institutional and environmental – each representing a complex system of its own and affecting all the others at various structural and functional levels. An urban system is represented by a number of “human” agents, such as individuals and households, and “non-human” agents, such as buildings, establishments, transports, vehicles and infrastructures. These two categories of agents interact among them and simultaneously produce impact on the system they interact with. Try to understand the type of interactions, their spatial and temporal localisation to allow a very detailed simulation trough models, turn out to be a great effort and is the topic this research deals with. An analysis of urban system complexity is here presented and a state of the art review about the field of urban models is provided. Finally, six international models - MATSim, MobiSim, ANTONIN, TRANSIMS, UrbanSim, ILUTE - are illustrated and then compared.

Automatic Design of Boolean Networks for Modelling Differentiation Trees

Real living cell is a complex system governed by many process which are not yet fully understood: the process of cell differentiation is one of these. In this thesis work we make use of a cell differentiation model to develop gene regulatory networks (Boolean networks) with desired differentiation dynamics. To accomplish this task we have introduced techniques of automatic design and we have performed experiments using various differentiation trees. The results obtained have shown that the developed algorithms, except the Random algorithm, are able to generate Boolean networks with interesting differentiation dynamics. Moreover, we have presented some possible future applications and developments of the cell differentiation model in robotics and in medical research. Understanding the mechanisms involved in biological cells can gives us the possibility to explain some not yet understood dangerous disease, i.e the cancer. Le cellula è un sistema complesso governato da molti processi ancora non pienamente compresi: il differenziamento cellulare è uno di questi. In questa tesi utilizziamo un modello di differenziamento cellulare per sviluppare reti di regolazione genica (reti Booleane) con dinamiche di differenziamento desiderate. Per svolgere questo compito abbiamo introdotto tecniche di progettazione automatica e abbiamo eseguito esperimenti utilizzando vari alberi di differenziamento. I risultati ottenuti hanno mostrato che gli algoritmi sviluppati, eccetto l'algoritmo Random, sono in grado di poter generare reti Booleane con dinamiche di differenziamento interessanti. Inoltre, abbiamo presentato alcune possibili applicazioni e sviluppi futuri del modello di differenziamento in robotica e nella ricerca medica. Capire i meccanismi alla base del funzionamento cellulare può fornirci la possibilità di spiegare patologie ancora oggi non comprese, come il cancro.

A ROS-based Workspace Control and Trajectory Planner for a seven degrees of freedom Robotic arm

In this Bachelor Thesis I want to provide readers with tools and scripts for the control of a 7DOF manipulator, backed up by some theory of Robotics and Computer Science, in order to better contextualize the work done. In practice, we will see most common software, and developing environments, used to cope with our task: these include ROS, along with visual simulation by VREP and RVIZ, and an almost "stand-alone" ROS extension called MoveIt!, a very complete programming interface for trajectory planning and obstacle avoidance. As we will better appreciate and understand in the introduction chapter, the capability of detecting collision objects through a camera sensor, and re-plan to the desired end-effector pose, are not enough. In fact, this work is implemented in a more complex system, where recognition of particular objects is needed. Through a package of ROS and customized scripts, a detailed procedure will be provided on how to distinguish a particular object, retrieve its reference frame with respect to a known one, and then allow navigation to that target. Together with technical details, the aim is also to report working scripts and a specific appendix (A) you can refer to, if desiring to put things together.

Oxidative properties of the Iron - Thymine-1-acetic acid - Hydrogen peroxide catalytic system

The oxidation of alcohols and olefins is a pivotal reaction in organic synthesis. However, traditional oxidants are toxic and they often release a considerable amounts of by-products. Here, two IronIII-based systems are shown as oxidative catalyst, working in mild conditions with hydrogen peroxide as primary oxidant. An efficient catalytic system for the selective oxidation of several alcohols to their corresponding aldehydes and ketones was developed and characterized, [Fe(phen)2Cl2]NO3 (phen=1,10-Phenantroline). It was demonstrated that the adoption of a buffered aqueous solution is of crucial importance to ensure both considerable activity and selectivity.The Iron - Thymine-1-acetic acid in-situ complex was studied as catalyst in alcohol oxidations and C-H oxidative functionalization, involving hydrogen peroxide as primary oxidant in mild reaction conditions. The catalytic ability in alcohol oxidations was investigated by Density Functional Theory calculations, however the catalyst still has uncertain structure. The system shows satisfactory activity in alcohol oxidation and aliphatic rings functionalization. The Fe-THA system was studied in cyclohexene oxidation and oxidative halogenations. Halide salts such as NBu4X and NH4X were introduced in the catalytic system as halogens source to obtain cyclohexene derivatives such as halohydrins, important synthetic intermediates.The purpose of this dissertation is to contribute in testing new catalytic systems for alcohol oxidations and C-H functionalization. In particular, most of the efforts in this work focus on studying the Iron - Thymine-1-acetic acid (THA) systems as non-heme oxidative model, which present: •an iron metal centre(s) as a coordinative active site, •hydrogen peroxide as a primary oxidant, •THA as an eco-friendly, biocompatible, low cost coordinating ligand.

Data dissemination over complex networks through gossip

This thesis offers a practical and theoretical evaluations about gossip-epidemic algorithms, comparing those most common in the literature with new proposed algorithms and analyzing their behavior. Tests have been executed using one hundred graphs that has been randomly generated by Large Unstructured NEtwork Simulator (LUNES), a simulation software provided by Parallel and Distributed Simulation Research Group (PADS), of the Department of Computer Science, Università di Bologna and simulated using Advanced RTI System (ARTÌS), based on the High Level Architecture standard. Literatures algorithms have been analyzed and taken as base for new algorithms.

Phage therapy: A software system for phage quantification and kinetic model inference.

One of the most serious problems of the modern medicine is the growing emergence of antibiotic resistance among pathogenic bacteria. In this circumstance, different and innovative approaches for treating infections caused by multidrug-resistant bacteria are imperatively required. Bacteriophage Therapy is one among the fascinating approaches to be taken into account. This consists of the use of bacteriophages, viruses that infect bacteria, in order to defeat specific bacterial pathogens. Phage therapy is not an innovative idea, indeed, it was widely used around the world in the 1930s and 1940s, in order to treat various infection diseases, and it is still used in Eastern Europe and the former Soviet Union. Nevertheless, Western scientists mostly lost interest in further use and study of phage therapy and abandoned it after the discovery and the spread of antibiotics. The advancement of scientific knowledge of the last years, together with the encouraging results from recent animal studies using phages to treat bacterial infections, and above all the urgent need for novel and effective antimicrobials, have given a prompt for additional rigorous researches in this field. In particular, in the laboratory of synthetic biology of the department of Life Sciences at the University of Warwick, a novel approach was adopted, starting from the original concept of phage therapy, in order to study a concrete alternative to antibiotics. The innovative idea of the project consists in the development of experimental methodologies, which allow to engineer a programmable synthetic phage system using a combination of directed evolution, automation and microfluidics. The main aim is to make “the therapeutics of tomorrow individualized, specific, and self-regulated” (Jaramillo, 2015). In this context, one of the most important key points is the Bacteriophage Quantification. Therefore, in this research work, a mathematical model describing complex dynamics occurring in biological systems involving continuous growth of bacteriophages, modulated by the performance of the host organisms, was implemented as algorithms into a working software using MATLAB. The developed program is able to predict different unknown concentrations of phages much faster than the classical overnight Plaque Assay. What is more, it gives a meaning and an explanation to the obtained data, making inference about the parameter set of the model, that are representative of the bacteriophage-host interaction.

An integrated system for building and running reproducible research

Our generation of computational scientists is living in an exciting time: not only do we get to pioneer important algorithms and computations, we also get to set standards on how computational research should be conducted and published. From Euclid’s reasoning and Galileo’s experiments, it took hundreds of years for the theoretical and experimental branches of science to develop standards for publication and peer review. Computational science, rightly regarded as the third branch, can walk the same road much faster. The success and credibility of science are anchored in the willingness of scientists to expose their ideas and results to independent testing and replication by other scientists. This requires the complete and open exchange of data, procedures and materials. The idea of a “replication by other scientists” in reference to computations is more commonly known as “reproducible research”. In this context the journal “EAI Endorsed Transactions on Performance & Modeling, Simulation, Experimentation and Complex Systems” had the exciting and original idea to make the scientist able to submit simultaneously the article and the computation materials (software, data, etc..) which has been used to produce the contents of the article. The goal of this procedure is to allow the scientific community to verify the content of the paper, reproducing it in the platform independently from the OS chosen, confirm or invalidate it and especially allow its reuse to reproduce new results. This procedure is therefore not helpful if there is no minimum methodological support. In fact, the raw data sets and the software are difficult to exploit without the logic that guided their use or their production. This led us to think that in addition to the data sets and the software, an additional element must be provided: the workflow that relies all of them.

A framework for cyber-physical system simulation

In these last years, systems engineering has became one of the major research domains. The complexity of systems has increased constantly and nowadays Cyber-Physical Systems (CPS) are a category of particular interest: these, are systems composed by a cyber part (computer-based algorithms) that monitor and control some physical processes. Their development and simulation are both complex due to the importance of the interaction between the cyber and the physical entities: there are a lot of models written in different languages that need to exchange information among each other. Normally people use an orchestrator that takes care of the simulation of the models and the exchange of informations. This orchestrator is developed manually and this is a tedious and long work. Our proposition is to achieve to generate the orchestrator automatically through the use of Co-Modeling, i.e. by modeling the coordination. Before achieving this ultimate goal, it is important to understand the mechanisms and de facto standards that could be used in a co-modeling framework. So, I studied the use of a technology employed for co-simulation in the industry: FMI. In order to better understand the FMI standard, I realized an automatic export, in the FMI format, of the models realized in an existing software for discrete modeling: TimeSquare. I also developed a simple physical model in the existing open source openmodelica tool. Later, I started to understand how works an orchestrator, developing a simple one: this will be useful in future to generate an orchestrator automatically.