Many-core Algorithms for Combinatorial Optimization

Combinatorial Optimization is becoming ever more crucial, in these days. From natural sciences to economics, passing through urban centers administration and personnel management, methodologies and algorithms with a strong theoretical background and a consolidated real-word effectiveness is more and more requested, in order to find, quickly, good solutions to complex strategical problems. Resource optimization is, nowadays, a fundamental ground for building the basements of successful projects. From the theoretical point of view, Combinatorial Optimization rests on stable and strong foundations, that allow researchers to face ever more challenging problems. However, from the application point of view, it seems that the rate of theoretical developments cannot cope with that enjoyed by modern hardware technologies, especially with reference to the one of processors industry. In this work we propose new parallel algorithms, designed for exploiting the new parallel architectures available on the market. We found that, exposing the inherent parallelism of some resolution techniques (like Dynamic Programming), the computational benefits are remarkable, lowering the execution times by more than an order of magnitude, and allowing to address instances with dimensions not possible before. We approached four Combinatorial Optimization’s notable problems: Packing Problem, Vehicle Routing Problem, Single Source Shortest Path Problem and a Network Design problem. For each of these problems we propose a collection of effective parallel solution algorithms, either for solving the full problem (Guillotine Cuts and SSSPP) or for enhancing a fundamental part of the solution method (VRP and ND). We endorse our claim by presenting computational results for all problems, either on standard benchmarks from the literature or, when possible, on data from real-world applications, where speed-ups of one order of magnitude are usually attained, not uncommonly scaling up to 40 X factors.

Spectral estimates and preconditioning for saddle point systems arising from optimization problems

In this thesis, we consider the problem of solving large and sparse linear systems of saddle point type stemming from optimization problems. The focus of the thesis is on iterative methods, and new preconditioning srategies are proposed, along with novel spectral estimtates for the matrices involved.

Optimization of molecular and crystalline forms of drugs, agrochemicals, pesticides in relation to activity, bioavailability, patentability and to the fabrication of polymorphs, solvates, co-crystals with green chemistry methods

This doctorate was funded by the Regione Emilia Romagna, within a Spinner PhD project coordinated by the University of Parma, and involving the universities of Bologna, Ferrara and Modena. The aim of the project was: - Production of polymorphs, solvates, hydrates and co-crystals of active pharmaceutical ingredients (APIs) and agrochemicals with green chemistry methods; - Optimization of molecular and crystalline forms of APIs and pesticides in relation to activity, bioavailability and patentability. In the last decades, a growing interest in the solid-state properties of drugs in addition to their solution chemistry has blossomed. The achievement of the desired and/or the more stable polymorph during the production process can be a challenge for the industry. The study of crystalline forms could be a valuable step to produce new polymorphs and/or co-crystals with better physical-chemical properties such as solubility, permeability, thermal stability, habit, bulk density, compressibility, friability, hygroscopicity and dissolution rate in order to have potential industrial applications. Selected APIs (active pharmaceutical ingredients) were studied and their relationship between crystal structure and properties investigated, both in the solid state and in solution. Polymorph screening and synthesis of solvates and molecular/ionic co-crystals were performed according to green chemistry principles. Part of this project was developed in collaboration with chemical/pharmaceutical companies such as BASF (Germany) and UCB (Belgium). We focused on on the optimization of conditions and parameters of crystallization processes (additives, concentration, temperature), and on the synthesis and characterization of ionic co-crystals. Moreover, during a four-months research period in the laboratories of Professor Nair Rodriguez-Hormedo (University of Michigan), the stability in aqueous solution at the equilibrium of ionic co-crystals (ICCs) of the API piracetam was investigated, to understand the relationship between their solid-state and solution properties, in view of future design of new crystalline drugs with predefined solid and solution properties.

Models and Algorihtm for the Optimization of Real-World Routing and Logistics Problems

Logistics involves planning, managing, and organizing the flows of goods from the point of origin to the point of destination in order to meet some requirements. Logistics and transportation aspects are very important and represent a relevant costs for producing and shipping companies, but also for public administration and private citizens. The optimization of resources and the improvement in the organization of operations is crucial for all branches of logistics, from the operation management to the transportation. As we will have the chance to see in this work, optimization techniques, models, and algorithms represent important methods to solve the always new and more complex problems arising in different segments of logistics. Many operation management and transportation problems are related to the optimization class of problems called Vehicle Routing Problems (VRPs). In this work, we consider several real-world deterministic and stochastic problems that are included in the wide class of the VRPs, and we solve them by means of exact and heuristic methods. We treat three classes of real-world routing and logistics problems. We deal with one of the most important tactical problems that arises in the managing of the bike sharing systems, that is the Bike sharing Rebalancing Problem (BRP). We propose models and algorithms for real-world earthwork optimization problems. We describe the 3DP process and we highlight several optimization issues in 3DP. Among those, we define the problem related to the tool path definition in the 3DP process, the 3D Routing Problem (3DRP), which is a generalization of the arc routing problem. We present an ILP model and several heuristic algorithms to solve the 3DRP.

Contributions to exact approaches in combinatorial optimization

The focus of this thesis is to contribute to the development of new, exact solution approaches to different combinatorial optimization problems. In particular, we derive dedicated algorithms for a special class of Traveling Tournament Problems (TTPs), the Dial-A-Ride Problem (DARP), and the Vehicle Routing Problem with Time Windows and Temporal Synchronized Pickup and Delivery (VRPTWTSPD). Furthermore, we extend the concept of using dual-optimal inequalities for stabilized Column Generation (CG) and detail its application to improved CG algorithms for the cutting stock problem, the bin packing problem, the vertex coloring problem, and the bin packing problem with conflicts. In all approaches, we make use of some knowledge about the structure of the problem at hand to individualize and enhance existing algorithms. Specifically, we utilize knowledge about the input data (TTP), problem-specific constraints (DARP and VRPTWTSPD), and the dual solution space (stabilized CG). Extensive computational results proving the usefulness of the proposed methods are reported.

Optimization of RNA-based transgene expression by targeting Protein Kinase R

The aim of this thesis was to establish a method for repeated transfection of in vitro transcribed RNA (IVT-RNA) leading to a sustained protein expression lasting for days or even weeks. Once transfected cells recognize IVT-RNA as "non-self" and initiate defense pathways leading to an upregulated interferon (IFN) response and stalled translation. In this work Protein Kinase R (PKR) was identified as the main effector molecule mediating this cellular response. We assessed four strategies to inhibit PKR and the IFN response: A small molecule PKR inhibitor enhanced protein expression and hampered the induction of IFN-transcripts, but had to be excluded due to cytotoxicity. A siRNA mediated PKR knockdown and the overexpression of a kinase inactive PKR mutant elevated the protein expression, but the down-regulation of the IFN response was insufficient. The co-transfer of the viral inhibitors of PKR and the IFN response was most successful. The use of E3, K3 and B18R co-transfection enabled repeated IVT-RNA-based transfection of human fibroblasts. Thus, the developed protocol allows a continuous IVT-RNA encoded protein expression of proteins, which could be the basis for the generation of induced pluripotent stem cells (iPS) for several therapeutic applications in regenerative medicine or drug research.

Thermoelectric performance of p-type TiCoSb half-Heusler compounds - Intrinsic phase separation and charge carrier concentration optimization as key to high efficiency

The world's rising demand of energy turns the development of sustainable and more efficient technologies for energy production and storage into an inevitable task. Thermoelectric generators, composed of pairs of n-type and p-type semiconducting materials, di¬rectly transform waste heat into useful electricity. The efficiency of a thermoelectric mate¬rial depends on its electronic and lattice properties, summarized in its figure of merit ZT. Desirable are high electrical conductivity and Seebeck coefficients, and low thermal con¬ductivity. Half-Heusler materials are very promising candidates for thermoelectric applications in the medium¬ temperature range such as in industrial and automotive waste heat recovery. The advantage of Heusler compounds are excellent electronic properties and high thermal and mechanical stability, as well as their low toxicity and elemental abundance. Thus, the main obstacle to further enhance their thermoelectric performance is their relatively high thermal conductivity.rn rnIn this work, the thermoelectric properties of the p-type material (Ti/Zr/Hf)CoSb1-xSnx were optimized in a multistep process. The concept of an intrinsic phase separation has recently become a focus of research in the compatible n-type (Ti/Zr/Hf)NiSn system to achieve low thermal conductivities and boost the TE performance. This concept is successfully transferred to the TiCoSb system. The phase separation approach can form a significant alternative to the previous nanostructuring approach via ball milling and hot pressing, saving pro¬cessing time, energy consumption and increasing the thermoelectric efficiency. A fundamental concept to tune the performance of thermoelectric materials is charge carrier concentration optimization. The optimum carrier concentration is reached with a substitution level for Sn of x = 0.15, enhancing the ZT about 40% compared to previous state-of-the-art samples with x = 0.2. The TE performance can be enhanced further by a fine-tuning of the Ti-to-Hf ratio. A correlation of the microstructure and the thermoelectric properties is observed and a record figure of merit ZT = 1.2 at 710°C was reached with the composition Ti0.25Hf0.75CoSb0.85Sn0.15.rnTowards application, the long term stability of the material under actual conditions of operation are an important issue. The impact of such a heat treatment on the structural and thermoelectric properties is investigated. Particularly, the best and most reliable performance is achieved in Ti0.5Hf0.5CoSb0.85Sn0.15, which reached a maximum ZT of 1.1 at 700°C. The intrinsic phase separation and resulting microstructure is stable even after 500 heating and cooling cycles.

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.

Geometrical optimization of a short-stem hip implant for the reduction of proximal stress shielding (ottimizzazione geometrica di uno stelo corto di protesi d?anca per la riduzione della schermatura del carico prossimale)

Nowadays the number of hip joints arthroplasty operations continues to increase because the elderly population is growing. Moreover, the global life expectancy is increasing and people adopt a more active way of life. For this reasons, the demand of implant revision operations is becoming more frequent. The operation procedure includes the surgical removal of the old implant and its substitution with a new one. Every time a new implant is inserted, it generates an alteration in the internal femur strain distribution, jeopardizing the remodeling process with the possibility of bone tissue loss. This is of major concern, particularly in the proximal Gruen zones, which are considered critical for implant stability and longevity. Today, different implant designs exist in the market; however there is not a clear understanding of which are the best implant design parameters to achieve mechanical optimal conditions. The aim of the study is to investigate the stress shielding effect generated by different implant design parameters on proximal femur, evaluating which ranges of those parameters lead to the most physiological conditions.

Il sito web del Palio di San Donato: proposta di localizzazione e Search Engine Optimization

La presente tesi illustra e discute due attività legate all'ambito dei siti web, ovvero la localizzazione e l'ottimizzazione per i motori di ricerca (o SEO, dall'inglese "Search Engine Optimization"). Quest'ultima è un'attività mirata a permettere che i siti stessi ottengano un posizionamento migliore nella pagina dei risultati dei motori di ricerca e siano dunque più visibili agli utenti. Poiché la SEO prevede vari interventi sui siti web, alcuni dei quali implicano la manipolazione di codice HTML, essa viene spesso considerata come un'attività strettamente informatica. L'obiettivo della presente tesi, dunque, è quello di illustrare come i traduttori possano sfruttare le proprie competenze linguistiche per dedicarsi non soltanto alla localizzazione di siti web, ma anche alla loro ottimizzazione per i motori di ricerca. Per dimostrare l'applicabilità di tali tecniche è stato utilizzato come esempio pratico il sito web de "Il Palio di San Donato", un sito gestito dal Comune di Cividale del Friuli e finalizzato alla descrizione dell'omonima rievocazione storica cittadina. La tesi si compone di quattro capitoli. Nel primo capitolo vengono introdotti i principi teorici alla base della localizzazione di siti web, della SEO, della scrittura per il web e della traduzione per il settore turistico. Nel secondo capitolo, invece, viene descritto il sito del Palio di San Donato, esaminandone in particolare la struttura e i contenuti. Il terzo capitolo è dedicato alla descrizione del progetto di localizzazione a cui è stato sottoposto il sito in esame. Infine, il quarto capitolo contiene un breve commento relativo alle problematiche linguistiche, culturali e tecnologiche riscontrate durante il processo traduttivo e un elenco di strategie di SEO applicate a cinque pagine del sito web in esame, selezionate sulla base della possibilità di illustrare il maggior numero possibile di interventi di SEO attuabili dai traduttori.

Integrare Search Engine Optimization e Website usability al processo di localizzazione di un sito Web. Proposta di localizzazione dal francese all’italiano del sito del Parc de loisirs du Lac de Maine.

Ce mémoire a comme objectif de montrer le processus de localisation en langue italienne d’un site Internet français, celui du Parc de loisir du Lac de Maine. En particulier, le but du mémoire est de démontrer que, lorsqu’on parle de localisation pour le Web, on doit tenir compte de deux facteurs essentiels, qui contribuent de manière exceptionnelle au succès du site sur le Réseau Internet. D’un côté, l’utilisabilité du site Web, dite également ergonomie du Web, qui a pour objectif de rendre les sites Web plus aisés d'utilisation pour l'utilisateur final, de manière que son rapprochement au site soit intuitif et simple. De l’autre côté, l’optimisation pour les moteurs de recherche, couramment appelée « SEO », acronyme de son appellation anglais, qui cherche à découvrir les meilleures techniques visant à optimiser la visibilité d'un site web dans les pages de résultats de recherche. En améliorant le positionnement d'une page web dans les pages de résultats de recherche des moteurs, le site a beaucoup plus de possibilités d’augmenter son trafic et, donc, son succès. Le premier chapitre de ce mémoire introduit la localisation, avec une approche théorique qui en illustre les caractéristiques principales ; il contient aussi des références à la naissance et l’origine de la localisation. On introduit aussi le domaine du site qu’on va localiser, c’est-à-dire le domaine du tourisme, en soulignant l’importance de la langue spéciale du tourisme. Le deuxième chapitre est dédié à l’optimisation pour les moteurs de recherche et à l’ergonomie Web. Enfin, le dernier chapitre est consacré au travail de localisation sur le site du Parc : on analyse le site, ses problèmes d’optimisation et d’ergonomie, et on montre toutes les phases du processus de localisation, y compris l’intégration de plusieurs techniques visant à améliorer la facilité d’emploi par les utilisateurs finaux, ainsi que le positionnement du site dans les pages de résultats des moteurs de recherche.

Application and optimization of a thermal energy storage on a cruise ship

The thesis, developed in collaboration between the team Systems and Equipment for Energy and Environment of Bologna University and Chalmers University of Technology in Goteborg, aims to study the benefits resulting from the adoption of a thermal storage system for marine application. To that purpose a chruis ship has been considered. To reach the purpose has been used the software EGO (Energy Greed Optimization) developed by University of Bologna.

Search Engine Optimization: principi e tecniche di ottimizzazione di siti web per i motori di ricerca

La tesi tratta i concetti fondamentali legati alla "Search Engine Optimization", ovvero all’ottimizzazione dei siti web per i motori di ricerca. La SEO è un’attività multidisciplinare che coinvolge aspetti tecnici dello sviluppo web e princìpi di web marketing, allo scopo di migliorare la visibilità di un sito nelle pagine di risposta di un motore di ricerca. All’interno dell’elaborato viene analizzato dapprima il funzionamento dei motori di ricerca, con particolare riferimento al mondo Google; in seguito vengono esaminate le diverse tecniche di ottimizzazione “on-page” di un sito (codice, architettura, contenuti) e le strategie “off-page” volte a migliorare reputazione, popolarità e autorevolezza del sito stesso.

64-section multidetector CT of the upper abdomen: optimization of a saline chaser injection protocol for improved vascular and parenchymal contrast enhancement

To prospectively investigate the effect of varying the injection flow rates of a saline chaser on vascular and parenchymal contrast enhancement during abdominal MDCT.

Thermal model for optimization of vascular laser tissue soldering

Laser tissue soldering (LTS) is a promising technique for tissue fusion based on a heat-denaturation process of proteins. Thermal damage of the fused tissue during the laser procedure has always been an important and challenging problem. Particularly in LTS of arterial blood vessels strong heating of the endothelium should be avoided to minimize the risk of thrombosis. A precise knowledge of the temperature distribution within the vessel wall during laser irradiation is inevitable. The authors developed a finite element model (FEM) to simulate the temperature distribution within blood vessels during LTS. Temperature measurements were used to verify and calibrate the model. Different parameters such as laser power, solder absorption coefficient, thickness of the solder layer, cooling of the vessel and continuous vs. pulsed energy deposition were tested to elucidate their impact on the temperature distribution within the soldering joint in order to reduce the amount of further animal experiments. A pulsed irradiation with high laser power and high absorbing solder yields the best results.