Software Defined Applications in Cellular and Optical Networks

abstract: Small wireless cells have the potential to overcome bottlenecks in wireless access through the sharing of spectrum resources. A novel access backhaul network architecture based on a Smart Gateway (Sm-GW) between the small cell base stations, e.g., LTE eNBs, and the conventional backhaul gateways, e.g., LTE Servicing/Packet Gateways (S/P-GWs) has been introduced to address the bottleneck. The Sm-GW flexibly schedules uplink transmissions for the eNBs. Based on software defined networking (SDN) a management mechanism that allows multiple operator to flexibly inter-operate via multiple Sm-GWs with a multitude of small cells has been proposed. This dissertation also comprehensively survey the studies that examine the SDN paradigm in optical networks. Along with the PHY functional split improvements, the performance of Distributed Converged Cable Access Platform (DCCAP) in the cable architectures especially for the Remote-PHY and Remote-MACPHY nodes has been evaluated. In the PHY functional split, in addition to the re-use of infrastructure with a common FFT module for multiple technologies, a novel cross functional split interaction to cache the repetitive QAM symbols across time at the remote node to reduce the transmission rate requirement of the fronthaul link has been proposed.Dissertation/ThesisDoctoral Dissertation Electrical Engineering 201

Spectrum Sharing, Latency, and Security in 5G Networks with Application to IoT and Smart Grid

The surge of mobile devices, such as smartphones, and tables, demands additional capacity. On the other hand, Internet-of-Things (IoT) and smart grid, which connects numerous sensors, devices, and machines require ubiquitous connectivity and data security. Additionally, some use cases, such as automated manufacturing process, automated transportation, and smart grid, require latency as low as 1 ms, and reliability as high as 99.99\%. To enhance throughput and support massive connectivity, sharing of the unlicensed spectrum (3.5 GHz, 5GHz, and mmWave) is a potential solution. On the other hand, to address the latency, drastic changes in the network architecture is required. The fifth generation (5G) cellular networks will embrace the spectrum sharing and network architecture modifications to address the throughput enhancement, massive connectivity, and low latency. To utilize the unlicensed spectrum, we propose a fixed duty cycle based coexistence of LTE and WiFi, in which the duty cycle of LTE transmission can be adjusted based on the amount of data. In the second approach, a multi-arm bandit learning based coexistence of LTE and WiFi has been developed. The duty cycle of transmission and downlink power are adapted through the exploration and exploitation. This approach improves the aggregated capacity by 33\%, along with cell edge and energy efficiency enhancement. We also investigate the performance of LTE and ZigBee coexistence using smart grid as a scenario. In case of low latency, we summarize the existing works into three domains in the context of 5G networks: core, radio and caching networks. Along with this, fundamental constraints for achieving low latency are identified followed by a general overview of exemplary 5G networks. Besides that, a loop-free, low latency and local-decision based routing protocol is derived in the context of smart grid. This approach ensures low latency and reliable data communication for stationary devices. To address data security in wireless communication, we introduce a geo-location based data encryption, along with node authentication by k-nearest neighbor algorithm. In the second approach, node authentication by the support vector machine, along with public-private key management, is proposed. Both approaches ensure data security without increasing the packet overhead compared to the existing approaches

Resource allocation in networks via coalitional games

The main goal of this dissertation is to manage resource allocation in network engineering problems and to introduce efficient cooperative algorithms to obtain high performance, ensuring fairness and stability. Specifically, this dissertation introduces new approaches for resource allocation in Orthogonal Frequency Division Multiple Access (OFDMA) wireless networks and in smart power grids by casting the problems to the coalitional game framework and by providing a constructive iterative algorithm based on dynamic learning theory.  Software Engineering (Software)Algorithms and the Foundations of Software technolog

In silico studies of the effect of phenolic compounds from grape seed extracts on the activity of phosphoinositide 3-kinase (PI3K) and the farnesoid x receptor (FXR)

In silico studies of the effect of phenolic compounds from grape seed extracts on the activity of phosphoinositide 3-kinase (PI3K) and farnesoid X receptor (FXR)Montserrat Vaqué Marquès En aquesta tesis es pretén aplicar metodologies computacionals (generació de farmacòfors i docking proteïna lligand) en l'àmbit de la nutigenòmica (ciència que pretén entendre, a nivell molecular, com els nutrients afecten la salut). S'aplicaran metodologies in silico per entendre a nivell molecular com productes naturals com els compostos fenòlics presents en la nostra dieta, poden modular la funció d'una diana comportant un efect en la salut. Aquest efecte es creu que podria ser degut a la seva interacció directa amb proteïnes de vies de senyalització molecular o bé a la modificació indirecta de l'expressió gènica. Donat que el coneixement de l'estructura del complex lligand-receptor és bàsic per entendre el mecanisme d'acció d'aquests lligands s'aplica la metodologia docking per predir l'estructura tridimensional del complex. En aquest sentit, un dels programes de docking és AutoGrid/AutoDock (un dels més citats). No obstant, l'automatització d'AutoGrid/AutoDock no és trivial tan per (a) la cerca virtual en una llibreria de lligands contra un grup de possibles receptors, (b) l'ús de flexibilitat, i (c) realitzar un docking a cegues utilitzant tota la superfície del receptor. Per aquest motiu, es dissenya una interfície gràfica de fàcil ús per utilitzar AutoGrid/AutoDock. Blind Docking Tester (BDT) és una aplicació gràfica que s'executa sobre quatre programes escrits en Fortran i que controla les condicions de les execucions d'AutoGrid i AutoDock. BDT pot ser utilitzat per equips d'investigadors en el camp de la química i de ciències de la vida interessats en dur a terme aquest tipus d'experiments però que no tenen suficient habilitats en programació. En la modulació del metabolisme de la glucosa, treballs in vivio i in vitro en el nostre grup de recerca s'han atribuït els efectes beneficiosos de l'extracte de pinyol de raïm en induir captació de glucosa (punt crític pel manteniment de l'homeostasis de la glucosa). No obstant alguns compostos fenòlics no tenen efecte en la captació de la glucosa, d'altres l'inhibeixen reversiblement. En alguns casos aquesta inhibició és el resultat de la competició dels compostos fenòlics amb ATP pel lloc d'unió de l'ATP de la subunitat catalítica de la fosfatidil inositol 3-kinasa (PI3K). Estudis recents amb inhibidors específics d'isoforma han identificat la p110α (la subunitat catalítica de PI3Kα) com la isoforma crucial per la captació de glucosa estimulada per insulina en algunes línies cel·lulars. Els programes computacionals han estat aplicats per tal de correlacionar l'activitat biològica dels compostos fenòlics amb informació estructural per obtenir una relació quantitativa estructura-activitat (3D-QSAR) i obtenir informació dels requeriments estructura-lligand per augmentar l'afinitat i/o selectivitat amb la diana (proteïna). Tot hi haver-se demostrat que l'adició d'extractes de compostos fenòlics en l'aliment pot tenir en general un benefici per la salut, s'ha de tenir en compte que l'estudi 3D-QSAR (construït a partir d'inhibidors sintètics de p110α) prediu que algunes d'aquestes molècules poden agreujar la resistència a la insulina en individus susceptibles dificultant la capatació de glucosa en múscul i teixit adipós i, per tant, produir un efecte secundari indesitjat. Resultats en el nostre grup de recerca han demostrat que compostos fenòlics presents en extractes de llavor de raïm incrementen l'activitat del receptor "farnesoid x receptor" (FXR) de manera dosi depenent quan el lligand natural de FXR (CDCA) és present. Les metodologies in silico, docking i 3D-QSAR, han estat aplicades juntament amb dades biològiques d'agonistes no esteroidals de FXR que s'uneixen a un lloc d'unió proper però diferent al lligand esteroidal 6CDCA. Els resultats han mostrat que els compostos fenòlics no són capaços d'activar FXR per ells mateixos però poden afegir noves interaccions que estabilitzarien la conformació activa de FXR en presència del lligand natural CDCA. Els compostos fenòlics podrien induir canvis conformacionals específics que augmentarien l'activitat de FXR. In silico studies of the effect of phenolic compounds from grape seed extracts on the activity of phosphoinositide 3-kinase (PI3K) and farnesoid X receptor (FXR)Montserrat Vaqué Marquès This thesis was written with the aim of applying computational methods that have already been developed for molecular design and simulation (i.e. pharmacophore generation and protein-ligand docking) to nutrigenomics. So, in silico tools that are routinely used by the pharmaceutical industry to develop drugs have been used to understand, at the molecular level, how natural products such as phenolic compounds (i.e. molecules that are commonly found in fruits and vegetables) can improve health and prevent diseases. Therefore, we first focused on predicting the structure of protein-ligand complexes. The docking algorithms can use the individual structures from receptor and ligand to predict (1) whether they can form a complex and (2) if so, the structure of the resulting complex. This prediction can be made, for instance, with AutoGrid/AutoDock, the most cited docking software in the literature. The automation of AutoGrid/AutoDock is not trivial for tasks such as (1) the virtual screening of a library of ligands against a set of possible receptors; (2) the use of receptor flexibility and (3) making a blind-docking experiment with the whole receptor surface. Therefore, in order to circumvent these limitations, we have designed BDT (i.e. blind-docking tester; http://www.quimica.urv.cat/~pujadas/BDT), an easy-to-use graphic interface for using AutoGrid/AutoDock. BDT is a Tcl/Tk graphic front-end application that runs on top of four Fortran programs and which controls the conditions of the AutoGrid and AutoDock runs. As far as the modulation of the glucose metabolism is concerned, several in vivo and in vitro results obtained by our group have shown that grape seed procyanidin extracts (GSPE) stimulate glucose uptake in 3T3-L1 adipocytes and thus help to maintain their glucose homeostasis. In contrast, it is also well known that although some phenolic compounds do not affect glucose uptake, others reversibly inhibit it in several cell lines. Moreover, for at least some of these phenolic compounds, this inhibition is the result of their competition with ATP for the ATP-binding site in p110α (i.e. the α isoform of the catalytic subunit of phosphoinositide 3-kinase or PI3Kα). Furthermore, recent studies with isoform-specific inhibitors have identified p110α as the crucial isoform for insulin-stimulated glucose-uptake in some cell lines. Therefore, although it has been proved that the addition of phenolic compound extracts to food can have an overall benefit on health, it should be taken into account that some of these molecules may exacerbate insulin resistance in susceptible individuals via impaired glucose uptake in muscle and adipose tissues and, therefore, produce an undesirable side effect. In this context, we have applied computational approaches (i.e. protein-ligand docking and 3D-QSAR) to predict the IC50 (i.e. the concentration that reduces the p110α activity to 50%). Our results agree with previous experimental results and predict that some compounds are potential inhibitors of this enzyme. Recent results in our research group have demonstrated that the phenolic compounds in GSPE increase the activity of the farnesoid X receptor (i.e. FXR) in a dose-dependent way when the natural ligand of FXR (i.e. CDCA) is also present. The phenolic compounds might induce specific conformational changes that increase FXR activity and then contribute to cardioprotection through mechanisms that are independent of their intrinsic antioxidant capacities but that involve direct interaction with FXR to modulate gene expression. Taking into account this hypothesis a 3D-QSAR analysis was made in an attempt to understand how phenolic compounds activate FXR. So, our results explain why phenolic compounds cannot activate FXR by themselves and how they can add new interactions to stabilize the active conformation of FXR when its natural ligand (i.e. CDCA) is present. Therefore, we proposed a mechanism of FXR activation by dietary phenolic compounds in which they may enhance bile acid-bound FXR activity