Conventional TCP is window based, which exploits the sliding window mechanism to conduct the flow control. It increases the sending window additively and decreases the sending window multiplicatively in response to successful transmission and, packet loss/timeout events respectively. While the mechanism works quite well in normal networks, TCP can hardly reach the ideal bandwidth utilization in long fat networks (LFNs) due to long delay and bursts of packet losses. Besides, as wireless and mobile computing has become popular today, packet loss in such networks may occur due to noise, interference and handoff across different domains. TCP could not react to different situations effectively as it sees all packet losses as an indication of network congestion. In this thesis, we proposed a new transmission control mechanism called Active Rate Anchoring TCP (ARCH-TCP). In ARCH-TCP, we explicitly integrate bandwidth measurement into TCP to solve the aforementioned problem. Specifically, we exploit packet-pair measurement to quickly estimate bandwidth share and then RTT variation is observed to compensate measurement error. We built the model in J-Sim network simulator to evaluate the effectiveness of our proposal. We found that ARCH-TCP can react to network conditions quickly and precisely in both wired and wireless networks and both in the normal networks and LFNs.

Expanding the global Internet to include mobile devices is an exciting area of current research. Because of the vast size of the Internet, and because the protocols in it are already widely deployed, mobile devices must inter-operate with those protocols. Although most of the incompatiblities with mobiles have been solved, the protocols that deliver data reliably, and that account for the majority of Internet traffic, perform very poorly. A change in location causes a disruption in traffic, and disruption is dealt with by algorithms tailored only for stationary hosts. The Transmission Control Protocol (TCP) is the predominant transport-layer protocol in the Internet. In this thesis, we look at the performance of TCP in mobile environments. We provide a complete explanation for poor performance; we conduct a large number of experiments, simulations, and analyses that prove and quantify poor performance;and we propose simple and scalable solutions that address the limitations.

Expanding the global Internet to include mobile devices is an exciting area of current research. Because of the vast size of the Internet, and because the protocols in it are already widely deployed, mobile devices must inter-operate with those protocols. Although most of the incompatiblities with mobiles have been solved, the protocols that deliver data reliably, and that account for the majority of Internet traffic, perform very poorly. A change in location causes a disruption in traffic, and disruption is dealt with by algorithms tailored only for stationary hosts. The Transmission Control Protocol (TCP) is the predominant transport-layer protocol in the Internet. In this thesis, we look at the performance of TCP in mobile environments. We provide a complete explanation for poor performance; we conduct a large number of experiments, simulations, and analyses that prove and quantify poor performance;and we propose simple and scalable solutions that address the limitations.

This thesis investigates TCP connection management mechanisms in order to understand the behaviour and improve the performance of Internet servers during overload conditions such as flash crowds. We study several alternatives for implementing TCP connection establishment, reviewing approaches taken by existing TCP stacks as well as proposing new mechanisms to improve server throughput and reduce client response times under overload. We implement some of these connection establishment mechanisms in the Linux TCP stack and evaluate their performance in a variety of environments. We also evaluate the cost of supporting half-closed connections at the server and assess the impact of an abortive release of connections by clients on the throughput of an overloaded server. Our evaluation demonstrates that connection establishment mechanisms that eliminate the TCP-level retransmission of connection attempts by clients increase server throughput by up to 40% and reduce client response times by two orders of magnitude. Connection termination mechanisms that preclude support for half-closed connections additionally improve server throughput by up to 18%.

The explosive growth of the Internet during the last few years, has been propelled by the TCP/IP protocol suite and the best effort packet forwarding service. However, quality of service (QoS) is far from being a reality especially for multimedia services like video streaming and video conferencing. In the case of wireless and mobile networks, the problem becomes even worse due to the physics of the medium, resulting into further deterioration of the system performance. Goal of this dissertation is the systematic development of comprehensive models that jointly characterize the performance of transport protocols and media delivery in heterogeneous wireless networks. At the core of our novel methodology, is the use of analytical models for driving the design of media transport algorithms, so that the delivery of conversational and non-interactive multimedia data is enhanced in terms of throughput, delay, and jitter. More speciffically, we develop analytical models that characterize the throughput and goodput of the transmission control protocol (TCP) and the transmission friendly rate control (TFRC) protocol, when CBR and VBR multimedia workloads are considered. Subsequently, we enhance the transport protocol models with new parameters that capture the playback buffer performance and the expected video distortion at the receiver. In this way a complete end-to-end model for media streaming is obtained. This model is used as a basis for a new algorithm for rate-distortion optimized mode selection in video streaming appli- cations. As a next step, we extend the developed models for the aforementioned protocols, so that heterogeneous wireless networks can be accommodated. Subsequently, new algorithms are proposed in order to enhance the developed media streaming algorithms when heterogeneous wireless networks are also included. Finally, the aforementioned models and algorithms are extended for the case of concurrent multipath media transport over several hybrid wired/wireless links.

In this dissertation, we present performance prediction models for rate-based and window¡Vbased flow control mechanisms. For rate-based flow control, such as in ATM network, we derive two analytical models to predict the ACR rates for congestion-free and congestion networks, respectively. To coordinate the cooperative problems of TCP over ATM networks, we propose a new algorithm to monitor the states of ATM switches and adjust TCP congestion window size based on RM cells. For window-based flow control mechanisms, such as in TCP-Reno and TCP-SACK, we respectively present analytical models to systematically capture the characteristics of multiple consecutive packet losses in TCP windows. Through fast retransmission, the lost packets may or may not be recovered. Thus, we present upper bound analyses for slow start and congestion avoidance phases to study the effects of multiple packet losses on TCP performance. Above the proposed upper bounds, the lost packets may not be successfully recovered through fast retransmission. Finally, we develop a model to study the TCP performance in terms of throughput degradation resulted from multiple consecutive packet losses. The analytical results from the throughput degradation model are validated through OPNET simulation.

Despite the persistent change and growth that characterizes the Internet, the Transmission Control Protocol (TCP) still dominates at the transport layer, carrying more than 90\% of the global traffic. Despite its astonishing success, it has been observed that TCP can cause poor end-to-end performance, especially for large transfers and in network paths with high bandwidth-delay product. In this thesis, we focus on mechanisms that can address key problems in TCP performance, without any modification in the protocol itself. This evolutionary approach is important in practice, as the deployment of clean-slate transport protocols in the Internet has been proved to be extremely difficult. Specifically, we identify a number of TCP-related problems that can cause poor end-to-end performance. These problems include poorly dimensioned socket buffer sizes at the end-hosts, suboptimal buffer sizing at routers and switches, and congestion unresponsive TCP traffic aggregates. We propose solutions that can address these issues, without any modification to TCP. <br> <br> In network paths with significant available bandwidth, increasing the TCP window till observing loss can result in much lower throughput than the path's available bandwidth. We show that changes in TCP are {em not required} to utilize all the available bandwidth, and propose the application-layer SOcket Buffer Auto-Sizing (SOBAS) mechanism to achieve this goal. SOBAS relies on run-time estimation of the round trip time (RTT) and receive rate, and limits its socket buffer size when the receive rate approaches the path's available bandwidth. In a congested network, SOBAS does not limit its socket buffer size. Our experiment results show that SOBAS improves TCP throughput in uncongested network without hurting TCP performance in congested networks. <br> <br> Improper router buffer sizing can also result in poor TCP throughput. Previous research in router buffer sizing focused on network performance metrics such as link utilization or loss rate. Instead, we focus on the impact of buffer sizing on end-to-end TCP performance. We find that the router buffer size that optimizes TCP throughput is largely determined by the link's output to input capacity ratio. If that ratio is larger than one, the loss rate drops exponentially with the buffer size and the optimal buffer size is close to zero. Otherwise, if the output to input capacity ratio is lower than one, the loss rate follows a power-law reduction with the buffer size and significant buffering is needed. The amount of buffering required in this case depends on whether most flows end in the slow-start phase or in the congestion avoidance phase. <br> <br> TCP throughput also depends on whether the cross-traffic reduces its send rate upon congestion. We define this cross-traffic property as {em congestion responsiveness}. Since the majority of Internet traffic uses TCP, which reduces its send rate upon congestion, an aggregate of many TCP flows is believed to be congestion responsive. Here, we show that the congestion responsiveness of aggregate traffic also depends on the flow arrival process. If the flow arrival process follows an open-loop model, then even if the traffic consists exclusively of TCP transfers, the aggregate traffic can still be unresponsive to congestion. TCP flows that arrive in the network in a closed-loop manner are always congestion responsive, on the other hand. We also propose a scheme to estimate the fraction of traffic that follows the closed-loop model in a given link, and give practical guidelines to increase that fraction with simple application-layer modifications.

O florescimento é um processo chave no desenvolvimento vegetal. A mudança de identidade do meristema apical de vegetativo para reprodutivo desencadeia reprogramação genética com efeitos em todo o corpo vegetal. Arabidopsis thaliana é conhecida como o principal modelo de estudo para esse processo apresentando até o momento cinco principais vias genéticas regulatórias. Tais vias apresentam redundância, sendo complexa a eliminação total da transição de fase nessa espécie. A via AGE, regulada pela idade da planta, tem como principais reguladores o mir156 e seus alvos diretos, os fatores de transcrição da família SPL/SBP (SQUAMOSA PROMOTER BINDING PROTEIN-like). Uma segunda via é controlada pelo fitohormônio giberelina (GA), o qual atua de maneira oposta em Arabidopsis thaliana (arabidopsis) e Solanum lycopersicum L. (tomateiro). Em tomateiro, diferentemente de arabidopsis, o cruzamento entre mutantes com conteúdo alterado de GA e plantas transgênicas superexpressando o miR156 (156OE; SILVA et al., 2014) demonstraram efeito sinérgico no atraso do tempo de florescimento. A aplicação de GA3 em plantas 156OE apresenta efeito similar aos cruzamentos citados sobre a transição do meristema apical. Em um dos cruzamentos entre mutantes da via GA e plantas 156OE, foi possível obter plantas apresentando completo bloqueio da transição de fase vegetativo-reprodutivo. A oferta extra do florígeno SINGLE FLOWER TRUSS (SFT) via enxertia não foi suficiente para restaurar a transição de fase nessas plantas, sugerindo que vias associadas à GA e AGE regulam alvos em comum, os quais podem ser independentes da regulação por SFT. Além disso, a regulação transcricional, e possivelmente pós-transcricional de alguns genes SBPs por diferentes vias associadas à GA, sugere uma complexa inter-relação entre as vias GA e AGE em tomateiro durante o florescimento. A ação combinada das vias GA e AGE foi capaz de inibir completamente o florescimento em tomateiro, regulação oposta ao verificado na planta modelo Arabidopsis thaliana. O efeito inibitório de GA sobre o florescimento é também visualizado em plantas lenhosas, sugerindo que as descobertas científicas realizadas em tomateiro podem ser expandidas para essas espécies, nas quais a experimentação é lenta e laboriosa / The flowering process is a major developmental event during the plant life cicle. The meristem identity switches from vegetative to reproductive, triggering substantial genetic modifications that affect the whole plant body. Arabidopsis thaliana is a major model for flowering with five different pathways controlling this process. These pathways are redundant, making complex the complete elimination of phase change in this species. One of the pathways is termed AGE since it is regulated by the time of development. The miR156 and its direct target SBP (SQUAMOSA PROMOTER BINDING PROTEIN-like) are the main regulators of the AGE pathway. A second pathway is controlled by the phytohormone gibberellin (GA), which acts in opposite ways when comparing Arabidopsis thaliana and tomato. In tomato, unlike Arabidopsis, the cross between mutants with altered contents of GA and transgenic plants overexpressing the miR156 (156OE; SILVA et al, 2014) showed synergistic effect in delayed flowering time. Treatments of GA3 in plants 156OE lead to similar effects visualized on the crosses above related to meristem transition. Among the crosses between GA mutants and 156OE plants, one double mutant could completely abolish the phase change in tomato. An extra offer of the florigen (SINGLE FLOWER TRUSS or SFT) by grafting experiments was unable to restore the flowering process in this double mutant. It suggests, pathways associated to GA and AGE regulate common downstream targets, which could be independent of SFT regulation. Moreover, the transcriptional regulation, and possible the post-transcriptionally regulation of some SBP targets by different pathways associated to GA, suggest a complex network between GA and AGE during the flowering in tomato. The combined action of GA and AGE pathways can complete impaired the flowering in tomato, this interaction is opposed to the model Arabidopsis thaliana. The negative effect of GA over the time of flowering is presented in wood plants, suggesting the scientific discoveries in tomato could be expanded to these species, which experiments are slow and laborious

Orientador: Nobuo Oki / Banca: Artur Pantoja Marques / Banca: Dilvan de Abreu Moreira / Resumo: Com a globalização e a evolução tecnológica, a capilaridade das instituições, sejam elas públicas ou privadas, é realidade irreversível. O uso de computadores cada vez mais velozes e com elevada capacidade de armazenamento possibilitou a centralização das informações. Nesse contexto, surge a necessidade de interligar os sistemas computacionais com o objetivo de trocar informações, independentemente da região geográfica. A Internet, utilizando tecnologias de redes de dados, com arquitetura projetada para suportar em nível mundial a comunicação entre computadores, passa a ser a principal ferramenta utilizada na interligação de locais geograficamente distribuídos. Com a tecnologia e infraestrutura disponível para efetivar a comunicação, surge também a necessidade de garantir que os sistemas estejam ativos o maior tempo possível, atendendo a desempenho compatível às atividades desenvolvidas, pois as instituições passam a depender da interação entre os sistemas computacionais, independente do ponto do planeta em que estejam. Este trabalho propõe modelar, desenvolver e realizar ensaios de uma ferramenta que auxilie no monitoramento de pontos interligados por redes de comunicação dados sobre protocolo TCP/IP distribuídos geograficamente. O modelo consiste em monitorar um ou mais pontos, visualizados sobre um mapa com o traçado do perímetro político geográfico da área atendida. Em suma, propõe-se utilizar as ferramentas básicas de teste de conectividade nas redes de comunicação de dados, associadas aos conceitos de georreferenciamento e geoprocessamento / Abstract: The globalization and technological evolution, allowed the grow of institutions public or private over the entire world with highest capillarity. The development of computers becoming faster and with large storage capacity allowed the centralization of information. In this context the necessity of linking computer systems with the aim to exchange information regardless of geography became a reality. The technics and technologies used in Internet, envolving data communications, with architecture designed to support global communication between computers, becomes the main tool used in the interconnection of thousand geographically distributed sites. With the technology and infrastructure available for an effective communication, also arises the need to ensure that systems are active as long as possible, with a minimum of performance to the services, because the activities in the institutions are dependent upon interaction between computer systems, regardless of the point on the planet they are. This study proposes to model, develop and test a tool to assist in the monitoring of points connected by data communication networks over TCP / IP distributed geographically. The proposed format is to monitor one or more points, displayed on one or more maps with the route of political geographic boundaries of the area served. In short, it is proposed to use the basic tools to test network connectivity in data communications, combined with the concepts of GIS and georeferencing / Mestre

L'utilisation de TCP sur des liens asymétriques entraîne fréquemment des débits plus faibles qu'attendus au point de nuire sensiblement à la qualité de service ressentie par l'utilisateur. Ces baisses de performances peuvent prendre diverses formes parmi lesquelles une forte latence en début de connexion, une sous utilisation de la capacité du lien ou encore des latences excessivement hautes pour l'ensemble de la connexion. Afin de contrer ces effets, plusieurs approches sont possibles, que ce soit de bout-en-bout par des modifications de la pile TCP/IP ou en cœur de réseau avec divers mécanismes d'ordonnancement. L'objectif de cette thèse est d'explorer comment un résultat similaire à celui obtenu par des méthodes d'ordonnancement au goulot d'étranglement peut être obtenu en travaillant de bout-en-bout, c'est à dire là où les ressources de calcul et de mémoire sont les plus abondantes. Ce questionnement est accompagné par une analyse en profondeur des phénomènes causant une dégradation des performances, ainsi que l'évaluation des solutions existantes. Finalement, des solutions nouvelles, en cœur de réseau ainsi que de bout en bout, ont été apportées et testées sur banc d'essai. / Using TCP on asymmetric links may lead to unexpected and significant performance drops, severely degrading user experience. Those performance drops can come in various forms, among which a huge latency at the beginning of a connection, under-utilization of link capacities, or even excessive delays for the whole connection.In order to prevent those effects to happen, various approaches exist, either end-to-end through changes in the TCP/IP stack, or in the network core with a collection of scheduling algorithms.The first goal of this thesis is to explore if and how an end-to-end policy (i.e where CPU and memory resources are the most abundant) can achieve similar results as buffering policies in the core of the network. Secondly, we provide an in-depth analysis of the root cause of the performance drops, and evaluate existing algorithms. Finally, new solutions, both end-to-end and in the core of the network, are brought and tested in real life networks.