Wireless channels are vulnerable to interception. In some applications an end-to-end secure data transfer is required. However the use of cryptographic functions in communication over a wireless channel increases sensitivity to channel errors. As a result, the connection characteristics in terms of delay, throughput, and transmission energy worsen. Transmission energy is a key issue in some secure end-to-end wireless applications especially if they are running on mobile handheld devices with a limited source of energy such as batteries. That is why in most secure end-to-end wireless connections, the connection is dropped in poor channel conditions. In this thesis, models are proposed by which the performance is improved and transmission energy is lowered. A combination of a cross-layer controller, K Best Likelihood (K-BL) channel decoder, and a keyed error detection algorithm in the novel model supports the authorized receivers by a higher throughput, lower delay mean, and less transmission energy in a certain range of the Signal to Noise Ratio (SNR). This is done at the expense of additional computation at the receiving end. Ttradeoffs are examined and the simulation results of the new model are compared with those of conventional wireless communication systems. Another model is devised to mitigate the energy consumption of the Turbo Code channel decoder. The overall decoding energy consumption for each packet can be lowered by reducing the average number of iterations in the Turbo Code channel decoder. The proposed models achieve better energy consumption by reducing the number of iterations in a channel decoder that uses the Turbo decoder and by reducing the number of retransmissions in a trellis channel decoder. Furthermore, the security enhancement of the novel models is assessed in terms of the extent to which the enhancement is fully achieved.

IEEE 802.11 has become the standard in wireless LAN. Originally, 802.11 is designed for the best-effort services only. To support the increasing demand of delay-sensitive applications, IEEE 802.11 Task Group E is developing a QoS-aware MAC protocol, EDCF, for differentiated services. However, when the network becomes congested, there exists unexpected packet delay due to collisions and retransmissions. This thesis proposes a dynamic contention control (DCC) scheme to reduce packet delay and increase the percentage of packets arriving in time. DCC estimates per-hop delay, denoted as Mrtt, and end-to-end delay, denoted as Sigma_t, based on either the received MAC-layer ACK or the control packets of a reactive routing protocol. Then, Mrtt and Sigma_t are used to dynamically adjust the associated contention window for each priority. Besides, when a frame is retransmitted, the backoff time is determined according to the remaining end-to-end delay instead of a uniformly distributed random number. For the propose of evaluation, we perform simulations on the well-known network simulator, NS-2. DCC is compared with the EDCF and one previously proposed scheme, AEDCF. The simulation results demonstrate the effectiveness and superiority of DCC.

The increasing use of electronic components in today&rsquo / s automobiles demands more powerful in-vehicle network communication protocols. FlexRay protocol, which is expected to be the de-facto standard in the near future, is a deterministic, fault tolerant and fast protocol designed for in vehicle communication. The current de-facto in-vehicle communication standard, CAN, and the future in-vehicle communication standard FlexRay will exist together in future cars. Data exchange between these two standards will be performed via Gateway units. In this thesis, end-to-end performance of a FlexRay-CAN network connected by a Gateway is evaluated as well as Gateway functionality and processing delay. The results of the experiments, which are performed for a realistic message set with various scheduling schemes, are presented and discussed.

Quality of Service (QoS) in real-time media applications can be defined as the ability to guarantee the delivery of packets from source to destination over best-effort networks within some constraints. These constraints defined as the QoS metrics are end-to-end packet delay, delay jitter, throughtput, and packet losses. Transporting real-time media applications over best-effort networks, e.g. the Internet, is an area of current research. Both the Transmission Control Protocol (TCP) and the User Datagram Protocol (UDP) have failed to provide the desired QoS. This research aims at developing application-level end-to-end QoS controls to improve the user-perceived quality of real-time media applications over best-effort networks, such as, the public Internet. In this research an end-to-end packet based approach is developed. The end-to- end packet based approach consists of source buffer, network simulator ns-2, destina- tion buffer, and controller. Unconstrained model predictive control (MPC) methods are implemented by the controller at the application layer. The end-to-end packet based approach uses end-to-end network measurements and predictions as feedback signals. Effectiveness of the developed control methods are examined using Matlab and ns-2. The results demonstrate that sender-based control schemes utilizing UDP at transport layer are effective in providing QoS for real-time media applications transported over best-effort networks. Significant improvements in providing QoS are visible by the reduction of packet losses and the elimination of disruptions during the playback of real-time media. This is accompanied by either a decrease or increase in the playback start-time.

The paradigm of separate source-channel coding is inspired by Shannon's separation result, which implies the asymptotic optimality of designing source and channel coding independently from each other. The result exploits the fact that channel error probabilities can be made arbitrarily small, as long as the block length of the channel code can be made arbitrarily large. However, this is not possible in practice, where the block length is either fixed or restricted to a range of finite values. As a result, the optimality of source and channel coding separation becomes unknown, leading researchers to consider joint source-channel coding (JSCC) to further improve the performance of practical systems that must operate in the finite block length regime. With this motivation, this thesis investigates the application of JSCC principles for multimedia communications over point-to-point, broadcast, and relay channels. All analyses are conducted from the perspective of end-to-end distortion (EED) for results that are applicable to channel codes with finite block lengths in pursuing insights into practical design. The thesis first revisits the fundamental open problem of the separation of source and channel coding in the finite block length regime. Derived formulations and numerical analyses for a source-channel coding system reveal many scenarios where the EED reduction is positive when pairing the channel-optimized source quantizer (COSQ) with an optimal channel code, hence establishing the invalidity of the separation theorem in the finite block length regime. With this, further improvements to JSCC systems are considered by augmenting error detection codes with the COSQ. Closed-form EED expressions for such system are derived, from which necessary optimality conditions are identified and used in proposed algorithms for system design. Results for both the point-to-point and broadcast channels demonstrate significant reductions to the EED without sacrificing bandwidth when considering a tradeoff between quantization and error detection coding rates. Lastly, the JSCC system is considered under relay channels, for which a computable measure of the EED is derived for any relay channel conditions with nonzero channel error probabilities. To emphasize the importance of analyzing JSCC systems under finite block lengths, the large sub-optimality in performance is demonstrated when solving the power allocation configuration problem according to capacity-based formulations that disregard channel errors, as opposed to those based on the EED. Although this thesis only considers one JSCC setup of many, it is concluded that consideration of JSCC systems from a non-asymptotic perspective not only is more meaningful, but also reveals more relevant insight into practical system design. This thesis accomplishes such by maintaining the EED as a measure of system performance in each of the considered point-to-point, broadcast, and relay cases.

Marine ecosystem-based management requires end to end models, which are models capable of representing the entire ecosystem including physical, chemical and biological processes, anthropogenic activities, and multiple species with different sizes, life histories and from different trophic levels. To adequately represent ecosystem dynamics in shallow coastal regions, end-to-end models may need to include macrobiota species (wild and aquacultured) and may have to allow feedbacks (i.e. two-way coupling) between macrobiota and planktonic ecosystem dynamics. This is because the biomass of macrobiota can locally exceed the biomass of plankton, thus influencing the distribution of planktonic ecosystem tracers and altering the overall food web structure. Here, I describe a hybrid (Eulerian/Individual-Based) ecosystem framework, implemented in the Regional Ocean Modeling System (ROMS), a state-of-the-art 3-D ocean circulation model. The framework was applied to a model of a synthetic embayment containing seagrass, rockweed and kelp beds, a wild oyster reef, a mussel ranch and a fish farm. I found that two-way coupling is essential to reproduce expected spatial patterns of all variables and to conserve mass in the system. I also developed a shellfish ecophysiology model (SHELL E) and compared its results against water samples collected over 5 years in Ship Harbour, a fjord with mussel aquaculture in Nova Scotia, Eastern Canada. Also, from a high-resolution bio-optical survey of the fjord, I found that mussels decrease phytoplankton biomass inside the farm, but also cause a bloom of phytoplankton outside the farm. Using ROMS/SHELL-E, I determined that the increase of phytoplankton around the farm is caused by the waste products of the farmed bivalves, which have a fertilization effect, enhancing phytoplankton production outside the farm during nutrient-limited and light-replete conditions (i.e. late spring to late fall in Ship Harbour). The main conclusion of this thesis is that—in shallow coastal regions—ecosystem models must represent bilateral interactions between macrobiota and physical-planktonic dynamics, in a spatially-explicit setting, to adequately represent mass flows and ecosystem dynamics. The hybrid end-to-end modelling system provides a computationally efficient framework for describing these interactions and, through careful comparisons against observations, can be a powerful tool to test hypotheses and generate insights into coastal ecosystems.

Internet applications make use of the services provided by a transport protocol, such as TCP (a reliable, in-order stream protocol). We use this term Transport Service to mean the end-to- end service provided to application by the transport layer.   That service can only be provided correctly if information about the intended usage is supplied from the application. The application may determine this information at the design time, compile time, or run time, and it may include guidance on whether a feature is required, a preference by the application, or something in between. Multipath TCP (MPTCP) adds the capability of using multiple paths to a regular TCP session. Even though it is designed to be totally backward compatible to applications. The data transport differs compared to regular TCP, and there are several additional degrees of freedom that the particular application may want to exploit.   Multipath TCP is particularly useful in the context of wireless networks using both Wi-Fi and a mobile network is a typical use case. In addition to the gains in throughput from inverse multiplexing, links may be added or dropped as the user moves in or out of coverage without disrupting the end-to-end TCP connection. The problem of link handover is thus solved by abstraction in the transport layer, without any special mechanisms at the network or link level.   Handover functionality can then be implemented at the endpoints without requiring special functionality in the sub-networks according to the Internet's end-to-end principle. Multipath TCP can balance a single TCP connection across multiple interfaces and reach very high throughput.

Internet applications make use of the services provided by a transport protocol, such as TCP (a reliable, in-order stream protocol). We use the term Transport Service to mean the endtoend service provided to application by the transport layer. That service can only be provided correctly if information about the intended usage is supplied from the application. The application may determine this information at the design time, compile time, or run time, and it may include guidance on whether a feature is required, a preference by the application, or something in between. Multipath TCP (MPTCP) adds the capability of using multiple paths to a regular TCP session. Even though it is designed to be totally backward compatible to applications. The data transport differs compared to regular TCP, and there are several additional degrees of freedom that the particular application may want to exploit. Multipath TCP is particularly useful in the context of wireless networks using both Wi-Fi and a mobile network is a typical use case. In addition to the gains in throughput from inverse multiplexing, links may be added or dropped as the user moves in or out of coverage without disrupting the end-to-end TCP connection. The problem of link handover is thus solved by abstraction in the transport layer, without any special mechanisms at the network or link level. Handover functionality can then be implemented at the endpoints without requiring special functionality in the sub-networks according to the Internet's end-to-end principle. Multipath TCP can balance a single TCP connection across multiple interfaces and reach very high throughput.

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Wireless sensor networks have arrived because of further developments of themodern Internet, and this has been considered to be one of the most importanttechnologies of the 21st century. Currently, the wireless sensor network has becomean important technology in a variety of areas and is widely used in thefield of national defense, national security, environmental monitoring, trafficmanagement, anti-terrorism, anti-disaster, and so on. The majority of these applicationsrequire real-time communication as the WSNs are required to sendthe data to the data center within a specified time. In order to meet the real-timedemand for wireless sensor networks, this work mainly focuses on the analysisand measurement of the end-to-end delay, including both single-hop and multihopdelays. This thesis first analyzes the composition of the end-to-end delayand then describes the end-to-end delay measurement algorithms and methods.The measurement is implemented in TelosB motes within TinyOS. Finally thereport will show the evaluation of the end-to-end delay in wireless sensor networks.