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A Cooperative Cognitive Radio (CCR) network, which integrates a conventional cooperative system and cognitive radios (CRs) into a holistic system, is a promising paradigm for the next generation mobile communication systems. The spectral efficiency, power efficiency, bandwidth reduction and system complexity in CCR networks are the fundamental parameters of our system design and optimization. In this thesis, we focus our attention on opportunistically exploiting the underutilized spectrum band in the CR network with the aid of cooperative protocols. Furthermore, we invoke channel coding schemes in our CCR system in order to improve the overall system throughput. In our CCR system, the overlay based cooperation scheme of Primary Users (PUs) and Cognitive Users (CUs) is considered, which has the potential of leading to a transmission power reduction and transmission rate improvement for both the PU and the CU. More explicitly, our cooperative protocol allows a group of CUs to serve as Relay Nodes (RNs) for relaying the signal of the PUs’ transmitters to the PUs’ intended destinations. To elaborate further, both one way relaying and two-way relaying schemes are used in our proposed system, so that the bandwidth requirement of the PUs is reduced. Alternatively, the freed bandwidth may be leased to a group of CUs for their secondary communications. Our numerical and simulation results show that the bandwidth reduction attained by the proposed two-way relaying based CR scheme may approach as much as 80% of the PU’s bandwidth. Moreover, an Adaptive Dynamic Network Coding (ADNC) scheme is also conceived for this overlay CCR system, which is designed for supporting communications between multiple PUs and a common Base Station (BS). More particularly, the near-instantaneously Adaptive Turbo Trellis Coded Modulation (ATTCM) is employed for appropriately adjusting both the modulation mode as well as the channel coding rate and the network coding rate, according to the near-instantaneous channel conditions. In order to facilitate the recovery of the source information at the BS, the CUs invoke the ADNC technique, which is assisted by our cooperative protocol operating by exchanging the CCR-based control information between the near-instantaneously ATTCM and network coding codec as well as between the CUs and the BS. Additionally, the network encoder may also be activated in its adaptive mode for supporting the CUs, depending on the Boolean value of the feedback flags generated based on the success/failure of the ATTCMdecoder and of the network decoder, which is evaluated and fed back by the BS. Quantitatively, it was found that the joint holistic design of our ATTCM-ADNC-CCR scheme is either capable of freeing up an approximately 40% of the PU’s bandwidth in comparison to its non-cooperative counterpart, or increasing the attainable throughput by as much as 2 bit/symbol. Furthermore, a Pragmatic Distributed Algorithm (PDA) is proposed for supporting the efficient spectral access of multiple PUs and CUs in CCR networks. The novelty of our PDA is that the Pus negotiate with the CUs concerning the specific amount of relaying and transmission time, and the CU will decide either to accept or to decline this offer. These CUs relay the signal received from the PUs to the PUs’ receiver, but only when both the PUs’ and the CUs’ minimum rate requirements are satisfied. Moreover, we show that the cooperative spectral access based on our PDA reaches an equilibrium, when it is repeated for a sufficiently long duration. These benefits are achieved, because the PUs are motivated to cooperate by the incentive of achieving a higher PU rate, whilst defecting from cooperation can be discouraged with the aid of a limited-duration punishment. Therefore, our proposed PDA outperforms the benchmark, despite its significantly lower overhead and lower complexity. Finally, we present the joint design of coding, modulation, user-cooperation and CR techniques, which may lead to significant mutual benefits for both the PUs and the CUs.

The primary motor cortex (M1) is known for its general static correspondence between body parts and clustered sites on the physical cortical sheet – the somatotopic map. Under this view, it’s tempting to believe that the orchestration of motor output in M1 is as rigid as manipulating the movement of a marionette, where a fixed set of strings would reliably dictate the movements of corresponding body parts of the puppet. In this thesis work, we argue that motor representation on the M1 cortical sheet is in fact dynamic, from two perspectives: (1) the relationship between neural activity and muscle output is dynamic along movement execution; (2) the information-bearing neural activity itself is dynamically patterned across the cortical sheet during movement execution. The first part of the work shows that, rather than being a static mapping, the relationship between neural activity and muscle output is constantly evolving during simple point-to-point reaches. Any given location on the cortical sheet bears the most information about different muscles at different times; any muscle is represented by different cortical locations at different times. Furthermore, this dynamic representation is movement-specific and most stable around movement onset, possibly serving functional needs. These dynamics happen at significantly shorter time scales than training-induced neural plasticity, presumably reflecting neural multiplexing unfolding over time. The second part of the work shows that during movement execution M1 recruits spatially organized patterns of activity across the cortical sheet in a behaviorally specific manner. In particular, recruitment times form planar propagating patterns across the cortical sheet. The directions of those propagating patterns differ systematically according to reach directions, bearing important kinematic information. This finding expands the repertoire of spatio-temporally complex neural codes and points to their potential facilitative roles in neural computation. Together, this work speaks to the dynamic motor representation of the physical M1 cortical sheet. The effects that cortical activities have on the motor outputs are best understood by considering the interplay between space and time in characterizing population neural activity, and by considering the dynamic mapping between the cortex and effectors.

Epstein Barr-virus (EBV) is a ubiquitous herpesvirus that causes infectious mononucleosis and is associated with a variety of human cancers. Ordinarily, EBV persists in healthy individuals by establishing latent infection in the B-cell compartment. Immunosuppression can result in unchecked outgrowth of latently infected cells, culminating in lymphoproliferative disorders and lymphomas. How EBV induces and supports the physiological shift from quiescence to long-term growth and proliferation as modeled by in vitro lymphoblastic transformation is unknown. Multiplexed proteomics on de novo infected primary B-cells was performed to uncover metabolic and signaling pathways that facilitate outgrowth and survival of B-cells latently infected with EBV. By combining chemical inhibitor studies and clustered regularly interspaced short palindromic repeats (CRISPR) genetic perturbation experiments, we discovered viral upregulation of mitochondrial one-carbon (1C) metabolism and de novo synthesis of serine, cholesterol and fatty acids, to be crucial for EBV-positive B-cell proliferation and viability. We demonstrated that mitochondrial 1C metabolism broke down serine to generate formate for nucleotide synthesis, glycine for glutathione production and cellular reducing power in the form of NADPH. We also showed that intramitochondrial NADPH was important for efficient LCL proliferation. De novo serine synthesis (DNSS) may augment 1C metabolism and/or buffer the infected cells from external fluctuations in serine availability. Both mitochondrial 1C metabolism and DNSS depended on EBV-encoded nuclear antigen 2 (EBNA2) and its target MYC for activation. EBV-infected cells also utilized cholesterol and fatty acid synthetic pathways to produce geranylgeranyl pyrophosphate (GGPP) and palmitate, respectively, to reorganize the signaling milieu of the transforming cell. Rab geranylgeranyltransferase was specifically required for EBV-positive B-cell outgrowth and proliferation. We also identified RAB13 as a potent driver of latently infected cell growth and survival, whose expression was driven by EBNA3C and likely functioned as a chaperone for viral latent membrane proteins (LMPs) to maintain the latter’s oncogenic signaling capacities. Taken altogether, our results provide an expansive investigation into the pathways that underlie the transformative change of a B lymphocyte from quiescence to activation and growth and identify vulnerabilities in EBV-driven lymphoblastic disorders that may represent new therapeutic targets.

Electrostatic Discharge (ESD) has been one of the major reliability concerns in the advanced silicon technologies and it becomes more important with technology scaling. It has been reported that more than 35% of the failures in integrated circuits (ICs) are ESD induced. ESD event is a phenomenon that a finite amount of charges transfer between two objects with different potential in a quite short time. Such event contains a large energy and the ICs without proper ESD protection could be destroyed easily, so ESD protection solutions are essential to semiconductor industry. ESD protection design consists of on-chip and off-chip ESD protection design, and the research works in this dissertation are all conducted in on-chip level, which incorporate the ESD protection devices and circuits into the microchip, to provide with basic ESD protection from manufacturing to customer use. The basic idea of ESD protection design is to provide a path with low impedance which directs most of the ESD current to flow through itself instead of the core circuit, and the ESD protection path must be robust enough to make sure that it does not fail before the core circuit. In this way, proper design on protection devices and circuits should be considered carefully. To assist the understanding and design of ESD protection, the ESD event in real world has been classified into a few ESD model including Human Body Model (HBM), Machine Model (MM), Charged Device Model (CDM), etc. Some mainstream testing method and industry standard are also introduced, including Transmission Line Pulse (TLP), and IEC 61000-4-2. ESD protection devices including diode, Gate-Grounded N-type MOSFET (GGNMOS), Silicon Controlled Rectifier (SCR) are basic elements for ESD protection design. In this dissertation, the device characteristics in ESD event and their applications are introduced. From the perspective of the whole chip ESD protection design, the concept of circuit level ESD protection and the ESD clamps are also briefly introduced. Technology Computer Aided Design (TCAD) and Simulation Program with Integrated Circuit Emphasis (SPICE) simulation is widely used in ESD protection design. In this dissertation, TCAD and SPICE simulation are carried out for a few times for both of pre-tapeout evaluation on characteristics of the proposed device and circuit and post-tapeout analysis on structure operating mechanism. Automotive electronics has been a popular subject in semiconductor industry, and due to the special requirement of the automotive applications like the capacitive pins, the ESD protection device used in such applications need to be specially designed. In this dissertation, a few SCRs without snapback are discussed in detail. To avoid core circuit damages caused the displacement current induced by the large snapback in conventional SCR, an eliminated/minimized snapback is preferred in a selection of the protection device. Two novel SCRs are proposed for High Voltage (HV), Medium Voltage (MV), and Low Voltage (LV) automotive ESD protection. The typical operating temperature for ICs is up to 125°C, however in automotive applications, the operating temperature may extend up to 850°C. In this way, the characteristics of the ESD protection device under the elevated temperatures will be an essential part to investigate for automotive ESD protection design. In this dissertation, the high temperature characteristics of ESD protection devices including diode and a few SCRs is measured and discussed in detail. TCAD simulation are also conducted to explain the underlying physical mechanism. This work provides with a useful insight and information to ESD protection design in high temperature applications. Besides the high temperature environment, ESD protection are also highly needed for electronics working in other extreme environment like the space. Space is an environment that contains kinds of radiation source and at the same time can generate abundant ESD. The ESD adhering to the space systems could be a potential threat to the space electronics. At the same time, the characteristics of the ESD protection part especially the basic protection device used in the space electronics could be influenced after the irradiation in the space. Therefore, the investigation of the radiation effects on ESD protection devices are necessary. In this dissertation, the total ionizing dose (TID) effects on ESD protection devices are investigated. The devices are irradiated with 1.5 MeV He+ and characterized with TLP tester. The pre- and post-irradiation characteristics are compared and the variation on key ESD parameters are analyzed and discussed. This work offers a useful insight on ESD devices' operation under TID and help with the device designing on ESD protection devices for space electronics. Single ESD protection devices are essential part constructing the ESD protection network, however the optimization on ESD clamp circuit design is also important on building an efficient whole chip ESD protection network. In this dissertation, the design and simulation of a novel voltage triggered ESD detection circuit are introduced. The voltage triggered ESD detection circuit is proposed in a 0.18 um CMOS technology. Comparing with the conventional RC based detection circuit, the proposed circuit realizes a higher triggering efficiency with a much smaller footprint, and is immune to false triggering under fast power-up events. The proposed circuit has a better sensitivity to ESD event and is more reliable in ESD protection applications. The leakage current has been a concern with the scaling down of the thickness of the gate oxide. Therefore, a proper design of the ESD clamp for power rail ESD protection need to be specially considered. In this dissertation, a design of a novel ESD clamp with low leakage current is analyzed. The proposed clamp realized a pretty low leakage current up to 12 nA, and has a smaller footprint than conventional design. It also has a long hold-on time under ESD event and a quick turn-off mechanism for false triggering. SPICE simulation is carried out to evaluate the operation of the proposed ESD clamp.

Heating, ventilation and air conditioning (HVAC) is a mechanical system that provides thermal comfort and accepted indoor air quality often instrumented for large-scale buildings. The HVAC system takes a dominant portion of overall building energy consumption and accounts for 50% of the energy used in the U.S. commercial and residential buildings in 2012. The performance and energy saving of building HVAC systems can be significantly improved by the implementation of better and smarter control strategies. Therefore, it is of great benefits to develop automatic, intelligent, optimal and consistent model and control tools to ensure the normal operations of HVAC systems and increase the building energy efficiency.Motivated by these goals, this thesis presents a parametric modeling approach and a system-level control design for HVAC systems. For the modeling, we establish dynamical models for return air for the air-handiling-unit (AHU) of HVAC systems. The models include temperature and air flow rate models. These models follow the structure of the finite impulse response (FIR) model, and explicitly include the control variables from the AHU, the dynamical states, and the disturbances. Therefore, it is easy to apply this model to control design. Also, the model is flexible with prediction horizon and control horizon with a stability of the accuracy. In data processing, a convolution based low-pass digital filter, Savitzky-Golay filter is used for data smoothing. As a result, the return air flow rate model becomes more feasible with the smoothed data.Secondly, this thesis study develops a model preidctive control (MPC) algorithm with the application of the dynamical models for AHU optimization problems. This control strategy optimizes the energy consumption of the AHU, and tracks the set points the room temperatures, supply air flow and return air flow rate of the building. The strategy provides physical-based inherent connection between components in AHU by applying damper positions, supply air temperature and outside air flow rate as manipulated variables. The control inputs are explicitly implemented into both the models and objective functions and the optimization structure is computationally efficient. The optimal results show an energy saving average percentage over and track the supply air flow rate and set point of room temperatures in the building effectively. The thermal load, supply air flow rate set points are calculated from thirty-two VAVs, that ensures the internal cooling demand, the static pressure and the ventilation level of the building.In this thesis, all the data processing and modeling, model validation and implementation of the control algorithm are based on extensive data measurements collected from an office building on the campus of the University of California, at Merced. The control strategy is implemented into the online building automation system (BAS) of the building and can be easily incorporated with other BAS as well because of the explicit formulation.

In order to meet increasingly stringent total nitrogen limits, supplemental carbon must be added to improve the performance of the biological nutrient removal process. An industrial by-product that contained ethylene glycol and propylene glycol was used as a substitute carbon source for methanol in this study. The objectives of this study were to investigate the efficiency of using the glycol mixture as carbon source, including the calculation of denitrification rate and yield at two different initial concentrations of glycols. Possible inhibition effect on nitrification was also investigated. Three SBR reactors were operated by adding methanol, a low dosage of glycol, and a high dosage of glycol into the reactors. The low dosage glycol reactor exhibited the best performance, with the highest denitrification rate of 11.55 mg NOx-N/g MLVSS"h and the lowest yield of 0.21 mg VSS/mg COD. Small nitrite accumulation was observed in the low dosage glycol reactor (COD=185"•15 mg/L), but effluent quality was not influenced. Excess glycol in the reactor caused deteriorated performance. The high dosage glycol reactor (COD=345"•20 mg/L) performed with the lowest denitrfication rate of 8.56 mg NOx-N/g MLVSS"h and the highest yield of 0.55 mg VSS/ mg COD. The reactor with the high dosage of glycol also inhibited the lowest nitrification rate of 1.15 mg NH3-N oxidized/g MLVSS"h, which indicated that excess glycol may cause nitrification inhibition.

In a highly populated area such as university campus, there is limited space available to implement green solution outside the buildings. Roof tops provide opportunities to implement solution that can reduce the net emission of the building operation. However, they might come with a high capital cost and higher life-cycle emissions. By comparing the installation of three different building energy-saving technologies on a roof top of a 6640 ft2 education building located in Midwest area, we found that green roof is the best option of the green solutions considered. Green roof has the least negative net present value that ranges from -$95,423 to -$93,381 and a reduction of 595.16 metric tons of life-cycle CO2 emissions, the highest among the three. For asphalt roof, the net present value ranges from -$103,020 to -$102,730 and reduction of 579.21 metric tons of life-cycle CO2 emissions. Photovoltaic (PV) system is the most costly option. If we assume the efficiency of the PV system increases by 10 percent every decade without adding any capital cost, the net present value will range from -$340,132.17 to -$317,366.04 and the life-cycle CO2 emissions will increase by 605.69 metric tons. On the other hand, if the efficiency does not improve, the net present value will range from -$342,365.46 to -$321,828.95 and the life-cycle CO2 emissions will be 718.14 metric tons.

The increasing demand for ubiquitous Internet services imposes more security threats to communications due to open mediums in wireless networks. Thus, security mechanisms are proposed to protect communications, while putting more overheads on the transmission. As one of most widely used security mechanisms, authentication is used to identify mobile nodes (MNs), prevent unauthorized usage, and negotiate credentials with heavy overhead. Nevertheless, authentication mechanisms also induce heavy burdens, such as encryption/decryption load and long delay, in wireless networks. Although some solutions are proposed to reduce the burdens caused by the authentication, there have been little quantitative analysis, flexible protocol design, and optimized architecture implementation on the authentication that are adaptive to the quality of service (QoS) up to date. In this thesis, we propose in-depth design and analysis of the authentication protocol and architecture to improve the authentication efficiency, such as delay and call dropping probability, in single- and multi-hop wireless networks. In the single-hop wireless networks, we first analyze the impact of authentication on the security and QoS quantitatively. Then, we present enhanced protocols for net-to-net and mobile-to-net authentication on hierarchical authentication architecture (HAA), which is the most widely used in wireless networks. The enhanced protocols are designed with the dynamic security associations (SAs) based on different functions of metrics to reduce the authentication delay and cost. Moreover, considering that HAA is not sufficient to network manageability and security, we further propose a new architecture with two control schemes for net-to-net and mobile-to-net authentication. The architecture is composed of licensed authentication centers and intelligent control schemes based on a utility function. The design of this architecture is effective to reducing the authentication latency, improving network scalability, and enhancing the network security in terms of reducing the number of SAs when inter-domain roaming happens. In the multi-hop wireless networks, we propose reliable clustering algorithms to improve the service availability, which can cooperate with the proposed authentication protocols between clusters. In this design, the energy consumption and mobility of nodes are evaluated quantitatively, and the proposed authentication protocols are entangled with the construction of hierarchical clusters dynamically, which is not only able to handle the failure of nodes efficiently, but also able to guarantee the security even from the start of constructing network architectures when mobile nodes frequently join and leave the multi-hop wireless networks. As shown in the numerical and simulation results, by improving the authentication efficiency, such as delay and call dropping probability, in single- and multi-hop wireless networks significantly, our research demonstrates an in-depth impact of authentication on security and QoS in wireless networks, and builds a solid ground for future improvement of authentication protocols and architectures.

This thesis introduces three new feature selection methods based on sequential orthogonal search strategy that addresses three different contexts of feature selection problem being considered. The first method is a supervised feature selection called the maximum relevance–minimum multicollinearity (MRmMC), which can overcome some shortcomings associated with existing methods that apply the same form of feature selection criterion, especially those that are based on mutual information. In the proposed method, relevant features are measured by correlation characteristics based on conditional variance while redundancy elimination is achieved according to multiple correlation assessment using an orthogonal projection scheme. The second method is an unsupervised feature selection based on Locality Preserving Projection (LPP), which is incorporated in a sequential orthogonal search (SOS) strategy. Locality preserving criterion has been proved a successful measure to evaluate feature importance in many feature selection methods but most of which ignore feature correlation and this means these methods ignore redundant features. This problem has motivated the introduction of the second method that evaluates feature importance jointly rather than individually. In the method, the first LPP component which contains the information of local largest structure (LLS) is utilized as a reference variable to guide the search for significant features. This method is referred to as sequential orthogonal search for local largest structure (SOS-LLS). The third method is also an unsupervised feature selection with essentially the same SOS strategy but it is specifically designed to be robust on noisy data. As limited work has been reported concerning feature selection in the presence of attribute noise, the third method is thus attempts to make an effort towards this scarcity by further exploring the second proposed method. The third method is designed to deal with attribute noise in the search for significant features, and kernel pre-images (KPI) based on kernel PCA are used in the third method to replace the role of the first LPP component as the reference variable used in the second method. This feature selection scheme is referred to as sequential orthogonal search for kernel pre-images (SOS-KPI) method. The performance of these three feature selection methods are demonstrated based on some comprehensive analysis on public real datasets of different characteristics and comparative studies with a number of state-of-the-art methods. Results show that each of the proposed methods has the capacity to select more efficient feature subsets than the other feature selection methods in the comparative studies.

The research work presented on this thesis provides an alternative tool for characterising oil fields under fluid injection by analysing historical production/injection rates. In particular polynomial and radial basis Non Linear Autoregressive with Exogenous Input Model (NARX) models were developed; these models were capable of capturing the dynamics of an operating field in the North Sea. A Greedy Randomised Adaptive Search Procedure (GRASP) heuristic optimisation method was applied for estimating a future injection strategy. This approach is combined with a risk analysis methodology, a popular approach in financial mathematics. As a result, it is possible to estimate how likely it is to reach a production goal. According to the simulations, it is possible to increase oil production by 10% in one year by implementing a smart injection strategy with low statistical uncertainty. Resulting from this research project, a computational tool was developed. It is now possible to estimate NARX models from any field under fluid injection as well as finding the best future injection scenario.