Efficient -tensor determination and NH assignment of paramagnetic proteins

Anisotropic magnetic susceptibility tensors chi of paramagnetic metal ions are manifested in pseudocontact shifts, residual dipolar couplings, and other paramagnetic observables that present valuable long-range information for structure determinations of protein-ligand complexes. A program was developed for automatic determination of the chi-tensor anisotropy parameters and amide resonance assignments in proteins labeled with paramagnetic metal ions. The program requires knowledge of the three-dimensional structure of the protein, the backbone resonance assignments of the diamagnetic protein, and a pair of 2D N-15-HSQC or 3D HNCO spectra recorded with and without paramagnetic metal ion. It allows the determination of reliable chi-tensor anisotropy parameters from 2D spectra of uniformly N-15-labeled proteins of fairly high molecular weight. Examples are shown for the 185-residue N-terminal domain of the subunit epsilon from E. coli DNA polymerase III in complex with the subunit theta and La3+ in its diamagnetic and Dy3+, Tb3+, and Er3+ in its paramagnetic form.

Vehicle routing and crew scheduling for metropolitan mail distribution at Australia Post

This paper presents a new multi-depot combined vehicle and crew scheduling algorithm, and uses it, in conjunction with a heuristic vehicle routing algorithm, to solve the intra-city mail distribution problem faced by Australia Post. First we describe the Australia Post mail distribution problem and outline the heuristic vehicle routing algorithm used to find vehicle routes. We present a new multi-depot combined vehicle and crew scheduling algorithm based on set covering with column generation. The paper concludes with a computational investigation examining the affect of different types of vehicle routing solutions on the vehicle and crew scheduling solution, comparing the different levels of integration possible with the new vehicle and crew scheduling algorithm and comparing the results of sequential versus simultaneous vehicle and crew scheduling, using real life data for Australia Post distribution networks.

Molecular identification of 26 syntaxin genes and their assignment to the different trafficking pathways in Paramecium

SNARE proteins have been classified as vesicular (v)- and target (t)-SNAREs and play a central role in the various membrane interactions in eukaryotic cells. Based on the Paramecium genome project, we have identified a multigene family of at least 26 members encoding the t-SNARE syntaxin (PtSyx) that can be grouped into 15 subfamilies. Paramecium syntaxins match the classical build-up of syntaxins, being 'tail-anchored' membrane proteins with an N-terminal cytoplasmic domain and a membrane-bound single C-terminal hydrophobic domain. The membrane anchor is preceded by a conserved SNARE domain of approximately 60 amino acids that is supposed to participate in SNARE complex assembly. In a phylogenetic analysis, most of the Paramecium syntaxin genes were found to cluster in groups together with those from other organisms in a pathway-specific manner, allowing an assignment to different compartments in a homology-dependent way. However, some of them seem to have no counterparts in metazoans. In another approach, we fused one representative member of each of the syntaxin isoforms to green fluorescent protein and assessed the in vivo localization, which was further supported by immunolocalization of some syntaxins. This allowed us to assign syntaxins to all important trafficking pathways in Paramecium.

Adaptive Routing and Multi-Agent Control for Information Flows in IP-Networks

The principles of adaptive routing and multi-agent control for information flows in IP-networks.

Impact of inter-modal four-wave mixing on the performance of mode- and wavelength-division-multiplexing systems

In this paper, we investigate the impact of inter-modal four-wave mixing on mode- and wavelength-division-multiplexing systems. A set of coupled nonlinear Schrödinger equations, including linear mode coupling, is derived allowing to isolate the inter-modal four-wave mixing terms. The efficiency of inter-modal four-wave mixing between degenerate LP modes is found to be significantly higher than the intra-modal four-wave mixing efficiency. However, it is shown that the inter-modal four-wave mixing efficiency between degenerate modes is significantly reduced by the linear mode coupling.

Secure routing and trust computation in multihop infrastructureless networks

Today's wireless networks rely mostly on infrastructural support for their operation. With the concept of ubiquitous computing growing more popular, research on infrastructureless networks have been rapidly growing. However, such types of networks face serious security challenges when deployed. This dissertation focuses on designing a secure routing solution and trust modeling for these infrastructureless networks. ^ The dissertation presents a trusted routing protocol that is capable of finding a secure end-to-end route in the presence of malicious nodes acting either independently or in collusion, The solution protects the network from active internal attacks, known to be the most severe types of attacks in an ad hoc application. Route discovery is based on trust levels of the nodes, which need to be dynamically computed to reflect the malicious behavior in the network. As such, we have developed a trust computational model in conjunction with the secure routing protocol that analyzes the different malicious behavior and quantifies them in the model itself. Our work is the first step towards protecting an ad hoc network from colluding internal attack. To demonstrate the feasibility of the approach, extensive simulation has been carried out to evaluate the protocol efficiency and scalability with both network size and mobility. ^ This research has laid the foundation for developing a variety of techniques that will permit people to justifiably trust the use of ad hoc networks to perform critical functions, as well as to process sensitive information without depending on any infrastructural support and hence will enhance the use of ad hoc applications in both military and civilian domains. ^

Routing and dimensioning of 3G multi-service networks

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Routing and dimensioning of 3G multi-service networks

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

JOINT ENERGY BEAMFORMING AND TIME ASSIGNMENT FOR COOPERATIVE WIRELESS POWERED NETWORKS

Wireless power transfer (WPT) and radio frequency (RF)-based energy har- vesting arouses a new wireless network paradigm termed as wireless powered com- munication network (WPCN), where some energy-constrained nodes are enabled to harvest energy from the RF signals transferred by other energy-sufficient nodes to support the communication operations in the network, which brings a promising approach for future energy-constrained wireless network design. In this paper, we focus on the optimal WPCN design. We consider a net- work composed of two communication groups, where the first group has sufficient power supply but no available bandwidth, and the second group has licensed band- width but very limited power to perform required information transmission. For such a system, we introduce the power and bandwidth cooperation between the two groups so that both group can accomplish their expected information delivering tasks. Multiple antennas are employed at the hybrid access point (H-AP) to en- hance both energy and information transfer efficiency and the cooperative relaying is employed to help the power-limited group to enhance its information transmission throughput. Compared with existing works, cooperative relaying, time assignment, power allocation, and energy beamforming are jointly designed in a single system. Firstly, we propose a cooperative transmission protocol for the considered system, where group 1 transmits some power to group 2 to help group 2 with information transmission and then group 2 gives some bandwidth to group 1 in return. Sec- ondly, to explore the information transmission performance limit of the system, we formulate two optimization problems to maximize the system weighted sum rate by jointly optimizing the time assignment, power allocation, and energy beamforming under two different power constraints, i.e., the fixed power constraint and the aver- age power constraint, respectively. In order to make the cooperation between the two groups meaningful and guarantee the quality of service (QoS) requirements of both groups, the minimal required data rates of the two groups are considered as constraints for the optimal system design. As both problems are non-convex and have no known solutions, we solve it by using proper variable substitutions and the semi-definite relaxation (SDR). We theoretically prove that our proposed solution method can guarantee to find the global optimal solution. Thirdly, consider that the WPCN has promising application potentials in future energy-constrained net- works, e.g., wireless sensor network (WSN), wireless body area network (WBAN) and Internet of Things (IoT), where the power consumption is very critical. We investigate the minimal power consumption optimal design for the considered co- operation WPCN. For this, we formulate an optimization problem to minimize the total consumed power by jointly optimizing the time assignment, power allocation, and energy beamforming under required data rate constraints. As the problem is also non-convex and has no known solutions, we solve it by using some variable substitutions and the SDR method. We also theoretically prove that our proposed solution method for the minimal power consumption design guarantees the global optimal solution. Extensive experimental results are provided to discuss the system performance behaviors, which provide some useful insights for future WPCN design. It shows that the average power constrained system achieves higher weighted sum rate than the fixed power constrained system. Besides, it also shows that in such a WPCN, relay should be placed closer to the multi-antenna H-AP to achieve higher weighted sum rate and consume lower total power.

Computer Aided Design Algorithmic Technique for Very Large Scale Integrated Circuit Design and Smart Home Embedded System Design

To tackle the challenges at circuit level and system level VLSI and embedded system design, this dissertation proposes various novel algorithms to explore the efficient solutions. At the circuit level, a new reliability-driven minimum cost Steiner routing and layer assignment scheme is proposed, and the first transceiver insertion algorithmic framework for the optical interconnect is proposed. At the system level, a reliability-driven task scheduling scheme for multiprocessor real-time embedded systems, which optimizes system energy consumption under stochastic fault occurrences, is proposed. The embedded system design is also widely used in the smart home area for improving health, wellbeing and quality of life. The proposed scheduling scheme for multiprocessor embedded systems is hence extended to handle the energy consumption scheduling issues for smart homes. The extended scheme can arrange the household appliances for operation to minimize monetary expense of a customer based on the time-varying pricing model.

Vehicle routing and location routing problems with minimum latency: algorithms and models

Latency can be defined as the sum of the arrival times at the customers. Minimum latency problems are specially relevant in applications related to humanitarian logistics. This thesis presents algorithms for solving a family of vehicle routing problems with minimum latency. First the latency location routing problem (LLRP) is considered. It consists of determining the subset of depots to be opened, and the routes that a set of homogeneous capacitated vehicles must perform in order to visit a set of customers such that the sum of the demands of the customers assigned to each vehicle does not exceed the capacity of the vehicle. For solving this problem three metaheuristic algorithms combining simulated annealing and variable neighborhood descent, and an iterated local search (ILS) algorithm, are proposed. Furthermore, the multi-depot cumulative capacitated vehicle routing problem (MDCCVRP) and the multi-depot k-traveling repairman problem (MDk-TRP) are solved with the proposed ILS algorithm. The MDCCVRP is a special case of the LLRP in which all the depots can be opened, and the MDk-TRP is a special case of the MDCCVRP in which the capacity constraints are relaxed. Finally, a LLRP with stochastic travel times is studied. A two-stage stochastic programming model and a variable neighborhood search algorithm are proposed for solving the problem. Furthermore a sampling method is developed for tackling instances with an infinite number of scenarios. Extensive computational experiments show that the proposed methods are effective for solving the problems under study.

Cost-reduction using non-uniform traffic in optical networks

Next-generation networks are likely to be non-uniform in all their aspects, including number of lightpaths carried per link, number of wavelengths per link, number of fibres per link, asymmetry of the links, and traffic flows. Routing and wavelength allocation models generally assume that the optical network is uniform and that the number of wavelengths per link is a constant. In practice however, some nodes and links carry heavy traffic and additional wavelengths are needed in those links. We study a wavelength-routed optical network based on the UK JANET topology where traffic demands between nodes are assumed to be non-uniform. We investigate how network capacity can be increased by locating congested links and suggesting cost-effective upgrades. Different traffic demands patterns, hop distances, number of wavelengths per link, and routing algorithms are considered. Numerical results show that a 95% increase in network capacity is possible by overlaying fibre on just 5% of existing links. We conclude that non-uniform traffic allocation can be beneficial to localize traffic in nodes and links deep in the network core and provisioning of additional resources there can efficiently and cost-effectively increase network capacity. © 2013 IEEE.

Energy Cooperation in Energy Harvesting Communication Systems

In energy harvesting communications, users transmit messages using energy harvested from nature. In such systems, transmission policies of the users need to be carefully designed according to the energy arrival profiles. When the energy management policies are optimized, the resulting performance of the system depends only on the energy arrival profiles. In this dissertation, we introduce and analyze the notion of energy cooperation in energy harvesting communications where users can share a portion of their harvested energy with the other users via wireless energy transfer. This energy cooperation enables us to control and optimize the energy arrivals at users to the extent possible. In the classical setting of cooperation, users help each other in the transmission of their data by exploiting the broadcast nature of wireless communications and the resulting overheard information. In contrast to the usual notion of cooperation, which is at the signal level, energy cooperation we introduce here is at the battery energy level. In a multi-user setting, energy may be abundant in one user in which case the loss incurred by transferring it to another user may be less than the gain it yields for the other user. It is this cooperation that we explore in this dissertation for several multi-user scenarios, where energy can be transferred from one user to another through a separate wireless energy transfer unit. We first consider the offline optimal energy management problem for several basic multi-user network structures with energy harvesting transmitters and one-way wireless energy transfer. In energy harvesting transmitters, energy arrivals in time impose energy causality constraints on the transmission policies of the users. In the presence of wireless energy transfer, energy causality constraints take a new form: energy can flow in time from the past to the future for each user, and from one user to the other at each time. This requires a careful joint management of energy flow in two separate dimensions, and different management policies are required depending on how users share the common wireless medium and interact over it. In this context, we analyze several basic multi-user energy harvesting network structures with wireless energy transfer. To capture the main trade-offs and insights that arise due to wireless energy transfer, we focus our attention on simple two- and three-user communication systems, such as the relay channel, multiple access channel and the two-way channel. Next, we focus on the delay minimization problem for networks. We consider a general network topology of energy harvesting and energy cooperating nodes. Each node harvests energy from nature and all nodes may share a portion of their harvested energies with neighboring nodes through energy cooperation. We consider the joint data routing and capacity assignment problem for this setting under fixed data and energy routing topologies. We determine the joint routing of energy and data in a general multi-user scenario with data and energy transfer. Next, we consider the cooperative energy harvesting diamond channel, where the source and two relays harvest energy from nature and the physical layer is modeled as a concatenation of a broadcast and a multiple access channel. Since the broadcast channel is degraded, one of the relays has the message of the other relay. Therefore, the multiple access channel is an extended multiple access channel with common data. We determine the optimum power and rate allocation policies of the users in order to maximize the end-to-end throughput of this system. Finally, we consider the two-user cooperative multiple access channel with energy harvesting users. The users cooperate at the physical layer (data cooperation) by establishing common messages through overheard signals and then cooperatively sending them. For this channel model, we investigate the effect of intermittent data arrivals to the users. We find the optimal offline transmit power and rate allocation policy that maximize the departure region. When the users can further cooperate at the battery level (energy cooperation), we find the jointly optimal offline transmit power and rate allocation policy together with the energy transfer policy that maximize the departure region.

Equilibrium Assignments in Competitive and Cooperative Traffic Flow Routing

Part 18: Optimization in Collaborative Networks