Optimization of biochemical systems through mathematical programming: Methods and applications

In this work we present a general (mono and multiobjective) optimization framework for the technological improvement of biochemical systems. The starting point of the method is a mathematical model in ordinary differential equations (ODEs) of the investigated system, based on qualitative biological knowledge and quantitative experimental data. In the method we take advantage of the special structural features of a family of ODEs called power-law models to reduce the computational complexity of the optimization program. In this way, the genetic manipulation of a biochemical system to meet a certain biotechnological goal can be expressed as an optimization program with some desired properties such as linearity or convexity.The general method of optimization is presented and discussed in its linear and geometric programming versions. We furthermore illustrate the use of the method by several real case studies. We conclude that the technological improvement of microorganisms can be afforded using the combination of mathematical modelling and optimization. The systematic nature of this approach facilitates the redesign of biochemical systems and makes this a predictive exercise rather than a trial-and-error procedure.     

Stability conditions for integral delay systems

In this paper we consider a special class of integral delay systems arising in several stability problems of time‐delay systems. For these integral systems we derive stability and robust stability conditions in terms of Lyapunov–Krasovskii functionals. More explicitly, after providing the stability conditions we compute quadratic functionals and apply them to derive exponential estimates for solutions, and robust stability conditions for perturbed integral delay systems. Copyright © 2008 John Wiley & Sons, Ltd.     

Network interfaces for programmable NICs and multicore platforms

The availability of multicore processors and programmable NICs, such as TOEs (TCP/IP Offloading Engines), provides new opportunities for designing efficient network interfaces to cope with the gap between the improvement rates of link bandwidths and microprocessor performance. This gap poses important challenges related with the high computational requirements associated to the traffic volumes and wider functionality that the network interface has to support. This way, taking into account the rate of link bandwidth improvement and the ever changing and increasing application demands, efficient network interface architectures require scalability and flexibility. An opportunity to reach these goals comes from the exploitation of the parallelism in the communication path by distributing the protocol processing work across processors which are available in the computer, i.e. multicore microprocessors and programmable NICs.Thus, after a brief review of the different solutions that have been previously proposed for speeding up network interfaces, this paper analyzes the onloading and offloading alternatives. Both strategies try to release host CPU cycles by taking advantage of the communication workload execution in other processors present in the node. Nevertheless, whereas onloading uses another general-purpose processor, either included in a chip multiprocessor (CMP) or in a symmetric multiprocessor (SMP), offloading takes advantage of processors in programmable network interface cards (NICs). From our experiments, implemented by using a full-system simulator, we provide a fair and more complete comparison between onloading and offloading. Thus, it is shown that the relative improvement on peak throughput offered by offloading and onloading depends on the rate of application workload to communication overhead, the message sizes, and on the characteristics of the system architecture, more specifically the bandwidth of the buses and the way the NIC is connected to the system processor and memory. In our implementations, offloading provides lower latencies than onloading, although the CPU utilization and interrupts are lower for onloading. Taking into account the conclusions of our experimental results, we propose a hybrid network interface that can take advantage of both, programmable NICs and multicore processors.     

Accelerating network applications by distributed interfaces on heterogeneous multiprocessor architectures

Hosts with several, possibly heterogeneous and/or multicore, processors provide new challenges and opportunities to accelerate applications with high communications bandwidth requirements. Many opportunities to scale these network applications with the increase in the link bandwidths are related to the exploitation of the available parallelism provided by the presence of several processing cores in the servers, not only for computing the workload of the user application but also for decreasing the overhead associated to the network interface and the system software.     

Optimization of interval type-2 fuzzy logic controllers for a perturbed autonomous wheeled mobile robot using genetic algorithms

We describe a tracking controller for the dynamic model of a unicycle mobile robot by integrating a kinematic and a torque controller based on type-2 fuzzy logic theory and genetic algorithms. Computer simulations are presented confirming the performance of the tracking controller and its application to different navigation problems.     

LAMED — A PRNG for EPC Class-1 Generation-2 RFID specification

RFID is a relatively heterogenous radio technology, where it is necessary to put an extra effort on security and privacy-related issues. As early as 2004, some authors suggested the use of a PRNG for increasing security. This was later questioned because many thought a PRNG implementation may go well beyond the very limited computational capabilities of low-cost RFID tags. However, its use has been ratified by EPCGlobal (EPC Class-1 Generation-2) and ISO (ISO/IEC 18000-6C). This motivates our proposal of a new PRNG, named LAMED, which is compliant with the standards and successfully passes several batteries of very demanding randomness tests (ENT, DIEHARD, NIST, and SEXTON). A study of its hardware complexity shows that LAMED can be implemented with slightly less than 1.6 K gates, and that pseudo-random numbers can be generated each 1.8 ms. So we can affirm this is a realist proposal both conforming with the EPC-G1C2 standard, and suitable for low-cost RFID tags.     

Co-design of H∞ jump observers for event-based measurements over networks

This work presents a strategy to minimise the network usage and the energy consumption of wireless battery-powered sensors in the observer problem over networks. The sensor nodes implement a periodic send-on-delta approach, sending new measurements when a measure deviates considerably from the previous sent one. The estimator node implements a jump observer whose gains are computed offline and depend on the combination of available new measurements. We bound the estimator performance as a function of the sending policies and then state the design procedure of the observer under fixed sending thresholds as a semidefinite programming problem. We address this problem first in a deterministic way and, to reduce conservativeness, in a stochastic one after obtaining bounds on the probabilities of having new measurements and applying robust optimisation problem over the possible probabilities using sum of squares decomposition. We relate the network usage with the sending thresholds and propose an iterative procedure for the design of those thresholds, minimising the network usage while guaranteeing a prescribed estimation performance. Simulation results and experimental analysis show the validity of the proposal and the reduction of network resources that can be achieved with the stochastic approach.     

Multilayer Cognitive Maps in the Resolution of Problems using the FCM Designer Tool

Cognitive maps are a tool to represent knowledge from a qualitative perspective, allowing to create models of complex systems where an exact mathematical model cannot be used because of the complexity of the system. In the literature, several tools have been proposed to develop cognitive maps and fuzzy cognitive maps (FCMs); one of them is FCM Designer. This paper designs and implements an extension to the FCM Designer tool that allows creating multilayer FCM. With this extension, it is possible to have several FCMs for the same problem, where each one expresses a different level of knowledge of the system under study, but interlinked. Thus, one can have a first level of detailed abstraction of the system with specific information and then more general levels. In addition, we can have different levels where the variables of one level depend on those of another level. That is, the multilayer approach enriches the modeled systems with flow of information between layers, to derive information about the concepts involved in layers from the concepts in other layers. In our multilayer approach, the relationship between the cognitive maps in different layers can be carried out in various ways: with fuzzy rules, connections with weights and with mathematical equations. This work presents the design and the implementation of the extension of the FCM Designer tool, and several test cases in different domains: a FCM to analyze emergent properties of Wikipedia a FCM for medical analysis for diagnosis, and another like recommender system.     

Resilient overlay network for real-time interactive multimedia sessions in corporate networks

Real-time interactive multimedia communications are becoming increasingly useful for education, business, e-commerce and e-government, providing an enriched user experience in teleconferencing, e-meetings, distance training and product demonstrations. Large corporations are usually located at several sites, so real-time multipoint sessions within corporations are especially difficult. IP multicast is available or feasible within each site of an organization. Thus, corporate networks can be considered as various multicast-capable networks interconnected through a wide area network without multicast connectivity. This paper proposes a resilient self-managed overlay network to support real-time multipoint interactive sessions within corporate networks. The proposed overlay takes advantage of the configuration of corporate networks to self-organize and provide an efficient media delivery service, making use of multicast communications wherever available. Various self-healing techniques are implemented allowing for the continuity of ongoing sessions in spite of network disruptions and entity failures. Extensive simulations and tests have been carried out to assess the performance and resilience of the overlay facing several types of disruptions.