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.     

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.     

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.     

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.     

Hand gesture recognition from depth and infrared Kinect data for CAVE applications interaction

This paper presents a real-time framework that combines depth data and infrared laser speckle pattern (ILSP) images, captured from a Kinect device, for static hand gesture recognition to interact with CAVE applications. At the startup of the system, background removal and hand position detection are performed using only the depth map. After that, tracking is started using the hand positions of the previous frames in order to seek for the hand centroid of the current one. The obtained point is used as a seed for a region growing algorithm to perform hand segmentation in the depth map. The result is a mask that will be used for hand segmentation in the ILSP frame sequence. Next, we apply motion restrictions for gesture spotting in order to mark each image as a ‘Gesture’ or ‘Non-Gesture’. The ILSP counterparts of the frames labeled as “Gesture” are enhanced by using mask subtraction, contrast stretching, median filter, and histogram equalization. The result is used as the input for the feature extraction using a scale invariant feature transform algorithm (SIFT), bag-of-visual-words construction and classification through a multi-class support vector machine (SVM) classifier. Finally, we build a grammar based on the hand gesture classes to convert the classification results in control commands for the CAVE application. The performed tests and comparisons show that the implemented plugin is an efficient solution. We achieve state-of-the-art recognition accuracy as well as efficient object manipulation in a virtual scene visualized in the CAVE.     

Standard process monitoring and traceability programming in collaborative CAD/CAM/CNC manufacturing scenarios

The paper focuses on collaborative STEP-based CAD/CAM/CNC supply chains to program and automate machining process data monitoring and traceability activities. A traceability interface (traceability nc_functions) is defined for the new CNC programming standard ISO STEP-NC. CAM systems will be able to program monitoring and data access activities by inserting traceability nc_function calls in CNC programs. On the shop floor, controllers will automatically interpret these nc_functions to access process data while machining and will relate data records with the corresponding machining operations in a STEP-NC part program. With both types of information—process data and standard machining program (STEP-NC part program)—spread and technologically heterogeneous engineering systems will have full knowledge about what has happened in production. Traceability data access automation will assure data reliability. The paper describes a traceability scenario where standards such as MTConnect and ISA-95 support, rather than interfere with, the STEP-NC traceability proposal.     

A Framework for Integrating Non-Functional Requirements into Conceptual Models

The development of complex information systems calls for conceptual models that describe aspects beyond entities and activities. In particular, recent research has pointed out that conceptual models need to model goals, in order to capture the intentions which underlie complex situations within an organisational context. This paper focuses on one class of goals, namely non-functional requirements (NFR), which need to be captured and analysed from the very early phases of the software development process. The paper presents a framework for integrating NFRs into the ER and OO models. This framework has been validated by two case studies, one of which is very large. The results of the case studies suggest that goal modelling during early phases can lead to a more productive and complete modelling activity.       

Protein radial distribution function (P-RDF) and Bayesian-Regularized Genetic Neural Networks for modeling protein conformational stability: chymotrypsin inhibitor 2 mutants

Development of novel computational approaches for modeling protein properties is a main goal in applied Proteomics. In this work, we reported the extension of the radial distribution function (RDF) scores formalism to proteins for encoding 3D structural information with modeling purposes. Protein-RDF (P-RDF) scores measure spherical distributions on protein 3D structure of 48 amino acids/residues properties selected from the AAindex data base. P-RDF scores were tested for building predictive models of the change of thermal unfolding Gibbs free energy change (DeltaDeltaG) of chymotrypsin inhibitor 2 upon mutations. In this sense, an ensemble of Bayesian-Regularized Genetic Neural Networks (BRGNNs) yielded an optimum nonlinear model for the conformational stability. The ensemble predictor described about 84% and 70% variance of the data in training and test sets, respectively.     

Conformational analyses and docking studies of a series of 5-nitrofuran- and 5-nitrothiophen-semicarbazone derivatives in three possible binding sites of trypanothione and glutathione reductases

To explore three possible binding sites of trypanothione and glutathione reductase, namely, the active, the dimer interface and the coenzyme NADPH binding site, a series of eight compounds, nitrofurans and nitrothiophenes derivatives, were docked, using their crystallographic and modeled conformations. Docking results showed that, for both families and both enzymes, compounds are more likely to bind in the interface site, even though there is some probability of binding in the active site. These studies are in agreement with experimental data, which suggest that these class of compounds can act either as uncompetitive or mixed type inhibitors, and also with the finding that there is an alpha-helix which connects the active with the interface site, thus allowing charge transference between them.