Ligand-Induced structural changes in TEM‑1 probed by molecular dynamics and relative binding free energy calculations

The TEM family of enzymes has had a crucial impact on the pharmaceutical industry due to their important role in antibiotic resistance. Even with the latest technologies in structural biology and genomics, no 3D structure of a TEM- 1/antibiotic complex is known previous to acylation. Therefore, the comprehension of their capability in acylate antibiotics is based on the protein macromolecular structure uncomplexed. In this work, molecular docking, molecular dynamic simulations, and relative free energy calculations were applied in order to get a comprehensive and thorough analysis of TEM-1/ampicillin and TEM-1/amoxicillin complexes. We described the complexes and analyzed the effect of ligand binding on the overall structure. We clearly demonstrate that the key residues involved in the stability of the ligand (hot-spots) vary with the nature of the ligand. Structural effects such as (i) the distances between interfacial residues (Ser70−Oγ and Lys73−Nζ, Lys73−Nζ and Ser130−Oγ, and Ser70−Oγ−Ser130−Oγ), (ii) side chain rotamer variation (Tyr105 and Glu240), and (iii) the presence of conserved waters can be also influenced by ligand binding. This study supports the hypothesis that TEM-1 suffers structural modifications upon ligand binding.

Energy storage systems (sistemas de armazenamento de energia)

O armazenamento de energia pode ser efetuado sobre cinco categorias, designadamente, elétrica, eletromecânica, mecânica, térmica e química. Contudo, o assunto aqui debatido é sobre meios de armazenamento de energia elétrica, sendo que o armazenamento de eletricidade é usualmente efetuado recorrendo a outros géneros de energia, tais como, química, mecânica, térmica ou, até, em energia potencial. [1]. Há nos dias de hoje uma crescente preocupação na forma como é gerido o setor elétrico, uma vez que este implica um elevado impacto ambiental. Neste sentido tem havido algumas alterações, nomeadamente, no que diz respeito à produção de energia elétrica. A utilização de energias renováveis estão cada vez mais presentes na produção de eletricidade (Figura 1), pois permitem diminuir de forma indireta a utilização dos combustíveis fósseis, sendo esta a principal vantagem face às centrais de produção convencionais.

Energy-conscious tasks partitioning onto a heterogeneous multi-core platform

Modern multicore processors for the embedded market are often heterogeneous in nature. One feature often available are multiple sleep states with varying transition cost for entering and leaving said sleep states. This research effort explores the energy efficient task-mapping on such a heterogeneous multicore platform to reduce overall energy consumption of the system. This is performed in the context of a partitioned scheduling approach and a very realistic power model, which improves over some of the simplifying assumptions often made in the state-of-the-art. The developed heuristic consists of two phases, in the first phase, tasks are allocated to minimise their active energy consumption, while the second phase trades off a higher active energy consumption for an increased ability to exploit savings through more efficient sleep states. Extensive simulations demonstrate the effectiveness of the approach.

JamLab: augmenting sensornet testbeds with realistic and controlled interference generation

Radio interference drastically affects the performance of sensor-net communications, leading to packet loss and reduced energy-efficiency. As an increasing number of wireless devices operates on the same ISM frequencies, there is a strong need for understanding and debugging the performance of existing sensornet protocols under interference. Doing so requires a low-cost flexible testbed infrastructure that allows the repeatable generation of a wide range of interference patterns. Unfortunately, to date, existing sensornet testbeds lack such capabilities, and do not permit to study easily the coexistence problems between devices sharing the same frequencies. This paper addresses the current lack of such an infrastructure by using off-the-shelf sensor motes to record and playback interference patterns as well as to generate customizable and repeat-able interference in real-time. We propose and develop JamLab: a low-cost infrastructure to augment existing sensornet testbeds with accurate interference generation while limiting the overhead to a simple upload of the appropriate software. We explain how we tackle the hardware limitations and get an accurate measurement and regeneration of interference, and we experimentally evaluate the accuracy of JamLab with respect to time, space, and intensity. We further use JamLab to characterize the impact of interference on sensornet MAC protocols.

Enhanced Race-to-halt: a leakage-aware energy management approach for dynamic priority systems

With progressing CMOS technology miniaturization, the leakage power consumption starts to dominate the dynamic power consumption. The recent technology trends have equipped the modern embedded processors with the several sleep states and reduced their overhead (energy/time) of the sleep transition. The dynamic voltage frequency scaling (DVFS) potential to save energy is diminishing due to efficient (low overhead) sleep states and increased static (leakage) power consumption. The state-of-the-art research on static power reduction at system level is based on assumptions that cannot easily be integrated into practical systems. We propose a novel enhanced race-to-halt approach (ERTH) to reduce the overall system energy consumption. The exhaustive simulations demonstrate the effectiveness of our approach showing an improvement of up to 8 % over an existing work.

Scalable and efficient data processing in networked control systems

Network control systems (NCSs) are spatially distributed systems in which the communication between sensors, actuators and controllers occurs through a shared band-limited digital communication network. However, the use of a shared communication network, in contrast to using several dedicated independent connections, introduces new challenges which are even more acute in large scale and dense networked control systems. In this paper we investigate a recently introduced technique of gathering information from a dense sensor network to be used in networked control applications. Obtaining efficiently an approximate interpolation of the sensed data is exploited as offering a good tradeoff between accuracy in the measurement of the input signals and the delay to the actuation. These are important aspects to take into account for the quality of control. We introduce a variation to the state-of-the-art algorithms which we prove to perform relatively better because it takes into account the changes over time of the input signal within the process of obtaining an approximate interpolation.

Experiences on the implementation of a cooperative embedded system framework

As the complexity of embedded systems increases, multiple services have to compete for the limited resources of a single device. This situation is particularly critical for small embedded devices used in consumer electronics, telecommunication, industrial automation, or automotive systems. In fact, in order to satisfy a set of constraints related to weight, space, and energy consumption, these systems are typically built using microprocessors with lower processing power and limited resources. The CooperatES framework has recently been proposed to tackle these challenges, allowing resource constrained devices to collectively execute services with their neighbours in order to fulfil the complex Quality of Service (QoS) constraints imposed by users and applications. In order to demonstrate the framework's concepts, a prototype is being implemented in the Android platform. This paper discusses key challenges that must be addressed and possible directions to incorporate the desired real-time behaviour in Android.

Energy efficient scheduling for cluster-tree wireless sensor networks with time-bounded data flows: application to IEEE 802.15.4/ZigBee

Cluster scheduling and collision avoidance are crucial issues in large-scale cluster-tree Wireless Sensor Networks (WSNs). The paper presents a methodology that provides a Time Division Cluster Scheduling (TDCS) mechanism based on the cyclic extension of RCPS/TC (Resource Constrained Project Scheduling with Temporal Constraints) problem for a cluster-tree WSN, assuming bounded communication errors. The objective is to meet all end-to-end deadlines of a predefined set of time-bounded data flows while minimizing the energy consumption of the nodes by setting the TDCS period as long as possible. Sinceeach cluster is active only once during the period, the end-to-end delay of a given flow may span over several periods when there are the flows with opposite direction. The scheduling tool enables system designers to efficiently configure all required parameters of the IEEE 802.15.4/ZigBee beaconenabled cluster-tree WSNs in the network design time. The performance evaluation of thescheduling tool shows that the problems with dozens of nodes can be solved while using optimal solvers.

Wind energy technology

Electricity is regarded as one of the indispensable means to growth of any country’s economy. This source of power is the heartbeat of everything from the huge metropolitans, industries, worldwide computer networks and our global communication systems down to our homes. Electrical energy is the lifeline for any economic and societal development of a region or country. It is central to develop countries for maintaining acquired life styles and essential to developing countries for industrialisation and escaping poverty.

Simulation study of energy efficient scheduling for IEEE 802.15.4/ZigBee cluster-treeWireless Sensor Networks with time-bounded data flows

The simulation analysis is important approach to developing and evaluating the systems in terms of development time and cost. This paper demonstrates the application of Time Division Cluster Scheduling (TDCS) tool for the configuration of IEEE 802.15.4/ZigBee beaconenabled cluster-tree WSNs using the simulation analysis, as an illustrative example that confirms the practical applicability of the tool. The simulation study analyses how the number of retransmissions impacts the reliability of data transmission, the energy consumption of the nodes and the end-to-end communication delay, based on the simulation model that was implemented in the Opnet Modeler. The configuration parameters of the network are obtained directly from the TDCS tool. The simulation results show that the number of retransmissions impacts the reliability, the energy consumption and the end-to-end delay, in a way that improving the one may degrade the others.

Elements of scalable data processing

Cooperating objects (COs) is a recently coined term used to signify the convergence of classical embedded computer systems, wireless sensor networks and robotics and control. We present essential elements of a reference architecture for scalable data processing for the CO paradigm.

Slow down or race to halt: towards managing complexity of real-time energy management decisions

Existing work in the context of energy management for real-time systems often ignores the substantial cost of making DVFS and sleep state decisions in terms of time and energy and/or assume very simple models. Within this paper we attempt to explore the parameter space for such decisions and possible constraints faced.

Energy and delay trade-off of the GTS allocation mechanism in IEEE 802.15.4 for wireless sensor networks

The IEEE 802.15.4 protocol proposes a flexible communication solution for Low-Rate Wireless Personal Area Networks (LR-WPAN) including wireless sensor networks (WSNs). It presents the advantage to fit different requirements of potential applications by adequately setting its parameters. When in beaconenabled mode, the protocol can provide timeliness guarantees by using its Guaranteed Time Slot (GTS) mechanism. However, power-efficiency and timeliness guarantees are often two antagonistic requirements in wireless sensor networks. The purpose of this paper is to analyze and propose a methodology for setting the relevant parameters of IEEE 802.15.4-compliant WSNs that takes into account a proper trade-off between power-efficiency and delay bound guarantees. First, we propose two accurate models of service curves for a GTS allocation as a function of the IEEE 802.15.4 parameters, using Network Calculus formalism. We then evaluate the delay bound guaranteed by a GTS allocation and express it as a function of the duty cycle. Based on the relation between the delay requirement and the duty cycle, we propose a power-efficient superframe selection method that simultaneously reduces power consumption and enables meeting the delay requirements of real-time flows allocating GTSs. The results of this work may pave the way for a powerefficient management of the GTS mechanism in an IEEE 802.15.4 cluster.

A sensitivity study of the WRF model in wind simulation for an area of high wind energy

The performance of the Weather Research and Forecast (WRF) model in wind simulation was evaluated under different numerical and physical options for an area of Portugal, located in complex terrain and characterized by its significant wind energy resource. The grid nudging and integration time of the simulations were the tested numerical options. Since the goal is to simulate the near-surface wind, the physical parameterization schemes regarding the boundary layer were the ones under evaluation. Also, the influences of the local terrain complexity and simulation domain resolution on the model results were also studied. Data from three wind measuring stations located within the chosen area were compared with the model results, in terms of Root Mean Square Error, Standard Deviation Error and Bias. Wind speed histograms, occurrences and energy wind roses were also used for model evaluation. Globally, the model accurately reproduced the local wind regime, despite a significant underestimation of the wind speed. The wind direction is reasonably simulated by the model especially in wind regimes where there is a clear dominant sector, but in the presence of low wind speeds the characterization of the wind direction (observed and simulated) is very subjective and led to higher deviations between simulations and observations. Within the tested options, results show that the use of grid nudging in simulations that should not exceed an integration time of 2 days is the best numerical configuration, and the parameterization set composed by the physical schemes MM5–Yonsei University–Noah are the most suitable for this site. Results were poorer in sites with higher terrain complexity, mainly due to limitations of the terrain data supplied to the model. The increase of the simulation domain resolution alone is not enough to significantly improve the model performance. Results suggest that error minimization in the wind simulation can be achieved by testing and choosing a suitable numerical and physical configuration for the region of interest together with the use of high resolution terrain data, if available.

Experimental backlash study in mechanical manipulators

The behavior of mechanical manipulators with backlash is analyzed. In order to acquire and study the signals an experimental setup is implemented. The signal processing capabilities of the wavelets are used for de-noising the experimental signals and the energy of the obtained components is analyzed. To evaluate the backlash effect upon the robotic system, it is proposed an index based on the pseudo phase plane representation. Several tests are developed that demonstrate the coherence of the results.