Dynamics of RNA with A6 bulge loop

In order to understand the behavior of RNAs with large bulges In solution, molecular dynamics was performed on the RNA molecule in water with A6 bulge. The result of simulation showed that nonstacked conformation Is the main conformation in large bulges, and the backbone of large bulge is of great conformational flexibility, but bulges-induced bends are relatively rigid. The fluctuation in bulge has little influence on the bend angle of RNAs.

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Algorithm-based continuous pulse duration tuning and performance control of a mode-locked laser diode.

A control algorithm is presented that addresses the stability issues inherent to the operation of monolithic mode-locked laser diodes. It enables a continuous pulse duration tuning without any onset of Q-switching instabilities. A demonstration of the algorithm performance is presented for two radically different laser diode geometries and continuous pulse duration tuning between 0.5 ps to 2.2 ps and 1.2 ps to 10.2 ps is achieved. With practical applications in mind, this algorithm also facilitates control over performance parameters such as output power and wavelength during pulse duration tuning. The developed algorithm enables the user to harness the operational flexibility from such a laser with 'push-button' simplicity.

Superconducting fault current limiter design using parallel-connected YBCO thin films

Superconducting Fault Current Limiters (SFCLs) are able to reduce fault currents to an acceptable value, reducing potential mechanical and thermal damage to power system apparatus and allowing more flexibility in power system design and operation. The device can also help avoid replacing circuit breakers whose capacity has been exceeded. Due to limitations in current YBCO thin film manufacturing processes, it is not easy to obtain one large thin film that satisfies the specifications for high voltage and large current applications. The combination of standardized thin films has merit to reduce costs and maintain device quality, and it is necessary to connect these thin films in different series and parallel configurations in order to meet these specifications. In this paper, the design of a resistive type SFCL using parallel-connected YBCO thin films is discussed, including the role of a parallel resistor and the influence of individual thin film characteristics, based on both theory and experimental results. © 2009 IEEE.

Experimental study on an SFCL using series-connected YBCO thin films

Superconducting Fault Current Limiters (SFCLs) are able to reduce fault currents to an acceptable value, reducing potential mechanical and thermal damage and allowing more flexibility in an electric power system's design. Due to limitations in current YBCO thin film manufacturing techniques, it is necessary to connect a number of thin films in different series and parallel configurations in order to realise a practical SFCL for electric power system applications. The amount of resistance generated (i.e. the degree of current limitation), the characteristics of the S-N transition, and the time at which they operate is different depending on their comparative characteristics. However, it is desirable for series-connected thin films to have an operating time difference as small as possible to avoid placing an excess burden on certain thin films. The role of a parallel resistance, along with the influence of thin film characteristics, such as critical current (Ic), are discussed in regards to the design of SFCLs using YBCO thin films. © 2008 IOP Publishing Ltd.

Comparison of manual and user guided methodologies for the classification and retrieval of construction site images

The amount of original imaging information produced yearly during the last decade has experienced a tremendous growth in all industries due to the technological breakthroughs in digital imaging and electronic storage capabilities. This trend is affecting the construction industry as well, where digital cameras and image databases are gradually replacing traditional photography. Owners demand complete site photograph logs and engineers store thousands of images for each project to use in a number of construction management tasks like monitoring an activity's progress and keeping evidence of the "as built" in case any disputes arise. So far, retrieval methodologies are done manually with the user being responsible for imaging classification according to specific rules that serve a limited number of construction management tasks. New methods that, with the guidance of the user, can automatically classify and retrieve construction site images are being developed and promise to remove the heavy burden of manually indexing images. In this paper, both the existing methods and a novel image retrieval method developed by the authors for the classification and retrieval of construction site images are described and compared. Specifically a number of examples are deployed in order to present their advantages and limitations. The results from this comparison demonstrates that the content based image retrieval method developed by the authors can reduce the overall time spent for the classification and retrieval of construction images while providing the user with the flexibility to retrieve images according different classification schemes.

The response of piled buildings to deep excavations

This paper explores the influence of the piled foundation on the building response to excavation-induced deformations. The influence of the type of foundation, the position of positive and negative skin friction zones, and the flexibility of the piles is evaluated with respect to both horizontal and vertical soil deformations. Case histories from the Netherlands are included from Amsterdam (North South Line) and Rotterdam (a building adjacent to the Willemspoortunnel). Most of the buildings are founded on timber piles ranging in length from 12-17 m. Conclusions are drawn about the interaction between the piled building and the soil deformation. © 2012 Taylor & Francis Group.

Vibration response of a wind-turbine planetary gear set in the presence of a localized planet bearing defect

In a wind-turbine gearbox, planet bearings exhibit a high failure rate and are considered as one of the most critical components. Development of efficient vibration based fault detection methods for these bearings requires a thorough understanding of their vibration signature. Much work has been done to study the vibration properties of healthy planetary gear sets and to identify fault frequencies in fixed-axis bearings. However, vibration characteristics of planetary gear sets containing localized planet bearing defects (spalls or pits) have not been studied so far. In this paper, we propose a novel analytical model of a planetary gear set with ring gear flexibility and localized bearing defects as two key features. The model is used to simulate the vibration response of a planetary system in the presence of a defective planet bearing with faults on inner or outer raceway. The characteristic fault signature of a planetary bearing defect is determined and sources of modulation sidebands are identified. The findings from this work will be useful to improve existing sensor placement strategies and to develop more sophisticated fault detection algorithms. Copyright © 2011 by ASME.

Bayesian non-parametrics and the probabilistic approach to modelling.

Modelling is fundamental to many fields of science and engineering. A model can be thought of as a representation of possible data one could predict from a system. The probabilistic approach to modelling uses probability theory to express all aspects of uncertainty in the model. The probabilistic approach is synonymous with Bayesian modelling, which simply uses the rules of probability theory in order to make predictions, compare alternative models, and learn model parameters and structure from data. This simple and elegant framework is most powerful when coupled with flexible probabilistic models. Flexibility is achieved through the use of Bayesian non-parametrics. This article provides an overview of probabilistic modelling and an accessible survey of some of the main tools in Bayesian non-parametrics. The survey covers the use of Bayesian non-parametrics for modelling unknown functions, density estimation, clustering, time-series modelling, and representing sparsity, hierarchies, and covariance structure. More specifically, it gives brief non-technical overviews of Gaussian processes, Dirichlet processes, infinite hidden Markov models, Indian buffet processes, Kingman's coalescent, Dirichlet diffusion trees and Wishart processes.

Design of a compact reconfigurable optical interconnection using nematic liquid crystal spatial light modulator

The wavelength-division multiplexing (WDM) has been proposed as a promising technology to efficiently use the available bandwidth of a single optical fibre. This can be achieved by transmitting different channels on the optical fibre with each channel modulating a different wavelength. The aim of this paper is to propose a compact design (35 mm×65 mm) of a reconfigurable holographic optical switch in order to access and manipulate 4 channels at a node of a fibre-optic communication network. A vital component of such a switch is a nematic liquid crystal spatial light modulator offering control and flexibility at the channel manipulation stage and providing the ability to redirect light into the desired output fibre. This is achieved by the use of a 2-D analogue phase computer generated hologram (CGH) based on liquid crystal on silicon (LCOS) technology. © 2012 SPIE.

Dead-time minimisation using active voltage control gate drive for high-power IGBT converters

High-power converters usually need longer dead-times than their lower-power counterparts and a lower switching frequency. Also due to the complicated assembly layout and severe variations in parasitics, in practice the conventional dead-time specific adjustment or compensation for high-power converters is less effective, and usually this process is time-consuming and bespoke. For general applications, minimising or eliminating dead-time in the gate drive technology is a desirable solution. With the growing acceptance of power electronics building blocks (PEBB) and intelligent power modules (IPM), gate drives with intelligent functions are in demand. Smart functions including dead time elimination/minimisation can improve modularity, flexibility and reliability. In this paper, a dead-time minimisation using Active Voltage Control (AVC) gate drive is presented. © 2012 IEEE.

Proposal for a novel and simple WDM NRZ-DPSK system

A novel and simple non-return-to-zero differential phase shift keying (NRZ-DPSK) wavelength division multiplexing (WDM) system, which can simultaneously demultiplex and demodulate multiple wavelengths, is proposed and investigated in this paper. The phase-to-intensity demodulation principle is based on detuned filtering, which is achieved by using a single commercial array waveguide grating (AWG) in our scheme. By properly choosing appropriate AWG channels at the transmitter, the AWG at the receiver can act as both the demultiplexer and the demodulator of the DPSK signals. Simulations at 10, 20, and 40 Gbit/s show good flexibility and performance for the proposed system. © 2009 Higher Education Press and Springer-Verlag GmbH.

Tomorrow's cities - a framework for building resilience

Urbanisation is the great driving force of the twenty-first century. Cities are associated with both productivity and creativity, and the benefits offered by closely connected and high density living and working contribute to sustainability. At the same time, cities need extensive infrastructure – like water, power, sanitation and transportation systems – to operate effectively. Cities therefore comprise multiple components, forming both static and dynamic systems that are interconnected directly and indirectly on a number of levels, all forming the backdrop for the interaction of people and processes. Bringing together large numbers of people and complex products in rich interactions can lead to vulnerability from hazards, threats and even trends, whether natural hazards, epidemics, political upheaval, demographic changes, economic instability and/or mechanical failures; The key to countering vulnerability is the identification of critical systems and clear understanding of their interactions and dependencies. Critical systems can be assessed methodically to determine the implications of their failure and their interconnectivities with other systems to identify options. The overriding need is to support resilience – defined here as the degree to which a system or systems can continue to function effectively in a changing environment. Cities need to recognise the significance of devising adaptation strategies and processes to address a multitude of uncertainties relating to climate, economy, growth and demography. In this paper we put forward a framework to support cities in understanding the hazards, threats and trends that can make them vulnerable to unexpected changes and unpredictable shocks. The framework draws on an asset model of the city, in which components that contribute to resilience include social capital, economic assets, manufactured assets, and governance. The paper reviews the field, and draws together an overarching framework intended to help cities plan a robust trajectory towards increased resilience through flexibility, resourcefulness and responsiveness. It presents some brief case studies demonstrating the applicability of the proposed framework to a wide variety of circumstances.

Performance assessment of XACML authorizations for supply chain traceability web services

Service-Oriented Architecture (SOA) and Web Services (WS) offer advanced flexibility and interoperability capabilities. However they imply significant performance overheads that need to be carefully considered. Supply Chain Management (SCM) and Traceability systems are an interesting domain for the use of WS technologies that are usually deemed to be too complex and unnecessary in practical applications, especially regarding security. This paper presents an externalized security architecture that uses the eXtensible Access Control Markup Language (XACML) authorization standard to enforce visibility restrictions on trace-ability data in a supply chain where multiple companies collaborate; the performance overheads are assessed by comparing 'raw' authorization implementations - Access Control Lists, Tokens, and RDF Assertions - with their XACML-equivalents. © 2012 IEEE.

Determining vibration signature of a defective planet bearing in a wind turbine epicyclic gearbox

Planet bearings of wind turbine epicyclic gearboxes are considered as one of the most critical components due to their high failure rate. In order to develop effective vibration based detection algorithms for these bearings, a thorough understanding of their vibration signature is required. In this paper, we investigate the vibration behaviour of an epicyclic gearbox in the presence of a defective planet bearing both theoretically and experimentally. We also identify different sources of modulation sidebands using an analytical model which includes ring gear flexibility and planet bearing defects. The findings from this work will help engineers to develop more effective fault detection algorithms.