Analysis of the energies of the triple base triplets

Sixty-four sets of three-dimensional models of DNA triplex base triplets (TBT) were built up based on codons by homologous modeling method and their energies were minimized. According to sequence of TBT and orientation of the third ODN strand third, the energies of monomers and water-K+-TBT ternary complexes of TBT were analyzed. The results showed: (i) The energies of the symmetric parallel monomers are generally lower than those of the symmetric anti-parallel monomers of TBT, but the energies of the symmetric parallel ternary complexes are higher than those of the symmetric anti-parallel ternary complexes of TBT. (ii) No matter TBTs are monomers or ternary complexes, the energies of asymmetric parallel TBTs are generally lower than those of the asymmetric anti-parallel ones. (iii) Although the energies of the parallel TBTs are correlated with those of the anti-parallel ones, the energy differences are significant between them. The results here suggest the sequences of TBTs and the orientations of the third ODN strands are two of the key factors that can influence the formation and stability of TBT. (C) 2002 Elsevier Science B.V. All rights reserved.

The comparative analysis of the energies of conjugated triple base triplets and their applications

We built 64 sets of 3D models of DNA triplex base triplets (TBT) and minimized their energies. The TBTs were divided into 32 pairs of conjugated ones on the basis of their sequence characteristic, and the energies of each pair of them were compared and analyzed, the results showed: (i) The duplex DNA of which any strand contains at least a couple of A or T, has a preference for selecting the oligodeoxyribonucleic acid (ODN) strand containing abundant T to form TBT. (ii) The duplex DNA of which any strand contains at least a couple of G or C has a preference for selecting ODN containing abundant G to form symmetric antiparallel TBT, but selecting ODN containing abundant C to form asymmetric parallel TBT. (iii) The duplex DNA of which any strand contains only one of A, T, G or C has a preference for selecting ODN containing abundant pyrimidines (T or C) to form antiparallel TBT. Additionally, two examples of TBTs applications, in designing ODN to form triplex with duplex were presented. The energy calculation result revealed that 15-TCG is the best ligand of the HIV PPT duplex. The comparative analysis of energies of the conjugated TBTs provides directive significance for designing ODN strand that is easy to form triplex in theory. (C) 2002 Elsevier Science B.V. All rights reserved.

On-line policy optimisation of spoken dialogue systems via live interaction with human subjects

Statistical dialogue models have required a large number of dialogues to optimise the dialogue policy, relying on the use of a simulated user. This results in a mismatch between training and live conditions, and significant development costs for the simulator thereby mitigating many of the claimed benefits of such models. Recent work on Gaussian process reinforcement learning, has shown that learning can be substantially accelerated. This paper reports on an experiment to learn a policy for a real-world task directly from human interaction using rewards provided by users. It shows that a usable policy can be learnt in just a few hundred dialogues without needing a user simulator and, using a learning strategy that reduces the risk of taking bad actions. The paper also investigates adaptation behaviour when the system continues learning for several thousand dialogues and highlights the need for robustness to noisy rewards. © 2011 IEEE.

Effects of initial soil fabric and mode of shearing on quasi-steady state line for monotonic undrained behavior

The effects of initial soil fabric and mode of shearing on quasi-steady state line in void ratiostress space are studied by employing the Distinct Element Method numerical analysis. The results show that the initial soil fabric and the mode of shearing have a profound effect on the location of the quasi-steady state line. The evolution of the soil fabric during the course of undrained shearing shows that the specimens with different initial soil fabrics reach quasi-steady state at various soil fabric conditions. At quasi-steady state, the soil fabric has a significant adjustment to change its behavior from contractive to dilative. As the stress state approaches the steady state, the soil fabrics of different initial conditions become similar. The numerical analysis results are compared qualitatively with the published experimental data and the effects of specimen reconstitution methods and mode of shearing found in the experimental studies canbe systematically explained by the numerical analysis. © 2009 Taylor & Francis Group.

Vehicle trajectory linearisation to enable efficient optimisation of the constant speed racing line

A driver model is presented capable of optimising the trajectory of a simple dynamic nonlinear vehicle, at constant forward speed, so that progression along a predefined track is maximised as a function of time. In doing so, the model is able to continually operate a vehicle at its lateral-handling limit, maximising vehicle performance. The technique used forms a part of the solution to the motor racing objective of minimising lap time. A new approach of formulating the minimum lap time problem is motivated by the need for a more computationally efficient and robust tool-set for understanding on-the-limit driving behaviour. This has been achieved through set point-dependent linearisation of the vehicle model and coupling the vehicle-track system using an intrinsic coordinate description. Through this, the geometric vehicle trajectory had been linearised relative to the track reference, leading to new path optimisation algorithm which can be formed as a computationally efficient convex quadratic programming problem. © 2012 Copyright Taylor and Francis Group, LLC.

Recovering 3D Structure of Poorly Textured Infrastructure Scenes Using Point and Line Features

Most of the existing automated machine vision-based techniques for as-built documentation of civil infrastructure utilize only point features to recover the 3D structure of a scene. However it is often the case in man-made structures that not enough point features can be reliably detected (e.g. buildings and roofs); this can potentially lead to the failure of these techniques. To address the problem, this paper utilizes the prominence of straight lines in infrastructure scenes. It presents a hybrid approach that benefits from both point and line features. A calibrated stereo set of video cameras is used to collect data. Point and line features are then detected and matched across video frames. Finally, the 3D structure of the scene is recovered by finding 3D coordinates of the matched features. The proposed approach has been tested on realistic outdoor environments and preliminary results indicate its capability to deal with a variety of scenes.

Blade loading and its application in the mean-line design of low pressure turbines

In order to minimize the number of iterations to a turbine design, reasonable choices of the key parameters must be made at the earliest possible opportunity. The choice of blade loading is of particular concern in the low pressure (LP) turbine of civil aero engines, where the use of high-lift blades is widespread. This paper presents an analytical mean-line design study for a repeating-stage, axial-flow Low Pressure (LP) turbine. The problem of how to measure blade loading is first addressed. The analysis demonstrates that the Zweifel coefficient [1] is not a reasonable gauge of blade loading because it inherently depends on the flow angles. A more appropriate coefficient based on blade circulation is proposed. Without a large set of turbine test data it is not possible to directly evaluate the accuracy of a particular loss correlation. The analysis therefore focuses on the efficiency trends with respect to flow coefficient, stage loading, lift coefficient and Reynolds number. Of the various loss correlations examined, those based on Ainley and Mathieson ([2], [3], [4]) do not produce realistic trends. The profile loss model of Coull and Hodson [5] and the secondary loss models of Craig and Cox [6] and Traupel [7] gave the most reasonable results. The analysis suggests that designs with the highest flow turning are the least sensitive to increases in blade loading. The increase in Reynolds number lapse with loading is also captured, achieving reasonable agreement with experiments. Copyright © 2011 by ASME.

Uncertainty management for on-line optimisation of a POMDP-based large-scale spoken dialogue system

The optimization of dialogue policies using reinforcement learning (RL) is now an accepted part of the state of the art in spoken dialogue systems (SDS). Yet, it is still the case that the commonly used training algorithms for SDS require a large number of dialogues and hence most systems still rely on artificial data generated by a user simulator. Optimization is therefore performed off-line before releasing the system to real users. Gaussian Processes (GP) for RL have recently been applied to dialogue systems. One advantage of GP is that they compute an explicit measure of uncertainty in the value function estimates computed during learning. In this paper, a class of novel learning strategies is described which use uncertainty to control exploration on-line. Comparisons between several exploration schemes show that significant improvements to learning speed can be obtained and that rapid and safe online optimisation is possible, even on a complex task. Copyright © 2011 ISCA.

Overview and status of bottom-up silicon nanowire electronics

This review summarises the recent advances in the field of silicon nanowire electronics from bottom-up assembled materials. The aim is to draw a comparison between bottom-up and top-down approaches, examining respective achievements and evaluating advantages and disadvantages of each methodology. Existing techniques for synthesis and doping are discussed to provide the framework in which practical electronic applications can be developed. Next, key device categories are reviewed, emphasising current challenges and proposed solutions. Finally, field perspectives are outlined. © 2012 Elsevier Ltd.

Blade Loading and Its Application in the Mean-Line Design of Low Pressure Turbines

In order to minimize the number of iterations to a turbine design, reasonable choices of the key parameters must be made at the preliminary design stage. The choice of blade loading is of particular concern in the low pressure (LP) turbine of civil aero engines, where the use of high-lift blades is widespread. This paper considers how blade loading should be measured, compares the performance of various loss correlations, and explores the impact of blade lift on performance and lapse rates. To these ends, an analytical design study is presented for a repeating-stage, axial-flow LP turbine. It is demonstrated that the long-established Zweifel lift coefficient (Zweifel, 1945, "The Spacing of Turbomachine Blading, Especially with Large Angular Deflection" Brown Boveri Rev., 32(1), pp. 436-444) is flawed because it does not account for the blade camber. As a result the Zweifel coefficient is only meaningful for a fixed set of flow angles and cannot be used as an absolute measure of blade loading. A lift coefficient based on circulation is instead proposed that accounts for the blade curvature and is independent of the flow angles. Various existing profile and secondary loss correlations are examined for their suitability to preliminary design. A largely qualitative comparison demonstrates that the loss correlations based on Ainley and Mathieson (Ainley and Mathieson, 1957, "A Method of Performance Estimation for Axial-Flow Turbines," ARC Reports and Memoranda No. 2974; Dunham and Came, 1970, "Improvements to the Ainley-Mathieson Method of Turbine Performance Prediction," Trans. ASME: J. Eng. Gas Turbines Power, July, pp. 252-256; Kacker and Okapuu, 1982, "A Mean Line Performance Method for Axial Flow Turbine Efficiency," J. Eng. Power, 104, pp. 111-119). are not realistic, while the profile loss model of Coull and Hodson (Coull and Hodson, 2011, "Predicting the Profile Loss of High-Lift Low Pressure Turbines," J. Turbomach., 134(2), pp. 021002) and the secondary loss model of (Traupel, W, 1977, Thermische Turbomaschinen, Springer-Verlag, Berlin) are arguably the most reasonable. A quantitative comparison with multistage rig data indicates that, together, these methods over-predict lapse rates by around 30%, highlighting the need for improved loss models and a better understanding of the multistage environment. By examining the influence of blade lift across the Smith efficiency chart, the analysis demonstrates that designs with higher flow turning will tend to be less sensitive to increases in blade loading. © 2013 American Society of Mechanical Engineers.

Measurement of the Interaction Between Recombinant I-domain from Integrin alpha 2 beta 1 and a Triple Helical Collagen Peptide with the GFOGER Binding Motif Using Molecular Force Spectroscopy.

The role of the collagen-platelet interaction is of crucial importance to the haemostatic response during both injury and pathogenesis of the blood vessel wall. Of particular interest is the high affinity interaction of the platelet transmembrane receptor, alpha 2 beta 1, responsible for firm attachment of platelets to collagen at and around injury sites. We employ single molecule force spectroscopy (SMFS) using the atomic force microscope (AFM) to study the interaction of the I-domain from integrin alpha 2 beta 1 with a synthetic collagen related triple-helical peptide containing the high-affinity integrin-binding GFOGER motif, and a control peptide lacking this sequence, referred to as GPP. By utilising synthetic peptides in this manner we are able to study at the molecular level subtleties that would otherwise be lost when considering cell-to-collagen matrix interactions using ensemble techniques. We demonstrate for the first time the complexity of this interaction as illustrated by the complex multi-peaked force spectra and confirm specificity using control blocking experiments. In addition we observe specific interaction of the GPP peptide sequence with the I-domain. We propose a model to explain these observations.