Probing biomolecular interaction forces using an anharmonic acoustic technique for selective detection of bacterial spores

Receptor-based detection of pathogens often suffers from non-specific interactions, and as most detection techniques cannot distinguish between affinities of interactions, false positive responses remain a plaguing reality. Here, we report an anharmonic acoustic based method of detection that addresses the inherent weakness of current ligand dependant assays. Spores of Bacillus subtilis (Bacillus anthracis simulant) were immobilized on a thickness-shear mode AT-cut quartz crystal functionalized with anti-spore antibody and the sensor was driven by a pure sinusoidal oscillation at increasing amplitude. Biomolecular interaction forces between the coupled spores and the accelerating surface caused a nonlinear modulation of the acoustic response of the crystal. In particular, the deviation in the third harmonic of the transduced electrical response versus oscillation amplitude of the sensor (signal) was found to be significant. Signals from the specifically-bound spores were clearly distinguishable in shape from those of the physisorbed streptavidin-coated polystyrene microbeads. The analytical model presented here enables estimation of the biomolecular interaction forces from the measured response. Thus, probing biomolecular interaction forces using the described technique can quantitatively detect pathogens and distinguish specific from non-specific interactions, with potential applicability to rapid point-of-care detection. This also serves as a potential tool for rapid force-spectroscopy, affinity-based biomolecular screening and mapping of molecular interaction networks. © 2011 Elsevier B.V.

Robust airfoil design with respect to boundary layer transition

In order to disign an airfoil of which maximum lift coefficient (CL max) is not sensitive to location of forced top boundary layer transition. Taking maximizing mean value of CL max and minimizing standard deviation as biobjective, leading edge radius, manximum thickness and its location, maximum camber and its location as deterministic design variables, location of forced top boundary layer transition as stochastic variable, XFOIL as deterministic CFD solver, non-intrusive polynomial chaos as substitute of Monte Carlo method, we completed a robust airfoil design problem. Results demonstrate performance of initial airfoil is enhanced through reducing standard deviation of CL max. Besides, we also know maximum thickness has the most dominating effect on mean value of CL max, location of maximum thickness has the most dominating effect on standard deviation of CL max, maximum camber has a little effect on both mean value and standard deviation, and maximum camber is the only element of which increase can lead increase of mean value and standard deviation at the same time. Copyright © 2009 by the American Institute of Aeronautics and Astronautics, Inc.

Robust estimation of local genetic ancestry in admixed populations using a nonparametric Bayesian approach.

We present a new haplotype-based approach for inferring local genetic ancestry of individuals in an admixed population. Most existing approaches for local ancestry estimation ignore the latent genetic relatedness between ancestral populations and treat them as independent. In this article, we exploit such information by building an inheritance model that describes both the ancestral populations and the admixed population jointly in a unified framework. Based on an assumption that the common hypothetical founder haplotypes give rise to both the ancestral and the admixed population haplotypes, we employ an infinite hidden Markov model to characterize each ancestral population and further extend it to generate the admixed population. Through an effective utilization of the population structural information under a principled nonparametric Bayesian framework, the resulting model is significantly less sensitive to the choice and the amount of training data for ancestral populations than state-of-the-art algorithms. We also improve the robustness under deviation from common modeling assumptions by incorporating population-specific scale parameters that allow variable recombination rates in different populations. Our method is applicable to an admixed population from an arbitrary number of ancestral populations and also performs competitively in terms of spurious ancestry proportions under a general multiway admixture assumption. We validate the proposed method by simulation under various admixing scenarios and present empirical analysis results from a worldwide-distributed dataset from the Human Genome Diversity Project.

Re-examination of the coefficient of determination (r2) using road materials engineering case studies

The analysis of scientific data is integral to materials engineering and science. The correlation between measured variables is often quantified by estimating the coefficient of determination or the r2 value. This is the recognised procedure for determining linear relationships. The authors review the derivation of the r2 value and derive an associated quantity, termed the relative deviation (RD), which is the ratio of the root mean square of the deviations about the fitted line to the root mean square of the deviations about the y bar line expressed as a percentage. The relative deviation has an advantage over the coefficient of determination in that it has greater numerical sensitivity to changes in the spread of data about the fitted line, especially when the scatter is small. In addition, the relative deviation is able to define, in percentage terms, the reduction in scatter when different independent variables are correlated with a common dependent variable. Four case studies in the materials field (aggregate crushing value, Atterberg limits, permeability and creep of asphalt) from work carried out at the Queensland Main Roads Department are presented to show the use of the new parameter RD.

Dasher

Dasher is an information-efficient text-entry interface, which can be driven by natural continuous pointing gestures or by pressing buttons. Dasher is a competitive text-entry system wherever a full-size keyboard cannot be used - for example, when operating a computer one-handed, by joystick, touchscreen, trackball, or mouse; when operating a computer with zero hands (i.e., by head-mouse or by eyetracker); on a palmtop computer; on a wearable computer. The gazetracking version of Dasher allows an experienced user to write text as fast as normal handwriting - 29 words per minute; using a mouse, experienced users can write at 39 words per minute. Dasher can be used to write efficiently in any language. Dasher is free software (distributed under the GPL) and is available for many computer platforms, including linux, windows, and android.

Impact of mode localization on the motional resistance of coupled MEMS resonators

This paper investigates the effect of mode-localization that arises from structural asymmetry induced by manufacturing tolerances in mechanically coupled, electrically transduced Si MEMS resonators. We demonstrate that in the case of such mechanically coupled resonators, the achievable series motional resistance (R x) is dependent not only on the quality factor (Q) but also on the variations in the eigenvector of the chosen mode of vibration induced by mode localization due to manufacturing tolerances during the fabrication process. We study this effect of mode-localization both theoretically and experimentally in two pairs of coupled double-ended tuning fork resonators with different levels of initial structural asymmetry. The measured series R x is minimal when the system is close to perfect symmetry and any deviation from structural symmetry induced by fabrication tolerances leads to a degradation in the effective R x. Mechanical tuning experiments of the stiffness of one of the coupled resonators was also conducted to study variations in R x as a function of structural asymmetry within the system, the results of which demonstrated consistent variations in motional resistance with predictions. © 2012 IEEE.

The foundations of a new approach to additive manufacturing: Characteristics of free space metal deposition

In this paper, we report on the realisation of a free space deposition process (FSD). For the first time the use of a moving support structure to deposit tracks of metal starting from a substrate and extending into free space is characterised. The ability to write metal shapes in free space has wide ranging applications in additive manufacturing and rapid prototyping where the tracks can be layered to build overhanging features without the use of fixed support structures (such as is used in selective laser melting (SLM) and stereo lithography (SLA)). We demonstrate and perform a preliminary characterisation of the process in which a soldering iron was used to deposit lead free solder tracks. The factors affecting the stability of tracks and the effect of operating parameters, temperature, velocity, initial track starting diameter and starting volume were measured. A series of 10 tracks at each setting were compared with a control group of tracks; the track width, taper and variation between tracks were compared. Notable results in free space track deposition were that the initial track diameter and volume affected the repeatability and quality of tracks. The standard deviation of mean track width of tracks from the constrained initial diameter group were half that of the unconstrained group. The amount of material fed to the soldering iron before commencing deposition affected the taper of tracks. At an initial volume of 7 mm3 and an initial track diameter of 0.8 mm, none of the ten tracks deposited broke or showed taper > ∼1°. The maximum deposition velocity for free space track deposition using lead-free solder was limited to 1.5 mm s-1. © 2011 Elsevier B.V. All rights reserved.

Status of vibrational structure in Ni62

Measurements consisting of γ-ray excitation functions and angular distributions were performed using the (n,n′γ) reaction on Ni62. The excitation function data allowed us to check the consistency of the placement of transitions in the level scheme. From γ-ray angular distributions, the lifetimes of levels up to ~3.8 MeV in excitation energy were extracted with the Doppler-shift attenuation method. The experimentally deduced values of reduced transition probabilities were compared with the predictions of the quadrupole vibrator model and with large-scale shell model calculations in the fp shell configuration space. Two-phonon states were found to exist with some notable deviation from the predictions of the quadrupole vibrator model, but no evidence for the existence of three-phonon states could be established. Z=28 proton core excitations played a major role in understanding the observed structure. © 2011 American Physical Society.

Risk based lifetime costs assessment of a ground source heat pump (GSHP) system design: Methodology and case study

Space heating accounts for a large portion of the world's carbon dioxide emissions. Ground Source Heat Pumps (GSHPs) are a technology which can reduce carbon emissions from heating and cooling. GSHP system performance is however highly sensitive to deviation from design values of the actual annual energy extraction/rejection rates from/to the ground. In order to prevent failure and/or performance deterioration of GSHP systems it is possible to incorporate a safety factor in the design of the GSHP by over-sizing the ground heat exchanger (GHE). A methodology to evaluate the financial risk involved in over-sizing the GHE is proposed is this paper. A probability based approach is used to evaluate the economic feasibility of a hypothetical full-size GSHP system as compared to four alternative Heating Ventilation and Air Conditioning (HVAC) system configurations. The model of the GSHP system is developed in the TRNSYS energy simulation platform and calibrated with data from an actual hybrid GSHP system installed in the Department of Earth Science, University of Oxford, UK. Results of the analysis show that potential savings from a full-size GSHP system largely depend on projected HVAC system efficiencies and gas and electricity prices. Results of the risk analysis also suggest that a full-size GSHP with auxiliary back up is potentially the most economical system configuration. © 2012 Elsevier Ltd.

Stiffness of sands through a laboratory test database

Deformations of sandy soils around geotechnical structures generally involve strains in the range small (0·01%) to medium (0·5%). In this strain range the soil exhibits non-linear stress-strain behaviour, which should be incorporated in any deformation analysis. In order to capture the possible variability in the non-linear behaviour of various sands, a database was constructed including the secant shear modulus degradation curves of 454 tests from the literature. By obtaining a unique S-shaped curve of shear modulus degradation, a modified hyperbolic relationship was fitted. The three curve-fitting parameters are: an elastic threshold strain γe, up to which the elastic shear modulus is effectively constant at G0; a reference strain γr, defined as the shear strain at which the secant modulus has reduced to 0·5G0; and a curvature parameter a, which controls the rate of modulus reduction. The two characteristic strains γe and γr were found to vary with sand type (i.e. uniformity coefficient), soil state (i.e. void ratio, relative density) and mean effective stress. The new empirical expression for shear modulus reduction G/G0 is shown to make predictions that are accurate within a factor of 1·13 for one standard deviation of random error, as determined from 3860 data points. The initial elastic shear modulus, G0, should always be measured if possible, but a new empirical relation is shown to provide estimates within a factor of 1·6 for one standard deviation of random error, as determined from 379 tests. The new expressions for non-linear deformation are easy to apply in practice, and should be useful in the analysis of geotechnical structures under static loading.

Light absorption in silicon quantum dots embedded in silica

The photon absorption in Si quantum dots (QDs) embedded in SiO2 has been systematically investigated by varying several parameters of the QD synthesis. Plasma-enhanced chemical vapor deposition (PECVD) or magnetron cosputtering (MS) have been used to deposit, upon quartz substrates, single layer, or multilayer structures of Si-rich- SiO2 (SRO) with different Si content (43-46 at. %). SRO samples have been annealed for 1 h in the 450-1250 °C range and characterized by optical absorption measurements, photoluminescence analysis, Rutherford backscattering spectrometry and x-ray Photoelectron Spectroscopy. After annealing up to 900 °C SRO films grown by MS show a higher absorption coefficient and a lower optical bandgap (∼2.0 eV) in comparison with that of PECVD samples, due to the lower density of Si-Si bonds and to the presence of nitrogen in PECVD materials. By increasing the Si content a reduction in the optical bandgap has been recorded, pointing out the role of Si-Si bonds density in the absorption process in small amorphous Si QDs. Both the photon absorption probability and energy threshold in amorphous Si QDs are higher than in bulk amorphous Si, evidencing a quantum confinement effect. For temperatures higher than 900 °C both the materials show an increase in the optical bandgap due to the amorphous-crystalline transition of the Si QDs. Fixed the SRO stoichiometry, no difference in the optical bandgap trend of multilayer or single layer structures is evidenced. These data can be profitably used to better implement Si QDs for future PV technologies. © 2009 American Institute of Physics.

Studying adsorbent dynamics on a quartz crystal resonator using its nonlinear electrical response

The quartz crystal resonator has been traditionally employed in studying surface-confined physisorbed films and particles by measuring dissipation and frequency shifts. However, theoretical interpretation of the experimental observations is often challenged due to limited understanding of physical interaction mechanisms at the interfaces involved. Here we model a physisorbed interaction between particles and gold electrode surface of a quartz crystal and demonstrate how the nonlinear modulation of the electric response of the crystal due to the nonlinear interaction forces may be used to study the dynamics of the particles. In particular, we show that the graphs of the deviation in the third Fourier harmonic response versus oscillation amplitude provide important information about the onset, progress and nature of sliding of the particles. The graphs also present a signature of the surface-particle interaction and could be used to estimate the interaction energy profile. Interestingly, the insights gained from the model help to explain some of the experimental observations with physisorbed streptavidin-coated polystyrene microbeads on quartz resonators. © 2012 Elsevier B.V. All rights reserved.

Characterization of vertical Mo/diamond Schottky barrier diode from non-ideal I-V and C-V measurements based on MIS model

In this study, we investigated non-ideal characteristics of a diamond Schottky barrier diode with Molybdenum (Mo) Schottky metal fabricated by Microwave Plasma Chemical Vapour Deposition (MPCVD) technique. Extraction from forward bias I-V and reverse bias C- 2-V measurements yields ideality factor of 1.3, Schottky barrier height of 1.872 eV, and on-resistance of 32.63 mö·cm2. The deviation of extracted Schottky barrier height from an ideal value of 2.24 eV (considering Mo workfunction of 4.53 eV) indicates Fermi level pinning at the interface. We attributed such non-ideal behavior to the existence of thin interfacial layer and interface states between metal and diamond which forms Metal-Interfacial layer-Semiconductor (MIS) structure. Oxygen surface treatment during fabrication process might have induced them. From forward bias C-V characteristics, the minimum thickness of the interfacial layer is approximately 0.248 nm. Energy distribution profile of the interface state density is then evaluated from the forward bias I-V characteristics based on the MIS model. The interface state density is found to be uniformly distributed with values around 1013 eV - 1·cm- 2. © 2013 Elsevier B.V.

HTGR fuel element depletion benchmark: Stage one results

In this paper, we reported the results of the first stage of HTGR fuel element depletion benchmark obtained with BGCore and HELIOS depletion codes. The results of the k-inf are generally in good agreement. However, significant deviation in concentrations of several nuclides between MCNP based and HELIOS codes was observed.

Consideration of reactivity initiated accidents for TRU recycling in LWRs

Response of a PWR core loaded with Combined Non-Fertile and UO2 (CONFU) fuel assemblies to control rod ejection accident was evaluated. A number of core arrangements and TRU fuel compositions were considered and the results were compared with the performance of a reference all-UO2 core. The comparison was based on the results of a simple point kinetics model with thermal reactivity feedbacks and temperature dependant materials properties. The reactivity coefficients and core average kinetics parameters were obtained from the full core 3D neutronic simulations. The results show that application of the CONFU assembly concept causes only minor deviation of fuel performance characteristics in reactivity initiated accidents. This is a consequence of relatively small loadings of TRU in the CONFU assembly and therefore dominating role of conventional UO2 fuel in the neutronic performance of the core.