Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm.

We live in an era of abundant data. This has necessitated the development of new and innovative statistical algorithms to get the most from experimental data. For example, faster algorithms make practical the analysis of larger genomic data sets, allowing us to extend the utility of cutting-edge statistical methods. We present a randomised algorithm that accelerates the clustering of time series data using the Bayesian Hierarchical Clustering (BHC) statistical method. BHC is a general method for clustering any discretely sampled time series data. In this paper we focus on a particular application to microarray gene expression data. We define and analyse the randomised algorithm, before presenting results on both synthetic and real biological data sets. We show that the randomised algorithm leads to substantial gains in speed with minimal loss in clustering quality. The randomised time series BHC algorithm is available as part of the R package BHC, which is available for download from Bioconductor (version 2.10 and above) via http://bioconductor.org/packages/2.10/bioc/html/BHC.html. We have also made available a set of R scripts which can be used to reproduce the analyses carried out in this paper. These are available from the following URL. https://sites.google.com/site/randomisedbhc/.

Measurement of the magnetic field inside the holes of a drilled bulk high-Tc superconductor

We use macroscopic holes drilled in a bulk YBCO superconductor to probe its magnetic properties in the volume of the sample. The sample is subjected to an AC magnetic flux with a density ranging from 30mT to 130mT and the flux in the superconductor is probed by miniature coils inserted in the holes. In a given hole, three different penetration regimes can be observed: (i) the shielded regime, where no magnetic flux threads the hole; (ii) the gradual penetration regime, where the waveform of the magnetic field has a clipped sine shape whose fundamental component scales with the applied field; and (iii) the flux concentration regime, where the waveform of the magnetic field is nearly a sine wave, with an amplitude exceeding that of the applied field by up to a factor of two. The distribution of the penetration regimes in the holes is compared with that of the magnetic flux density at the top and bottom surfaces of the sample, and is interpreted with the help of optical polarized light micrographs of these surfaces. We show that the measurement of the magnetic field inside the holes can be used as a local characterization of the bulk magnetic properties of the sample.

UEGO based measurement of EGR rate and residual gas fraction

A technique is presented for measuring the exhaust gas recirculation (EGR) and residual gas fraction (RGF) using a fast UEGO based O2 measurement of the manifold or in-cylinder gases, and of the exhaust gases. The technique has some advantages over the more common CO2-based method. In the case of an RGF measurement, fuel interference must be eliminated and special fuelling arrangements are is required. It is shown how a UEGO-based measurement, though sensitive to reactive species in the exhaust (such as H 2), as a system reports EGR/ RGF rates faithfully. Preliminary tests showed that EGR and RGF measurements using the O2 approach agreed well with CO2-based measurements. Copyright © 2011 SAE International.

Measurement of the unburnt gas temperature in an IC engine by means of a pressure transducer

A novel method of measuring cylinder gas temperature in an internal combustion engine cylinder is introduced. The physical basis for the technique is that the flow rate through an orifice is a function of the temperature of the gas flowing through the orifice. Using a pressure transducer in the cylinder, and another in a chamber connected to the cylinder via an orifice, it is shown how the cylinder temperature can be determined with useful sensitivity. In this paper the governing equations are derived, which show that the heat transfer characteristics of the chamber are critical to the performance of the system, and that isothermal or adiabatic conditions give the optimum performance. For a typical internal combustion engine, it is found that the pre-compression cylinder temperature is related to the chamber pressure late in the compression process with sensitivity of the order of 0.005 bar/K. Copyright © 2010 SAE International.

A novel measurement of dynamic friction

A tribometer, based on a pin-on-disc machine, uses a PZT drive to produce small sinusoidal fluctuations of sliding speed. The frequency and amplitude of these fluctuations can be controlled, and the dynamic response measured. Preliminary test results show that the dynamic friction variation is influenced by the contact materials, normal force, oscillation frequency and steady sliding speed. The variation of friction force amplitude and phase with frequency gives clues about the underlying state variables determining the friction. Modelling studies illustrate the expected behaviour for idealized friction laws governed by, for example, sliding speed, contact temperature, and "rate-state" laws. © 2008 SAE International.

Investigation of the dilution process for measurement of particulate matter from spark-ignition engines

Measurements of particulate matter (PM) from spark ignition (SI) engine exhaust using dilution tunnels will become more prevalent as emission standards are tightened. Hence, a study of the dilution process was undertaken in order to understand how various dilution related parameters affect the accuracy with which PM sizes and concentrations can be determined. A SI and a compression ignition (CI) engine were separately used to examine parameters of the dilution process; the present work discusses the results in the context of SI exhaust dilution. A Scanning Mobility Particle Sizer (SMPS) was used to measure the size distribution, number density, and volume fraction of PM. Temperature measurements in the exhaust pipe and dilution tunnel reveal the degree of mixing between exhaust and dilution air, the effect of flowrate on heat transfer from undiluted and diluted exhaust to the environment, and the minimum permissible dilution ratio for a maximum sample temperature of 52°C. Measurements of PM concentrations as a function of dilution ratio show the competing effects of temperature and particle/vapor concentrations on particle growth dynamics, which result in a range of dilution ratios-from 13 to 18-where the effect of dilution ratio, independent of flowrate, is kept to a minimum. This range of dilution ratios is therefore optimal in order to achieve repeatable PM concentration measurements. Particle dynamics during transit through the tunnel operating at the optimal dilution ratio was found statistically insignificant compared to data scatter. Such small differences in number concentration may be qualitatively representative of particle losses for SI exhaust, but small increases in PM volume fraction during transit through the tunnel may significantly underestimate accretion of mass due to unburned hydrocarbons (HCs) emitted by SI engines. The fraction of SI-derived PM mass due to adsorbed/absorbed vapor, estimated from these data, is consistent with previous chemical analyses of PM. © 1998 Society of Automotive Engineers, Inc.

Measurement of filling-factor-dependent magnetophonon resonances in graphene using Raman spectroscopy

We perform polarization-resolved Raman spectroscopy on graphene in magnetic fields up to 45 T. This reveals a filling-factor-dependent, multicomponent anticrossing structure of the Raman G peak, resulting from magnetophonon resonances between magnetoexcitons and E2g phonons. This is explained with a model of Raman scattering taking into account the effects of spatially inhomogeneous carrier densities and strain. Random fluctuations of strain-induced pseudomagnetic fields lead to increased scattering intensity inside the anticrossing gap, consistent with the experiments. © 2013 American Physical Society.

Noncontact measurement of charge carrier lifetime and mobility in GaN nanowires

The first noncontact photoconductivity measurements of gallium nitride nanowires (NWs) are presented, revealing a high crystallographic and optoelectronic quality achieved by use of catalyst-free molecular beam epitaxy. In comparison with bulk material, the NWs exhibit a long conductivity lifetime (>2 ns) and a high mobility (820 ± 120 cm 2/(V s)). This is due to the weak influence of surface traps with respect to other III-V semiconducting NWs and to the favorable crystalline structure of the NWs achieved via strain-relieved growth. © 2012 American Chemical Society.

Continuous weak measurement of a trapped electron using a percolation field effect transistor

We investigate the use of a percolation-field-effect-transistor for the continuous weak measurement of a spatially Rabi oscillating trapped electron through the change in percolation pathway of the transistor channel. In contrast to conventional devices, this detection mechanism in principle does not require a change in the stored energy of the gate capacitance to modify the drain current, so reducing the measurement back-action. The signal-to-noise ratio and measurement bandwidth are seen to be improved compared to conventional devices, allowing further aspects of the dynamic behaviour to be observed. © 2013 AIP Publishing LLC.

Measurement of third-order dispersion in a hong-ou-mandel interferometer

The effect of third-order dispersion in a Hong-Ou-Mandel interferometer is investigated using a ZnSe crystal as a dispersive medium. A value for the TOD coefficient of ZnSe is extracted which is consistent with literature values. © OSA 2013.

Measurement of Residual Stresses in Ferroelectric Pb(Zr

The residual stresses in Pb(Zr0.3Ti0.7)O3thin films were measured by the \sin^{2}\Psi method using the normal X-ray incidence. The spacing of different planes (hkl) parallel to the film surface were converted to the spacing of a set of inclined planes (100). The angles between (100) and (hkl) were equivalent to the tilting angles of (100) from the normal of film surface. The residual stresses were extracted from the linear slope of the strain difference between the equivalent inclined direction and normal direction with respect to the \sin^{2}\Psi. The results were in consistency with that derived from the conventional \sin^{2}\Psi method.

High resolution direct measurement of temperature distribution in silicon nanophotonics devices.

Following the miniaturization of photonic devices and the increase in data rates, the issues of self heating and heat removal in active nanophotonic devices should be considered and studied in more details. In this paper we use the approach of Scanning Thermal Microscopy (SThM) to obtain an image of the temperature field of a silicon micro ring resonator with sub-micron spatial resolution. The temperature rise in the device is a result of self heating which is caused by free carrier absorption in the doped silicon. The temperature is measured locally and directly using a temperature sensitive AFM probe. We show that this local temperature measurement is feasible in the photonic device despite the perturbation that is introduced by the probe. Using the above method we observed a significant self heating of about 10 degrees within the device.

Measurement of residual stresses in ferroelectric Pb(Zr 0.3Ti0.7)O3 thin films by X-ray diffraction

The residual stresses in Pb(Zr0.3Ti0.7)O3 thin films were measured by the sin2 Ψ method using the normal X-ray incidence. The spacing of different planes (hkl) parallel to the film surface were converted to the spacing of a set of inclined planes (100). The angles between (100) and (hkl) were equivalent to the tilting angles of (100) from the normal of film surface. The residual stresses were extracted from the linear slope of the strain difference between the equivalent inclined direction and normal direction with respect to the sin2 Ψ. The results were in consistency with that derived from the conventional sin2 Ψ method. © 2013 The Japan Society of Applied Physics.