On representing chemical environments

We review some recently published methods to represent atomic neighbourhood environments, and analyse their relative merits in terms of their faithfulness and suitability for fitting potential energy surfaces. The crucial properties that such representations (sometimes called descriptors) must have are differentiability with respect to moving the atoms, and invariance to the basic symmetries of physics: rotation, reflection, translation, and permutation of atoms of the same species. We demonstrate that certain widely used descriptors that initially look quite different are specific cases of a general approach, in which a finite set of basis functions with increasing angular wave numbers are used to expand the atomic neighbourhood density function. Using the example system of small clusters, we quantitatively show that this expansion needs to be carried to higher and higher wave numbers as the number of neighbours increases in order to obtain a faithful representation, and that variants of the descriptors converge at very different rates. We also propose an altogether new approach, called Smooth Overlap of Atomic Positions (SOAP), that sidesteps these difficulties by directly defining the similarity between any two neighbourhood environments, and show that it is still closely connected to the invariant descriptors. We test the performance of the various representations by fitting models to the potential energy surface of small silicon clusters and the bulk crystal.

Quantification of the effects of antibodies on the extra- and intracellular dynamics of Salmonella enterica.

Antibodies are known to be essential in controlling Salmonella infection, but their exact role remains elusive. We recently developed an in vitro model to investigate the relative efficiency of four different human immunoglobulin G (IgG) subclasses in modulating the interaction of the bacteria with human phagocytes. Our results indicated that different IgG subclasses affect the efficacy of Salmonella uptake by human phagocytes. In this study, we aim to quantify the effects of IgG on intracellular dynamics of infection by combining distributions of bacterial numbers per phagocyte observed by fluorescence microscopy with a mathematical model that simulates the in vitro dynamics. We then use maximum likelihood to estimate the model parameters and compare them across IgG subclasses. The analysis reveals heterogeneity in the division rates of the bacteria, strongly suggesting that a subpopulation of intracellular Salmonella, while visible under the microscope, is not dividing. Clear differences in the observed distributions among the four IgG subclasses are best explained by variations in phagocytosis and intracellular dynamics. We propose and compare potential factors affecting the replication and death of bacteria within phagocytes, and we discuss these results in the light of recent findings on dormancy of Salmonella.

Comparison of bleed and micro-vortex generator effects on supersonic boundary-layers

An experimental study of bleed and vortex generators in supersonic ow has been conducted. Methods were developed to analyze and directly compare the two systems' effects on turbulent boundary layers to better understand their potential to mitigate ow separation. LDA was used to measure two components of velocity in the boundary-layer for three cases|baseline, with bleed, or with a VG|at Mach numbers of 1.3, 1.5 and 1.8. The bleed system was comprised of a series of 2mm diameter normal holes operated at different suction rates, removing up to 10% of the incoming boundary layer. Three VG shapes were tested only at Mach 1.5 and 1.8. Measurements of the evolution of Hi and Cf downstream of each device indicate that Hi is not an appropriate parameter to gauge the effectiveness of vortex generators due to boundary layer wake distortion. The skin friction coeficient Cf may be a more appropriate measure. Similar increases in Cf were generated by VGs and bleed. The recovery to baseline conditions downstream of bleed was sensitive to Mach number, and more investigation of that effect will be required. Copyright © 2012 by University of Cambridge.

Effects of turbulent reynolds number on the performance of algebraic flame surface density models for large eddy simulation in the thin reaction zones regime: A direct numerical simulation analysis

A direct numerical simulation (DNS) database of freely propagating statistically planar turbulent premixed flames with a range of different turbulent Reynolds numbers has been used to assess the performance of algebraic flame surface density (FSD) models based on a fractal representation of the flame wrinkling factor. The turbulent Reynolds number Ret has been varied by modifying the Karlovitz number Ka and the Damköhler number Da independently of each other in such a way that the flames remain within the thin reaction zones regime. It has been found that the turbulent Reynolds number and the Karlovitz number both have a significant influence on the fractal dimension, which is found to increase with increasing Ret and Ka before reaching an asymptotic value for large values of Ret and Ka. A parameterisation of the fractal dimension is presented in which the effects of the Reynolds and the Karlovitz numbers are explicitly taken into account. By contrast, the inner cut-off scale normalised by the Zel'dovich flame thickness ηi/δz does not exhibit any significant dependence on Ret for the cases considered here. The performance of several algebraic FSD models has been assessed based on various criteria. Most of the algebraic models show a deterioration in performance with increasing the LES filter width. © 2012 Mohit Katragadda et al.

Measuring EGFR Separations on Cells with ∼10 nm Resolution via Fluorophore Localization Imaging with Photobleaching

Detecting receptor dimerisation and other forms of clustering on the cell surface depends on methods capable of determining protein-protein separations with high resolution in the ∼10-50 nm range. However, this distance range poses a significant challenge because it is too large for fluorescence resonance energy transfer and contains distances too small for all other techniques capable of high-resolution in cells. Here we have adapted the technique of fluorophore localisation imaging with photobleaching to measure inter-receptor separations in the cellular environment. Using the epidermal growth factor receptor, a key cancer target molecule, we demonstrate ∼10 nm resolution while continuously covering the range of ∼10-80 nm. By labelling the receptor on cells expressing low receptor numbers with a fluorescent antagonist we have found inter-receptor separations all the way up from 8 nm to 59 nm. Our data are consistent with epidermal growth factor receptors being able to form homo-polymers of at least 10 receptors in the absence of activating ligands. © 2013 Needham et al.

Cryogenic on-chip multiplexer for the study of quantum transport in 256 split-gate devices

We present a multiplexing scheme for the measurement of large numbers of mesoscopic devices in cryogenic systems. The multiplexer is used to contact an array of 256 split gates on a GaAs/AlGaAs heterostructure, in which each split gate can be measured individually. The low-temperature conductance of split-gate devices is governed by quantum mechanics, leading to the appearance of conductance plateaux at intervals of 2e^2/h. A fabrication-limited yield of 94% is achieved for the array, and a "quantum yield" is also defined, to account for disorder affecting the quantum behaviour of the devices. The quantum yield rose from 55% to 86% after illuminating the sample, explained by the corresponding increase in carrier density and mobility of the two-dimensional electron gas. The multiplexer is a scalable architecture, and can be extended to other forms of mesoscopic devices. It overcomes previous limits on the number of devices that can be fabricated on a single chip due to the number of electrical contacts available, without the need to alter existing experimental set ups.

The rhythm of fountains: The length and time scales of rise height fluctuations at low and high Froude numbers

The magnitude and frequency of vertical fluctuations of the top of an axisymmetric miscible Boussinesq fountain forms the focus of this work. We present measurements of these quantities for saline-aqueous fountains in uniform quiescent surroundings. Our results span source Froude numbers 0.3 ≤ Fr 0 ≤ 40 and, thereby, encompass very weak, weak, intermediate and forced classes of fountain. We identify distinct scalings, based on known quantities at the fountain source, for the frequency of fountain height fluctuations which collapse our data within bands of Fr0. Notably, our scalings reveal that the (dimensionless) frequency takes a constant value within each band. These results highlight characteristic time scales for the fluctuations which we decompose into a single, physically apparent, length scale and velocity scale within each band. Moreover, within one particular band, spanning source Froude numbers towards the lower end of the full range considered, we identify unexpectedly long-period fluctuations indicating a near balance of inertia and (opposing) buoyancy at the source. Our analysis identifies four distinct classes of fluctuation behaviour (four bands of Fr 0) and this classification matches well with existing classifications of fountains based on rise heights. As such, we show that an analysis of the behaviour of the fountain top alone, rather than the entire fountain, provides an alternative approach to classifying fountains. The similarity of classifications based on the two different methods confirms that the boundaries between classes mark tangible changes in the physics of fountains. For high Fr0 we show that the dominant fluctuations occur at the scale of the largest eddies which can be contained within the fountain near its top. Extending this, we develop a Strouhal number, Strtop, based on experimental measures of the fountain top, defined such that Strtop = 1 would suggest the dominant fluctuations are caused by a continual cycle of eddies forming and collapsing at this largest physical scale. For high- Fr 0 fountains we find Strtop ≈ 0. 9. © 2013 Cambridge University Press.

Mixing and internal dynamics of droplets impacting and coalescing on a solid surface.

The coalescence and mixing of a sessile and an impacting liquid droplet on a solid surface are studied experimentally and numerically in terms of lateral separation and droplet speed. Two droplet generators are used to produce differently colored droplets. Two high-speed imaging systems are used to investigate the impact and coalescence of the droplets in color from a side view with a simultaneous gray-scale view from below. Millimeter-sized droplets were used with dynamical conditions, based on the Reynolds and Weber numbers, relevant to microfluidics and commercial inkjet printing. Experimental measurements of advancing and receding static contact angles are used to calibrate a contact angle hysteresis model within a lattice Boltzmann framework, which is shown to capture the observed dynamics qualitatively and the final droplet configuration quantitatively. Our results show that no detectable mixing occurs during impact and coalescence of similar-sized droplets, but when the sessile droplet is sufficiently larger than the impacting droplet vortex ring generation can be observed. Finally we show how a gradient of wettability on the substrate can potentially enhance mixing.

The influence of boundary conditions on tip leakage flow

Most of the current understanding of tip leakage flows has been derived from detailed cascade experiments. However, the cascade model is inherently approximate since it is difficult to simulate the boundary conditions present in a real machine, particularly the secondary flows convecting from the upstream stator row and the relative motion of the casing and blade. This problem is further complicated when considering the high pressure turbine rotors of aero engines, where the high Mach numbers must also be matched in order to correctly model the aerodynamics and heat transfer. More realistic tests can be performed on high-speed turbines, but the experimental fidelity and resolution achievable in such set-ups is limited. In order to examine the differences between cascade models and real-engine behavior, the influence of boundary conditions on the tip leakage flow in an unshrouded high pressure turbine rotor is investigated using RANS calculations. This study examines the influence of the rotor inlet condition and relative casing motion. A baseline calculation with a simplified inlet condition and no relative endwall motion exhibits similar behavior to cascade studies. Only minor changes to the leakage flow are induced by introducing either a more realistic inlet condition or relative casing motion. However when both of these conditions are applied simultaneously the pattern of leakage flow is very different, with ingestion of flow over much of the early suction surface. The paper explores the physical processes driving this change and the impact on leakage losses and modeling requirements. Copyright © 2013 by ASME.

On the laminar-turbulent transition of the rotating-disk flow: The role of absolute instability

© 2014 Cambridge University Press. This paper describes a detailed experimental study using hot-wire anemometry of the laminar-turbulent transition region of a rotating-disk boundary-layer flow without any imposed excitation of the boundary layer. The measured data are separated into stationary and unsteady disturbance fields in order to elaborate on the roles that the stationary and the travelling modes have in the transition process. We show the onset of nonlinearity consistently at Reynolds numbers, R, of ∼ 510, i.e. at the onset of Lingwood's (J. Fluid Mech., vol. 299, 1995, pp. 17-33) local absolute instability, and the growth of stationary vortices saturates at a Reynolds number of ∼ 550. The nonlinear saturation and subsequent turbulent breakdown of individual stationary vortices independently of their amplitudes, which vary azimuthally, seem to be determined by well-defined Reynolds numbers. We identify unstable travelling disturbances in our power spectra, which continue to grow, saturating at around R=585, whereupon turbulent breakdown of the boundary layer ensues. The nonlinear saturation amplitude of the total disturbance field is approximately constant for all considered cases, i.e. different rotation rates and edge Reynolds numbers. We also identify a travelling secondary instability. Our results suggest that it is the travelling disturbances that are fundamentally important to the transition to turbulence for a clean disk, rather than the stationary vortices. Here, the results appear to show a primary nonlinear steep-fronted (travelling) global mode at the boundary between the local convectively and absolutely unstable regions, which develops nonlinearly interacting with the stationary vortices and which saturates and is unstable to a secondary instability. This leads to a rapid transition to turbulence outward of the primary front from approximately R=565 to 590 and to a fully turbulent boundary layer above 650.