Bacterial growth rate and host factors as determinants of intracellular bacterial distributions in systemic Salmonella enterica infections.

Bacteria of the species Salmonella enterica cause a range of life-threatening diseases in humans and animals worldwide. The within-host quantitative, spatial, and temporal dynamics of S. enterica interactions are key to understanding how immunity acts on these infections and how bacteria evade immune surveillance. In this study, we test hypotheses generated from mathematical models of in vivo dynamics of Salmonella infections with experimental observation of bacteria at the single-cell level in infected mouse organs to improve our understanding of the dynamic interactions between host and bacterial mechanisms that determine net growth rates of S. enterica within the host. We show that both bacterial and host factors determine the numerical distributions of bacteria within host cells and thus the level of dispersiveness of the infection.

Fluid-structure interaction with mean flow: Over-scattering and unstable resonance growth

It is known theoretically [1-3] that infinitely long fluid loaded plates in mean flow exhibit a range of unusual phenomena in the 'long time' limit. These include convective instability, absolute instability and negative energy waves which are destabilized by dissipation. However, structures are necessarily of finite length and may have discontinuities. Moreover, linear instability waves can only grow over a limited number of cycles before non-linear effects become dominant. We have undertaken an analytical and computational study to investigate the response of finite, discontinuous plates to ascertain if these unusual effects might be realized in practice. Analytically, we take a "wave scattering" [2,4] - as opposed to a "modal superposition" [5] - view of the fluttering plate problem. First, we solve for the scattering coefficients of localized plate discontinuities and identify a range of parameter space, well outside the convective instability regime, where over-scattering or amplified reflection/transmission occurs. These are scattering processes that draw energy from the mean flow into the plate. Next, we use the Wiener-Hopf technique to solve for the scattering coefficients from the leading and trailing edges of a baffled plate. Finally, we construct the response of a finite, baffled plate by a superposition of infinite plate propagating waves continuously scattering off the plate ends and solve for the unstable resonance frequencies and temporal growth rates for long plates. We present a comparison between our computational results and the infinite plate theory. In particular, the resonance response of a moderately sized plate is shown to be in excellent agreement with our long plate analytical predictions. Copyright © 2010 by ASME.

High rate deposition of ta-C:H using an electron cyclotron wave resonance plasma source

A compact electron cyclotron wave resonance (ECWR) source has been developed for the high rate deposition of hydrogenated tetrahedral amorphous carbon (ta-C:H). The ECWR provides growth rates of up to 1.5 nm/s over a 4-inch diameter and an independent control of the deposition rate and ion energy. The ta-C:H was deposited using acetylene as the source gas and was characterized as having an sp3 content of up to 77%, plasmon energy of 27 eV, refractive index of 2.45, hydrogen content of about 30%, optical gap of up to 2.1 eV and RMS surface roughness of 0.04 nm. © 1999 Elsevier Science S.A. All rights reserved.

High rate deposition of Ta-C:H using an electron cyclotron wave resonance plasma source

A compact electron cyclotron wave resonance (ECWR) source has been developed for the high rate deposition of hydrogenated tetrahedral amorphous carbon (ta-C:H). The ECWR provides growth rates of up to 900 angstrom/min and an independent control of the deposition rate and ion energy. The ta-C:H was deposited using acetylene as the source gas and was characterized in terms of its bonding, stress and friction coefficient. The results indicated that the ta-C:H produced using this source fulfills the necessary requirements for applications requiring enhanced tribological performance.

The preparation, characterization and tribological properties of TA-C : H deposited using an electron cyclotron wave resonance plasma beam source

A compact electron cyclotron wave resonance (ECWR) source has been developed for the high rate deposition of hydrogenated tetrahedral amorphous carbon (ta-C:H). The ECWR provides growth rates of up to 900 Å/min over a 4″ diameter and an independent control of the deposition rate and ion energy. The ta-C:H was deposited using acetylene as the source gas and was characterized in terms of its sp3 content, mass density, intrinsic stress, hydrogen content, C-H bonding, Raman spectra, optical gap, surface roughness and friction coefficient. The results obtained indicated that the film properties were maximized at an ion energy of approximately 167 eV, corresponding to an energy per daughter carbon ion of 76 eV. The relationship between the incident ion energy and film densification was also explained in terms of the subsurface implantation of carbon ions into the growing film.

Nucleated polymerization with secondary pathways. I. Time evolution of the principal moments.

Self-assembly processes resulting in linear structures are often observed in molecular biology, and include the formation of functional filaments such as actin and tubulin, as well as generally dysfunctional ones such as amyloid aggregates. Although the basic kinetic equations describing these phenomena are well-established, it has proved to be challenging, due to their non-linear nature, to derive solutions to these equations except for special cases. The availability of general analytical solutions provides a route for determining the rates of molecular level processes from the analysis of macroscopic experimental measurements of the growth kinetics, in addition to the phenomenological parameters, such as lag times and maximal growth rates that are already obtainable from standard fitting procedures. We describe here an analytical approach based on fixed-point analysis, which provides self-consistent solutions for the growth of filamentous structures that can, in addition to elongation, undergo internal fracturing and monomer-dependent nucleation as mechanisms for generating new free ends acting as growth sites. Our results generalise the analytical expression for sigmoidal growth kinetics from the Oosawa theory for nucleated polymerisation to the case of fragmenting filaments. We determine the corresponding growth laws in closed form and derive from first principles a number of relationships which have been empirically established for the kinetics of the self-assembly of amyloid fibrils.

HYDROGENATED AMORPHOUS SILICON THIN-FILM DEPOSITION BY DIRECT PHOTO-ENHANCED DECOMPOSITION OF SILANE USING AN INTERNAL HYDROGEN DISCHARGE LAMP.

Hydrogenated amorphous silicon (a-Si:H) thin films have been deposited from silane using a novel photo-enhanced decomposition technique. The system comprises a hydrogen discharge lamp contained within the reaction vessel; this unified approach allows high energy photon excitation of the silane molecules without absorption by window materials or the need for mercury sensitisation. The film growth rates (exceeding 4 Angstrom/s) and material properties obtained are comparable to those of films produced by plasma-enhanced CVD techniques. The reduction of energetic charged particles in the film growth region should enable the fabrication of cleaner semiconductor/insulator interfaces in thin-film transistors.

Tailoring the morphology of carbon nanotube assemblies using microgradients in the catalyst thickness

In addition to the structural control of individual carbon nanotubes (CNTs), the morphological control of their assemblies is crucial to realize miniaturized CNT devices. Microgradients in the thickness of catalyst are used to enrich the variety of available self-organized morphologies of CNTs. Microtrenches were fabricated in gate/spacer/cathode trilayers using a conventional self-aligned top-down process and catalyst exhibiting a microgradient in its thickness was formed on the cathode by sputter deposition through gate slits. CNTs, including single-walled CNTs, of up to 1μm in length were grown within 5-15 s by chemical vapor deposition. The tendency of thin CNTs to aggregate caused interactions between CNTs with different growth rates, yielding various morphologies dependent on the thickness of the catalyst. The field emission properties of several types of CNT assemblies were evaluated. The ability to produce CNTs with tailored morphologies by engineering the spatial distribution of catalysts will enhance their performance in devices. © 2011 The Japan Society of Applied Physics.

Combustion rumble prediction with integrated computational-fluid-dynamics/ low-order-model methods

The pressure oscillation within combustion chambers of aeroengines and industrial gas turbines is a major technical challenge to the development of high-performance and low-emission propulsion systems. In this paper, an approach integrating computational fluid dynamics and one-dimensional linear stability analysis is developed to predict the modes of oscillation in a combustor and their frequencies and growth rates. Linear acoustic theory was used to describe the acoustic waves propagating upstream and downstream of the combustion zone, which enables the computational fluid dynamics calculation to be efficiently concentrated on the combustion zone. A combustion oscillation was found to occur with its predicted frequency in agreement with experimental measurements. Furthermore, results from the computational fluid dynamics calculation provide the flame transfer function to describe unsteady heat release rate. Departures from ideal one-dimensional flows are described by shape factors. Combined with this information, low-order models can work out the possible oscillation modes and their initial growth rates. The approach developed here can be used in more general situations for the analysis of combustion oscillations. Copyright © 2012 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.

Attenuated Salmonella Typhimurium lacking the pathogenicity island-2 type 3 secretion system grow to high bacterial numbers inside phagocytes in mice.

Intracellular replication within specialized vacuoles and cell-to-cell spread in the tissue are essential for the virulence of Salmonella enterica. By observing infection dynamics at the single-cell level in vivo, we have discovered that the Salmonella pathogenicity island 2 (SPI-2) type 3 secretory system (T3SS) is dispensable for growth to high intracellular densities. This challenges the concept that intracellular replication absolutely requires proteins delivered by SPI-2 T3SS, which has been derived largely by inference from in vitro cell experiments and from unrefined measurement of net growth in mouse organs. Furthermore, we infer from our data that the SPI-2 T3SS mediates exit from infected cells, with consequent formation of new infection foci resulting in bacterial spread in the tissues. This suggests a new role for SPI-2 in vivo as a mediator of bacterial spread in the body. In addition, we demonstrate that very similar net growth rates of attenuated salmonellae in organs can be derived from very different underlying intracellular growth dynamics.

Sensitivity analysis of a time-delayed thermo-acoustic system via an adjoint-based approach

We apply adjoint-based sensitivity analysis to a time-delayed thermo-acoustic system: a Rijke tube containing a hot wire. We calculate how the growth rate and frequency of small oscillations about a base state are affected either by a generic passive control element in the system (the structural sensitivity analysis) or by a generic change to its base state (the base-state sensitivity analysis). We illustrate the structural sensitivity by calculating the effect of a second hot wire with a small heat-release parameter. In a single calculation, this shows how the second hot wire changes the growth rate and frequency of the small oscillations, as a function of its position in the tube. We then examine the components of the structural sensitivity in order to determine the passive control mechanism that has the strongest influence on the growth rate. We find that a force applied to the acoustic momentum equation in the opposite direction to the instantaneous velocity is the most stabilizing feedback mechanism. We also find that its effect is maximized when it is placed at the downstream end of the tube. This feedback mechanism could be supplied, for example, by an adiabatic mesh. We illustrate the base-state sensitivity by calculating the effects of small variations in the damping factor, the heat-release time-delay coefficient, the heat-release parameter, and the hot-wire location. The successful application of sensitivity analysis to thermo-acoustics opens up new possibilities for the passive control of thermo-acoustic oscillations by providing gradient information that can be combined with constrained optimization algorithms in order to reduce linear growth rates. © Cambridge University Press 2013.

Structural sensitivity of spiral vortex breakdown

Previous numerical simulations have shown that vortex breakdown starts with the formation of a steady axisymmetric bubble and that an unsteady spiralling mode then develops on top of this. We investigate this spiral mode with a linear global stability analysis around the steady bubble and its wake. We obtain the linear direct and adjoint global modes of the linearized Navier-Stokes equations and overlap these to obtain the structural sensitivity of the spiral mode, which identifies the wavemaker region. We also identify regions of absolute instability with a local stability analysis. At moderate swirls, we find that the m=-1 azimuthal mode is the most unstable and that the wavemaker regions of the m=-1 mode lie around the bubble, which is absolutely unstable. The mode is most sensitive to feedback involving the radial and azimuthal components of momentum in the region just upstream of the bubble. To a lesser extent, the mode is also sensitive to feedback involving the axial component of momentum in regions of high shear around the bubble. At an intermediate swirl, in which the bubble and wake have similar absolute growth rates, other researchers have found that the wavemaker of the nonlinear global mode lies in the wake. We agree with their analysis but find that the regions around the bubble are more influential than the wake in determining the growth rate and frequency of the linear global mode. The results from this paper provide the first steps towards passive control strategies for spiral vortex breakdown. © 2013 Cambridge University Press.

When will a flame describing function approach to thermoacoustics work well?

In any thermoacoustic analysis, it is important not only to predict linear frequencies and growth rates, but also the amplitude and frequencies of any limit cycles. The Flame Describing Function (FDF) approach is a quasi-linear analysis which allows the prediction of both the linear and nonlinear behaviour of a thermoacoustic system. This means that one can predict linear growth rates and frequencies, and also the amplitudes and frequencies of any limit cycles. The FDF achieves this by assuming that the acoustics are linear and that the flame, which is the only nonlinear element in the thermoacoustic system, can be adequately described by considering only its response at the frequency at which it is forced. Therefore any harmonics generated by the flame's nonlinear response are not considered. This implies that these nonlinear harmonics are small or that they are sufficiently filtered out by the linear dynamics of the system (the low-pass filter assumption). In this paper, a flame model with a simple saturation nonlinearity is coupled to simple duct acoustics, and the success of the FDF in predicting limit cycles is studied over a range of flame positions and acoustic damping parameters. Although these two parameters affect only the linear acoustics and not the nonlinear flame dynamics, they determine the validity of the low-pass filter assumption made in applying the flame describing function approach. Their importance is highlighted by studying the level of success of an FDF-based analysis as they are varied. This is achieved by comparing the FDF's prediction of limit-cycle amplitudes to the amplitudes seen in time domain simulations.

Precursor flow rate manipulation for the controlled fabrication of twin-free GaAs nanowires on silicon substrates

Vertically oriented GaAs nanowires (NWs) are grown on Si(111) substrates using metal-organic chemical vapor deposition. Controlled epitaxial growth along the 111 direction is demonstrated following the deposition of thin GaAs buffer layers and the elimination of structural defects, such as twin defects and stacking faults, is found for high growth rates. By systematically manipulating the AsH 3 (group-V) and TMGa (group-III) precursor flow rates, it is found that the TMGa flow rate has the most significant effect on the nanowire quality. After capping the minimal tapering and twin-free GaAs NWs with an AlGaAs shell, long exciton lifetimes (over 700ps) are obtained for high TMGa flow rate samples. It is observed that the Ga adatom concentration significantly affects the growth of GaAs NWs, with a high concentration and rapid growth leading to desirable characteristics for optoelectronic nanowire device applications including improved morphology, crystal structure and optical performance. © 2012 IOP Publishing Ltd.