Non-Newtonian behavior in simple fluids

Using nonequilibrium molecular dynamics simulations, we study the non-Newtonian rheology of a microscopic sample of simple fluid. The calculations were performed using a configurational thermostat which unlike previous nonequilibrium molecular dynamics or nonequilibrium Brownian dynamics methods does not exert any additional constraint on the flow profile. Our findings are in agreement with experimental results on concentrated "hard sphere"-like colloidal suspensions. We observe: (i) a shear thickening regime under steady shear; (ii) a strain thickening regime under oscillatory shear at low frequencies; and (iii) shear-induced ordering under oscillatory shear at higher frequencies. These results significantly differ from previous simulation results which showed systematically a strong ordering for all frequencies. They also indicate that shear thickening can occur even in the absence of a solvent.J.D. acknowledges support from the Research School of Chemistry ~ANU! through a visiting fellowship

On the effects of assuming flow profiles in nonequilibrium simulations

Atomic simulation methods modelling fluid flows often incorporate in the equations of motion the steady state flow profile predicted by Navier–Stokes equations. We show in this work that this may lead to significant errors such as spurious shear induced ordering, unphysical steady state flow profiles or artificial dampening of thermal motion even at shear rates regarded as low in simulation applications. Our results also suggest that nonequilibrium molecular dynamics coupled with the recently developed configurational thermostat, which makes no assumption at all on the flow profile, provides a much more realistic way to study these phenomena

Homogeneous shear flow of a hard-sphere fluid: Analytic solutions

Recently, a solution for collision-free trajectories in an N particle thermostatted hard-sphere system undergoing homogeneous shear (the so-called "Sllod" equations of motion) led to a kinetic theory of dilute hard-sphere gases under shear. However, a solution for collisions, necessary for a complete theory at higher densities, has been missing. We present an analytic solution to this problem, which provides surprising insights into the mechanical aspects of thermostatting a system in an external field. The equivalence of constant temperature and constant energy ensembles in the thermodynamic limit in equilibrium, the conditions for the nature of heat exchange with the environment (entropy creation and reduction) in the system, and the condition for appearance of the artificial string phase follow from our solution

Selectivity of nanocavities and dislocations for gettering of Cu and Fe in silicon

The selectivity of interstitial-based extended defects (loops) and nanocavities for the gettering of Cu and Fe in Si has been studied. Controlled amounts of Cu and Fe were introduced by ion implantation into wafers containing pre-existing nanocavities and/or dislocations. Results show that Cu has a strong preference for gettering to open volume defects, even when high concentrations of interstitial-based loops are present in close proximity. However, the gettering of Fe in samples containing both vacancy- and interstitial-type defects is more complex, with Fe accumulation at all regions in the sample which contain defects, whether they are vacancy- or interstitial-like in character

2D and 3D Dense-Fluid Shear Flows via Nonequilibrium Molecular Dynamics. Comparison of Time-and-Space-Averaged Tensor Temperature and Normal Stresses from Doll's, Sllod, and Boundary-Driven Shear Algorithms

Homogeneous shear flows (with constant strainrate du/dy) are generated with the Doll's and Sllod algorithms and compared to corresponding inhomogeneous boundary-driven flows. We use one-, two-, and three-dimensional smooth-particle weight functions for computing instantaneous spatial averages. The nonlinear stress differences are small, but significant, in both two and three space dimensions. In homogeneous systems the sign and magnitude of the shearplane stress difference, P(xx) - P(yy), depend on both the thermostat type and the chosen shearflow algorithm. The Doll's and Sllod algorithms predict opposite signs for this stress difference, with the Sllod approach definitely wrong, but somewhat closer to the (boundary-driven) truth. Neither of the homogeneous shear algorithms predicts the correct ordering of the kinetic temperatures, T(xx) > T(zz) > T(yy).Comment: 34 pages with 12 figures, under consideration by Physical Review

Formation of defects in boron nitride by low energy ion bombardment

Formation of defects in hexagonal and cubic boron nitride (h -BN and c -BN, respectively) under low-energy argon or nitrogen ion-bombardment has been studied by near-edge x-ray absorption fine structure (NEXAFS) around boron and nitrogen K -edges. Breaking of B-N bonds for both argon and nitrogen bombardment and formation of nitrogen vacancies, VN, has been identified from the B K -edge of both h -BN and c -BN, followed by the formation of molecular nitrogen, N2, at interstitial positions. The presence of N 2 produces an additional peak in photoemission spectra around N 1s core level and a sharp resonance in the low-resolution NEXAFS spectra around N K -edge, showing the characteristic vibrational fine structure in high-resolution measurements. In addition, several new peaks within the energy gap of BN, identified by NEXAFS around B and N K -edges, have been assigned to boron or nitrogen interstitials, in good agreement with theoretical predictions. Ion bombardment destroys the cubic phase of c -BN and produces a phase similar to a damaged hexagonal phase. &copy; 2009 American Institute of Physics.<br /

Vaccination and Timing Influence SIV Immune Escape Viral Dynamics In Vivo

CD8+ cytotoxic T lymphocytes (CTL) can be effective at controlling HIV-1 in humans and SIV in macaques, but their utility is partly offset by mutational escape. The kinetics of CTL escape and reversion of escape mutant viruses upon transmission to MHC-mismatched hosts can help us understand CTL-mediated viral control and the fitness cost extracted by immune escape mutation. Traditional methods for following CTL escape and reversion are, however, insensitive to minor viral quasispecies. We developed sensitive quantitative real-time PCR assays to track the viral load of SIV Gag164–172 KP9 wild-type (WT) and escape mutant (EM) variants in pigtail macaques. Rapid outgrowth of EM virus occurs during the first few weeks of infection. However, the rate of escape plateaued soon after, revealing a prolonged persistence of WT viremia not detectable by standard cloning and sequencing methods. The rate of escape of KP9 correlated with levels of vaccine-primed KP9-specific CD8+ T cells present at that time. Similarly, when non-KP9 responder (lacking the restricting Mane-A*10 allele) macaques were infected with SHIVmn229 stock containing a mixture of EM and WT virus, rapid reversion to WT was observed over the first 2 weeks following infection. However, the rate of reversion to WT slowed dramatically over the first month of infection. The serial quantitation of escape mutant viruses evolving during SIV infection shows that rapid dynamics of immune escape and reversion can be observed in early infection, particularly when CD8 T cells are primed by vaccination. However, these early rapid rates of escape and reversion are transient and followed by a significant slowing in these rates later during infection, highlighting that the rate of escape is significantly influenced by the timing of its occurrence

Lyapunov Exponent Pairing for a Thermostatted Hard-Sphere Gas under Shear in the Thermodynamic Limit

We demonstrate why for a sheared gas of hard spheres, described by the SLLOD equations with an iso-kinetic Gaussian thermostat in between collisions, deviations of the conjugate pairing rule for the Lyapunov spectrum are to be expected, employing a previous result that for a large number of particles $N$, the iso-kinetic Gaussian thermostat is equivalent to a constant friction thermostat, up to $1/\sqrt{N}$ fluctuations. We also show that these deviations are at most of the order of the fourth power in the shear rate.Comment: 4 pages, to appear in Rapid Comm., Phys. Rev.

Optima Nutrition: an allocative efficiency tool to reduce childhood stunting by better targeting of nutrition-related interventions.

BACKGROUND: Child stunting due to chronic malnutrition is a major problem in low- and middle-income countries due, in part, to inadequate nutrition-related practices and insufficient access to services. Limited budgets for nutritional interventions mean that available resources must be targeted in the most cost-effective manner to have the greatest impact. Quantitative tools can help guide budget allocation decisions. METHODS: The Optima approach is an established framework to conduct resource allocation optimization analyses. We applied this approach to develop a new tool, 'Optima Nutrition', for conducting allocative efficiency analyses that address childhood stunting. At the core of the Optima approach is an epidemiological model for assessing the burden of disease; we use an adapted version of the Lives Saved Tool (LiST). Six nutritional interventions have been included in the first release of the tool: antenatal micronutrient supplementation, balanced energy-protein supplementation, exclusive breastfeeding promotion, promotion of improved infant and young child feeding (IYCF) practices, public provision of complementary foods, and vitamin A supplementation. To demonstrate the use of this tool, we applied it to evaluate the optimal allocation of resources in 7 districts in Bangladesh, using both publicly available data (such as through DHS) and data from a complementary costing study. RESULTS: Optima Nutrition can be used to estimate how to target resources to improve nutrition outcomes. Specifically, for the Bangladesh example, despite only limited nutrition-related funding available (an estimated $0.75 per person in need per year), even without any extra resources, better targeting of investments in nutrition programming could increase the cumulative number of children living without stunting by 1.3 million (an extra 5%) by 2030 compared to the current resource allocation. To minimize stunting, priority interventions should include promotion of improved IYCF practices as well as vitamin A supplementation. Once these programs are adequately funded, the public provision of complementary foods should be funded as the next priority. Programmatic efforts should give greatest emphasis to the regions of Dhaka and Chittagong, which have the greatest number of stunted children. CONCLUSIONS: A resource optimization tool can provide important guidance for targeting nutrition investments to achieve greater impact