Numerical simulations of immiscible generalised Newtonian fluids

We present a numerical methodology for three-dimensional large-scale simulations of two-fluid flow for generalised Newtonian fluids exhibiting non-Newtonian behaviour such as a non-zero yield stress and power-law dependency on strain-rate. The incompressible continuity and Cauchy momentum equations, along with appropriate rheological models, are solved using a computational framework initially developed at Lawrence Berkeley National Laboratory. The solver uses second-order Godunov method- ology for the advective terms and semi-implicit diffusion in the context of an approximate projection method to evolve the system in time. We have extended the algorithm to en- able the simulation of Herschel-Bulkley fluids by means of a mathematical regularisation of the constitutive equation which describes the fluid rheology. Additionally, interfaces between fluids with different properties are treated using a passively advected indicator function. The performance of the software is validated for two-dimensional displacement flow and tested on a three-dimensional viscoplastic dambreak.Funding and technical support from BP through the BP International Centre for Advanced Materials (BP-ICAM) which made this research possible

Sensorimotor temporal recalibration within and across limbs

Deciding precisely when we have acted is challenging, as actions involve a train of neural events spread across both space and time. Repeated delays between actions and consequent events can result in a shift, such that immediate feedback can seem to precede the causative act. Here we examined which neurocognitive representations are affected during such sensorimotor temporal recalibration, by testing if the effect generalizes across limbs and whether it might reflect altered decision criteria for temporal judgments. Hand or foot adaptation phases were interspersed with simultaneity judgments about actions involving the same or opposite limb. Shifts in the distribution of participants' simultaneity responses were quantified using a detection-theoretic model, where a shift of both boundaries together gives a stronger indication that the effect is not simply a result of decision bias. By demonstrating that temporal recalibration occurs in the foot as well as the hand, we confirmed that it is a robust motor phenomenon: Both low and high boundaries shifted reliably in the same-limb conditions. However, in cross-limb conditions only the high boundary shifted reliably. These two patterns are interpreted to reflect a genuine change in how the time of action is represented, and a timing criterion shift, respectively. (PsycINFO Database Record (c) 2013 APA, all rights reserved)

Using knowledge: the dilemmas of 'bridging research and policy'

The 'knowledge agenda' has become a central part of development discourse. This paper addresses one aspect of this discourse - the use of policy research in the social sciences - and the dilemmas that have been encountered by both development agencies and researchers in communicating and making use of that research. Development agencies as well as NGOs have initiated work to evaluate and document the effectiveness of research partnerships, knowledge capacity building and (social) science policy impact. As a multilateral initiative, the Global Development Network (GDN), and especially its 'Bridging Research and Policy' project, provides a vehicle to address issues related to research impact. Twelve perspectives on improving research and policy linkages are outlined to reveal that how the problem is defined shapes policy responses. Taken together, these explanations provide a multifaceted picture of the research-policy nexus indicating that there are many possible routes to 'bridging' research and policy. These diverse perspectives will be categorised into three broad categories of explanation: (i) supply-side; (ii) demand-led; and (iii) policy currents. However, knowledge is part of the solution to many development problems but not of itself a panacea

Simulating carbon capture by enhanced weathering with global croplands: an overview of key processes highlighting areas of future model development

Enhanced weathering (EW) aims to amplify a natural sink for CO2 by incorporating powdered silicate rock with high reactive surface area into agricultural soils. The goal is to achieve rapid dissolution of minerals and release of alkalinity with accompanying dissolution of CO2 into soils and drainage waters. EW could counteract phosphorus limitation and greenhouse gas (GHG) emissions in tropical soils, and soil acidification, a common agricultural problem studied with numerical process models over several decades. Here, we review the processes leading to soil acidification in croplands and how the soil weathering CO2 sink is represented in models. Mathematical models capturing the dominant processes and human interventions governing cropland soil chemistry and GHG emissions neglect weathering, while most weathering models neglect agricultural processes. We discuss current approaches to modelling EW and highlight several classes of model having the potential to simulate EW in croplands. Finally, we argue for further integration of process knowledge in mathematical models to capture feedbacks affecting both longer-term CO2 consumption and crop growth and yields

A repurposing strategy for Hsp90 inhibitors demonstrates their potency against filarial nematodes

Novel drugs are required for the elimination of infections caused by filarial worms, as most commonly used drugs largely target the microfilariae or first stage larvae of these infections. Previous studies, conducted in vitro, have shown that inhibition of Hsp90 kills adult Brugia pahangi. As numerous small molecule inhibitors of Hsp90 have been developed for use in cancer chemotherapy, we tested the activity of several novel Hsp90 inhibitors in a fluorescence polarization assay and against microfilariae and adult worms of Brugia in vitro. The results from all three assays correlated reasonably well and one particular compound, NVP-AUY922, was shown to be particularly active, inhibiting Mf output from female worms at concentrations as low as 5.0 nanomolar after 6 days exposure to drug. NVP-AUY922 was also active on adult worms after a short 24 h exposure to drug. Based on these in vitro data, NVP-AUY922 was tested in vivo in a mouse model and was shown to significantly reduce the recovery of both adult worms and microfilariae. These studies provide proof of principle that the repurposing of currently available Hsp90 inhibitors may have potential for the development of novel agents with macrofilaricidal properties

Quantitative localized proton-promoted dissolution kinetics of calcite using scanning electrochemical microscopy (SECM)

Scanning electrochemical microscopy (SECM) has been used to determine quantitatively the kinetics of proton-promoted dissolution of the calcite (101̅4) cleavage surface (from natural “Iceland Spar”) at the microscopic scale. By working under conditions where the probe size is much less than the characteristic dislocation spacing (as revealed from etching), it has been possible to measure kinetics mainly in regions of the surface which are free from dislocations, for the first time. To clearly reveal the locations of measurements, studies focused on cleaved “mirror” surfaces, where one of the two faces produced by cleavage was etched freely to reveal defects intersecting the surface, while the other (mirror) face was etched locally (and quantitatively) using SECM to generate high proton fluxes with a 25 μm diameter Pt disk ultramicroelectrode (UME) positioned at a defined (known) distance from a crystal surface. The etch pits formed at various etch times were measured using white light interferometry to ascertain pit dimensions. To determine quantitative dissolution kinetics, a moving boundary finite element model was formulated in which experimental time-dependent pit expansion data formed the input for simulations, from which solution and interfacial concentrations of key chemical species, and interfacial fluxes, could then be determined and visualized. This novel analysis allowed the rate constant for proton attack on calcite, and the order of the reaction with respect to the interfacial proton concentration, to be determined unambiguously. The process was found to be first order in terms of interfacial proton concentration with a rate constant k = 6.3 (± 1.3) × 10–4 m s–1. Significantly, this value is similar to previous macroscopic rate measurements of calcite dissolution which averaged over large areas and many dislocation sites, and where such sites provided a continuous source of steps for dissolution. Since the local measurements reported herein are mainly made in regions without dislocations, this study demonstrates that dislocations and steps that arise from such sites are not needed for fast proton-promoted calcite dissolution. Other sites, such as point defects, which are naturally abundant in calcite, are likely to be key reaction sites

Viral trans-factor independent replication of human papillomavirus genomes

<p>Abstract</p> <p>Background</p> <p>Papillomaviruses (PVs) establish a persistent infection in the proliferating basal cells of the epithelium. The viral genome is replicated and maintained as a low-copy nuclear plasmid in basal keratinocytes. Bovine and human papillomaviruses (BPV and HPV) are known to utilize two viral proteins; E1, a DNA helicase, and E2, a transcription factor, which have been considered essential for viral DNA replication. However, growing evidence suggests that E1 and E2 are not entirely essential for stable replication of HPV.</p> <p>Results</p> <p>Here we report that multiple HPV16 mutants, lacking either or both E1 and E2 open reading frame (ORFs) and the long control region (LCR), still support extrachromosomal replication. Our data clearly indicate that HPV16 has a mode of replication, independent of viral trans-factors, E1 and E2, which is achieved by origin activity located outside of the LCR.</p