Computer simulations of the diffusion of Na+ and Cl− ions across POPC lipid bilayer membranes

We have carried out molecular dynamics simulations using NAMD to study the diffusivity of Na and Cl ions across a POPC lipid bilayer membrane. We show that an imbalance of positively and negatively charged ions on either side of the membrane leads to the diffusion of ions and water molecules. We considered the cases of both weak and very strong charge imbalance across the membrane. The diffusion coefficients of the ions have been determined from the mean square displacements of the particles as a function of time. We find that for strong electrochemical gradients, both the Na and Cl ions diffuse rapidly through pores in the membrane with diffusion coefficients up to ten times larger than in water. Rather surprisingly, we found that although the Na ions are the first to begin the permeation process due to the lower potential barrier that they experience compared to the Cl ions, the latter complete the permeation across the barrier more quickly due to their faster diffusion rates

Molecular dynamics studies of the melting of copper with vacancies and dislocations at high pressures

Molecular dynamics simulations of the melting process of bulk copper were performed using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) with the interatomic potentials being described by the embedded atom method. The aim of the study was to understand the effects of high pressures and defects on the melting temperature. The simulations were visualised using Visual Molecular Dynamics (VMD). The melting temperature of a perfect copper crystal, was found to be slightly higher than the experimentally observed value. The melting temperature as a function of pressure was determined and compared with experiment. Point and line defects, in the form of dislocations, were then introduced into crystal and the new melting temperature of the crystal determined. We find that the melting temperature decreases as the defect density is increased. Additionally, the slope of the melting temperature curve was found to decrease as the pressure was increased while the vacancy formation energy increases with pressure

Three-dimensional geometry, ore distribution and time-integrated mass transfer through the quartz-tourmaline-gold vein network of the Sigma deposit (Abitibi belt, Canada)

We present a reconstruction of the three-dimensional (3D) geometry and gold grade distribution of shear zone-hosted, Au-mineralized, quartz-tourmaline veins of the Sigma deposit (Abitibi belt). Host shears and veins form a network of anastomosing, steeply dipping structures associated with smaller subhorizontal extensional veins. Our reconstruction has been carried out using the exceptionally large geological database of the mine. From this database, we extracted the geometric position, thickness and gold grades of geometrically best-defined steep veins contained in a representative subvolume of the deposit. These data allowed the 3D representation of 53 veins, which have been constructed by fitting surfaces through the geometrical data and by contouring thickness and gold grade. The geometry of the network is mainly characterized by: (i) a few large segmented veins, with sinuous and helicoidal shape, and typical vertical dimension of >100 m; (ii) a large number of smaller vertical veins, some of which splay off the steep veins with high dip angles; (iii) subhorizontal extension veins (joints) located at, or close to, the tips of steep veins. The absolute thickness of the vertically short veins is the same as that of the large veins, suggesting that they formed simultaneously, but only a few of them interconnect to form vertically continuous bodies. Patchy, vertically elongated zones of high dilation are present in the large veins, and are poorly correlated with Au-rich zones. They presumably represent former high-permeability zones of the network. The highest gold grades occur at the interconnections between the large veins and small splays or subhorizontal joints. This indicates the important role of vein interconnection for fluid flow and gold precipitation within the network. Combining the calculation of the volume of the network with the estimation of tourmaline abundance in the veins, we calculate that 2.1 × 106 m3 of tourmaline and 3.2 × 106 m3 of quartz precipitated during Au deposition

Coarse grained molecular dynamic simulations of the interaction a carbon nanotube with a bilayer membrane

In coarse grained molecular dynamics (CGMD) simulations, small groups of atoms are treated as single particles (beads) and the forces between these particles are derived from the interatomic forces. The effect of this is to severely reduce the number of particles in a simulation, thereby allowing for the consideration of a larger number of atoms. It has also proven to be a valuable tool in probing time and length scales of systems beyond that used in all-atom molecular dynamics (AAMD) simulations. The down side of this is that the inter-particle interactions are less accurate. However, if these coarse grained particles are chosen carefully, such simulations can provide much useful information. There are different levels of how the coarse grains are constructed. For example, CG systems have been developed using tens or hundreds of atoms per CG bead in some studies of amino acids in biological science. By contrast, for other systems, a single CG bead is used to replace just two or three atoms. In this paper, the interaction of a carbon nanotube (CNT) with a lipid bilayer membrane is studied using both coarse grained and atomistic MD in an effort to understand the usefulness of the CGMD method for such simulations. Our preliminary studies of the interaction of a CNT with a lipid bilayer points indicates that such nano-tubes inserted into a membrane could be stable. This means that it could be used as an agent in the delivery of drugs. It would be good if these simulations could be repeated using AAMD simulations to confirm the validity of these results

Strain Distribution During Growth of Ge/Si(001) and the Effect of Surfactant Layers

Grazing incidence X-ray diffraction has been employed to determine directly the distribution of strain in the plane of the interface during deposition of Ge onto Si(001). The corresponding strain distribution has also been deduced for a relaxed island whose atomic structure has been determined by molecular dynamics. The results illustrate the central role of elastic deformation of islands in the initial stage of strain relief. The results are also compared with those for growth with a Sb surfactant layer which suppresses island formation. An investigation of surfactant-like behaviour is also presented for homoepitaxial growth of Ag on Ag(111), where sub-monolayer coverages of Sb promote a layer-by-layer growth mode over a wide temperature range

Simulation Studies of Polymer Translocation through a Channel

Monte Carlo simulation studies of the translocation of homopolymers of length N driven through a channel have been performed. We find that the translocation time τ depends on temperature in a nontrivial way. For temperatures below some critical temperature θc, τ∼T-1.4, whereas for T>θc, τ increases with temperature. The low temperature results are in good agreement with experimental findings as is the dependence of τ on the driving field strength. The velocity of translocation displays the same characteristics as found in experiment but the N dependence of τ shows the linear relationship observed in experiment only for large values of N. A possible reason for this is suggested

Effect of strain on surface diffusion in semiconductor heteroepitaxy

We present a first-principles analysis of the strain renormalization of the cation diffusivity on the GaAs(001) surface. For the example of In/GaAs(001)-c(4x4) it is shown that the binding of In is increased when the substrate lattice is expanded. The diffusion barrier \Delta E(e) has a non-monotonic strain dependence with a maximum at compressive strain values (e 0) studied. We discuss the consequences of spatial variations of both the binding energy and the diffusion barrier of an adatom caused by the strain field around a heteroepitaxial island. For a simplified geometry, we evaluate the speed of growth of two coherently strained islands on the GaAs(001) surface and identify a growth regime where island sizes tend to equalize during growth due to the strain dependence of surface diffusion.Comment: 10 pages, 8 figures, LaTeX2e, to appear in Phys. Rev. B (2001). Other related publications can be found at http://www.rz-berlin.mpg.de/th/paper.htm

Planck Intermediate Results II: Comparison of Sunyaev-Zeldovich measurements from Planck and from the Arcminute Microkelvin Imager for 11 galaxy clusters

A comparison is presented of Sunyaev-Zeldovich measurements for 11 galaxy clusters as obtained by Planck and by the ground-based interferometer, the Arcminute Microkelvin Imager. Assuming a universal spherically-symmetric Generalised Navarro, Frenk & White (GNFW) model for the cluster gas pressure profile, we jointly constrain the integrated Compton-Y parameter (Y_500) and the scale radius (theta_500) of each cluster. Our resulting constraints in the Y_500-theta_500 2D parameter space derived from the two instruments overlap significantly for eight of the clusters, although, overall, there is a tendency for AMI to find the Sunyaev-Zeldovich signal to be smaller in angular size and fainter than Planck. Significant discrepancies exist for the three remaining clusters in the sample, namely A1413, A1914, and the newly-discovered Planck cluster PLCKESZ G139.59+24.18. The robustness of the analysis of both the Planck and AMI data is demonstrated through the use of detailed simulations, which also discount confusion from residual point (radio) sources and from diffuse astrophysical foregrounds as possible explanations for the discrepancies found. For a subset of our cluster sample, we have investigated the dependence of our results on the assumed pressure profile by repeating the analysis adopting the best-fitting GNFW profile shape which best matches X-ray observations. Adopting the best-fitting profile shape from the X-ray data does not, in general, resolve the discrepancies found in this subset of five clusters. Though based on a small sample, our results suggest that the adopted GNFW model may not be sufficiently flexible to describe clusters universally.Comment: update to metadata author list onl

Planck Intermediate Results. IX. Detection of the Galactic haze with Planck

Using precise full-sky observations from Planck, and applying several methods of component separation, we identify and characterize the emission from the Galactic "haze" at microwave wavelengths. The haze is a distinct component of diffuse Galactic emission, roughly centered on the Galactic centre, and extends to |b| ~35 deg in Galactic latitude and |l| ~15 deg in longitude. By combining the Planck data with observations from the WMAP we are able to determine the spectrum of this emission to high accuracy, unhindered by the large systematic biases present in previous analyses. The derived spectrum is consistent with power-law emission with a spectral index of -2.55 +/- 0.05, thus excluding free-free emission as the source and instead favouring hard-spectrum synchrotron radiation from an electron population with a spectrum (number density per energy) dN/dE ~ E^-2.1. At Galactic latitudes |b|<30 deg, the microwave haze morphology is consistent with that of the Fermi gamma-ray "haze" or "bubbles," indicating that we have a multi-wavelength view of a distinct component of our Galaxy. Given both the very hard spectrum and the extended nature of the emission, it is highly unlikely that the haze electrons result from supernova shocks in the Galactic disk. Instead, a new mechanism for cosmic-ray acceleration in the centre of our Galaxy is implied.Comment: 15 pages, 9 figures, submitted to Astronomy and Astrophysic

Rapid tests and urine sampling techniques for the diagnosis of urinary tract infection (UTI) in children under five years: a systematic review

Background: Urinary tract infection (UTI) is one of the most common sources of infection in children under five. Prompt diagnosis and treatment is important to reduce the risk of renal scarring. Rapid, cost-effective, methods of UTI diagnosis are required as an alternative to culture. Methods: We conducted a systematic review to determine the diagnostic accuracy of rapid tests for detecting UTI in children under five years of age. Results: The evidence supports the use of dipstick positive for both leukocyte esterase and nitrite (pooled LR+ = 28.2, 95% CI: 17.3, 46.0) or microscopy positive for both pyuria and bacteriuria (pooled LR+ = 37.0, 95% CI: 11.0, 125.9) to rule in UTI. Similarly dipstick negative for both LE and nitrite (Pooled LR- = 0.20, 95% CI: 0.16, 0.26) or microscopy negative for both pyuria and bacteriuria (Pooled LR- = 0.11, 95% CI: 0.05, 0.23) can be used to rule out UTI. A test for glucose showed promise in potty-trained children. However, all studies were over 30 years old. Further evaluation of this test may be useful. Conclusion: Dipstick negative for both LE and nitrite or microscopic analysis negative for both pyuria and bacteriuria of a clean voided urine, bag, or nappy/pad specimen may reasonably be used to rule out UTI. These patients can then reasonably be excluded from further investigation, without the need for confirmatory culture. Similarly, combinations of positive tests could be used to rule in UTI, and trigger further investigation