Bioinformatics for Membrane Lipid Simulations: Models, Computational Methods, and Web Server Tools

Biological membranes are complex environments consisting of different types of lipids and membrane proteins. The structure of a lipid bilayer is typically difficult to study because the membrane liquid crystalline state is made up of multiple disordered lipid molecules. This complicates the description of the lipid membrane properties by the conformation of any single lipid molecule. Molecular dynamics (MD) simulations have been used extensively to investigate properties of membrane lipids, lipid vesicles, and membrane protein systems. All-atom membrane models can elucidate detailed contacts between membrane proteins and its surrounding lipids, while united-atom and coarse-grained description have allowed larger models and longer timescales up to microsecond mark to be probed. Additionally, membrane models with mixed phospholipids and lipopolysaccharide content have made it possible to model improved views of biological membranes. Here, we present an overview of commonly used lipid force fields by the biosimulation community, useful tools for membrane MD simulations, and recent advances in membrane simulations

Fundamental thickness limit of itinerant ferromagnetic SrRuO3_3 thin films

We report on a fundamental thickness limit of the itinerant ferromagnetic oxide SrRuO$_3$ that might arise from the orbital-selective quantum confinement effects. Experimentally, SrRuO$_3$ films remain metallic even for a thickness of 2 unit cells (uc), but the Curie temperature, T$_C$, starts to decrease at 4 uc and becomes zero at 2 uc. Using the Stoner model, we attributed the T$_C$ decrease to a decrease in the density of states (N$_o$). Namely, in the thin film geometry, the hybridized Ru-d$_yz,zx$ orbitals are terminated by top and bottom interfaces, resulting in quantum confinement and reduction of N$_o$.Comment: 20 pages, 4 figure

The Full Range of Predictions for B Physics From Iso-singlet Down Quark Mixing

We extend the range of predictions of the isosinglet (or vector) down quark model to the fully allowed physical ranges, and also update this with the effect of new physics constraints. We constrain the present allowed ranges of sin(2*beta) and sin(2*alpha), gamma, x_s, and A_{B_s}. In models allowing mixing to a new isosinglet down quark (as in E_6) flavor changing neutral currents are induced that allow a Z^0 mediated contribution to B-Bbar mixing and which bring in new phases. In (rho, eta), (x_s, sin(gamma)), and (x_s, A_{B_s}) plots for the extra isosinglet down quark model which are herein extended to the full physical range, we find new allowed regions that will require experiments on sin(gamma) and/or x_s to verify or to rule out an extra down quark contribution.Comment: 13 pages in RevTeX, 7 postscript figure

Iso-singlet Down Quark Mixing And CP Violation Experiments

We confront the new physics models with extra iso-singlet down quarks in the new CP violation experimental era with $\sin{(2\beta)}$ and $\epsilon'/\epsilon$ measurements, $K^+ \to \pi^+ \nu \bar{\nu}$ events, and $x_s$ limits. The closeness of the new experimental results to the standard model theory requires us to include full SM amplitudes in the analysis. In models allowing mixing to a new isosinglet down quark, as in E$_6$, flavor changing neutral currents are induced that allow a $Z^0$ mediated contribution to $B-\bar B$ mixing and which bring in new phases. In $(\rho,\eta)$, $(x_s,\sin{(\gamma)})$, and $(x_s, \sin{(2\phi_s)})$ plots we still find much larger regions in the four down quark model than in the SM, reaching down to $\eta \approx 0$, $0 \leq \sin{(\gamma)} \leq 1$, $-.75 \leq \sin{(2\alpha)} \leq 0.15$, and $\sin{(2\phi_s)}$ down to zero, all at 1$\sigma$. We elucidate the nature of the cancellation in an order $\lambda^5$ four down quark mixing matrix element which satisfies the experiments and reduces the number of independent angles and phases. We also evaluate tests of unitarity for the $3\times3$ CKM submatrix.Comment: 14 pages, 16 figures, REVTeX

Microwave-Assisted Synthesis of Porous ZnO/SnS 2

Porous ZnO/SnS2 nanocomposites with adjustable SnS2 contents were prepared via microwave-assisted heating of different aqueous solutions of SnS2 precursors in the presence of fixed amount of ZnCO3 nanoparticles at pH 7. The structures, compositions, BET specific surface areas, and optical properties of the as-prepared products were characterized by X-ray diffraction, energy dispersive X-ray spectroscopy, transmission electron microscopy, N2 adsorption, and UV-Vis absorption spectra. Photocatalytic activities of the samples were tested by the removal of aqueous ciprofloxacin, CrVI, and methylene blue under visible-light (λ>420 nm) irradiation. The experimental results reveal that the as-prepared heterogeneous nanostructures exhibit much higher visible-light-driven photocatalytic activity for the degradation of the pollutants than pure SnS2 nanocrystals. The photocatalytic degradation rates Ct/C0 of the pollutants for the most active heterogeneous nanostructure are about 10, 49, and 9 times higher than that of pure SnS2. The enhanced photocatalytic activities exhibited by the heterojunctions could be ascribed to the synergetic effect of enhanced absorption in the visible region and the reduced rate of charge carrier recombination because of efficient separation and electron transfer from the SnS2 to ZnO nanoparticles

Synthesis of CdS Sensitized TiO 2

A series of CdS/TiO2 nanocomposites with different Cd to Ti molar ratio were synthesized from P25-TiO2 nanopowder using microwave-assisted hydrothermal method. The as-produced powders were characterized by XRD, electron microscopy, EDX, and UV-Vis diffuse reflectance spectroscopy. The adsorption capacity and photocatalytic activity of the samples were investigated using methylene blue as a model pollutant. Sorption tests revealed that the adsorption of MB onto the samples obeys the Freundlich-Langmuir isotherm model. The sorption capacity decreased as follows: TiO2>TCd2>TCd1>TCd3>TCd4. The results of the photocatalytic tests under high-intensity discharge (HID) lamp revealed that CdS/TiO2 powders with low Cd to Ti molar ratios exhibited much higher activities than P25-TiO2. The CdS/TiO2 sample with 20% CdS/(TCd2) showed the most activity among all these samples. The results also show that the Cd to Ti molar ratio of the nanocomposite has a significant effect on the photodegradation of MB and the enhanced activities exhibited by the nanocomposites are because of the low rate of electron-hole recombination

Constraints on the Mass and Mixing of the 4th Generation Quark From Direct CP Violationϵ′/ϵ\epsilon^{\prime}/\epsilon and Rare K Decays

We investigate the $\epsilon^{\prime} /\epsilon$ for $K\to \pi\pi$ in a sequential fourth generation model. By giving the basic formulae for $\epsilon^{\prime}/\epsilon$ in this model, we analyze the numerical results which are dependent of $m_{t^{\prime}}$ and imaginary part of the fourth CKM factor, ${Im}V^{*}_{t^{'}s}V_{t^{'}d}$ (or $V^{*}_{t^{'}s}V_{t^{'}d}$ and the fourth generation CKM matrix phase $\theta$). We find that, unlike the SM, when taking the central values of all parameters for $\epsilon^{\prime}/\epsilon$, the values of $\epsilon^{\prime}/ \epsilon$ can easily fit to the current experimental data for all values of hadronic matrix elements estimated from various approaches. Also, we show that the experimental values of $\epsilon^{\prime}/\epsilon$ and rare K decays can provide a strong constraint on both mass and mixing of the fourth generation quark. When taking the values of hadronic matrix elements from the lattice or 1/N expansion calculations, a large region of the up-type quark mass $m_{t^{\prime}}$ is excluded.Comment: 18 pages, 4 eps figure

Evidence for the Decay Sigma+ -> p mu+ mu-

We report the first evidence for the decay Sigma+ -> p mu+ mu- from data taken by the HyperCP experiment(E871) at Fermilab. Based on three observed events, the branching ratio is B(Sigma+ -> p,mu+,mu-) = [8.6 +6.6,-5.4(stat) +/-5.5(syst)] x 10**-8. The narrow range of dimuon masses may indicate that the decay proceeds via a neutral intermediate state, Sigma+ -> p P0, P0 -> mu+ mu-, with a P0 mass of 214.3 +/- 0.5 MeV/c**2 and branching ratio B(Sigma+ -> p P0; P0 -> mu+ mu-) = [3.1 +2.4,-1.(stat) +/-1.5(syst)] x 10**-8.Comment: As published in PR