Study of the antimicrobial peptide indolicidin and a mutant in micelle medium by molecular dynamics simulation

The antimicrobial peptide indolicidin (IND) and the mutant CP10A in hydrated micelles were studied using molecular dynamics simulations in order to observe whether the molecular dynamics and experimental data could be sufficiently correlated and a detailed description of the interaction of the antimicrobial peptides with a model of the membrane provided by a hydrated micelle system could be obtained. In agreement with the experiments, the simulations showed that the peptides are located near the surface of the micelles. Peptide insertions agree with available experimental data, showing deeper insertion of the mutant compared with the peptide IND. Major insertion into the hydrophobic core of the micelle by all tryptophan and mutated residues of CP10A in relation to IND was observed. The charged residues of the terminus regions of both peptides present similar behavior, indicating that the major differences in the interactions with the micelles of the peptides IND and CP10A occur in the case of the hydrophobic residues.

Sequential analysis of global gene expression profiles in immature and in vitro matured bovine oocytes: potential molecular markers of oocyte maturation

Background: Without intensive selection, the majority of bovine oocytes submitted to in vitro embryo production (IVP) fail to develop to the blastocyst stage. This is attributed partly to their maturation status and competences. Using the Affymetrix GeneChip Bovine Genome Array, global mRNA expression analysis of immature (GV) and in vitro matured (IVM) bovine oocytes was carried out to characterize the transcriptome of bovine oocytes and then use a variety of approaches to determine whether the observed transcriptional changes during IVM was real or an artifact of the techniques used during analysis. Results: 8489 transcripts were detected across the two oocyte groups, of which similar to 25.0% (2117 transcripts) were differentially expressed (p < 0.001); corresponding to 589 over-expressed and 1528 under-expressed transcripts in the IVM oocytes compared to their immature counterparts. Over expression of transcripts by IVM oocytes is particularly interesting, therefore, a variety of approaches were employed to determine whether the observed transcriptional changes during IVM were real or an artifact of the techniques used during analysis, including the analysis of transcript abundance in oocytes in vitro matured in the presence of a-amanitin. Subsets of the differentially expressed genes were also validated by quantitative real-time PCR (qPCR) and the gene expression data was classified according to gene ontology and pathway enrichment. Numerous cell cycle linked (CDC2, CDK5, CDK8, HSPA2, MAPK14, TXNL4B), molecular transport (STX5, STX17, SEC22A, SEC22B), and differentiation (NACA) related genes were found to be among the several over-expressed transcripts in GV oocytes compared to the matured counterparts, while ANXA1, PLAU, STC1and LUM were among the over-expressed genes after oocyte maturation. Conclusion: Using sequential experiments, we have shown and confirmed transcriptional changes during oocyte maturation. This dataset provides a unique reference resource for studies concerned with the molecular mechanisms controlling oocyte meiotic maturation in cattle, addresses the existing conflicting issue of transcription during meiotic maturation and contributes to the global goal of improving assisted reproductive technology.

Fossil groups in the Millennium Simulation Evolution of the brightest galaxies

Aims. We create a catalogue of simulated fossil groups and study their properties, in particular the merging histories of their first-ranked galaxies. We compare the simulated fossil group properties with those of both simulated non-fossil and observed fossil groups. Methods. Using simulations and a mock galaxy catalogue, we searched for massive (>5 x 10(13) h(-1) M-circle dot) fossil groups in the Millennium Simulation Galaxy Catalogue. In addition, we attempted to identify observed fossil groups in the Sloan Digital Sky Survey Data Release 6 using identical selection criteria. Results. Our predictions on the basis of the simulation data are: (a) fossil groups comprise about 5.5% of the total population of groups/clusters with masses larger than 5 x 10(13) h(-1) M-circle dot. This fraction is consistent with the fraction of fossil groups identified in the SDSS, after all observational biases have been taken into account; (b) about 88% of the dominant central objects in fossil groups are elliptical galaxies that have a median R-band absolute magnitude of similar to-23.5-5 log h, which is typical of the observed fossil groups known in the literature; (c) first-ranked galaxies of systems with M > 5 x 10(13) h(-1) M-circle dot, regardless of whether they are either fossil or non-fossil, are mainly formed by gas-poor mergers; (d) although fossil groups, in general, assembled most of their virial masses at higher redshifts in comparison with non-fossil groups, first-ranked galaxies in fossil groups merged later, i.e. at lower redshifts, compared with their non-fossil-group counterparts. Conclusions. We therefore expect to observe a number of luminous galaxies in the centres of fossil groups that show signs of a recent major merger.

Fossil groups in the Millennium simulation Their environment and its evolution

Context. Fossil systems are defined to be X- ray bright galaxy groups ( or clusters) with a two- magnitude difference between their two brightest galaxies within half the projected virial radius, and represent an interesting extreme of the population of galaxy agglomerations. However, the physical conditions and processes leading to their formation are still poorly constrained. Aims. We compare the outskirts of fossil systems with that of normal groups to understand whether environmental conditions play a significant role in their formation. We study the groups of galaxies in both, numerical simulations and observations. Methods. We use a variety of statistical tools including the spatial cross- correlation function and the local density parameter Delta(5) to probe differences in the density and structure of the environments of "" normal"" and "" fossil"" systems in the Millennium simulation. Results. We find that the number density of galaxies surrounding fossil systems evolves from greater than that observed around normal systems at z = 0.69, to lower than the normal systems by z = 0. Both fossil and normal systems exhibit an increment in their otherwise radially declining local density measure (Delta(5)) at distances of order 2.5 r(vir) from the system centre. We show that this increment is more noticeable for fossil systems than normal systems and demonstrate that this difference is linked to the earlier formation epoch of fossil groups. Despite the importance of the assembly time, we show that the environment is different for fossil and non- fossil systems with similar masses and formation times along their evolution. We also confirm that the physical characteristics identified in the Millennium simulation can also be detected in SDSS observations. Conclusions. Our results confirm the commonly held belief that fossil systems assembled earlier than normal systems but also show that the surroundings of fossil groups could be responsible for the formation of their large magnitude gap.

First Direct Observation of Muon Antineutrino Disappearance

This Letter reports the first direct observation of muon antineutrino disappearance. The MINOS experiment has taken data with an accelerator beam optimized for (nu) over bar (mu) production, accumulating an exposure of 1.71 x 10(20) protons on target. In the Far Detector, 97 charged current (nu) over bar (mu) events are observed. The no-oscillation hypothesis predicts 156 events and is excluded at 6.3 sigma. The best fit to oscillation yields vertical bar Delta(m) over bar (2)vertical bar = [3.36(-0.40)(+0.46)(stat) +/- 0.06(sys)] x 10(-3) eV(2), sin(2)(2 (theta) over bar) = 0.86(-0.12)(+0.11)(stat) +/- 0.01(syst). The MINOS nu(mu) and (nu) over bar (mu) measurements are consistent at the 2.0% confidence level, assuming identical underlying oscillation parameters.

Precise measurements of direct CP violation, CPT symmetry, and other parameters in the neutral kaon system

We present precise tests of CP and CPT symmetry based on the full data set of K -> pi pi decays collected by the KTeV experiment at Fermi National Accelerator Laboratory during 1996, 1997, and 1999. This data set contains 16 x 10(6) K -> pi(0)pi(0) and 69 x 10(6) K -> pi(+)pi(-) decays. We measure the direct CP violation parameter Re(epsilon'/epsilon) = (19.2 +/- 2.1) x 10(-4). We find the K(L) -> K(S) mass difference Delta m = (5270 +/- 12) x 10(6) (h) over tilde s(-1) and the K(S) lifetime tau(S) = (89.62 +/- 0.05) x 10(-12) s. We also measure several parameters that test CPT invariance. We find the difference between the phase of the indirect CP violation parameter epsilon and the superweak phase: phi(epsilon) - phi(SW) =(0.40 +/- 0.56)degrees. We measure the difference of the relative phases between the CP violating and CP conserving decay amplitudes for K -> pi(+)pi(-) (phi(+-)) and for K -> pi(0)pi(0) (phi(00)): Delta phi = (0.30 +/- 0.35)degrees. From these phase measurements, we place a limit on the mass difference between K(0) and (K) over bar (0): Delta M < 4.8 x 10(-19) GeV/c(2) at 95% C.L. These results are consistent with those of other experiments, our own earlier measurements, and CPT symmetry.

High p(T) direct photon and pi(0) triggered azimuthal jet correlations and measurement of k(T) for isolated direct photons in p plus p collisions at root s=200 GeV

Correlations of charged hadrons of 1< p(T) < 10 Gev/c with high pT direct photons and pi(0) mesons in the range 5< p(T) < 15 Gev/c are used to study jet fragmentation in the gamma + jet and dijet channels, respectively. The magnitude of the partonic transverse momentum, k(T), is obtained by comparing to a model incorporating a Gaussian kT smearing. The sensitivity of the associated charged hadron spectra to the underlying fragmentation function is tested and the data are compared to calculations using recent global fit results. The shape of the direct photon-associated hadron spectrum as well as its charge asymmetry are found to be consistent with a sample dominated by quark-gluon Compton scattering. No significant evidence of fragmentation photon correlated production is observed within experimental uncertainties.

Enhanced Production of Direct Photons in Au plus Au Collisions at root s(NN)=200 GeV and Implications for the Initial Temperature

The production of e(+)e(-) pairs for m(e+e-) < 0.3 GeV/c(2) and 1< p(T) < 5 GeV/c is measured in p + p and Au + Au collisions at root s(NN) = 200 GeV. An enhanced yield above hadronic sources is observed. Treating the excess as photon internal conversions, the invariant yield of direct photons is deduced. In central Au + Au collisions, the excess of the direct photon yield over p + p is exponential in transverse momentum, with an inverse slope T = 221 +/- 19(stat) +/- 19(syst) MeV. Hydrodynamical models with initial temperatures ranging from T(init) similar to 300-600 MeV at times of similar to 0.6-0.15 fm/c after the collision are in qualitative agreement with the data. Lattice QCD predicts a phase transition to quark gluon plasma at similar to 170 MeV.

Detailed measurement of the e(+)e(-) pair continuum in p plus p and Au plus Au collisions at root s(NN)=200 GeV and implications for direct photon production

PHENIX has measured the e(+)e(-) pair continuum in root s(NN) = 200 GeV Au+Au and p+p collisions over a wide range of mass and transverse momenta. The e(+)e(-) yield is compared to the expectations from hadronic sources, based on PHENIX measurements. In the intermediate-mass region, between the masses of the phi and the J/psi meson, the yield is consistent with expectations from correlated c (c) over bar production, although other mechanisms are not ruled out. In the low-mass region, below the phi, the p+p inclusive mass spectrum is well described by known contributions from light meson decays. In contrast, the Au+Au minimum bias inclusive mass spectrum in this region shows an enhancement by a factor of 4.7 +/- 0.4(stat) +/- 1.5(syst) +/- 0.9(model). At low mass (m(ee) < 0.3 GeV/c(2)) and high p(T) (1 < p(T) < 5 GeV/c) an enhanced e(+)e(-) pair yield is observed that is consistent with production of virtual direct photons. This excess is used to infer the yield of real direct photons. In central Au+Au collisions, the excess of the direct photon yield over the p+p is exponential in p(T), with inverse slope T = 221 +/- 19(stat) +/- 19(syst) MeV. Hydrodynamical models with initial temperatures ranging from T(init) similar or equal to 300-600 MeV at times of 0.6-0.15 fm/c after the collision are in qualitative agreement with the direct photon data in Au+Au. For low p(T) < 1 GeV/c the low-mass region shows a further significant enhancement that increases with centrality and has an inverse slope of T similar or equal to 100 MeV. Theoretical models underpredict the low-mass, low-p(T) enhancement.

Study of the optical and magnetic properties of pyrimidine in water combining PCM and QM/MM methodologies

The solvent effects on the low-lying absorption spectrum and on the (15)N chemical shielding of pyrimidine in water are calculated using the combined and sequential Monte Carlo simulation and quantum mechanical calculations. Special attention is devoted to the solute polarization. This is included by an iterative procedure previously developed where the solute is electrostatically equilibrated with the solvent. In addition, we verify the simple yet unexplored alternative of combining the polarizable continuum model (PCM) and the hybrid QM/MM method. We use PCM to obtain the average solute polarization and include this in the MM part of the sequential QM/MM methodology, PCM-MM/QM. These procedures are compared and further used in the discrete and the explicit solvent models. The use of the PCM polarization implemented in the MM part seems to generate a very good description of the average solute polarization leading to very good results for the n-pi* excitation energy and the (15)N nuclear chemical shield of pyrimidine in aqueous environment. The best results obtained here using the solute pyrimidine surrounded by 28 explicit water molecules embedded in the electrostatic field of the remaining 472 molecules give the statistically converged values for the low lying n-pi* absorption transition in water of 36 900 +/- 100 (PCM polarization) and 36 950 +/- 100 cm(-1) (iterative polarization), in excellent agreement among one another and with the experimental value observed with a band maximum at 36 900 cm(-1). For the nuclear shielding (15)N the corresponding gas-water chemical shift obtained using the solute pyrimidine surrounded by 9 explicit water molecules embedded in the electrostatic field of the remaining 491 molecules give the statistically converged values of 24.4 +/- 0.8 and 28.5 +/- 0.8 ppm, compared with the inferred experimental value of 19 +/- 2 ppm. Considering the simplicity of the PCM over the iterative polarization this is an important aspect and the computational savings point to the possibility of dealing with larger solute molecules. This PCM-MM/QM approach reconciles the simplicity of the PCM model with the reliability of the combined QM/MM approaches.

Hydrogen bond interactions between acetone and supercritical water

Hydrogen bond interactions between acetone and supercritical water are investigated using a combined and sequential Monte Carlo/quantum mechanics (S-MC/QM) approach. Simulation results show a dominant presence of con. gurations with one hydrogen bond for different supercritical states, indicating that this specific interaction plays an important role on the solvation properties of acetone in supercritical water. Using QM MP2/aug-cc-pVDZ the calculated average interaction energy reveals that the hydrogen-bonded acetone-water complex is energetically more stable under supercritical conditions than ambient conditions and its stability is little affected by variations of temperature and/or pressure. All average results reported here are statistically converged.

Dynamic polarizability, Cauchy moments, and the optical absorption spectrum of liquid water: A sequential molecular dynamics/quantum mechanical approach

The dynamic polarizability and optical absorption spectrum of liquid water in the 6-15 eV energy range are investigated by a sequential molecular dynamics (MD)/quantum mechanical approach. The MD simulations are based on a polarizable model for liquid water. Calculation of electronic properties relies on time-dependent density functional and equation-of-motion coupled-cluster theories. Results for the dynamic polarizability, Cauchy moments, S(-2), S(-4), S(-6), and dielectric properties of liquid water are reported. The theoretical predictions for the optical absorption spectrum of liquid water are in good agreement with experimental information.

Combined Monte Carlo and quantum mechanics study of the solvatochromism of phenol in water. The origin of the blue shift of the lowest pi-pi* transition

A combined and sequential use of Monte Carlo simulations and quantum mechanical calculations is made to analyze the spectral shift of the lowest pi-pi* transition of phenol in water. The solute polarization is included using electrostatic embedded calculations at the MP2/aug-cc-pVDZ level giving a dipole moment of 2.25 D, corresponding to an increase of 76% compared to the calculated gas-phase value. Using statistically uncorrelated configurations sampled from the MC simulation,first-principle size-extensive calculations are performed to obtain the solvatochromic shift. Analysis is then made of the origin of the blue shift. Results both at the optimized geometry and in room-temperature liquid water show that hydrogen bonds of water with phenol promote a red shift when phenol is the proton-donor and a blue shift when phenol is the proton-acceptor. In the case of the optimized clusters the calculated shifts are in very good agreement with results obtained from mass-selected free jet expansion experiments. In the liquid case the contribution of the solute-solvent hydrogen bonds partially cancels and the total shift obtained is dominated by the contribution of the outer solvent water molecules. Our best result, including both inner and outer water molecules, is 570 +/- 35 cm(-1), in very good agreement with the small experimental shift of 460 cm(-1) for the absorption maximum.

Electronic properties of liquid ammonia: A sequential molecular dynamics/quantum mechanics approach

The electronic properties of liquid ammonia are investigated by a sequential molecular dynamics/quantum mechanics approach. Quantum mechanics calculations for the liquid phase are based on a reparametrized hybrid exchange-correlation functional that reproduces the electronic properties of ammonia clusters [(NH(3))(n); n=1-5]. For these small clusters, electron binding energies based on Green's function or electron propagator theory, coupled cluster with single, double, and perturbative triple excitations, and density functional theory (DFT) are compared. Reparametrized DFT results for the dipole moment, electron binding energies, and electronic density of states of liquid ammonia are reported. The calculated average dipole moment of liquid ammonia (2.05 +/- 0.09 D) corresponds to an increase of 27% compared to the gas phase value and it is 0.23 D above a prediction based on a polarizable model of liquid ammonia [Deng , J. Chem. Phys. 100, 7590 (1994)]. Our estimate for the ionization potential of liquid ammonia is 9.74 +/- 0.73 eV, which is approximately 1.0 eV below the gas phase value for the isolated molecule. The theoretical vertical electron affinity of liquid ammonia is predicted as 0.16 +/- 0.22 eV, in good agreement with the experimental result for the location of the bottom of the conduction band (-V(0)=0.2 eV). Vertical ionization potentials and electron affinities correlate with the total dipole moment of ammonia aggregates. (c) 2008 American Institute of Physics.

Bilayer graphene dual-gate nanodevice: An ab initio simulation

We study the electronic transport properties of a dual-gated bilayer graphene nanodevice via first-principles calculations. We investigate the electric current as a function of gate length and temperature. Under the action of an external electrical field we show that even for gate lengths up 100 angstrom, a nonzero current is exhibited. The results can be explained by the presence of a tunneling regime due the remanescent states in the gap. We also discuss the conditions to reach the charge neutrality point in a system free of defects and extrinsic carrier doping.