OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application

The semiempirical methods of the OMx family (orthogonalization models OM1, OM2, and OM3) are known to describe biochemical systems more accurately than standard semiempirical approaches such as AM1. We investigate the benefits of augmenting these methods with an empirical dispersion term (OMx-D) taken from recent density functional work, without modifying the standard OMx parameters. Significant improvements are achieved for non-covalent interactions, with mean unsigned errors of 1.41 kcal/mol (OM2-D) and 1.31 kcal/mol (OM3-D) for the binding energy of the complexes in the JSCH-2005 data base. This supports the use of these augmented methods in quantum mechanical/molecular mechanical (QM/MM) studies of biomolecules, for example during system preparation and equilibration. As an illustrative application, we present QM and QM/MM calculations on the binding between antibody 34E4 and a hapten, where OM3-D performs better than the methods without dispersion terms (AM1, OM3)

Tribute to Donald A. Winslow

This article is comprised of a series of tributes to Donald A. Winslow, who was a law professor at the University of Kentucky College of Law

Differential vaginal expression of interleukin-1 system cytokines in the presence of Mycoplasma hominis and Ureaplasma urealyticum in pregnant women.

OBJECTIVE: The genital mycoplasmas, Ureaplasma urealyticum and Mycoplasma hominis, are commonly identified in the vagina of healthy pregnant women. However, these microorganisms are the most common isolates from the amniotic fluids of women in preterm labor. The mechanisms responsible for vaginal colonization and ascent to the uterus remain undetermined. We evaluated the association between U. urealyticum and M. hominis vaginal colonization and the presence of pro-inflammatory and anti-inflammatory interleukin-1 system components in asymptomatic pregnant women of different ethnicities. METHODS: Vaginal specimens, obtained from 224 first trimester pregnant women, were assayed for interleukin-1beta (IL-1beta) and IL-1 receptor antagonist (IL-1ra) concentrations by ELISA. U. urealyticum and M. hominis vaginal colonization were identified by polymerase chain reaction (PCR). RESULTS: Vaginal colonization with M. hominis was identified in 37 (16.5%) women, and was more prevalent in black (18.9%) and Hispanic (20.9%) than in white (4.2%) women (p = 0.01). U. urealyticum was present in 84 (37.5%) women and there was no ethnic disparity in its detection. M. hominis colonization was associated with elevated median vaginal IL-1beta concentrations in both black women (p = 0.02) and Hispanic women (p = 0.04), and was unrelated to vaginal IL-1ra concentrations. In marked contrast, U. urealyticum colonization was associated with elevations in vaginal IL-1ra levels, but not with IL-1beta concentrations, in black women (p = 0.02) and Hispanic women (p < 0.0001) and marginally in white women (p = 0.06). CONCLUSION: M. hominis colonization in healthy pregnant women is associated with localized pro-inflammatory immune activation, while U. urealyticum colonization is associated with immune suppression

Two-Neutron Sequential Decay of 24^{24}O

A two-neutron unbound excited state of $^{24}$O was populated through a (d,d') reaction at 83.4 MeV/nucleon. A state at $E = 715 \pm 110$ (stat) $\pm 45$ (sys) keV with a width of $\Gamma < 2$ MeV was observed above the two-neutron separation energy placing it at 7.65 $\pm$ 0.2 MeV with respect to the ground state. Three-body correlations for the decay of $^{24}$O $\rightarrow$ $^{22}$O + $2n$ show clear evidence for a sequential decay through an intermediate state in $^{23}$O. Neither a di-neutron nor phase-space model for the three-body breakup were able to describe these correlations

Elucidation of the bonding of a near infrared dye to hollow gold nanospheres : a chalcogen tripod

Infrared surface enhanced Raman scattering (SERS) is an attractive technique for the in situ detection of nanoprobes in biological samples due to the greater depth of penetration and reduced interference compared to SERS in the visible region. A key challenge is to understand the surface layer formed in suspension when a specific label is added to the SERS substrate in aqueous suspension. SERS taken at different wavelengths, theoretical calculations, and surface-selective sum frequency generation vibrational spectroscopy (SFG-VS) were used to define the surface orientation and manner of attachment of a new class of infrared SERS label with a thiopyrylium core and four pendant 2-selenophenyl rings. Hollow gold nanospheres (HGNs) were used as the enhancing substrate and two distinct types of SERS spectra were obtained. With excitation close to resonance with both the near infrared electronic transition in the label (max 826 nm) and the plasmon resonance maximum (690 nm), surface enhanced resonance Raman scattering (SERRS) was obtained. SERRS indicates that the major axis of the core is near to perpendicular to the surface plane and SFG-VS obtained from a dried gold film gave a similar orientation with the major axis at an angle 64°-85° from the surface plane. Longer excitation wavelengths give SERS with little or no molecular resonance contribution and new vibrations appeared with significant displacements between the thiopyrylium core and the pendant selenophene rings. Analysis using calculated spectra with one or two rings rotated indicates that two rings on one end are rotated towards the metal surface to give an arrangement of two selenium and one sulphur atoms directly facing the gold structure. The spectra, together with a space filled model, indicate that the molecule is strongly adsorbed to the surface through the selenium and sulphur atoms in an arrangement which will facilitate layer formation

A Brief Introduction to Wilson Loops and Large N

A pedagogical introduction to Wilson loops, lattice gauge theory and the 1/N-expansion of QCD is presented. The three introductory lectures were given at the 37th ITEP Winter School of Physics, Moscow, February 9-16, 2009.Comment: 14 pages, 14 figures, Lectures at the 37th ITEP Winter School of Physic

Effect of hydrogen on ground state structures of small silicon clusters

We present results for ground state structures of small Si$_{n}$H (2 \leq \emph{n} \leq 10) clusters using the Car-Parrinello molecular dynamics. In particular, we focus on how the addition of a hydrogen atom affects the ground state geometry, total energy and the first excited electronic level gap of an Si$_{n}$ cluster. We discuss the nature of bonding of hydrogen in these clusters. We find that hydrogen bonds with two silicon atoms only in Si$_{2}$H, Si$_{3}$H and Si$_{5}$H clusters, while in other clusters (i.e. Si$_{4}$H, Si$_{6}$H, Si$_{7}$H, Si$_{8}$H, Si$_{9}$H and Si$_{10}$H) hydrogen is bonded to only one silicon atom. Also in the case of a compact and closed silicon cluster hydrogen bonds to the cluster from outside. We find that the first excited electronic level gap of Si$_{n}$ and Si$_{n}$H fluctuates as a function of size and this may provide a first principles basis for the short-range potential fluctuations in hydrogenated amorphous silicon. Our results show that the addition of a single hydrogen can cause large changes in the electronic structure of a silicon cluster, though the geometry is not much affected. Our calculation of the lowest energy fragmentation products of Si$_{n}$H clusters shows that hydrogen is easily removed from Si$_{n}$H clusters.Comment: one latex file named script.tex including table and figure caption. Six postscript figure files. figure_1a.ps and figure_1b.ps are files representing Fig. 1 in the main tex

Lightning arrestor connector lead magnesium niobate qualification pellet test procedures.

Enhanced knowledge preservation for DOE DP technical component activities has recently received much attention. As part of this recent knowledge preservation effort, improved documentation of the sample preparation and electrical testing procedures for lead magnesium niobate--lead titanate (PMN/PT) qualification pellets was completed. The qualification pellets are fabricated from the same parent powders used to produce PMN/PT lightning arrestor connector (LAC) granules at HWF&amp;T. In our report, the procedures for fired pellet surface preparation, electrode deposition, electrical testing and data recording are described. The dielectric measurements described in our report are an information only test. Technical reasons for selecting the electrode material, electrode size and geometry are presented. The electrical testing is based on measuring the dielectric constant and dissipation factor of the pellet during cooling from 280 C to 220 C. The most important data are the temperature for which the peak dielectric constant occurs (Curie Point temperature) and the peak dielectric constant magnitude. We determined that the peak dielectric constant for our procedure would be that measured at 1 kHz at the Curie Point. Both the peak dielectric constant and the Curie point parameters provide semi-quantitative information concerning the chemical and microstructural homogeneity of the parent material used for the production of PMN/PT granules for LACs. Finally, we have proposed flag limits for the dielectric data for the pellets. Specifically, if the temperature of the peak dielectric constant falls outside the range of 250 C {+-} 30 C we propose that a flag limit be imposed that will initiate communication between production agency and design agency personnel. If the peak dielectric constant measured falls outside the range 25,000 {+-} 10,000 we also propose that a flag limit be imposed

Synthesis and properties of novel star-shaped oligofluorene conjugated systems with BODIPY cores

Star-shaped conjugated systems with varying oligofluorene arm length and substitution patterns of the central BODIPY core have been synthesised, leading to two families of compounds, T-B1-T-B4 and Y-B1-Y-B4, with T- and Y-shaped motifs, respectively. Thermal stability, cyclic voltammetry, absorption and photoluminescence spectroscopy of each member of these two families were studied in order to determine their suitability as emissive materials in photonic applications

The Layer 0 Inner Silicon Detector of the D0 Experiment

This paper describes the design, fabrication, installation and performance of the new inner layer called Layer 0 (L0) that was inserted in the existing Run IIa Silicon Micro-Strip Tracker (SMT) of the D0 experiment at the Fermilab Tevatron collider. L0 provides tracking information from two layers of sensors, which are mounted with center lines at a radial distance of 16.1 mm and 17.6 mm respectively from the beam axis. The sensors and readout electronics are mounted on a specially designed and fabricated carbon fiber structure that includes cooling for sensor and readout electronics. The structure has a thin polyimide circuit bonded to it so that the circuit couples electrically to the carbon fiber allowing the support structure to be used both for detector grounding and a low impedance connection between the remotely mounted hybrids and the sensors.Comment: 28 pages, 9 figure