Site-selective adsorption of naphthalene-tetracarboxylic-dianhydride on Ag(110): First-principles calculations

The mechanism of adsorption of the 1,4,5,8-naphthalene-tetracarboxylic-dianhydride (NTCDA) molecule on the Ag(110) surface is elucidated on the basis of extensive density functional theory calculations. This molecule, together with its perylene counterpart, PTCDA, are archetype organic semiconductors investigated experimentally over the past 20 years. We find that the bonding of the molecule to the substrate is highly site-selective, being determined by electron transfer to the LUMO of the molecule and local electrostatic attraction between negatively charged carboxyl oxygens and positively charged silver atoms in [1-10] atomic rows. The adsorption energy in the most stable site is 0.9eV. A similar mechanism is expected to govern the adsorption of PTCDA on Ag(110) as well.Comment: 8 pages, 4 figures, high-quality figures available upon reques

Kepler Presearch Data Conditioning II - A Bayesian Approach to Systematic Error Correction

With the unprecedented photometric precision of the Kepler Spacecraft, significant systematic and stochastic errors on transit signal levels are observable in the Kepler photometric data. These errors, which include discontinuities, outliers, systematic trends and other instrumental signatures, obscure astrophysical signals. The Presearch Data Conditioning (PDC) module of the Kepler data analysis pipeline tries to remove these errors while preserving planet transits and other astrophysically interesting signals. The completely new noise and stellar variability regime observed in Kepler data poses a significant problem to standard cotrending methods such as SYSREM and TFA. Variable stars are often of particular astrophysical interest so the preservation of their signals is of significant importance to the astrophysical community. We present a Bayesian Maximum A Posteriori (MAP) approach where a subset of highly correlated and quiet stars is used to generate a cotrending basis vector set which is in turn used to establish a range of "reasonable" robust fit parameters. These robust fit parameters are then used to generate a Bayesian Prior and a Bayesian Posterior Probability Distribution Function (PDF) which when maximized finds the best fit that simultaneously removes systematic effects while reducing the signal distortion and noise injection which commonly afflicts simple least-squares (LS) fitting. A numerical and empirical approach is taken where the Bayesian Prior PDFs are generated from fits to the light curve distributions themselves.Comment: 43 pages, 21 figures, Submitted for publication in PASP. Also see companion paper "Kepler Presearch Data Conditioning I - Architecture and Algorithms for Error Correction in Kepler Light Curves" by Martin C. Stumpe, et a

Direct observation of molecular cooperativity near the glass transition

We describe direct observations of molecular cooperativity near the glass transition in poly-vinyl-acetate (PVAc), through nanometer-scale probing of dielectric fluctuations. Molecular clusters switched spontaneously between two to four distinct configurations, producing complex random-telegraph-signals (RTS). Analysis of the RTS and their power spectra shows that individual clusters exhibit both transient dynamical heterogeneity and non-exponential kinetics.Comment: 14 pages pdf, need Acrobat Reade

Health professionals, their medical interventions and uncertainty : a study focusing on women at midlife

Health professionals face a tension between focusing on the individual and attending to health issues for the population as a whole. This tension is intrinsic to medicine and gives rise to medical uncertainty, which here is explored through accounts of three medical interventions focused on women at midlife: breast screening, hormone replacement therapy and bone densitometry. The accounts come from interviews with UK health professionals using these medical interventions in their daily work. Drawing on the analysis of Fox [(2002). Health and Healing: The public/private divide (pp. 236–253). London: Routledge] we distinguish three aspects of medical uncertainty and explore each one of them in relation to one of the interventions. First is uncertainty about the balance between the individual and distributive ethic of medicine, explored in relation to breast screening. Second is the dilemma faced by health professionals when using medicial evidence generated through studies of populations and applying this to individuals. We explore this dilemma for hormone replacement therapy. Thirdly there is uncertainty because of the lack of a conceptual framework for understanding how new micro knowledge, such as human genetic information, can be combined with knowledge of other biological and social dimensions of health. The accounts from the bone denistometry clinic indicate the beginnings of an understanding of the need for such a framework, which would acknowledge complexity, recognising that factors from many different levels of analysis, from heredity through to social factors, interact with each other and influence the individual and their health. However, our analysis suggests biomedicine continues to be dominated by an individualised, context free, concept of health and health risk with individuals alone responsible for their own health and for the health of the population. This may continue to dominate how we perceive responsibilities for health until we establish a conceptual framework that recognises the complex interaction of many factors at macro and micro level affecting health

Kinetic Roughening in Surfaces of Crystals Growing on Disordered Substrates

Substrate disorder effects on the scaling properties of growing crystalline surfaces in solidification or epitaxial deposition processes are investigated. Within the harmonic approach there is a phase transition into a low-temperature (low-noise) superrough phase with a continuously varying dynamic exponent z>2 and a non-linear response. In the presence of the KPZ nonlinearity the disorder causes the lattice efects to decay on large scales with an intermediate crossover behavior. The mobility of the rough surface hes a complex dependence on the temperature and the other physical parameters.Comment: 13 pages, 2 figures (not included). Submitted to Phys. Rev. Letts. Use Latex twic

Inconsistent boundaries

Research on this paper was supported by a grant from the Marsden Fund, Royal Society of New Zealand.Mereotopology is a theory of connected parts. The existence of boundaries, as parts of everyday objects, is basic to any such theory; but in classical mereotopology, there is a problem: if boundaries exist, then either distinct entities cannot be in contact, or else space is not topologically connected (Varzi in Noûs 31:26–58, 1997). In this paper we urge that this problem can be met with a paraconsistent mereotopology, and sketch the details of one such approach. The resulting theory focuses attention on the role of empty parts, in delivering a balanced and bounded metaphysics of naive space.PostprintPeer reviewe

Dynamics of Particles Deposition on a Disordered Substrate: II. Far-from Equilibrium Behavior. -

The deposition dynamics of particles (or the growth of a rigid crystal) on a disordered substrate at a finite deposition rate is explored. We begin with an equation of motion which includes, in addition to the disorder, the periodic potential due to the discrete size of the particles (or to the lattice structure of the crystal) as well as the term introduced by Kardar, Parisi, and Zhang (KPZ) to account for the lateral growth at a finite growth rate. A generating functional for the correlation and response functions of this process is derived using the approach of Martin, Sigga, and Rose. A consistent renormalized perturbation expansion to first order in the non-Gaussian couplings requires the calculation of diagrams up to three loops. To this order we show, for the first time for this class of models which violates the the fluctuation-dissipation theorem, that the theory is renormalizable. We find that the effects of the periodic potential and the disorder decay on very large scales and asymptotically the KPZ term dominates the behavior. However, strong non-trivial crossover effects are found for large intermediate scales.Comment: 52 pages & 17 Figs in uucompressed file. UR-CM 94-090

The Halo and Rings of the Planetary Nebula NGC 40 in the Mid-Infrared

We present imaging and spectroscopy of NGC 40 acquired using the Spitzer Space Telescope (Spitzer), and the Infrared Space observatory (ISO). These are used to investigate the nature of emission from the central nebular shell, from the nebular halo, and from the associated circumnebular rings. It is pointed out that a variety of mechanisms may contribute to the mid-infrared (MIR) fluxes, and there is evidence for a cool dust continuum, strong ionic transitions, and appreciable emission by polycyclic aromatic hydrocarbons (PAHs). Prior observations at shorter wavelengths also indicate the presence of warmer grains, and the possible contribution of H2 transitions. It is suggested that an apparent jet-like structure to the NE of the halo represents one of the many emission spokes that permeate the shell. The spokes are likely to be caused by the percolation of UV photons through a clumpy interior shell, whilst the jet-like feature is enhanced due to locally elevated electron densities; a result of interaction between NGC 40 and the interstellar medium. It is finally noted that the presence of the PAH, 21 microns and 30 microns spectral features testifies to appreciable C/O ratios within the main nebular shell. Such a result is consistent with abundance determinations using collisionally excited lines, but not with those determined using optical recombination linesComment: 13 pages, 8 figures, Accepted for publication in MNRAS. 37 pages in arXi

Pseudo–Messenger RNA: Phantoms of the Transcriptome

The mammalian transcriptome harbours shadowy entities that resist classification and analysis. In analogy with pseudogenes, we define pseudo–messenger RNA to be RNA molecules that resemble protein-coding mRNA, but cannot encode full-length proteins owing to disruptions of the reading frame. Using a rigorous computational pipeline, which rules out sequencing errors, we identify 10,679 pseudo–messenger RNAs (approximately half of which are transposon-associated) among the 102,801 FANTOM3 mouse cDNAs: just over 10% of the FANTOM3 transcriptome. These comprise not only transcribed pseudogenes, but also disrupted splice variants of otherwise protein-coding genes. Some may encode truncated proteins, only a minority of which appear subject to nonsense-mediated decay. The presence of an excess of transcripts whose only disruptions are opal stop codons suggests that there are more selenoproteins than currently estimated. We also describe compensatory frameshifts, where a segment of the gene has changed frame but remains translatable. In summary, we survey a large class of non-standard but potentially functional transcripts that are likely to encode genetic information and effect biological processes in novel ways. Many of these transcripts do not correspond cleanly to any identifiable object in the genome, implying fundamental limits to the goal of annotating all functional elements at the genome sequence level

Two-Loop Renormalization Group Analysis of the Burgers-Kardar-Parisi-Zhang Equation

A systematic analysis of the Burgers--Kardar--Parisi--Zhang equation in $d+1$ dimensions by dynamic renormalization group theory is described. The fixed points and exponents are calculated to two--loop order. We use the dimensional regularization scheme, carefully keeping the full $d$ dependence originating from the angular parts of the loop integrals. For dimensions less than $d_c=2$ we find a strong--coupling fixed point, which diverges at $d=2$, indicating that there is non--perturbative strong--coupling behavior for all $d \geq 2$. At $d=1$ our method yields the identical fixed point as in the one--loop approximation, and the two--loop contributions to the scaling functions are non--singular. For $d>2$ dimensions, there is no finite strong--coupling fixed point. In the framework of a $2+\epsilon$ expansion, we find the dynamic exponent corresponding to the unstable fixed point, which describes the non--equilibrium roughening transition, to be $z = 2 + {\cal O} (\epsilon^3)$, in agreement with a recent scaling argument by Doty and Kosterlitz. Similarly, our result for the correlation length exponent at the transition is $1/\nu = \epsilon + {\cal O} (\epsilon^3)$. For the smooth phase, some aspects of the crossover from Gaussian to critical behavior are discussed.Comment: 24 pages, written in LaTeX, 8 figures appended as postscript, EF/UCT--94/3, to be published in Phys. Rev. E