MEIS investigations of surface structure

The early work of the FOM-AMOLF group in Amsterdam clearly demonstrated the potential of medium energy ion scattering (MEIS), typically using 100 keV H+ incident ions, to investigate the structure of surfaces, but most current applications of the method are focussed on near-surface compositional studies of non-crystalline films. However, the key strengths of the MEIS technique, notably the use of blocking curves in double-alignment experiments and absolute yield measurements, are extremely effective in providing detailed near-surface structural information for a wide range of crystalline materials. This potential and the underlying methodology, is illustrated through examples of applications to the study of layer-dependent composition and structure in alloy surfaces, in studies of the surface crystallography of an oxide surface (rutile TiO2(1 1 0)) and in investigations of complex adsorbate-induced reconstruction of metal surfaces, including the pseudo-(1 0 0) reconstruction of Cu(1 1 1) induced by adsorption of atomic N and molecular methylthiolate (CH3S–). In addition to the use of calibrated blocking curves, the use of the detailed spectral shape of the surface peak in the scattered ion energy spectra, as a means of providing single-atomic layer resolution of the surface structure, is also discussed

Adsorbate-induced surface stress, surface strain and surface reconstruction : S on Cu(100) and Ni(100)

Density functional theory (DFT) calculations have been applied to investigate the known difference in behaviour of S adsorption on Cu(100) and Ni(100). Both surfaces form a 0.25 ML (2 × 2) adsorption phase, but while at higher coverage a 0.5 ML c(2 × 2) phase forms on Ni(100), on Cu(100) only a reconstructed 0.47 ML (√17 × √17)R14° structure occurs. Calculations of the energy, structure, and surface stress of (2 × 2) and c(2 × 2) phases on both substrates show there is an energy advantage on both surfaces to form the higher coverage phase, but that both surfaces show local surface strain around the S atoms in the (2 × 2) phase, a phenomenon previously investigated only on Cu(100). More than forty different structural models of the Cu(100)(√17 × √17)R14°-S phase have been investigated. The pseudo-(100)c(2 × 2) structure previously proposed, containing 16 Cu adatoms per unit mesh in the reconstructed layer, is found to be less energetically favourable than many other possible structures, even after taking account of local structural relaxations. Significantly more favourable is a structure with 12 Cu adatoms per (√17 × √17)R14° unit mesh, previously proposed on the basis of scanning tunnelling microscopy (STM), and found to yield simulated STM images in good agreement with experiment. This model has all S atoms in local 4-fold coordinated hollows relative to the Cu atoms below, half being located above Cu adatoms with the remainder lying above the underlying outermost substrate layer. However, an alternative model with only 4 Cu adatoms and with half the S atoms at 3-fold coordinated sites on the periphery of the Cu adatom cluster, has an even lower energy and gives simulated STM images in excellent agreement with experiment

Renormalisation-theoretic analysis of non-equilibrium phase transitions II: The effect of perturbations on rate coefficients in the Becker-Doring equations

We study in detail the application of renormalisation theory to models of cluster aggregation and fragmentation of relevance to nucleation and growth processes. In particular, we investigate the Becker-Doring (BD) equations, originally formulated to describe and analyse non-equilibrium phase transitions, but more recently generalised to describe a wide range of physicochemical problems. We consider here rate coefficients which depend on the cluster size in a power-law fashion, but now perturbed by small amplitude random noise. Power-law rate coefficients arise naturally in the theory of surface-controlled nucleation and growth processes. The noisy perturbations on these rates reflect the effect of microscopic variations in such mean-field coefficients, thermal fluctuations and/or experimental uncertainties. In the present paper we generalise our earlier work that identified the nine classes into which all dynamical behaviour must fall by investigating how random perturbations of the rate coefficients influence the steady-state and kinetic behaviour of the coarse-grained, renormalised system. We are hence able to confirm the existence of a set of up to nine universality classes for such BD systems.Comment: 30 pages, to appear in J Phys A Math Ge

Studies of the translesion synthesis DNA ploymerase eta in Saccharomyces cerevisiae

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2008.Includes bibliographical references.All organisms must control the effects of DNA damage to protect the integrity of their genomes. In addition to DNA repair, this requires DNA damage tolerance pathways, which allow the continuation of essential processes in the presence of DNA damage. One such mechanism is translesion synthesis (TLS), in which a specialized polymerase replicates a damaged DNA template. These studies address the regulation of the eukaryotic TLS polymerase eta, which is particularly important for accurately bypassing UV-induced DNA damage. Here I identify a regulatory domain of Saccharomyces cerevisiae polymerase eta and show that it is essential for pol eta's function. This domain interacts with ubiquitin, and has been named the UBZ (ubiquitin binding zinc finger) domain because its human homolog is a zinc finger. However, results presented here demonstrate that, in S. cerevisiae, neither the sequence nor the functional significance of the zinc finger within the UBZ domain is conserved. I present the first analysis of DNA-association of S. cerevisiae pol eta, demonstrating a UBZ-dependent increase in its chromatin-association in response to DNA damage. These results are consistent with the UBZ domain of S. cerevisiae pol eta forming a zincless finger, similar in structure and function to its human counterpart, and mediating a physical interaction with ubiquitinated PCNA to promote pol eta's association with damaged DNA. Another eukaryotic TLS polymerase is Rev1, which is thought to play a structural role in TLS by binding the other TLS polymerases. In mammals, Rev and pol eta robustly interact. Here, I show that any physical interaction between Rev and pol eta in S. cerevisiae is too weak or conditional to observe by coimmunoprecipitation.(cont.) Finally, I describe a genetic study to elucidate the functional interactions of pol eta with Rev and another TLS polymerase, pol zeta. The results presented here are consistent with TLS during two distinct periods during the cell cycle, with pol eta contributing most to S-phase TLS. Pol eta's complex genetic relationships with the other polymerases show that pol eta generally acts independently, but may cooperate with the other polymerases in a damage-induced pathway. Alternative explanations of the data are also discussed.by Rachel Van Etten Woodruff.Ph.D

AGB Variables and the Mira Period-Luminosity Relation

Published data for large amplitude asymptotic giant branch variables in the Large Magellanic Cloud are re-analysed to establish the constants for an infrared (K) period-luminosity relation of the form: Mk=rho[log P-2.38] + delta. A slope of rho=-3.51+/-0.20 and a zero point of delta=-7.15+/-0.06 are found for oxygen-rich Miras (if a distance modulus of 18.39+/-0.05 is used for the LMC). Assuming this slope is applicable to Galactic Miras we discuss the zero-point for these stars using the revised Hipparcos parallaxes together with published VLBI parallaxes for OH Masers and Miras in Globular Clusters. These result in a mean zero-point of delta=-7.25+/-0.07 for O-rich Galactic Miras. The zero-point for Miras in the Galactic Bulge is not significantly different from this value. Carbon-rich stars are also discussed and provide results that are consistent with the above numbers, but with higher uncertainties. Within the uncertainties there is no evidence for a significant difference between the period-luminosity relation zero-points for systems with different metallicity.Comment: 15 pages, 3 figures, accepted for MNRA

Renormalisation-theoretic analysis of non-equilibrium phase transitions I: The Becker-Doring equations with power law rate coefficients

We study in detail the application of renormalisation theory to models of cluster aggregation and fragmentation of relevance to nucleation and growth processes. We investigate the Becker-Dorging equations, originally formulated to describe and analyse non-equilibrium phase transitions, and more recently generalised to describe a wide range of physicochemical problems. In the present paper we analyse how the systematic coarse-graining renormalisation of the \BD system of equations affects the aggregation and fragmentation rate coefficients. We consider the case of power-law size-dependent cluster rate coefficients which we show lead to only three classes of system that require analysis: coagulation-dominated systems, fragmentation-dominated systems and those where coagulation and fragmentation are exactly balanced. We analyse the late-time asymptotics associated with each class.Comment: 18 pages, to appear in J Phys A Math Ge

The interface structure of n-alkylthiolate self-assembled monolayers on coinage metal surfaces

The current state of understanding of the structure of the metal/thiolate interface of n-alkylthiolate self-assembled monolayers (SAMs) on Cu(111), Ag(111) and Au(111) is reviewed. On Cu(111) and Ag(111) there is now clear evidence that adsorbate-induced reconstruction of the outermost metal layer occurs to a less atomically-dense structure, with the S head-group atom bonded to four-fold and three-fold coordinated hollow sites, respectively, and that intermolecular interaction plays some role in the periodicity of the resulting SAMs. On the far more heavily-studied Au(111) surface, the detailed interface structure remains controversial, but there is growing evidence for the role of Au-adatom-thiolate moieties in the layer ordering

The Pulsation of Chi Cygni Imaged by Optical Interferometry; a Novel Technique to Derive Distance and Mass of Mira Stars

We present infrared interferometric imaging of the S-type Mira star Chi Cygni. The object was observed at four different epochs in 2005-2006 with the IOTA optical interferometer (H band). Images show up to 40% variation in the stellar diameter, as well as significant changes in the limb darkening and stellar inhomogeneities. Model fitting gave precise time-dependent values of the stellar diameter, and reveals presence and displacement of a warm molecular layer. The star radius, corrected for limb darkening, has a mean value of 12.1 mas and shows a 5.1mas amplitude pulsation. Minimum diameter was observed at phase 0.94+/-0.01. Maximum temperature was observed several days later at phase 1.02+/-0.02. We also show that combining the angular acceleration of the molecular layer with CO (Delta v = 3) radial velocity measurements yields a 5.9+/-1.5 mas parallax. The constant acceleration of the CO molecules -- during 80% of the pulsation cycle -- lead us to argument for a free-falling layer. The acceleration is compatible with a gravitational field produced by a 2.1(+1.5/-0.7) solar mass star. This last value is in agreement with fundamental mode pulsator models. We foresee increased development of techniques consisting in combining radial velocity with interferometric angular measurements, ultimately allowing total mapping of the speed, density, and position of the diverse species in pulsation driven atmospheres.Comment: 36 pages, accepted in Ap