Understanding the disorder of the DNA base cytosine on the Au(111) surface

Using ultrahigh vacuum scanning tunneling microscopy (STM) and ab initio density functional theory, we have investigated in detail structures formed by cytosine on the Au(111) surface in clean ultrahigh vacuum conditions. In spite of the fact that the ground state of this DNA base on the surface is shown to be an ordered arrangement of cytosine one-dimensional branches (filaments), this structure has never been observed in our STM experiments. Instead, disordered structures are observed, which can be explained by only a few elementary structural motifs: filaments, five- and sixfold rings, which randomly interconnect with each other forming bent chains, T junctions, and nanocages. The latter may have trapped smaller structures inside. The formation of such an unusual assembly is explained by simple kinetic arguments as a liquid-glass transition. © 2008 American Institute of Physics

Looking at electronic wave functions on metal surfaces

The project described here is not only a beautiful example of the visual side tophysics, it is also a beautiful example of international cooperation. The first use of the idea—to apply a Fourier transform to STM pictures to see electron waves instead of just the surface atoms—came out of a collaboration between Plummer, Sprunger and the Aarhus group headed by Besenbacher. Hofman, who had beenworking at Tennessee, took Be(1010) samples to Berlin where the images shown in this pictorial were taken. All of the participants are now preparing a paper on the use of a Fourier transform to map the Fermi contour at metal surfaces

High-coverage structures of carbon monoxide adsorbed on Pt(111) studied by high-pressure scanning tunneling microscopy

High-pressure scanning tunneling microscopy was used to study the room-temperature adsorption of CO on a Pt(111) single-crystal surface in equilibrium with the gas phase. The coverage was found to vary continuously, and over the entire range from 10(-6)-760 Torr pressure-dependent moire patterns were observed, characteristic of a hexagonal or nearly hexagonal CO overlayer. Two different pressure ranges can be distinguished: below 10(-2) Tort, the moire lattice vector is oriented along a 30degrees high-symmetry direction of the substrate, corresponding to a pressure-dependent rotation of the CO overlayer with respect to the (1 x 1) Pt surface lattice, while above 10(-2) Torr, the CO layer angle is independent of the pressure. This behavior is analyzed in terms of the interplay of the repulsive CO-CO interaction potential and the substrate potential

Adsorption configuration effects on the surface diffusion of large organic molecules: The case of Violet Lander

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Violet Lander (C108H104) is a large organic molecule that when deposited on Cu(110) surface exhibits lock-and-key like behavior [Otero et al., Nature Mater. 3, 779 (2004)]. In this work, we report a detailed fully atomistic molecular mechanics and molecular dynamics study of this phenomenon. Our results show that it has its physical basis on the interplay of the molecular hydrogens and the Cu(110) atomic spacing, which is a direct consequence of the matching between molecule and surface dimensions. This information could be used to find new molecules capable of displaying lock-and-key behavior with new potential applications in nanotechnology. (C) 2010 American Institute of Physics. [doi:10.1063/1.3512623]13322Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

A self-interaction corrected pseudopotential scheme for magnetic and strongly-correlated systems

Local-spin-density functional calculations may be affected by severe errors when applied to the study of magnetic and strongly-correlated materials. Some of these faults can be traced back to the presence of the spurious self-interaction in the density functional. Since the application of a fully self-consistent self-interaction correction is highly demanding even for moderately large systems, we pursue a strategy of approximating the self-interaction corrected potential with a non-local, pseudopotential-like projector, first generated within the isolated atom and then updated during the self-consistent cycle in the crystal. This scheme, whose implementation is totally uncomplicated and particularly suited for the pseudopotental formalism, dramatically improves the LSDA results for a variety of compounds with a minimal increase of computing cost.Comment: 18 pages, 14 figure

The spectral and magnetic properties of α\alpha- and γ\gamma-Ce from the Dynamical Mean-Field Theory and Local Density Approximation

We have calculated ground state properties and excitation spectra for Ce metal with the {\it ab initio} computational scheme combining local density approximation and dynamical mean-field theory (LDA+DMFT). We considered all electronic states, i.e. correlated f-states and non-correlated s-, p- and d-states. The strong local correlations (Coulomb interaction) among the f-states lead to typical many-body resonances in the partial f-density, such as lower and upper Hubbard band. Additionally the well known Kondo resonance is observed. The s-, p- and d-densities show small to mediate renormalization effects due to hybridization. We observe different Kondo temperatures for $\alpha$- and $\gamma$-Ce ($T_{K,\alpha}\approx 1000 K$ and $T_{K,\gamma}\approx 30 K$), due to strong volume dependence of the effective hybridization strength for the localized f-electrons. Finally we compare our results with a variety of experimental data, i.e. from photoemission spectroscopy (PES), inverse photoemission spectroscopy (BIS), resonant inverse photoemission spectroscopy (RIPES) and magnetic susceptibility measurements.Comment: 7 pages, 4 figure

Modelling charge self-trapping in wide-gap dielectrics: Localization problem in local density functionals

We discuss the adiabatic self-trapping of small polarons within the density functional theory (DFT). In particular, we carried out plane-wave pseudo-potential calculations of the triplet exciton in NaCl and found no energy minimum corresponding to the self-trapped exciton (STE) contrary to the experimental evidence and previous calculations. To explore the origin of this problem we modelled the self-trapped hole in NaCl using hybrid density functionals and an embedded cluster method. Calculations show that the stability of the self-trapped state of the hole drastically depends on the amount of the exact exchange in the density functional: at less than 30% of the Hartree-Fock exchange, only delocalized hole is stable, at 50% - both delocalized and self-trapped states are stable, while further increase of exact exchange results in only the self-trapped state being stable. We argue that the main contributions to the self-trapping energy such as the kinetic energy of the localizing charge, the chemical bond formation of the di-halogen quasi molecule, and the lattice polarization, are represented incorrectly within the Kohn-Sham (KS) based approaches.Comment: 6 figures, 1 tabl

Label-free biosensing with high sensitivity in dual-core microstructured polymer optical fibers

We present experimentally feasible designs of a dual-core microstructured polymer optical fiber (mPOF), which can act as a highly sensitive, label-free, and selective biosensor. An immobilized antigen sensing layer on the walls of the holes in the mPOF provides the ability to selectively capture antibody biomolecules. The change of the layer thickness of biomolecules can then be detected as a change in the coupling length between the two cores. We compare mPOF structures with 1, 2, and 3 air-holes between the solid cores and show that the sensitivity increases with increasing distance between the cores. Numerical calculations indicate a record sensitivity up to 20 nm/nm (defined as the shift in the resonance wavelength per nm biolayer) at visible wavelengths, where the mPOF has low loss.9 page(s