176 research outputs found
Grain Boundary Loops in Graphene
Topological defects can affect the physical properties of graphene in
unexpected ways. Harnessing their influence may lead to enhanced control of
both material strength and electrical properties. Here we present a new class
of topological defects in graphene composed of a rotating sequence of
dislocations that close on themselves, forming grain boundary loops that either
conserve the number of atoms in the hexagonal lattice or accommodate
vacancy/interstitial reconstruction, while leaving no unsatisfied bonds. One
grain boundary loop is observed as a "flower" pattern in scanning tunneling
microscopy (STM) studies of epitaxial graphene grown on SiC(0001). We show that
the flower defect has the lowest energy per dislocation core of any known
topological defect in graphene, providing a natural explanation for its growth
via the coalescence of mobile dislocations.Comment: 23 pages, 7 figures. Revised title; expanded; updated reference
Incoherent Transport through Molecules on Silicon in the vicinity of a Dangling Bond
We theoretically study the effect of a localized unpaired dangling bond (DB)
on occupied molecular orbital conduction through a styrene molecule bonded to a
n++ H:Si(001)-(2x1) surface. For molecules relatively far from the DB, we find
good agreement with the reported experiment using a model that accounts for the
electrostatic contribution of the DB, provided we include some dephasing due to
low lying phonon modes. However, for molecules within 10 angstrom to the DB, we
have to include electronic contribution as well along with higher dephasing to
explain the transport features.Comment: 9 pages, 5 figure
Silicon-based molecular electronics
Molecular electronics on silicon has distinct advantages over its metallic
counterpart. We describe a theoretical formalism for transport through
semiconductor-molecule heterostructures, combining a semi-empirical treatment
of the bulk silicon bandstructure with a first-principles description of the
molecular chemistry and its bonding with silicon. Using this method, we
demonstrate that the presence of a semiconducting band-edge can lead to a novel
molecular resonant tunneling diode (RTD) that shows negative differential
resistance (NDR) when the molecular levels are driven by an STM potential into
the semiconducting band-gap. The peaks appear for positive bias on a p-doped
and negative for an n-doped substrate. Charging in these devices is compromised
by the RTD action, allowing possible identification of several molecular
highest occupied (HOMO) and lowest unoccupied (LUMO) levels. Recent experiments
by Hersam et al. [1] support our theoretical predictions.Comment: Author list is reverse alphabetical. All authors contributed equally.
Email: rakshit/liangg/ ghosha/[email protected]
Fourier Transform Scanning Tunneling Spectroscopy: the possibility to obtain constant energy maps and the band dispersion using a local measurement
We present here an overview of the Fourier Transform Scanning Tunneling
spectroscopy technique (FT-STS). This technique allows one to probe the
electronic properties of a two-dimensional system by analyzing the standing
waves formed in the vicinity of defects. We review both the experimental and
theoretical aspects of this approach, basing our analysis on some of our
previous results, as well as on other results described in the literature. We
explain how the topology of the constant energy maps can be deduced from the FT
of dI/dV map images which exhibit standing waves patterns. We show that not
only the position of the features observed in the FT maps, but also their shape
can be explained using different theoretical models of different levels of
approximation. Thus, starting with the classical and well known expression of
the Lindhard susceptibility which describes the screening of electron in a free
electron gas, we show that from the momentum dependence of the susceptibility
we can deduce the topology of the constant energy maps in a joint density of
states approximation (JDOS). We describe how some of the specific features
predicted by the JDOS are (or are not) observed experimentally in the FT maps.
The role of the phase factors which are neglected in the rough JDOS
approximation is described using the stationary phase conditions. We present
also the technique of the T-matrix approximation, which takes into account
accurately these phase factors. This technique has been successfully applied to
normal metals, as well as to systems with more complicated constant energy
contours. We present results recently obtained on graphene systems which
demonstrate the power of this technique, and the usefulness of local
measurements for determining the band structure, the map of the Fermi energy
and the constant-energy maps.Comment: 33 pages, 15 figures; invited review article, to appear in Journal of
Physics D: Applied Physic
Ab initio simulations of the kinetic properties of the hydrogen monomer on graphene
The understanding of the kinetic properties of hydrogen (isotopes) adatoms on
graphene is important in many fields. The kinetic properties of
hydrogen-isotope (H, D and T) monomers were simulated using a composite method
consisting of density functional theory, density functional perturbation theory
and harmonic transition state theory. The kinetic changes of the magnetic
property and the aromatic bond of the hydrogenated graphene during the
desorption and diffusion of the hydrogen monomer was discussed. The vibrational
zero-point energy corrections in the activation energies were found to be
significant, ranging from 0.072 to 0.205 eV. The results obtained from
quantum-mechanically modified harmonic transition state theory were compared
with the ones obtained from classical-limit harmonic transition state theory
over a wide temperature range. The phonon spectra of hydrogenated graphene were
used to closely explain the (reversed) isotope effects in the prefactor,
activation energy and jump frequency of the hydrogen monomer. The kinetic
properties of the hydrogen-isotope monomers were simulated under conditions of
annealing for 10 minutes and of heating at a constant rate (1.0 K/s). The
isotope effect was observed; that is, a hydrogen monomer of lower mass is
desorbed and diffuses more easily (with lower activation energies). The results
presented herein are very similar to other reported experimental observations.
This study of the kinetic properties of the hydrogen monomer and many other
involved implicit mechanisms provides a better understanding of the interaction
between hydrogen and graphene.Comment: Accepted by J. Phys. Chem.
Electrical resistance: an atomistic view
This tutorial article presents a "bottom-up" view of electrical resistance
starting from something really small, like a molecule, and then discussing the
issues that arises as we move to bigger conductors. Remarkably, no serious
quantum mechanics is needed to understand electrical conduction through
something really small, except for unusual things like the Kondo effect that
are seen only for a special range of parameters. This article starts with
energy level diagrams (section 2), shows that the broadening that accompanies
coupling limits the conductance to a maximum of q^2/h per level (sections 3,
4), describes how a change in the shape of the self-consistent potential
profile can turn a symmetric current-voltage characteristic into a rectifying
one (sections 5, 6), shows that many interesting effects in molecular
electronics can be understood in terms of a simple model (section 7),
introduces the non-equilibrium Green function (NEGF) formalism as a
sophisticated version of this simple model with ordinary numbers replaced by
appropriate matrices (section 8) and ends with a personal view of unsolved
problems in the field of nanoscale electron transport (section 9). Appendix A
discusses the Coulomb blockade regime of transport, while appendix B presents a
formal derivation of the NEGF equations. MATLAB codes for numerical examples
are listed in the appendix C
Structural and Electronic Decoupling of C_(60) from Epitaxial Graphene on SiC
We have investigated the initial stages of growth and the electronic structure of C_(60) molecules on graphene grown epitaxially on SiC(0001) at the single-molecule level using cryogenic ultrahigh vacuum scanning tunneling microscopy and spectroscopy. We observe that the first layer of C_(60) molecules self-assembles into a well-ordered, close-packed arrangement on graphene upon molecular deposition at room temperature while exhibiting a subtle C_(60) superlattice. We measure a highest occupied molecular orbital–lowest unoccupied molecular orbital gap of ~ 3.5 eV for the C_(60) molecules on graphene in submonolayer regime, indicating a significantly smaller amount of charge transfer from the graphene to C_(60) and substrate-induced screening as compared to C_(60) adsorbed on metallic substrates. Our results have important implications for the use of graphene for future device applications that require electronic decoupling between functional molecular adsorbates and substrates
Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing
<p>Abstract</p> <p>Background</p> <p>Milkweeds (<it>Asclepias </it>L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (<it>Asclepias syriaca </it>L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing <it>A. syriaca </it>as a model in ecology and evolution.</p> <p>Results</p> <p>A 0.5× genome of <it>A. syriaca </it>was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: <it>accD, clpP</it>, and <it>ycf1</it>. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/<it>copia</it>-like retroelements are the most common repeat type in the milkweed genome. At least one <it>A. syriaca </it>microread hit 88% of <it>Catharanthus roseus </it>(Apocynaceae) unigenes (median coverage of 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). From this partial characterization of the <it>A. syriaca </it>genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed.</p> <p>Conclusions</p> <p>The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives. This study represents a first step in the development of a community resource for further study of plant-insect co-evolution, anti-herbivore defense, floral developmental genetics, reproductive biology, chemical evolution, population genetics, and comparative genomics using milkweeds, and <it>A. syriaca </it>in particular, as ecological and evolutionary models.</p
Episodic Evolution and Adaptation of Chloroplast Genomes in Ancestral Grasses
It has been suggested that the chloroplast genomes of the grass family, Poaceae, have undergone an elevated evolutionary rate compared to most other angiosperms, yet the details of this phenomenon have remained obscure. To know how the rate change occurred during evolution, estimation of the time-scale with reliable calibrations is needed. The recent finding of 65 Ma grass phytoliths in Cretaceous dinosaur coprolites places the diversification of the grasses to the Cretaceous period, and provides a reliable calibration in studying the tempo and mode of grass chloroplast evolution.By using chloroplast genome data from angiosperms and by taking account of new paleontological evidence, we now show that episodic rate acceleration both in terms of non-synonymous and synonymous substitutions occurred in the common ancestral branch of the core Poaceae (a group formed by rice, wheat, maize, and their allies) accompanied by adaptive evolution in several chloroplast proteins, while the rate reverted to the slow rate typical of most monocot species in the terminal branches.Our finding of episodic rate acceleration in the ancestral grasses accompanied by adaptive molecular evolution has a profound bearing on the evolution of grasses, which form a highly successful group of plants. The widely used model for estimating divergence times was based on the assumption of correlated rates between ancestral and descendant lineages. However, the assumption is proved to be inadequate in approximating the episodic rate acceleration in the ancestral grasses, and the assumption of independent rates is more appropriate. This finding has implications for studies of molecular evolutionary rates and time-scale of evolution in other groups of organisms
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