Harnessing the influence of reactive edges and defects of graphene substrates for achieving complete cycle of room-temperature molecular sensing

Molecular doping and detection are at the forefront of graphene research, a topic of great interest in physical and materials science. Molecules adsorb strongly on graphene, leading to a change in electrical conductivity at room temperature. However, a common impediment for practical applications reported by all studies to date is the excessively slow rate of desorption of important reactive gases such as ammonia and nitrogen dioxide. Annealing at high temperatures, or exposure to strong ultraviolet light under vacuum, is employed to facilitate desorption of these gases. In this article, the molecules adsorbed on graphene nanoflakes and on chemically derived graphene-nanomesh flakes are displaced rapidly at room temperature in air by the use of gaseous polar molecules such as water and ethanol. The mechanism for desorption is proposed to arise from the electrostatic forces exerted by the polar molecules, which decouples the overlap between substrate defect states, molecule states, and graphene states near the Fermi level. Using chemiresistors prepared from water-based dispersions of single-layer graphene on mesoporous alumina membranes, the study further shows that the edges of the graphene flakes (showing p-type responses to NO2 and NH3) and the edges of graphene nanomesh structures (showing n-type responses to NO2 and NH3) have enhanced sensitivity. The measured responses towards gases are comparable to or better than those which have been obtained using devices that are more sophisticated. The higher sensitivity and rapid regeneration of the sensor at room temperature provides a clear advancement towards practical molecule detection using graphene-based materials.

Combining Cartesian and polar coordinates in IBVS

Image-based visual servo (IBVS) is a simple, efficient and robust technique for vision-based control. Although technically a local method in practice it demonstrates almost global convergence. However IBVS performs very poorly for cases that involve large rotations about the optical axis. It is well known that re-parameterizing the problem by using polar, instead of Cartesian coordinates, of feature points overcomes this limitation. First, simulation and experimental results are presented to show the complementarity of these two parameter-izations. We then describe a new hybrid visual servo strategy based on combining polar and Cartesian image Jacobians. © 2009 IEEE.

Manipulating double-decker molecules at the liquid-solid interface

We have used a scanning tunneling microscope to manipulate heteroleptic phthalocyaninato, naphthalocyaninato, porphyrinato double-decker molecules at the liquid/solid interface between 1-phenyloctane solvent and graphite. We employed nano-grafting of phthalocyanines with eight octyl chains to place these molecules into a matrix of heteroleptic double-decker molecules; the overlayer structure is epitaxial on graphite. We have also used nano-grafting to place double-decker molecules in matrices of single-layer phthalocyanines with octyl chains. Rectangular scans with a scanning tunneling microscope at low bias voltage resulted in the removal of the adsorbed doubledecker molecular layer and substituted the double-decker molecules with bilayer-stacked phthalocyanines from phenyloctane solution. Single heteroleptic double-decker molecules with lutetium sandwiched between naphthalocyanine and octaethylporphyrin were decomposed with voltage pulses from the probe tip; the top octaethylporphyrin ligand was removed and the bottom naphthalocyanine ligand remained on the surface. A domain of decomposed molecules was formed within the double-decker molecular domain, and the boundary of the decomposed molecular domain self-cured to become rectangular. We demonstrated a molecular “sliding block puzzle” with cascades of double-decker molecules on the graphite surface.

Conceptualisation of articular cartilage as a giant reverse micelle: A hypothetical mechanism for joint biocushioning and lubrication

Phospholipid (PL) molecules form the main structure of the membrane that prevents the direct contact of opposing articular cartilage layers. In this paper we conceptualise articular cartilage as a giant reverse micelle (GRM) in which the highly hydrated three-dimensional network of phospholipids is electrically charged and able to resist compressive forces during joint movement, and hence loading. Using this hypothetical base, we describe a hydrophilic-hydrophilic (HL-HL) biopair model of joint lubrication by contacting cartilages, whose mechanism is reliant on lamellar cushioning. To demonstrate the viability of our concept, the electrokinetic properties of the membranous layer on the articular surface were determined by measuring via microelectrophoresis, the adsorption of ions H, OH, Na and Cl on phospholipid membrane of liposomes, leading to the calculation of the effective surface charge density. The surface charge density was found to be -0.08 ± 0.002 cm-2 (mean ± S.D.) for phospholipid membranes, in 0.155 M NaCl solution and physiological pH. This value was approximately five times less than that measured in 0.01 M NaCl. The addition of synovial fluid (SF) to the 0.155 M NaCl solution reduced the surface charge density by 30% which was attributed to the binding of synovial fluid macromolecules to the phospholipid membrane. Our experiments show that particles charge and interact strongly with the polar core of RM. We demonstrate that particles can have strong electrostatic interactions when ions and macromolecules are solubilized by reverse micelle (RM). Since ions are solubilized by reverse micelle, the surface entropy influences the change in the charge density of the phospholipid membrane on cartilage surfaces. Reverse micelles stabilize ions maintaining equilibrium, their surface charges contribute to the stability of particles, while providing additional screening for electrostatic processes. © 2008 Elsevier Ireland Ltd. All rights reserved.

Reduction of functionalized graphite oxides by trioctylphosphine in non-polar organic solvents

Graphene, functionalized with oleylamine (OA) and soluble in non-polar organic solvents, was produced on a large scale with a high yield by combining the Hummers process for graphite oxidation, an amine-coupling process to make OA-functionalized graphite oxide (OA-GO), and a novel reduction process using trioctylphosphine (TOP). TOP acts as both a reducing agent and an aggregation-prevention surfactant in the reduction of OA-GO in 1,2-dichlorobenzene (DCB). The reduction of OA-GO is confirmed by X-ray photoelectron spectroscopy, Fourier-transform infrared spectroscopy, X-ray diffraction, thermogravimetric analysis, and Raman spectroscopy. The exfoliation of GO, OA GO, and OA-functionalized graphene (OA-G) is verified by atomic force microscopy. The conductivity of TOP-reduced OA G, which is deduced from the current–voltage characteristics of a vacuum-filtered thin film, shows that the reduction of functionalized GO by TOP is as effective as the reduction of GO by hydrazine.

Molecules, morphology, and ecology indicate a recent, amphibious ancestry for echidnas

The semiaquatic platypus and terrestrial echidnas (spiny anteaters) are the only living egg-laying mammals (monotremes). The fossil record has provided few clues as to their origins and the evolution of their ecological specializations; however, recent reassignment of the Early Cretaceous Teinolophos and Steropodon to the platypus lineage implies that platypuses and echidnas diverged >112.5 million years ago, reinforcing the notion of monotremes as living fossils. This placement is based primarily on characters related to a single feature, the enlarged mandibular canal, which supplies blood vessels and dense electrosensory receptors to the platypus bill. Our reevaluation of the morphological data instead groups platypus and echidnas to the exclusion of Teinolophos and Steropodon and suggests that an enlarged mandibular canal is ancestral for monotremes (partly reversed in echidnas, in association with general mandibular reduction). A multigene evaluation of the echidna–platypus divergence using both a relaxed molecular clock and direct fossil calibrations reveals a recent split of 19–48 million years ago. Platypus-like monotremes (Monotrematum) predate this divergence, indicating that echidnas had aquatically foraging ancestors that reinvaded terrestrial ecosystems. This ecological shift and the associated radiation of echidnas represent a recent expansion of niche space despite potential competition from marsupials. Monotremes might have survived the invasion of marsupials into Australasia by exploiting ecological niches in which marsupials are restricted by their reproductive mode. Morphology, ecology, and molecular biology together indicate that Teinolophos and Steropodon are basal monotremes rather than platypus relatives, and that living monotremes are a relatively recent radiation.

Diversity of dicotyledenous-infecting geminiviruses and their associated DNA molecules in Southern Africa, including the South-west Indian Ocean Islands

The family Geminiviridae comprises a group of plant-infecting circular ssDNA viruses that severely constrain agricultural production throughout the temperate regions of the world, and are a particularly serious threat to food security in sub-Saharan Africa. While geminiviruses exhibit considerable diversity in terms of their nucleotide sequences, genome structures, host ranges and insect vectors, the best characterised and economically most important of these viruses are those in the genus Begomovirus. Whereas begomoviruses are generally considered to be either monopartite (one ssDNA component) or bipartite (two circular ssDNA components called DNA-A and DNA-B), many apparently monopartite begomoviruses are associated with additional subviral ssDNA satellite components, called alpha- (DNA-αs) or betasatellites (DNA-βs). Additionally, subgenomic molecules, also known as defective interfering (DIs) DNAs that are usually derived from the parent helper virus through deletions of parts of its genome, are also associated with bipartite and monopartite begomoviruses. The past three decades have witnessed the emergence and diversification of various new begomoviral species and associated DI DNAs, in southern Africa, East Africa, and proximal Indian Ocean islands, which today threaten important vegetable and commercial crops such as, tobacco, cassava, tomato, sweet potato, and beans. This review aims to describe what is known about these viruses and their impacts on sustainable production in this sensitive region of the world. © 2012 by the authors licensee MDPI, Basel, Switzerland.

Chimaeric HIV-1 subtype C Gag molecules with large in-frame C-terminal polypeptide fusions form virus-like particles

HIV-1 Pr55 Gag virus-like particles (VLPs) are strong immunogens with potential as candidate HIV vaccines. VLP immunogenicity can be broadened by making chimaeric Gag molecules: however, VLPs incorporating polypeptides longer than 200 aa fused in frame with Gag have not yet been reported. We constructed a range of gag-derived genes encoding in-frame C-terminal fusions of myristoylation-competent native Pr55Gag and p6-truncated Gag (Pr50Gag) to test the effects of polypeptide length and sequence on VLP formation and morphology, in an insect cell expression system. Fused sequences included a modified reverse transcriptase-Tat-Nef fusion polypeptide (RTTN, 778 aa), and truncated versions of RTTN ranging from 113 aa to 450 aa. Baculovirus-expressed chimaeric proteins were examined by western blot and electron microscopy. All chimaeras formed VLPs which could be purified by sucrose gradient centrifugation. VLP diameter increased with protein MW, from ∼100 nm for Pr55Gag to ∼250 nm for GagRTTN. The presence or absence of the Gag p6 region did not obviously affect VLP formation or appearance. GagRT chimaeric particles were successfully used in mice to boost T-cell responses to Gag and RT that were elicited by a DNA vaccine encoding a GagRTTN polypeptide, indicating the potential of such chimaeras to be used as candidate HIV vaccines. © 2008 Elsevier B.V. All rights reserved.

Automatic particle picking of biological molecules imaged by electron microscopy

One of the next great challenges of cell biology is the determination of the enormous number of protein structures encoded in genomes. In recent years, advances in electron cryo-microscopy and high-resolution single particle analysis have developed to the point where they now provide a methodology for high resolution structure determination. Using this approach, images of randomly oriented single particles are aligned computationally to reconstruct 3-D structures of proteins and even whole viruses. One of the limiting factors in obtaining high-resolution reconstructions is obtaining a large enough representative dataset ($>100,000$ particles). Traditionally particles have been manually picked which is an extremely labour intensive process. The problem is made especially difficult by the low signal-to-noise ratio of the images. This paper describes the development of automatic particle picking software, which has been tested with both negatively stained and cryo-electron micrographs. This algorithm has been shown to be capable of selecting most of the particles, with few false positives. Further work will involve extending the software to detect differently shaped and oriented particles.

Deposition of hydrocarbon molecules on diamond (001) surfaces : atomic scale modeling

The impact induced chemisorption of hydrocarbon molecules (CH3 and CH2) on H-terminated diamond (001)-(2x1) surface was investigated by molecular dynamics simulation using the many-body Brenner potential. The deposition dynamics of the CH3 radical at impact energies of 0.1-50 eV per molecule was studied and the energy threshold for chemisorption was calculated. The impact-induced decomposition of hydrogen atoms and the dimer opening mechanism on the surface was investigated. Furthermore, the probability for dimer opening event induced by chemisorption of CH, was simulated by randomly varying the impact position as well as the orientation of the molecule relative to the surface. Finally, the energetic hydrocarbons were modeled, slowing down one after the other to simulate the initial fabrication of diamond-like carbon (DLC) films. The structure characteristic in synthesized films with different hydrogen flux was studied. Our results indicate that CH3, CH2 and H are highly reactive and important species in diamond growth. Especially, the fraction of C-atoms in the film having sp(3) hybridization will be enhanced in the presence of H atoms, which is in good agreement with experimental observations. (C) 2002 Elsevier Science B.V. All rights reserved.