Bilayer graphene formed by passage of current through graphite: evidence for a three-dimensional structure

The passage of an electric current through graphite or few-layer graphene can result in a striking structural transformation, but there is disagreement about the precise nature of this process. Some workers have interpreted the phenomenon in terms of the sublimation and edge reconstruction of essentially flat graphitic structures. An alternative explanation is that the transformation actually involves a change from a flat to a three-dimensional structure. Here we describe detailed studies of carbon produced by the passage of a current through graphite which provide strong evidence that the transformed carbon is indeed three-dimensional. The evidence comes primarily from images obtained in the scanning transmission electron microscope using the technique of high-angle annular dark-field imaging, and from a detailed analysis of electron energy loss spectra. We discuss the possible mechanism of the transformation, and consider potential applications of “three-dimensional bilayer graphene”.

Can climate models capture the structure of extratropical cyclones?

Composites of wind speeds, equivalent potential temperature, mean sea level pressure, vertical velocity, and relative humidity have been produced for the 100 most intense extratropical cyclones in the Northern Hemisphere winter for the 40-yr ECMWF Re-Analysis (ERA-40) and the high resolution global environment model (HiGEM). Features of conceptual models of cyclone structure—the warm conveyor belt, cold conveyor belt, and dry intrusion—have been identified in the composites from ERA-40 and compared to HiGEM. Such features can be identified in the composite fields despite the smoothing that occurs in the compositing process. The surface features and the three-dimensional structure of the cyclones in HiGEM compare very well with those from ERA-40. The warm conveyor belt is identified in the temperature and wind fields as a mass of warm air undergoing moist isentropic uplift and is very similar in ERA-40 and HiGEM. The rate of ascent is lower in HiGEM, associated with a shallower slope of the moist isentropes in the warm sector. There are also differences in the relative humidity fields in the warm conveyor belt. In ERA-40, the high values of relative humidity are strongly associated with the moist isentropic uplift, whereas in HiGEM these are not so strongly associated. The cold conveyor belt is identified as rearward flowing air that undercuts the warm conveyor belt and produces a low-level jet, and is very similar in HiGEM and ERA-40. The dry intrusion is identified in the 500-hPa vertical velocity and relative humidity. The structure of the dry intrusion compares well between HiGEM and ERA-40 but the descent is weaker in HiGEM because of weaker along-isentrope flow behind the composite cyclone. HiGEM’s ability to represent the key features of extratropical cyclone structure can give confidence in future predictions from this model.

Microbial relatives of the seed storage proteins of higher plants: conservation of structure and diversification of function during evolution of the cupin superfamily.

This review summarizes the recent discovery of the cupin superfamily (from the Latin term "cupa," a small barrel) of functionally diverse proteins that initially were limited to several higher plant proteins such as seed storage proteins, germin (an oxalate oxidase), germin-like proteins, and auxin-binding protein. Knowledge of the three-dimensional structure of two vicilins, seed proteins with a characteristic beta-barrel core, led to the identification of a small number of conserved residues and thence to the discovery of several microbial proteins which share these key amino acids. In particular, there is a highly conserved pattern of two histidine-containing motifs with a varied intermotif spacing. This cupin signature is found as a central component of many microbial proteins including certain types of phosphomannose isomerase, polyketide synthase, epimerase, and dioxygenase. In addition, the signature has been identified within the N-terminal effector domain in a subgroup of bacterial AraC transcription factors. As well as these single-domain cupins, this survey has identified other classes of two-domain bicupins including bacterial gentisate 1, 2-dioxygenases and 1-hydroxy-2-naphthoate dioxygenases, fungal oxalate decarboxylases, and legume sucrose-binding proteins. Cupin evolution is discussed from the perspective of the structure-function relationships, using data from the genomes of several prokaryotes, especially Bacillus subtilis. Many of these functions involve aspects of sugar metabolism and cell wall synthesis and are concerned with responses to abiotic stress such as heat, desiccation, or starvation. Particular emphasis is also given to the oxalate-degrading enzymes from microbes, their biological significance, and their value in a range of medical and other applications.

Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold

The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for "middle of the SARS-unique domain") in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1 ''-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

NMR structure shows that the SARS-unique domain contains a macrodomain fold

The NMR structure of a central segment of the previously annotated "SARS-unique domain" (SUD-M; "middle of the SARS-unique domain") in the SARS coronavirus (SARS-CoV) non-structural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3-residues 528-648, and there is a flexibly extended N-terminal tail with the residues 513-527 and a C-terminal flexible tail of residues 649-651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527-651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly-A and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1''-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows 3D structure homology with several helicases and NTP-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

How may tropical cyclones change in a warmer climate?

Tropical Cyclones (TC) under different climate conditions in the Northern Hemisphere have been investigated with the Max Planck Institute (MPI) coupled (ECHAM5/MPIOM) and atmosphere (ECHAM5) climate models. The intensity and size of the TC depend crucially on resolution with higher wind speed and smaller scales at the higher resolutions. The typical size of the TC is reduced by a factor of 2.3 from T63 to T319 using the distance of the maximum wind speed from the centre of the storm as a measure. The full three dimensional structure of the storms becomes increasingly more realistic as the resolution is increased. For the T63 resolution, three ensemble runs are explored for the period 1860 until 2100 using the IPCC SRES scenario A1B and evaluated for three 30 year periods at the end of the 19th, 20th and 21st century, respectively. While there is no significant change between the 19th and the 20th century, there is a considerable reduction in the number of the TC by some 20% in the 21st century, but no change in the number of the more intense storms. Reduction in the number of storms occurs in all regions. A single additional experiment at T213 resolution was run for the two latter 30-year periods. The T213 is an atmospheric only experiment using the transient Sea Surface Temperatures (SST) of the T63 resolution experiment. Also in this case, there is a reduction by some 10% in the number of simulated TC in the 21st century compared to the 20th century but a marked increase in the number of intense storms. The number of storms with maximum wind speeds greater than 50ms-1 increases by a third. Most of the intensification takes place in 2 the Eastern Pacific and in the Atlantic where also the number of storms more or less stays the same. We identify two competing processes effecting TC in a warmer climate. First, the increase in the static stability and the reduced vertical circulation is suggested to contribute to the reduction in the number of storms. Second, the increase in temperature and water vapor provide more energy for the storms so that when favorable conditions occur, the higher SST and higher specific humidity will contribute to more intense storms. As the maximum intensity depends crucially on resolution, this will require higher resolution to have its full effect. The distribution of storms between different regions does not, at first approximation, depend on the temperature itself but on the distribution of the SST anomalies and their influence on the atmospheric circulation. Two additional transient experiments at T319 resolution where run for 20 years at the end of the 20th and 21st century, respectively using the same conditions as in the T213 experiments. The results are consistent with the T213 study. The total number of tropical cyclones were similar to the T213 experiment but were generally more intense. The change from the 20th to the 21st century was also similar with fewer TC in total but with more intense cyclones.

Dynamical evolution of the 2003 southern hemisphere stratospheric winter using Envisat trace-gas observations

Data from the MIPAS instrument on Envisat, supplemented by meteorological analyses from ECMWF and the Met Office, are used to study the meteorological and trace-gas evolution of the stratosphere in the southern hemisphere during winter and spring 2003. A pole-centred approach is used to interpret the data in the physically meaningful context of the evolving stratospheric polar vortex. The following salient dynamical and transport features are documented and analysed: the merger of anticyclones in the stratosphere; the development of an intense, quasi-stationary anticyclone in spring; the associated top-down breakdown of the polar vortex; the systematic descent of air into the polar vortex; and the formation of a three-dimensional structure of a tracer filament on a planetary scale. The paper confirms and extends existing paradigms of the southern hemisphere vortex evolution. The quality of the MIPAS observations is seen to be generally good. though the water vapour retrievals are unrealistic above 10 hPa in the high-latitude winter.

Atmospheric factors governing banded orographic convection

Atmospheric factors Governing Banded Orographic Convection The three-dimensional structure of shallow orographic convection is investigated through simulations performed with a cloud-resolving numerical model. In moist flows that overcome a given topographic barrier to form statically unstable cap clouds, the organization of the convection depends on both the atmospheric structure and the mechanism by which the convection is initiated. Convection initiated by background thermal fluctuations embedded in the flow over a smooth mountain (without any small-scale topographic features) tends to be cellular and disorganized except that shear-parallel bands may form in flows with strong unidirectional vertical shear. The development of well-organized bands is favored when there is weak static instability inside the cloud and when the dry air surrounding the cloud is strongly stable. These bands move with the flow and distribute their cumulative precipitation evenly over the mountain upslope. Similar shear-parallel bands also develop in flows where convection is initiated by small-scale topographic noise superimposed onto the main mountain profile, but in this case stronger circulations are also triggered that create stationary rainbands parallel to the low-level flow. This second dominant mode, which is less sensitive to the atmospheric structure and the strength of forcing, is triggered by lee waves that form over small-scale topographic bumps near the upstream edge of the main orographic cloud. Due to their stationarity, these flow-parallel bands can produce locally heavy precipitation amounts.

The synthesis and characterisation of four new antimony sulphides incorporating transition-metal complexes

Four new antimony sulphides, [T(dien)(2)]Sb6S10 center dot xH(2)O [T = Ni (1), Co (2) x approximate to 0.45], [Co(en)(3)]SbsSI(3) (3) and [Ni(en)(3)]Sb12S19 (4), have been synthesised under solvothermal conditions. In compounds (1) - (3), Sb12S228- secondary building units are connected to form layered structures. In (1) and (2), Sb-6 S-2- layers containing Sb16S16 heterorings are separated by [T(dien]2](2+) cations, whilst in (3), Sb8 S2- layers 10 13 contain [Co(en)3]2+ cations within large Sb22S22 pores. Compound (4) adopts a three-dimensional structure in which [Ni(en)3 12 cations lie within ca. 5 A wide channels. (c) 2007 Elsevier Ltd. All rights reserved.

Structural studies on acridine derivatives binding to telomeric DNA

Acridine derivatives can inhibit a variety of nuclear enzymes by binding or intercalating to DNA. This class of compounds is of great interest in the development of novel anticancer agents. Despite the availability of crystallographic data for some of the compounds complexed with DNA, uncertainties remain about the mechanisms of action, binding preferences and biological targets. To investigate the intercalation of several acridine derivatives, a variety of techniques are being employed. Single-crystal X-ray diffraction is being used to determine the high resolution three-dimensional structure of short sequences of quadruplex telomeric DNA with bound drug. This will be compared to the effect of drug binding to long segments of double-stranded DNA using fibre diffraction, with neutron diffraction studies planned to analyse the hydrogen bonding patterns of the DNA-drug complexes. Small-angle neutron scattering (SANS) will also be applied to study drug binding to both short and long sequences of quadruplex and double-stranded DNA in solution. Initial SANS measurements of the telomeric repeat d(TGGGGT) imply that this hexamer is present as a quadruplex. (c) 2006 Elsevier B.V. All rights reserved.

Path planning of robots in noisy workspaces using learning automata

The problem of a manipulator operating in a noisy workspace and required to move from an initial fixed position P0 to a final position Pf is considered. However, Pf is corrupted by noise, giving rise to Pˆf, which may be obtained by sensors. The use of learning automata is proposed to tackle this problem. An automaton is placed at each joint of the manipulator which moves according to the action chosen by the automaton (forward, backward, stationary) at each instant. The simultaneous reward or penalty of the automata enables avoiding any inverse kinematics computations that would be necessary if the distance of each joint from the final position had to be calculated. Three variable-structure learning algorithms are used, i.e., the discretized linear reward-penalty (DLR-P, the linear reward-penalty (LR-P ) and a nonlinear scheme. Each algorithm is separately tested with two (forward, backward) and three forward, backward, stationary) actions.

Dispersion of a point-source release of a passive scalar through an urban-like array for different wind directions

The dispersion of a point-source release of a passive scalar in a regular array of cubical, urban-like, obstacles is investigated by means of direct numerical simulations. The simulations are conducted under conditions of neutral stability and fully rough turbulent flow, at a roughness Reynolds number of Reτ = 500. The Navier–Stokes and scalar equations are integrated assuming a constant rate release from a point source close to the ground within the array. We focus on short-range dispersion, when most of the material is still within the building canopy. Mean and fluctuating concentrations are computed for three different pressure gradient directions (0◦ , 30◦ , 45◦). The results agree well with available experimental data measured in a water channel for a flow angle of 0◦ . Profiles of mean concentration and the three-dimensional structure of the dispersion pattern are compared for the different forcing angles. A number of processes affecting the plume structure are identified and discussed, including: (i) advection or channelling of scalar down ‘streets’, (ii) lateral dispersion by turbulent fluctuations and topological dispersion induced by dividing streamlines around buildings, (iii) skewing of the plume due to flow turning with height, (iv) detrainment by turbulent dispersion or mean recirculation, (v) entrainment and release of scalar in building wakes, giving rise to ‘secondary sources’, (vi) plume meandering due to unsteady turbulent fluctuations. Finally, results on relative concentration fluctuations are presented and compared with the literature for point source dispersion over flat terrain and urban arrays. Keywords Direct numerical simulation · Dispersion modelling · Urban array

A self-similar expansion model for use in solar wind transient propogation studies

Since the advent of wide-angle imaging of the inner heliosphere, a plethora of techniques have been developed to investigate the three-dimensional structure and kinematics of solar wind transients, such as coronal mass ejections, from their signatures in single- and multi-spacecraft imaging observations. These techniques, which range from the highly complex and computationally intensive to methods based on simple curve fitting, all have their inherent advantages and limitations. In the analysis of single-spacecraft imaging observations, much use has been made of the fixed φ fitting (FPF) and harmonic mean fitting (HMF) techniques, in which the solar wind transient is considered to be a radially propagating point source (fixed φ, FP, model) and a radially expanding circle anchored at Sun centre (harmonic mean, HM, model), respectively. Initially, we compare the radial speeds and propagation directions derived from application of the FPF and HMF techniques to a large set of STEREO/Heliospheric Imager (HI) observations. As the geometries on which these two techniques are founded constitute extreme descriptions of solar wind transients in terms of their extent along the line of sight, we describe a single-spacecraft fitting technique based on a more generalized model for which the FP and HM geometries form the limiting cases. In addition to providing estimates of a transient’s speed and propagation direction, the self-similar expansion fitting (SSEF) technique provides, in theory, the capability to estimate the transient’s angular extent in the plane orthogonal to the field of view. Using the HI observations, and also by performing a Monte Carlo simulation, we assess the potential of the SSEF technique.

Synthesis, characterisation and magnetic properties of a one-dimensional Iron(II) coordination polymer

A new iron(II) coordination polymer, [FeCl2(NC7H9)2(N2C12H12)], has been synthesized under solvothermal conditions and structurally characterized by single-crystal X-ray diffraction. This material crystallizes in the monoclinic space group C2/c, with a = 11.2850(6), b = 13.8925(7), c = 17.0988(9) Å and β = 94.300(3)º (Z = 4). The crystal structure consists of neutral zig-zag chains, in which the iron(II) ions are octahedrally coordinated. The infinite polymer chains are packed into a three-dimensional structure through C–H···Cl interactions. Magnetic susceptibility measurements reveal the existence of weak antiferromagnetic interactions between the iron(II) ions. The effective magnetic moment, μ eff = 5.33 μ B , is consistent with a high-spin iron(II) configuration.