Guanine specific binding at a DNA junction formed by d[CG(5-BrU)ACG]2 with a topoisomerase poison in the presence of Co2+Ions†,‡

The structure of the duplex d[CG(5-BrU)ACG]2 bound to 9-bromophenazine-4-carboxamide has been solved through MAD phasing at 2.0 Å resolution. It shows an unexpected and previously unreported intercalation cavity stabilized by the drug and novel binding modes of Co2+ ions at certain guanine N7 sites. For the intercalation cavity the terminal cytosine is rotated to pair with the guanine of a symmetry-related duplex to create a pseudo-Holliday junction geometry, with two such cavities linked through the minor groove interactions of the N2/N3 guanine sites at an angle of 40°, creating a quadruplex-like structure. The mode of binding of the drug is shown to be disordered, with the major conformations showing the side chain bound to the N7 position of adjacent guanines. The other end of the duplex exhibits a terminal base fraying in the presence of Co2+ ions linking symmetry-related guanines, causing the helices to intertwine through the minor groove. The stabilization of the structure by the intercalating drug shows that this class of compound may bind to DNA junctions as well as duplex DNA or to strand-nicked DNA (‘hemi-intercalated'), as in the cleavable complex. This suggests a structural basis for the dual poisoning of topoisomerase I and II enzymes by this family of drugs.

The correlation structure of spatial autoregressions

This paper investigates how the correlations implied by a first-order simultaneous autoregressive (SAR(1)) process are affected by the weights matrix and the autocorrelation parameter. A graph theoretic representation of the covariances in terms of walks connecting the spatial units helps to clarify a number of correlation properties of the processes. In particular, we study some implications of row-standardizing the weights matrix, the dependence of the correlations on graph distance, and the behavior of the correlations at the extremes of the parameter space. Throughout the analysis differences between directed and undirected networks are emphasized. The graph theoretic representation also clarifies why it is difficult to relate properties ofW to correlation properties of SAR(1) models defined on irregular lattices.

Symmetry-break in Voronoi tessellations

We analyse in a common framework the properties of the Voronoi tessellations resulting from regular 2D and 3D crystals and those of tessellations generated by Poisson distributions of points, thus joining on symmetry breaking processes and the approach to uniform random distributions of seeds. We perturb crystalline structures in 2D and 3D with a spatial Gaussian noise whose adimensional strength is α and analyse the statistical properties of the cells of the resulting Voronoi tessellations using an ensemble approach. In 2D we consider triangular, square and hexagonal regular lattices, resulting into hexagonal, square and triangular tessellations, respectively. In 3D we consider the simple cubic (SC), body-centred cubic (BCC), and face-centred cubic (FCC) crystals, whose corresponding Voronoi cells are the cube, the truncated octahedron, and the rhombic dodecahedron, respectively. In 2D, for all values α>0, hexagons constitute the most common class of cells. Noise destroys the triangular and square tessellations, which are structurally unstable, as their topological properties are discontinuous in α=0. On the contrary, the honeycomb hexagonal tessellation is topologically stable and, experimentally, all Voronoi cells are hexagonal for small but finite noise with α<0.12. Basically, the same happens in the 3D case, where only the tessellation of the BCC crystal is topologically stable even against noise of small but finite intensity. In both 2D and 3D cases, already for a moderate amount of Gaussian noise (α>0.5), memory of the specific initial unperturbed state is lost, because the statistical properties of the three perturbed regular tessellations are indistinguishable. When α>2, results converge to those of Poisson-Voronoi tessellations. In 2D, while the isoperimetric ratio increases with noise for the perturbed hexagonal tessellation, for the perturbed triangular and square tessellations it is optimised for specific value of noise intensity. The same applies in 3D, where noise degrades the isoperimetric ratio for perturbed FCC and BCC lattices, whereas the opposite holds for perturbed SCC lattices. This allows for formulating a weaker form of the Kelvin conjecture. By analysing jointly the statistical properties of the area and of the volume of the cells, we discover that also the cells shape heavily fluctuates when noise is introduced in the system. In 2D, the geometrical properties of n-sided cells change with α until the Poisson-Voronoi limit is reached for α>2; in this limit the Desch law for perimeters is shown to be not valid and a square root dependence on n is established, which agrees with exact asymptotic results. Anomalous scaling relations are observed between the perimeter and the area in the 2D and between the areas and the volumes of the cells in 3D: except for the hexagonal (2D) and FCC structure (3D), this applies also for infinitesimal noise. In the Poisson-Voronoi limit, the anomalous exponent is about 0.17 in both the 2D and 3D case. A positive anomaly in the scaling indicates that large cells preferentially feature large isoperimetric quotients. As the number of faces is strongly correlated with the sphericity (cells with more faces are bulkier), in 3D it is shown that the anomalous scaling is heavily reduced when we perform power law fits separately on cells with a specific number of faces.

Spatial coding of touch at the fingers: Insights from double simultaneous stimulation within and between hands

We studied the effect of tactile double simultaneous stimulation (DSS) within and between hands to examine spatial coding of touch at the fingers. Participants performed a go/no-go task to detect a tactile stimulus delivered to one target finger (e.g., right index), stimulated alone or with a concurrent non-target finger, either on the same hand (e.g., right middle finger) or on the other hand (e.g., left index finger=homologous; left middle finger=non-homologous). Across blocks we also changed the unseen hands posture (both hands palm down, or one hand rotated palm-up). When both hands were palm-down DSS interference effects emerged both within and between hands, but only when the non-homologous finger served as non-target. This suggests a clear segregation between the fingers of each hand, regardless of finger side. By contrast, when one hand was palm-up interference effects emerged only within hand, whereas between hands DSS interference was considerably reduced or absent. Thus, between hands interference was clearly affected by changes in hands posture. Taken together, these findings provide behavioral evidence in humans for multiple spatial coding of touch during tactile DSS at the fingers. In particular, they confirm the existence of representational stages of touch that distinguish between body-regions more than body-sides. Moreover, they show that the availability of tactile stimulation side becomes prominent when postural update is required.

Ternary erbium chromium sulfides : structural relationships and magnetic properties

Single crystals of four erbium-chromium sulfides have been grown by chemical vapor transport using iodine as the transporting agent. Single-crystal X-ray diffraction reveals that in Er(3)CrS(6) octahedral sites are occupied exclusively by Cr(3+) cations, leading to one-dimensional CrS(4)(5-) chains of edge-sharing octahedra, while in Er(2)CrS(4), Er(3+), and Cr(2+) cations occupy the available octahedral sites in an ordered manner. By contrast, in Er(6)Cr(2)S(11) and Er(4)CrS(7), Er(3+) and Cr(2+) ions are disordered over the octahedral sites. In Er(2)CrS(4), Er(6)Cr(2)S(11), and Er(4)CrS(7), the network of octahedra generates an anionic framework constructed from M(2)S(5) slabs of varying thickness, linked by one-dimensional octahedral chains. This suggests that these three phases belong to a series in which the anionic framework may be described by the general formula [M(2n+1)S(4n+3)](x-), with charge balancing provided by Er(3+) cations located in sites of high-coordination number within one-dimensional channels defined by the framework. Er(4)CrS(7), Er(6)Cr(2)S(11), and Er(2)CrS(4) may thus be considered as the n = 1, 2, and infinity members of this series. While Er(4)CrS(7) is paramagnetic, successive magnetic transitions associated with ordering of the chromium and erbium sub-lattices are observed on cooling Er(3)CrS(6) (T(C)(Cr) = 30 K; T(C)(Er) = 11 K) and Er(2)CrS(4) (T(N)(Cr) = 42 K, T(N)(Er) = 10 K) whereas Er(6)Cr(2)S(11) exhibits ordering of the chromium sub-lattice only (T(N) = 11.4 K).

The variable link between PNA and NAO in observations and in multi-century CGCM simulations

The link between the Pacific/North American pattern (PNA) and the North Atlantic Oscillation (NAO) is investigated in reanalysis data (NCEP, ERA40) and multi-century CGCM runs for present day climate using three versions of the ECHAM model. PNA and NAO patterns and indices are determined via rotated principal component analysis on monthly mean 500 hPa geopotential height fields using the varimax criteria. On average, the multi-century CGCM simulations show a significant anti-correlation between PNA and NAO. Further, multi-decadal periods with significantly enhanced (high anti-correlation, active phase) or weakened (low correlations, inactive phase) coupling are found in all CGCMs. In the simulated active phases, the storm track activity near Newfoundland has a stronger link with the PNA variability than during the inactive phases. On average, the reanalysis datasets show no significant anti-correlation between PNA and NAO indices, but during the sub-period 1973–1994 a significant anti-correlation is detected, suggesting that the present climate could correspond to an inactive period as detected in the CGCMs. An analysis of possible physical mechanisms suggests that the link between the patterns is established by the baroclinic waves forming the North Atlantic storm track. The geopotential height anomalies associated with negative PNA phases induce an increased advection of warm and moist air from the Gulf of Mexico and cold air from Canada. Both types of advection contribute to increase baroclinicity over eastern North America and also to increase the low level latent heat content of the warm air masses. Thus, growth conditions for eddies at the entrance of the North Atlantic storm track are enhanced. Considering the average temporal development during winter for the CGCM, results show an enhanced Newfoundland storm track maximum in the early winter for negative PNA, followed by a downstream enhancement of the Atlantic storm track in the subsequent months. In active (passive) phases, this seasonal development is enhanced (suppressed). As the storm track over the central and eastern Atlantic is closely related to the NAO variability, this development can be explained by the shift of the NAO index to more positive values.

Rheology of discrete failure regimes of anisotropic sea ice

A rheological model of sea ice is presented that incorporates the orientational distribution of ice thickness in leads embedded in isotropic floe ice. Sea ice internal stress is determined by coulombic, ridging and tensile failure at orientations where corresponding failure criteria are satisfied at minimum stresses. Because sea ice traction increases in thinner leads and cohesion is finite, such failure line angles are determined by the orientational distribution of sea ice thickness relative to the imposed stresses. In contrast to the isotropic case, sea ice thickness anisotropy results in these failure lines becoming dependent on the stress magnitude. Although generally a given failure criteria type can be satisfied at many directions, only two at most are considered. The strain rate is determined by shearing along slip lines accompanied by dilatancy and closing or opening across orientations affected by ridging or tensile failure. The rheology is illustrated by a yield curve determined by combining coulombic and ridging failure for the case of two pairs of isotropically formed leads of different thicknesses rotated with regard to each other, which models two events of coulombic failure followed by dilatancy and refreezing. The yield curve consists of linear segments describing coulombic and ridging yield as failure switches from one lead to another as the stress grows. Because sliding along slip lines is accompanied by dilatancy, at typical Arctic sea ice deformation rates a one-day-long deformation event produces enough open water that these freshly formed slip lines are preferential places of ridging failure.

Modelling the reorientation of sea-ice faults as the wind changes direction

A discrete-element model of sea ice is used to study how a 90° change in wind direction alters the pattern of faults generated through mechanical failure of the ice. The sea-ice domain is 400km in size and consists of polygonal floes obtained through a Voronoi tessellation. Initially the floes are frozen together through viscous–elastic joints that can break under sufficient compressive, tensile and shear deformation. A constant wind-stress gradient is applied until the initially frozen ice pack is broken into roughly diamond-shaped aggregates, with crack angles determined by wing-crack formation. Then partial refreezing of the cracks delineating the aggregates is modelled through reduction of their length by a particular fraction, the ice pack deformation is neglected and the wind stress is rotated by 90°. New cracks form, delineating aggregates with a different orientation. Our results show the new crack orientation depends on the refrozen fraction of the initial faults: as this fraction increases, the new cracks gradually rotate to the new wind direction, reaching 90° for fully refrozen faults. Such reorientation is determined by a competition between new cracks forming at a preferential angle determined by the wing-crack theory and at old cracks oriented at a less favourable angle but having higher stresses due to shorter contacts across the joints

Simulation of field-induced structural formation and transition in electromagnetorheological suspensions

A computer simulation method has been used to study the three-dimensional structural formation and transition of eleetromagnetorheological (EMR) suspensions under compatible electric and magnetic fields. When the fields are applied simultaneously and perpendicularly to each other, the particles rapidly arrange into single layer structures parallel to both fields. In each layer, there is a two-dimensional hexagonal lattice. The single layers then combine together to form thicker sheetlike structures. With the help of the thermal fluctuations, the thicker structures relax into three-dimensional close-packed structures, which may be face-centered cubic (fcc), hexagonal close-packed (hup) lattices, or, more probably, the mixture of them, depending on the initial configurations and the thermal fluctuations. On the other hand, if the electric field is applied first to induce the body-centered tetragonal (bct) columns in the system, and then the magnetic field is applied in the perpendicular direction, the bet to fee structure transition is observed in a very short time. Following that, the structure keeps on evolving due to the demagnetization effect and finally forms close-packed structures with fee and hcp lattice character. The simulation results are in agreement with the theoretical and experimental results.

On the structure and dynamics of Indian monsoon depressions

ERA-Interim reanalysis data from the past 35 years have been used with a newly-developed feature tracking algorithm to identify Indian monsoon depressions originating in or near the Bay of Bengal. These were then rotated, centralised and combined to give a fully three-dimensional 106-depression composite structure – a considerably larger sample than any previous detailed study on monsoon depressions and their structure. Many known features of depression structure are confirmed, particularly the existence of a maximum to the southwest of the centre in rainfall and other fields, and a westward axial tilt in others. Additionally, the depressions are found to have significant asymmetry due to the presence of the Himalayas; a bimodal mid-tropospheric potential vorticity core; a separation into thermally cold- (~–1.5K) and neutral- (~0K) cores near the surface with distinct properties; and that the centre has very large CAPE and very small CIN. Variability as a function of background state has also been explored, with land/coast/sea, diurnal, ENSO, active/break and Indian Ocean Dipole contrasts considered. Depressions are found to be markedly stronger during the active phase of the monsoon, as well as during La Niña. Depressions on land are shown to be more intense and more tightly constrained to the central axis. A detailed schematic diagram of a vertical cross-section through a composite depression is also presented, showing its inherent asymmetric structure.

Multi-instrument ground-based observations of a travelling convection vortices event

A coordinated ground-based observational campaign using the IMAGE magnetometer network, EISCAT radars and optical instruments on Svalbard has made possible detailed studies of a travelling convection vortices (TCV) event on 6 January 1992. Combining the data from these facilities allows us to draw a very detailed picture of the features and dynamics of this TCV event. On the way from the noon to the drawn meridian, the vortices went through a remarkable development. The propagation velocity in the ionosphere increased from 2.5 to 7.4 km s−1, and the orientation of the major axes of the vortices rotated from being almost parallel to the magnetic meridian near noon to essentially perpendicular at dawn. By combining electric fields obtained by EISCAT and ionospheric currents deduced from magnetic field recordings, conductivities associated with the vortices could be estimated. Contrary to expectations we found higher conductivities below the downward field aligned current (FAC) filament than below the upward directed. Unexpected results also emerged from the optical observations. For most of the time there were no discrete aurora at 557.7 nm associated with the TCVs. Only once did a discrete form appear at the foot of the upward FAC. This aurora subsequently expanded eastward and westward leaving its centre at the same longitude while the TCV continued to travel westward. Also we try to identify the source regions of TCVs in the magnetosphere and discuss possible generation mechanisms.

Ionospheric convection response to slow, strong variations in a northward interplanetary magnetic field: A case study for January 14, 1988

We analyze ionospheric convection patterns over the polar regions during the passage of an interplanetary magnetic cloud on January 14, 1988, when the interplanetary magnetic field (IMF) rotated slowly in direction and had a large amplitude. Using the assimilative mapping of ionospheric electrodynamics (AMIE) procedure, we combine simultaneous observations of ionospheric drifts and magnetic perturbations from many different instruments into consistent patterns of high-latitude electrodynamics, focusing on the period of northward IMF. By combining satellite data with ground-based observations, we have generated one of the most comprehensive data sets yet assembled and used it to produce convection maps for both hemispheres. We present evidence that a lobe convection cell was embedded within normal merging convection during a period when the IMF By and Bz components were large and positive. As the IMF became predominantly northward, a strong reversed convection pattern (afternoon-to-morning potential drop of around 100 kV) appeared in the southern (summer) polar cap, while convection in the northern (winter) hemisphere became weak and disordered with a dawn-to-dusk potential drop of the order of 30 kV. These patterns persisted for about 3 hours, until the IMF rotated significantly toward the west. We interpret this behavior in terms of a recently proposed merging model for northward IMF under solstice conditions, for which lobe field lines from the hemisphere tilted toward the Sun (summer hemisphere) drape over the dayside magnetosphere, producing reverse convection in the summer hemisphere and impeding direct contact between the solar wind and field lines connected to the winter polar cap. The positive IMF Bx component present at this time could have contributed to the observed hemispheric asymmetry. Reverse convection in the summer hemisphere broke down rapidly after the ratio |By/Bz| exceeded unity, while convection in the winter hemisphere strengthened. A dominant dawn-to-dusk potential drop was established in both hemispheres when the magnitude of By exceeded that of Bz, with potential drops of the order of 100 kV, even while Bz remained northward. The later transition to southward Bz produced a gradual intensification of the convection, but a greater qualitative change occurred at the transition through |By/Bz| = 1 than at the transition through Bz = 0. The various convection patterns we derive under northward IMF conditions illustrate all possibilities previously discussed in the literature: nearly single-cell and multicell, distorted and symmetric, ordered and unordered, and sunward and antisunward.

Auroral and plasma flow transients at magnetic noon

We present observations of a transient event in the dayside auroral ionosphere at magnetic noon. F-region plasma convection measurements were made by the EISCAT radar, operating in the beamswinging “Polar” experiment mode, and simultaneous observations of the dayside auroral emissions were made by optical meridian-scanning photometers and all-sky TV cameras at Ny Ålesund, Spitzbergen. The data were recorded on 9 January 1989, and a sequence of bursts of flow, with associated transient aurora, were observed between 08:45 and 11:00 U.T. In this paper we concentrate on an event around 09:05 U.T. because that is very close to local magnetic noon. The optical data show a transient intensification and widening (in latitude) of the cusp/cleft region, as seen in red line auroral emissions. Over an interval of about 10 min, the band of 630 nm aurora widened from about 1.5° of invariant latitude to over 5° and returned to its original width. Embedded within the widening band of 630 nm emissions were two intense, active 557.7 nm arc fragments with rays which persisted for about 2 min each. The flow data before and after the optical transient show eastward flows, with speeds increasing markedly with latitude across the band of 630 nm aurora. Strong, apparently westward, flows appeared inside the band while it was widening, but these rotated round to eastward, through northward, as the band shrunk to its original width. The observed ion temperatures verify that the flow speeds during the transient were, to a large extent, as derived using the beamswinging technique; but they also show that the flow increase initially occurred in the western azimuth only. This spatial gradient in the flow introduces ambiguity in the direction of these initial flows and they could have been north-eastward rather than westward. However, the westward direction derived by the beamswinging is consistent with the motion of the colocated and coincident active 557.7 nm arc fragment, A more stable transient 557.7 nm aurora was found close to the shear between the inferred westward flows and the persisting eastward flows to the North. Throughout the transient, northward flow was observed across the equatorward boundary of the 630 nm aurora. Interpretation of the data is made difficult by lack of IMF data, problems in distinguishing the cusp and cleft aurora and uncertainty over which field lines are open and which are closed. However, at magnetic noon there is a 50% probability that we were observing the cusp, in which case from its southerly location we infer that the IMF was southward and many features are suggestive of time-varying reconnection at a single X-line on the dayside magnetopause. This IMF orientation is also consistent with the polar rain precipitation observed simultaneously by the DMSP-F9 satellite in the southern polar cap. There is also a 25% chance that we were observing the cleft (or the mantle poleward of the cleft). In this case we infer that the IMF was northward and the transient is well explained by reconnection which is not only transient in time but occurs at various sites located randomly on the dayside magnetopause (i.e. patchy in space). Lastly, there is a 25% chance that we were observing the cusp poleward of the cleft, in which case we infer that IMF Bz was near zero and the transient is explained by a mixture of the previous two interpretations.

Evaluating perceptual separation in a pilot system for affective composition

Research evaluating perceptual responses to music has identified many structural features as correlates that might be incorporated in computer music systems for affectively charged algorithmic composition and/or expressive music performance. In order to investigate the possible integration of isolated musical features to such a system, a discrete feature known to correlate some with emotional responses – rhythmic density – was selected from a literature review and incorporated into a prototype system. This system produces variation in rhythm density via a transformative process. A stimulus set created using this system was then subjected to a perceptual evaluation. Pairwise comparisons were used to scale differences between 48 stimuli. Listener responses were analysed with Multidimensional scaling (MDS). The 2-Dimensional solution was then rotated to place the stimuli with the largest range of variation across the horizontal plane. Stimuli with variation in rhythmic density were placed further from the source material than stimuli that were generated by random permutation. This, combined with the striking similarity between the MDS scaling and that of the 2-dimensional emotional model used by some affective algorithmic composition systems, suggests that isolated musical feature manipulation can now be used to parametrically control affectively charged automated composition in a larger system.

Three-dimensional gallium sulphide open framework

The synthesis and crystal structure of four gallium sulphide open frameworks, built from supertetrahedral clusters, are described. The structures of [C4NH12]6[Ga10S18][C4NH12]6[Ga10S18](1) and [C4NH12]12[Ga20S35.5(S3)0.5O](2) contain supertetrahedral T3 clusters, while in the isostructural compounds [C4NH12]16[Ga10S18M4Ga16S33][C4NH12]16[Ga10S18M4Ga16S33] (M=CoM=Co(3), Zn (4)), T3 and T4 clusters alternate. These materials exhibit three-dimensional frameworks, with topologies consisting of two interpenetrating diamond lattices, and contain over 50% of solvent accessible void space. UV–Vis diffuse reflectance measurements indicate that these compounds are semiconducting, with band gaps over the range 3.4–4.1 eV.