North Atlantic subtropical mode waters and ocean memory in HadCM3

A study of the formation and propagation of volume anomalies in North Atlantic Mode Waters is presented, based on 100 yr of monthly mean fields taken from the control run of the Third Hadley Centre Coupled Ocean-Atmosphere GCM (HadCM3). Analysis of the temporal and. spatial variability in the thickness between pairs of isothermal surfaces bounding the central temperature of the three main North Atlantic subtropical mode waters shows that large-scale variability in formation occurs over time scales ranging from 5 to 20 yr. The largest formation anomalies are associated with a southward shift in the mixed layer isothermal distribution, possibly due to changes in the gyre dynamics and/or changes in the overlying wind field and air-sea heat fluxes. The persistence of these anomalies is shown to result from their subduction beneath the winter mixed layer base where they recirculate around the subtropical gyre in the background geostrophic flow. Anomalies in the warmest mode (18 degrees C) formed on the western side of the basin persist for up to 5 yr. They are removed by mixing transformation to warmer classes and are returned to the seasonal mixed layer near the Gulf Stream where the stored heat may be released to the atmosphere. Anomalies in the cooler modes (16 degrees and 14 degrees C) formed on the eastern side of the basin persist for up to 10 yr. There is no clear evidence of significant transformation of these cooler mode anomalies to adjacent classes. It has been proposed that the eastern anomalies are removed through a tropical-subtropical water mass exchange mechanism beneath the trade wind belt (south of 20 degrees N). The analysis shows that anomalous mode water formation plays a key role in the long-term storage of heat in the model, and that the release of heat associated with these anomalies suggests a predictable climate feedback mechanism.

Multi-mode approximations to wave scattering by an uneven bed

Approximations to the scattering of linear surface gravity waves on water of varying quiescent depth are Investigated by means of a variational approach. Previous authors have used wave modes associated with the constant depth case to approximate the velocity potential, leading to a system of coupled differential equations. Here it is shown that a transformation of the dependent variables results in a much simplified differential equation system which in turn leads to a new multi-mode 'mild-slope' approximation. Further, the effect of adding a bed mode is examined and clarified. A systematic analytic method is presented for evaluating inner products that arise and numerical experiments for two-dimensional scattering are used to examine the performance of the new approximations.

Ribonucleocapsid formation of severe acute respiratory syndrome coronavirus through molecular action of the N-terminal domain of N protein

Conserved among all coronaviruses are four structural proteins: the matrix (M), small envelope (E), and spike (S) proteins that are embedded in the viral membrane and the nucleocapsid phosphoprotein (N), which exists in a ribonucleoprotein complex in the lumen. The N-terminal domain of coronaviral N proteins (N-NTD) provides a scaffold for RNA binding, while the C-terminal domain (N-CTD) mainly acts as oligomerization modules during assembly. The C terminus of the N protein anchors it to the viral membrane by associating with M protein. We characterized the structures of N-NTD from severe acute respiratory syndrome coronavirus (SARS-CoV) in two crystal forms, at 1.17 A (monoclinic) and at 1.85 A (cubic), respectively, resolved by molecular replacement using the homologous avian infectious bronchitis virus (IBV) structure. Flexible loops in the solution structure of SARS-CoV N-NTD are now shown to be well ordered around the beta-sheet core. The functionally important positively charged beta-hairpin protrudes out of the core, is oriented similarly to that in the IBV N-NTD, and is involved in crystal packing in the monoclinic form. In the cubic form, the monomers form trimeric units that stack in a helical array. Comparison of crystal packing of SARS-CoV and IBV N-NTDs suggests a common mode of RNA recognition, but they probably associate differently in vivo during the formation of the ribonucleoprotein complex. Electrostatic potential distribution on the surface of homology models of related coronaviral N-NTDs suggests that they use different modes of both RNA recognition and oligomeric assembly, perhaps explaining why their nucleocapsids have different morphologies.

The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55)

Echovirus type 12 (EV12), an enterovirus of the Picornaviridae family, uses the complement regulator, decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF, consisting of short consensus repeat domains 3 and 4, from cryo-negative stain electron microscopy data (EMD #1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the two-fold symmetry axes. Despite this general similarity, our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF34 and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB #1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF-binding phenotype in these viruses.

Subspace system identification framework for the analysis of multimoded propagation of THz-transient signals

We provide a system identification framework for the analysis of THz-transient data. The subspace identification algorithm for both deterministic and stochastic systems is used to model the time-domain responses of structures under broadband excitation. Structures with additional time delays can be modelled within the state-space framework using additional state variables. We compare the numerical stability of the commonly used least-squares ARX models to that of the subspace N4SID algorithm by using examples of fourth-order and eighth-order systems under pulse and chirp excitation conditions. These models correspond to structures having two and four modes simultaneously propagating respectively. We show that chirp excitation combined with the subspace identification algorithm can provide a better identification of the underlying mode dynamics than the ARX model does as the complexity of the system increases. The use of an identified state-space model for mode demixing, upon transformation to a decoupled realization form is illustrated. Applications of state-space models and the N4SID algorithm to THz transient spectroscopy as well as to optical systems are highlighted.

Detection of neural correlates of self-paced motor activity using empirical mode decomposition phase locking analysis

Transient episodes of synchronisation of neuronal activity in particular frequency ranges are thought to underlie cognition. Empirical mode decomposition phase locking (EMDPL) analysis is a method for determining the frequency and timing of phase synchrony that is adaptive to intrinsic oscillations within data, alleviating the need for arbitrary bandpass filter cut-off selection. It is extended here to address the choice of reference electrode and removal of spurious synchrony resulting from volume conduction. Spline Laplacian transformation and independent component analysis (ICA) are performed as pre-processing steps, and preservation of phase synchrony between synthetic signals. combined using a simple forward model, is demonstrated. The method is contrasted with use of bandpass filtering following the same preprocessing steps, and filter cut-offs are shown to influence synchrony detection markedly. Furthermore, an approach to the assessment of multiple EEG trials using the method is introduced, and the assessment of statistical significance of phase locking episodes is extended to render it adaptive to local phase synchrony levels. EMDPL is validated in the analysis of real EEG data, during finger tapping. The time course of event-related (de)synchronisation (ERD/ERS) is shown to differ from that of longer range phase locking episodes, implying different roles for these different types of synchronisation. It is suggested that the increase in phase locking which occurs just prior to movement, coinciding with a reduction in power (or ERD) may result from selection of the neural assembly relevant to the particular movement. (C) 2009 Elsevier B.V. All rights reserved.

A single director switching mode for monodomain liquid crystal elastomer

We report rotation of a single director in a nematic monodomain, acrylate based side-chain elastomer which was subjected to mechanical fields applied at angles in the range to the director, , present at the time of network formation. Time and spatially resolving wide angle X-ray scattering, together with polarised light microscopy measurements revealed a pronounced, almost discontinuous switching mode at a critical extension as the strain was applied at angles approaching to , whereas a more continuous rotation was seen when the strain was applied at more acute angles. This director reorientation was more or less uniform across the complete sample and was accompanied by a modest decrease in orientation parameter . At strains sufficient to induce switching there was some continuous distribution of director orientations with fluctuations of 10 although there was no evidence for any localised director inhomogenities such as domain formation. The observed deformation behaviour of these acrylate-based nematic monodomains was in accord with the predictions of a theory developed by Bladon et al., in that the complete set of data could be accounted for through a single parameter describing the chain anisotropy. The experimentally deduced chain anisotropy parameter was in broad agreement with that obtained from small-angle neutron scattering procedures, but was somewhat greater than that obtained by spontaneous shape changes at the nematic-isotropic transition.

Sensitivity of simulated regional Arctic climate to the choice of coupled model domain

The climate over the Arctic has undergone changes in recent decades. In order to evaluate the coupled response of the Arctic system to external and internal forcing, our study focuses on the estimation of regional climate variability and its dependence on large-scale atmospheric and regional ocean circulations. A global ocean–sea ice model with regionally high horizontal resolution is coupled to an atmospheric regional model and global terrestrial hydrology model. This way of coupling divides the global ocean model setup into two different domains: one coupled, where the ocean and the atmosphere are interacting, and one uncoupled, where the ocean model is driven by prescribed atmospheric forcing and runs in a so-called stand-alone mode. Therefore, selecting a specific area for the regional atmosphere implies that the ocean–atmosphere system can develop ‘freely’ in that area, whereas for the rest of the global ocean, the circulation is driven by prescribed atmospheric forcing without any feedbacks. Five different coupled setups are chosen for ensemble simulations. The choice of the coupled domains was done to estimate the influences of the Subtropical Atlantic, Eurasian and North Pacific regions on northern North Atlantic and Arctic climate. Our simulations show that the regional coupled ocean–atmosphere model is sensitive to the choice of the modelled area. The different model configurations reproduce differently both the mean climate and its variability. Only two out of five model setups were able to reproduce the Arctic climate as observed under recent climate conditions (ERA-40 Reanalysis). Evidence is found that the main source of uncertainty for Arctic climate variability and its predictability is the North Pacific. The prescription of North Pacific conditions in the regional model leads to significant correlation with observations, even if the whole North Atlantic is within the coupled model domain. However, the inclusion of the North Pacific area into the coupled system drastically changes the Arctic climate variability to a point where the Arctic Oscillation becomes an ‘internal mode’ of variability and correlations of year-to-year variability with observational data vanish. In line with previous studies, our simulations provide evidence that Arctic sea ice export is mainly due to ‘internal variability’ within the Arctic region. We conclude that the choice of model domains should be based on physical knowledge of the atmospheric and oceanic processes and not on ‘geographic’ reasons. This is particularly the case for areas like the Arctic, which has very complex feedbacks between components of the regional climate system.