Interpreting the upper level structure of the Madden-Julian oscillation

The nonlinear response of a spherical shallow water model to an imposed heat source in the presence of realistic zonal mean zonal winds is investigated numerically. The solutions exhibit elongated, meridionally tilted ridges and troughs indicative of a poleward dispersion of wave activity. As the speed of the jets is increased, the equatorial Kelvin wave is unaffected but the global Rossby wave train coalesces to form a compact, amplified quadrupole structure that bears a striking resemblance to the observed upper level structure of the Madden-Julian oscillation. In the presence of strong subtropical westerly jets, the advection of planetary vorticity by the meridional flow and relative vorticity by the zonally averaged background flow conspire to create the distinctive quadrupole configuration of flanking Rossby waves.

Dynamics of the North American continent

The forces that cause deformation of western North America have been debated for decades. Recent studies, primarily based on analysis of crustal stresses in the western United States, have suggested that the deformation of the region is mainly controlled by gravitational potential energy (GPE) variations and boundary loads, with basal tractions due to mantle flow playing a relatively minor role. We address these issues by modelling the deviatoric stress field over western North America from a 3-D finite element mantle circulation model with lateral viscosity variations. Our approach takes into account the contribution from both topography and shallow lithosphere structure (GPE) as well as that from deeper mantle flow in one single model, as opposed to separate lithosphere and circulation models, as has been done so far. In addition to predicting the deviatoric stresses we also jointly fit the constraints of geoid, dynamic topography and plate motion both globally and over North America, in order to ensure that the forces that arise in our models are dynamically consistent. We examine the sensitivity of the dynamic models to different lateral viscosity variations. We find that circulation models that include upper mantle slabs yield a better fit to observed plate velocities. Our results indicate that a model of GPE variations coupled with mantle convection gives the best fit to the observational constraints. We argue that although GPE variations control a large part of the deformation of the western United States, deeper mantle tractions also play a significant role. The average deviatoric stress magnitudes in the western United States range 30-40 MPa. The cratonic region exhibits higher coupling to mantle flow than the rest of the continent. We find that a relatively strong San Andreas fault gives a better fit to the observational constraints, especially that of plate velocity in western North America.

The upper Bay of Bengal salinity structure in a high-resolution model

Salinity in the Bay of Bengal is highly heterogeneous, with extremely fresh waters found at the surface in the Northern part of the basin, and saltier waters at subsurface as well as to the south. This paper investigates the seasonal structure of sea surface salinity of the Bay in a regional high-resolution model forced by ERA-Interim reanalysis and various precipitation products. Surface circulation is believed to drive the spreading of northern Bay of Bengal fresh waters to the rest of the Indian Ocean. We first present a series of experiments to infer the sensitivity of modeled circulation to various numerical choices. Surface circulation is found to be sensitive to the horizontal resolution of the model, with the 1/12 degrees version appearing much more realistic than the 1/4 degrees version. The sidewall boundary condition is also drastically influencing the characteristics of the western boundary current simulated. We then investigate the sensitivity of the salinity response to the various precipitation products. We observe that ERA-Interim excess precipitation induces a fresh bias in the surface salinity response. Spaceborne precipitation products are more satisfactory. We then identify the pathways of the northern Bay freshwater mass, based on passive tracers experiments. Our model suggests that over timescales of a few months, vertical exchanges between the upper fresh layer and the underlying saltier layer appear to be the main export pathway for the freshwater. The horizontal circulation within the mixed layer also acts to convey fresh waters out of the Bay at these timescales, but in a lesser quantity compared to the vertical export. Beyond its intrinsic interest for the understanding of Bay of Bengal physics, this study highlights the need for a careful design of any realistic numerical model, in three key aspects: the choice of the resolution of the model, the choice of the sub-grid scale parameterizations, and the choice of the forcing fluxes. (C) 2013 Elsevier Ltd. All rights reserved.

Modular design of synthetic protein mimics. Crystal structure of two seven-residue helical peptide segments linked by .epsilon.-aminocaproic acid

Two seven-residue helical segments, Val-Ala-Leu-Aib-Val-Ala-Leu, were linked synthetically with an epsilon-aminocaproic acid (Acp) linker with the intention of making a stable antiparallel helix-helix motif. The crystal structure of the linked peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Acp-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe (1) shows the two helices displaced laterally from each other by the linker, but the linker has not folded the molecule into a close-packed antiparallel conformation. Two strong intermolecular NH...O = C hydrogen bonds are formed between the top of the lower helix of one molecule and the bottom of the upper helix in a laterally adjacent molecule to give the appearance of an extended single helix. The composite peptide with Boc and OMe end groups, C76H137N15O18.H2O, crystallize in space group P2(1) with a = 8.802 (1) angstrom, b = 20.409 (4) angstrom, c = 26.315 (3) angstrom, and beta = 90.72 (1)degrees; overall agreement R = 7.86% for 5030 observed reflections (\F(o)\ > 3-sigma(F)); resolution = 0.93 angstrom. Limited evidence for a more compact conformation in solution consistent with an antiparallel helix arrangement is obtained by comparison of the HPLC retention times and CD spectra of peptide 1 with well-characterized continuous helices of similar length and sequence.

Lazy structure sharing for query optimization

We study lazy structure sharing as a tool for optimizing equivalence testing on complex data types, We investigate a number of strategies for implementing lazy structure sharing and provide upper and lower bounds on their performance (how quickly they effect ideal configurations of our data structure). In most cases when the strategies are applied to a restricted case of the problem, the bounds provide nontrivial improvements over the naive linear-time equivalence-testing strategy that employs no optimization. Only one strategy, however, which employs path compression, seems promising for the most general case of the problem.

Tree structure for efficient data mining using rough sets

In data mining, an important goal is to generate an abstraction of the data. Such an abstraction helps in reducing the space and search time requirements of the overall decision making process. Further, it is important that the abstraction is generated from the data with a small number of disk scans. We propose a novel data structure, pattern count tree (PC-tree), that can be built by scanning the database only once. PC-tree is a minimal size complete representation of the data and it can be used to represent dynamic databases with the help of knowledge that is either static or changing. We show that further compactness can be achieved by constructing the PC-tree on segmented patterns. We exploit the flexibility offered by rough sets to realize a rough PC-tree and use it for efficient and effective rough classification. To be consistent with the sizes of the branches of the PC-tree, we use upper and lower approximations of feature sets in a manner different from the conventional rough set theory. We conducted experiments using the proposed classification scheme on a large-scale hand-written digit data set. We use the experimental results to establish the efficacy of the proposed approach. (C) 2002 Elsevier Science B.V. All rights reserved.

Predicting the lithospheric stress field and plate motions by joint modeling of lithosphere and mantle dynamics

The way in which basal tractions, associated with mantle convection, couples with the lithosphere is a fundamental problem in geodynamics. A successful lithosphere-mantle coupling model for the Earth will satisfy observations of plate motions, intraplate stresses, and the plate boundary zone deformation. We solve the depth integrated three-dimensional force balance equations in a global finite element model that takes into account effects of both topography and shallow lithosphere structure as well as tractions originating from deeper mantle convection. The contribution from topography and lithosphere structure is estimated by calculating gravitational potential energy differences. The basal tractions are derived from a fully dynamic flow model with both radial and lateral viscosity variations. We simultaneously fit stresses and plate motions in order to delineate a best-fit lithosphere-mantle coupling model. We use both the World Stress Map and the Global Strain Rate Model to constrain the models. We find that a strongly coupled model with a stiff lithosphere and 3-4 orders of lateral viscosity variations in the lithosphere are best able to match the observational constraints. Our predicted deviatoric stresses, which are dominated by contribution from mantle tractions, range between 20-70 MPa. The best-fitting coupled models predict strain rates that are consistent with observations. That is, the intraplate areas are nearly rigid whereas plate boundaries and some other continental deformation zones display high strain rates. Comparison of mantle tractions and surface velocities indicate that in most areas tractions are driving, although in a few regions, including western North America, tractions are resistive. Citation: Ghosh, A., W. E. Holt, and L. M. Wen (2013), Predicting the lithospheric stress field and plate motions by joint modeling of lithosphere and mantle dynamics.

ON POLYTOPAL UPPER BOUND SPHERES

Generalizing a result (the case k = 1) due to M. A. Perles, we show that any polytopal upper bound sphere of odd dimension 2k + 1 belongs to the generalized Walkup class K-k(2k + 1), i.e., all its vertex links are k-stacked spheres. This is surprising since it is far from obvious that the vertex links of polytopal upper bound spheres should have any special combinatorial structure. It has been conjectured that for d not equal 2k + 1, all (k + 1)-neighborly members of the class K-k(d) are tight. The result of this paper shows that the hypothesis d not equal 2k + 1 is essential for every value of k >= 1.

Elastic thickness structure of the Andaman subduction zone: Implications for convergence of the Ninetyeast Ridge

We use the Bouguer coherence (Morlet isostatic response function) technique to compute the spatial variation of effective elastic thickness (T-e) of the Andaman subduction zone. The recovered T-e map resolves regional-scale features that correlate well with known surface structures of the subducting Indian plate and the overriding Burma plate. The major structure on the India plate, the Ninetyeast Ridge (NER), exhibits a weak mechanical strength, which is consistent with the expected signature of an oceanic ridge of hotspot origin. However, a markedly low strength (0< T-e <3 km) in that region, where the NER is close to the Andaman trench (north of 10 N), receives our main attention in this study. The subduction geometry derived from the Bouguer gravity forward modeling suggests that the NER has indented beneath the Andaman arc. We infer that the bending stresses of the viscous plate, which were reinforced within the subducting oceanic plate as a result of the partial subduction of the NER buoyant load, have reduced the lithospheric strength. The correlation, T-e < T-s (seismogenic thickness) reveals that the upper crust is actively deforming beneath the frontal arc Andaman region. The occurrence of normal-fault earthquakes in the frontal arc, low Te zone, is indicative of structural heterogeneities within the subducting plate. The fact that the NER along with its buoyant root is subducting under the Andaman region is inhibiting the subduction processes, as suggested by the changes in trench line, interrupted back-arc volcanism, variation in seismicity mechanism, slow subduction, etc. The low T-e and thinned crustal structure of the Andaman back-arc basin are attributed to a thermomechanically weakened lithosphere. The present study reveals that the ongoing back-arc spreading and strike-slip motion along the West Andaman Fault coupled with the ridge subduction exerts an important control on the frequency and magnitude of seismicity in the Andaman region. (C) 2013 Elsevier Ltd. All rights reserved.

Spatial variations of effective elastic thickness over the Ninetyeast Ridge and implications for its structure and tectonic evolution

We present new data on the strength of oceanic lithosphere along the Ninetyeast Ridge (NER) from two independent methods: spectral analysis (Bouguer coherence) using the fan wavelet transform technique, and spatial analysis (flexure inversion) with the convolution method. The two methods provide effective elastic thickness (T-e) patterns that broadly complement each other, and correlate well with known surface structures and regional-scale features. Furthermore, our study presents a new high resolution database on the Moho configuration, which obeys flexural isostasy, and exhibit regional correlations with the T-e variations. A continuous ridge structure with a much lower T-e value than that of normal oceanic lithosphere provides strong support for the hotspot theory. The derived T-e values vary over the northern (higher T-e similar to 10-20 km), central (anomalously low T-e similar to 0-5 km), and southern (low T-e similar to 5 km) segments of the NER. The lack of correlation of the T-e value with the progressive aging of the lithosphere implies differences in thermo-mechanical setting of the crust and underlying mantle in different parts of the NER, again indicating diversity in their evolution. The anomalously low T-e and deeper Moho (similar to 22 km) estimates of the central NER (between 0.5 degrees N and 17 degrees S) are attributed to the interaction of a hotspot with the Wharton spreading ridge that caused significant thermal rejuvenation and hence weakening of the lithosphere. The higher mechanical strength values in the northern NER (north of 0.5 degrees N) may support the idea of off-ridge emplacement and a relatively large plate motion at the time of volcanism. The low T-e and deeper Moho (similar to 22 km) estimates in the southern part (south of 17 degrees S) suggest that the lithosphere was weak and therefore younger at the time of volcanism, and this supports the idea that the southern NER was emplaced on the edge of the Indian plate. (C) 2013 Elsevier B.V. All rights reserved.

Tectonic inheritance of the Indian Shield: New insights from its elastic thickness structure

A new evaluation of the elastic thickness (Te) structure of the Indian Shield, derived from isotropic fan wavelet methodology, documents spatial variations of lithospheric deformation in different tectonic provinces correlated with episodic tectono-thermal events. The Te variations corroborated by shear velocity, crustal thickness, and seismogenic thickness reveal the heterogeneous rheology of the Indian lithosphere. The thinned, attenuated lithosphere beneath Peninsular India is considered to be the reason for its mechanically weak strength (<30 km), where a decoupled crust-mantle rheology under different surface/subsurface loading structures may explain the prominent low Te patterns. The arcuate Te structure of the Western Dharwar province and a NNE-trending band of low Te anomaly in the Southern Granulite Terrane are intriguing patterns. The average Te values (40-50 km) of the Central Indian Tectonic Zone, the Bastar Craton, and the northern Eastern Ghats Mobile Belt are suggestive of old, stable, Indian lithosphere, which was not affected by any major tectono-thermal events after cratonic stabilization. We propose that the anomalously high Te (60-85 km) and high S-wave velocity zone to the north of the Narmada-Son Lineament, mainly in NW Himalaya, and the northern Aravalli and Bundelkhand Cratons, suggest that Archean lithosphere characterized by a high velocity mantle keel supports the orogenic topographic loads in/near the Himalaya. The Te map clearly segments the volcanic provinces of the Indian Shield, where the signatures of the Reunion, Marion, and Kerguelen hotspots are indicated by significantly low Te patterns that correlate with plume- and rift-related thermal and mechanical rejuvenation, magmatic underplating, and crustal necking. The correlations between Te variations and the occurrence of seismicity over seismically active zones reveal different causal relationships, which led to the current seismogenic zonation of the Indian Shield. (C) 2013 Elsevier B.V. All rights reserved.

Phytoplankton size structure in the southern Bay of Bengal modified by the Summer Monsoon Current and associated eddies: Implications on the vertical biogenic flux

The present study combines field and satellite observations to investigate how hydrographical transformations influence phytoplankton size structure in the southern Bay of Bengal during the peak Southwest Monsoon/Summer Monsoon (July-August). The intrusion of the Summer Monsoon Current (SMC) into the Bay of Bengal and associated changes in sea surface chemistry, traceable eastward up to 90 degrees E along 8 degrees N, seems to influence biology of the region significantly. Both in situ and satellite (MODIS) data revealed low surface chlorophyll except in the area influenced by the SMC During the study period, two well-developed cydonic eddies (north) and an anti-cyclonic eddy (south), closely linked to the main eastward flow of the SMC, were sampled. Considering the capping effect of the low-saline surface water that is characteristic of the Bay of Bengal, the impact of the cyclonic eddy, estimated in terms of enhanced nutrients and chlorophyll, was mostly restricted to the subsurface waters (below 20 m depth). Conversely, the anti-cyclonic eddy aided by the SMC was characterized by considerably higher nutrient concentration and chlorophyll in the upper water column (upper 60 m), which was contrary to the general characteristic of such eddies. Albeit smaller phytoplankton predominated the southern Bay of Bengal (60-95% of the total chlorophyll), the contribution of large phytoplankton was double in the regions influenced by the SMC and associated eddies. Multivariate analysis revealed the extent to which SMC-associated eddies spatially influence phytoplankton community structure. The study presents the first direct quantification of the size structure of phytoplankton from the southern Bay of Bengal and demonstrates that the SMC-associated hydrographical ramifications significantly increase the phytoplankton biomass contributed by larger phytoplankton and thereby influence the vertical opal and organic carbon flux in the region. (C) 2014 Elsevier B.V. All rights reserved.

X-Ray Studies On The Bilayer Structure Of Trypsin-Treated Rat-Brain Myelin

Trypsin-treated rat brain myelin was subjected to biochemical and X-ray studies. Untreated myelin gave rise to a pattern of three rings with a fundamental repeat period of 155 Angstrom consisting of two bilayers per repeat period, whereas myelin treated with trypsin showed a fundamental repeat period of 75 Angstrom with one bilayer per repeat period. The integrated raw intensity of the h=4 reflection with respect to the h=2 reflection is 0.38 for untreated myelin. The corresponding value reduced to 0.23, 0.18, 0.17 for myelin treated with 5, 10, 40 units of trypsin per mg of myelin, respectively, for 30 min at 30 degrees C. The decrease in relative raw intensity of the higher-order reflection relative to the lower-order reflection is suggestive of a disordering of the phosphate groups upon trypsin treatment or an increased mosaicity of the membrane or a combination of both these effects, However, trypsin treatment does not lead to a complete breakdown of the membrane, The integrated intensity of the h=1 reflection, though weak, is above the measurable threshold for untreated myelin, whereas the corresponding intensity is below the measurable threshold for trypsin-treated myelin, indicating a possible asymmetric to symmetric transition of the myelin bilayer structure about its centre after trypsin treatment.

X-ray Structure of Gelonin at 1.8 Å Resolution

Gelonin is a single chain ribosome inactivating protein (RIP) with potential application in the treatment of cancer and AIDS. Diffraction quality crystals grown using PEG3350, belong to the space group P2(1), with it a = 49.4 Angstrom b = 44.9 Angstrom, c = 137.4 Angstrom and beta = 98.4 degrees, and contain two molecules in the asymmetric unit. Diffraction data collected to 1.8 Angstrom resolution has a R(m) value of 7.3%. Structure of gelonin has been solved by the molecular replacement method, using ricin A chain as the search model. Crystallographic refinement using X-PLOR resulted in a model for which the r.m.s deviations from ideal bond lengths and bond angles are 0.012 Angstrom and 2.7 degrees, respectively The final R-factor is 18.4% for 39,806 reflections for which I > 1.0 sigma(I).The C-alpha atoms of the two molecules in the asymmetric unit superpose to within 0.38 Angstrom for 247 atom pairs. The overall fold of gelonin is similar to that of other RIPs such as ricin A chain and alpha-momorcharin, the r.m.s.d. for C-alpha superpositions being 1.3 and 1.4 Angstrom, respectively The-catalytic residues (Glu166, Arg169 and Tyr113) in the active site form a hydrogen bond scheme similar to that observed in other RIPs. The conformation of Tyr74 in the active site, however, is significantly different from that in alpha-momorcharin. Three well defined water molecules are located in the active site cavity and one of them, X319, superposes to within 0.2 Angstrom of a corresponding water molecule in the structure of alpha-momorcharin. Any of the three could be the substrate water molecule in the hydrolysis reaction catalysed by gelonin.Difference electron density for a N-linked sugar moiety has been observed near only one of the two potential glycosylation sites in the sequence. The amino acid at position 239 has been established as Lys by calculation of omit electron density maps.The two cysteine residues in the sequence, Cys44 and Cys50, form a disulphide bond, and are therefore not available for disulphide conjugation with antibodies. Based on the structure, the region of the molecule that is involved in intradimer interactions is suggested to be suitable for introducing a Cys residue for purposes of conjugation with an antibody to produce useful immunotoxins.

Solute induced liquid crystalline behaviour of a quaternary ammonium salt and its application to structure determination

A new liquid crystalline phase, induced by the addition of small amounts of a non-mesogenic solute (such as dimethyl sulphoxide or methyl iodide) to a quaternary ammonium salt, N-methyl-N,N,N-trioctadecylammonium iodide (MTAI), has been detected by NMR and optical microscopic studies. In some cases, there is a coexistence of nematic and smectic phases. Information on the ordering of the phases in the magnetic field of the spectrometer has been derived from NMR spectra of a dissolved molecule, C-13-enriched methyl iodide. The low order parameter of the pure thermotropic nematic phase of the salt provides first-order spectra of the dissolved oriented molecules. Analyses of spectra of cis,cis-mucononitrile exemplifies the utility of the MTAI nematic phase in the determination of structural parameters of the solute.