Does aluminium bind to histidine? an NMR investigation of Amyloid beta 12 and Amyloid beta 16 fragments

Aluminium and zinc are known to be the major triggering agents for aggregation of amyloid peptides leading to plaque formation in Alzheimer's disease. While zinc binding to histidine in A (amyloid ) fragments has been implicated as responsible for aggregation, not much information is available on the interaction of aluminium with histidine. In the NMR study of the N-terminal A fragments, DAEFRHDSGYEV (A12) and DAEFRHDSGYEVHHQK (A16) presented here, the interactions of the fragments with aluminium have been investigated. Significant chemical shifts were observed for few residues near the C-terminus when aluminium chloride was titrated with A12 and A16 peptides. Surprisingly, it is nonhistidine residues which seem to be involved in aluminium binding. Based on NMR constrained structure obtained by molecular modelling, aluminium-binding pockets in A12 were around charged residues such as Asp, Glu. The results are discussed in terms of native structure propagation, and the relevance of histidine residues in the sequences for metal-binding interactions. We expect that the study of such short amyloid peptide fragments will not only provide clues for plaque formation in aggregated conditions but also facilitate design of potential drugs for these targets.

Mechanism of crystal structure transformations. Part 3. - Factors affecting the anatase-rutile transformation

The particle size and crystallite size of anatase increase markedly in the region of the crystal structure transformation. The unit cell of anatase seems to expand prior to the transformation to rutile. This expansion has been attributed to a displacive transformation of the type defined by Buerger. Smaller particle size and larger surface area seem to favour the transformation. The kinetics of the transformation of anatase prepared by the hydrolysis of titanium sulphate have been studied at different temperatures and are found to be considerably different from the kinetics of the transformation of pure anatase. The transformation becomes immeasurably slow below ∼695 ± 10°C compared to ∼610°C for pure anatase. An induction period is observed in the transformation of anatase obtained from sulphate hydrolysis and the duration decreases with increase in temperature. The activation energy is ∼120 kcal/mole, a value higher than that for the pure anatase-rutile transformation. The results have been interpreted in terms of the relative rates of nucleation and propagation processes. The activation energy for the nucleation process seems to be much larger than for the propagation process. The kinetics of the transformation of anatase samples doped with different amounts of sulphate ion impurity have also been studied and the transformation is found to be progressively decelerated with increase in the impurity concentration. The energy of activation for the transformation appears to increase progressively with increase in impurity concentration.

Meridional propagation of large-scale monsoon convective zones

Observational studies indicate that the convective activity of the monsoon systems undergo intraseasonal variations with multi-week time scales. The zone of maximum monsoon convection exhibits substantial transient behavior with successive propagating from the North Indian Ocean to the heated continent. Over South Asia the zone achieves its maximum intensity. These propagations may extend over 3000 km in latitude and perhaps twice the distance in longitude and remain as coherent entities for periods greater than 2-3 weeks. Attempts to explain this phenomena using simple ocean-atmosphere models of the monsoon system had concluded that the interactive ground hydrology so modifies the total heating of the atmosphere that a steady state solution is not possible, thus promoting lateral propagation. That is, the ground hydrology forces the total heating of the atmosphere and the vertical velocity to be slightly out of phase, causing a migration of the convection towards the region of maximum heating. Whereas the lateral scale of the variations produced by the Webster (1983) model were essentially correct, they occurred at twice the frequency of the observed events and were formed near the coastal margin, rather than over the ocean. Webster's (1983) model used to pose the theories was deficient in a number of aspects. Particularly, both the ground moisture content and the thermal inertia of the model were severely underestimated. At the same time, the sea surface temperatures produced by the model between the equator and the model's land-sea boundary were far too cool. Both the atmosphere and the ocean model were modified to include a better hydrological cycle and ocean structure. The convective events produced by the modified model possessed the observed frequency and were generated well south of the coastline. The improved simulation of monsoon variability allowed the hydrological cycle feedback to be generalized. It was found that monsoon variability was constrained to lie within the bounds of a positive gradient of a convective intensity potential (I). The function depends primarily on the surface temperature, the availability of moisture and the stability of the lower atmosphere which varies very slowly on the time scale of months. The oscillations of the monsoon perturb the mean convective intensity potential causing local enhancements of the gradient. These perturbations are caused by the hydrological feedbacks, discussed above, or by the modification of the air-sea fluxes caused by variations of the low level wind during convective events. The final result is the slow northward propagation of convection within an even slower convective regime. The ECMWF analyses show very similar behavior of the convective intensity potential. Although it is considered premature to use the model to conduct simulations of the African monsoon system, the ECMWF analysis indicates similar behavior in the convective intensity potential suggesting, at least, that the same processes control the low frequency structure of the African monsoon. The implications of the hypotheses on numerical weather prediction of monsoon phenomenon are discussed.

Analysis of the effects of amino-acid-sequence on the structure of proteins

The conformation of amino acid side chains as observed in well-determined structures of globular proteins has earlier been extensively investigated. In contrast, the structural features of the polypeptide backbone that result from the occurrence of specific amino acids along the polypeptide have not been analysed. In this article, we present the statistically significant features in the backbone geometry that appear to be a consequence of the occurrence of rotamers of different amino acid side chains by analysing 102 well-refined structures that form a random collection of proteins. It is found that the persistence of helical segments around each residue is influenced by the residue type. Several residues exert asymmetrical influence between the carboxyl and amino terminal polypeptide segments. The degree to which secondary structures depart from an average geometry also appears to depend on residue type. These departures are correlated to the corresponding Chou and Fasman parameters of amino acid residues. The frequency distribution of the side chain rotamers is influenced by polypeptide secondary structure. In turn, the rotamer conformation of side chain affects the extension of the secondary structure of the backbone. The strongest correlation is found between the occurrence of g+ conformation and helix propagation on the carboxyl side of many residues.

Formation and propagation of bands in jerky flow:a coupled lattice map description

There has been revival of interest in Jerky flow from the point of view of dynamical systems. The earliest attempt in this direction was from our group. One of the predictions of the theory is that Jerky flow could be chaotic. This has been recently verified by us. We have recently extended the earlier model to account for the spatial aspect as well. Both these models are in the form of coupled set of nonlinear differential equations and hence, they are complicated in their structure. For this reason we wish to devise a model based on the results of these two theories in the form of coupled lattice map for the description of the formation and propagation of dislocation bands. We report here one such model and its results.

Hardness and Nitrogen Bonding Structure of A(x)Ti(1-x)N/CrN Multilayer Hard Coating

AlxTi1-xN/CrN multilayer coatings were fabricated by magnetron sputtering and those hardness variations were studied by observing the crack propagation and measuring the chemical bonding state of nitrides by Ti addition. While AlN/CrN multilayer shown stair-like crack propagation, AlxTi1-xN/CrN multilayer illustrated straight crack propagation. Most interestingly, Ti addition induced more broken nitrogen bonds in the nitride multilayers, leading to the reduction of hardness. However, the hardness of Al0.25Ti0.75N/CrN multilayer, having high Ti contents, increased by the formation of many Ti-N bond again instead of Al-N bond. From these results, we found that linear crack propagation behavior was dominated by broken nitrogen bonds in the AlxT1-xN/CrN multilayer coatings.

Wave propagation in single-walled carbon nanotube under longitudinal magnetic field using nonlocal Euler-Bernoulli beam theory

In the present work, the effect of longitudinal magnetic field on wave dispersion characteristics of equivalent continuum structure (ECS) of single-walled carbon nanotubes (SWCNT) embedded in elastic medium is studied. The ECS is modelled as an Euler-Bernoulli beam. The chemical bonds between a SWCNT and the elastic medium are assumed to be formed. The elastic matrix is described by Pasternak foundation model, which accounts for both normal pressure and the transverse shear deformation. The governing equations of motion for the ECS of SWCNT under a longitudinal magnetic field are derived by considering the Lorentz magnetic force obtained from Maxwell's relations within the frame work of nonlocal elasticity theory. The wave propagation analysis is performed using spectral analysis. The results obtained show that the velocity of flexural waves in SWCNTs increases with the increase of longitudinal magnetic field exerted on it in the frequency range: 0-20 THz. The present analysis also shows that the flexural wave dispersion in the ECS of SWCNT obtained by local and nonlocal elasticity theories differ. It is found that the nonlocality reduces the wave velocity irrespective of the presence of the magnetic field and does not influences it in the higher frequency region. Further it is found that the presence of elastic matrix introduces the frequency band gap in flexural wave mode. The band gap in the flexural wave is found to independent of strength of the longitudinal magnetic field. (C) 2011 Elsevier Inc. All rights reserved.

Exploiting the Structure of the Constraint Graph for Efficient Points-to Analysis

Points-to analysis is a key compiler analysis. Several memory related optimizations use points-to information to improve their effectiveness. Points-to analysis is performed by building a constraint graph of pointer variables and dynamically updating it to propagate more and more points-to information across its subset edges. So far, the structure of the constraint graph has been only trivially exploited for efficient propagation of information, e.g., in identifying cyclic components or to propagate information in topological order. We perform a careful study of its structure and propose a new inclusion-based flow-insensitive context-sensitive points-to analysis algorithm based on the notion of dominant pointers. We also propose a new kind of pointer-equivalence based on dominant pointers which provides significantly more opportunities for reducing the number of pointers tracked during the analysis. Based on this hitherto unexplored form of pointer-equivalence, we develop a new context-sensitive flow-insensitive points-to analysis algorithm which uses incremental dominator update to efficiently compute points-to information. Using a large suite of programs consisting of SPEC 2000 benchmarks and five large open source programs we show that our points-to analysis is 88% faster than BDD-based Lazy Cycle Detection and 2x faster than Deep Propagation. We argue that our approach of detecting dominator-based pointer-equivalence is a key to improve points-to analysis efficiency.

Wave propagation in a porous composite beam: Porosity determination, location and quantification

A wave-based method is developed to quantify the defect due to porosity and also to locate the porous regions, in a composite beam-type structure. Wave propagation problem for a porous laminated composite beam is modeled using spectral finite element method (SFEM), based on the modified rule of mixture approach, which is used to include the effect of porosity on the stiffness and density of the composite beam structure. The material properties are obtained from the modified rule of mixture model, which are used in a conventional SFEM to develop a new model for solving wave propagation problems in porous laminated composite beam. The influence of the porosity content on the group speed and also the effect of variation in theses parameters on the time responses are studied first, in the forward problem. The change in the time responses with the change in the porosity of the structure is used as a parameter to find the porosity content in a composite beam. The actual measured response from a structure and the numerically obtained time responses are used for the estimation of porosity, by solving a nonlinear optimization problem. The effect of the length of the porous region (in the propagation direction), on the time responses, is studied. The damage force indicator technique is used to locate the porous region in a beam and also to find its length, using the measured wave propagation responses. (C) 2012 Elsevier Ltd. All rights reserved.

A study of vertical cloud structure of the Indian summer monsoon using CloudSat data

Precise specification of the vertical distribution of cloud optical properties is important to reduce the uncertainty in quantifying the radiative impacts of clouds. The new global observations of vertical profiles of clouds from the CloudSat mission provide opportunities to describe cloud structures and to improve parameterization of clouds in the weather and climate prediction models. In this study, four years (2007-2010) of observations of vertical structure of clouds from the CloudSat cloud profiling radar have been used to document the mean vertical structure of clouds associated with the Indian summer monsoon (ISM) and its intra-seasonal variability. Active and break monsoon spells associated with the intra-seasonal variability of ISM have been identified by an objective criterion. For the present analysis, we considered CloudSat derived column integrated cloud liquid and ice water, and vertically profiles of cloud liquid and ice water content. Over the South Asian monsoon region, deep convective clouds with large vertical extent (up to 14 km) and large values of cloud water and ice content are observed over the north Bay of Bengal. Deep clouds with large ice water content are also observed over north Arabian Sea and adjoining northwest India, along the west coast of India and the south equatorial Indian Ocean. The active monsoon spells are characterized by enhanced deep convection over the Bay of Bengal, west coast of India and northeast Arabian Sea and suppressed convection over the equatorial Indian Ocean. Over the Bay of Bengal, cloud liquid water content and ice water content is enhanced by similar to 90 and similar to 200 % respectively during the active spells. An interesting feature associated with the active spell is the vertical tilting structure of positive CLWC and CIWC anomalies over the Arabian Sea and the Bay of Bengal, which suggests a pre-conditioning process for the northward propagation of the boreal summer intra-seasonal variability. It is also observed that during the break spells, clouds are not completely suppressed over central India. Instead, clouds with smaller vertical extent (3-5 km) are observed due to the presence of a heat low type of circulation. The present results will be useful for validating the vertical structure of clouds in weather and climate prediction models.

Wave propagation in stiffened structures using spectrally formulated finite element

In this work, the wave propagation analysis of built-up composite structures is performed using frequency domain spectral finite elements, to study the high frequency wave responses. The paper discusses basically two methods for modeling stiffened structures. In the first method, the concept of assembly of 2D spectral plate elements is used to model a built-up structure. In the second approach, spectral finite element method (SFEM) model is developed to model skin-stiffener structures, where the skin is considered as plate element and the stiffener as beam element. The SFEM model developed using the plate-beam coupling approach is then used to model wave propagation in a multiple stiffened structure and also extended to model the stiffened structures with different cross sections such as T-section, I-section and hat section. A number of parametric studies are performed to capture the mode coupling, that is, the flexural-axial coupling present in the wave responses.

Guided Ultrasonic Wave Propagation through Inaccessible Damage in a Folded Plate using Sensor-Actuator Network

Rapid diagnostics and virtual imaging of damages in complex structures like folded plate can help reduce the inspection time for guided wave based NDE and integrated SHM. Folded plate or box structure is one of the major structural components for increasing the structural strength. Damage in the folded plate, mostly in the form of surface breaking cracks in the inaccessible zone is a usual problem in aerospace structures. One side of the folded plate is attached (either riveted or bonded) to adjacent structure which is not accessible for immediate inspection. The sensor-actuator network in the form of a circular array is placed on the accessible side of the folded plate. In the present work, a circular array is employed for scanning the entire folded plate type structure for damage diagnosis and wave field visualization of entire structural panel. The method employs guided wave with relatively low frequency bandwidth of 100-300 kHz. Change in the response signal with respect to a baseline signal is used to construct a quantitative relationship with damage size parameters. Detecting damage in the folded plate by using this technique has significant potential for off-line and on-line SHM technologies. By employing this technique, surface breaking cracks on inaccessible face of the folded plate are detected without disassembly of structure in a realistic environment.

A Guided Wave approach for the detection of damage in a structure having elements with periodic damage

A wave propagation based approach for the detection of damage in components of structures having periodic damage has been proposed. Periodic damage pattern may arise in a structure due to periodicity in geometry and in loading. The method exploits the Block-Floquet band formation mechanism, a feature specific to structures with periodicity, to identify propagation bands (pass bands) and attenuation bands (stop bands) at different frequency ranges. The presence of damage modifies the wave propagation behaviour forming these bands. With proper positioning of sensors a damage force indicator (DFI) method can be used to locate the defect at an accuracy level of sensor to sensor distance. A wide range of transducer frequency may be used to obtain further information about the shape and size of the damage. The methodology is demonstrated using a few 1-D structures with different kinds of periodicity and damage. For this purpose, dynamic stiffness matrix is formed for the periodic elements to obtain the dispersion relationship using frequency domain spectral element and spectral super element method. The sensitivity of the damage force indicator for different types of periodic damages is also analysed.

Crack propagation in graphene

The crack initiation and growth mechanisms in an 2D graphene lattice structure are studied based on molecular dynamics simulations. Crack growth in an initial edge crack model in the arm-chair and the zig-zag lattice configurations of graphene are considered. Influence of the time steps on the post yielding behaviour of graphene is studied. Based on the results, a time step of 0.1 fs is recommended for consistent and accurate simulation of crack propagation. Effect of temperature on the crack propagation in graphene is also studied, considering adiabatic and isothermal conditions. Total energy and stress fields are analyzed. A systematic study of the bond stretching and bond reorientation phenomena is performed, which shows that the crack propagates after significant bond elongation and rotation in graphene. Variation of the crack speed with the change in crack length is estimated. (C) 2015 AIP Publishing LLC.

A comparison of the fine-scale structure of the diurnal cycle of tropical rain and lightning

In this study, the fine-scale structure of the diurnal variability of ground-based lightning is systematically compared with satellite-based rain. At the outset, it is shown that tropical variability of lightning exhibits a prominent diurnal mode, much like rain. A comparison of the geographical distribution of the timing of the diurnal maximum shows that there is very good agreement between the two observables over continental and coastal regions throughout the tropics. Following this global tropical comparison, we focus on two regions, Borneo and equatorial South America, both of which show the interplay between oceanward and landward propagations of the phase of the diurnal maximum. Over Borneo, both rain and lightning clearly show a climatological cycle of ``breathing in'' (afternoon to early morning) and ``breathing out'' (morning to early afternoon). Over the equatorial east coast of South America, landward propagation is noticed in rain and lightning from early afternoon to early morning. Along the Pacific coast of South America, both rain and lightning show oceanward propagation. Though qualitatively consistent, over both regions the propagation is seen to extend further in rainfall. Additionally, given that lightning highlights vigorous convection, the timing of its diurnal maximum often precedes that of rainfall in the convective life cycle. (C) 2015 Elsevier B.V. All rights reserved.