An FETI-preconditioned conjuerate gradient method for large-scale stochastic finite element problems

In the spectral stochastic finite element method for analyzing an uncertain system. the uncertainty is represented by a set of random variables, and a quantity of Interest such as the system response is considered as a function of these random variables Consequently, the underlying Galerkin projection yields a block system of deterministic equations where the blocks are sparse but coupled. The solution of this algebraic system of equations becomes rapidly challenging when the size of the physical system and/or the level of uncertainty is increased This paper addresses this challenge by presenting a preconditioned conjugate gradient method for such block systems where the preconditioning step is based on the dual-primal finite element tearing and interconnecting method equipped with a Krylov subspace reusage technique for accelerating the iterative solution of systems with multiple and repeated right-hand sides. Preliminary performance results on a Linux Cluster suggest that the proposed Solution method is numerically scalable and demonstrate its potential for making the uncertainty quantification Of realistic systems tractable.

Topology-based denoising of chaos

In this article, we propose a denoising algorithm to denoise a time series y(i) = x(i) + e(i), where {x(i)} is a time series obtained from a time- T map of a uniformly hyperbolic or Anosov flow, and {e(i)} a uniformly bounded sequence of independent and identically distributed (i.i.d.) random variables. Making use of observations up to time n, we create an estimate of x(i) for i<n. We show under typical limiting behaviours of the orbit and the recurrence properties of x(i), the estimation error converges to zero as n tends to infinity with probability 1.

Vitrification, relaxation and free volume in glycerol-water binary liquid mixture:Spin probe ESR studies

Glass transition and relaxation of the glycerol-water (G-W) binary mixture system have been studied over the glycerol concentration range of 5-85 mol% by using the highly sensitive technique of electron spin resonance (ESR). For the water rich mixture the glass transition,sensed by the dissolved spin probe, arises from the vitrified mesoscopic portion of the binary system. The concentration dependence of the glass transition temperature manifests a closely related molecular level cooperativity in the system. A drastic change in the mesoscopic structure of the system at the critical concentration of 40 mol is confirmed by an estimation of the spin probe effective volume in a temperature range where the tracer reorientation is strongly coupled to the system dynamics.

Nonlocal scale effects on wave propagation in multi-walled carbon nanotubes

This paper represents the effect of nonlocal scale parameter on the wave propagation in multi-walled carbon nanotubes (MWCNTs). Each wall of the MWCNT is modeled as first order shear deformation beams and the van der Waals interactions between the walls are modeled as distributed springs. The studies shows that the scale parameter introduces certain band gap region in both flexural and shear wave mode where no wave propagation occurs. This is manifested in the wavenumber plots as the region where the wavenumber tends to infinite (or group speed tends to zero). The frequency at which this phenomenon occurs is called the ``Escape frequency''. The analysis shows that, for a given N-walled carbon nanotube (CNT). the nonlocal scaling parameter has a significant effect on the shear wave modes of the N - 1 walls. The escape frequencies of the flexural and shear wave modes of the N-walls are inversely proportionl to the nonlocal scaling parameter. It is also shown that the cut-off frequencies are independent of the nonlocal scale parameter. (C) 2009 Elsevier B.V. All rights reserved.

Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks

The interdependence of the concept of allostery and enzymatic catalysis, and they being guided by conformational mobility is gaining increased prominence. However, to gain a molecular level understanding of llostery and hence of enzymatic catalysis, it is of utter importance that the networks of amino acids participating in allostery be deciphered. Our lab has been exploring the methods of network analysis combined with molecular dynamics simulations to understand allostery at molecular level. Earlier we had outlined methods to obtain communication paths and then to map the rigid/flexible regions of proteins through network parameters like the shortest correlated paths, cliques, and communities. In this article, we advance the methodology to estimate the conformational populations in terms of cliques/communities formed by interactions including the side-chains and then to compute the ligand-induced population shift. Finally, we obtain the free-energy landscape of the protein in equilibrium, characterizing the free-energy minima accessed by the protein complexes. We have chosen human tryptophanyl-tRNA synthetase (hTrpRS), a protein esponsible for charging tryptophan to its cognate tRNA during protein biosynthesis for this investigation. This is a multidomain protein exhibiting excellent allosteric communication. Our approach has provided valuable structural as well as functional insights into the protein. The methodology adopted here is highly generalized to illuminate the linkage between protein structure networks and conformational mobility involved in the allosteric mechanism in any protein with known structure.

Diurnal-scale signatures of monsoon rainfall over the Indian region from TRMM satellite observations

One of the most important modes of summer season precipitation variability over the Indian region, the diurnal cycle, is studied using the Tropical Rainfall Measuring Mission 3-hourly, 0.25 degrees x 0.25 degrees 3B42 rainfall product for nine years (1999-2007). Most previous studies have provided an analysis of a single year or a few years of satellite-or station-based rainfall data. Our study aims to systematically analyze the statistical characteristics of the diurnal-scale signature of rainfall over the Indian and surrounding regions. Using harmonic analysis, we extract the signal corresponding to diurnal and subdiurnal variability. Subsequently, the 3-hourly time period or the octet of rainfall peak for this filtered signal, referred to as the ``peak octet,'' is estimated, with care taken to eliminate spurious peaks arising out of Gibbs oscillations. Our analysis suggests that over the Bay of Bengal, there are three distinct modes of the peak octet of diurnal rainfall corresponding to 1130, 1430, and 1730 Indian standard time (IST), from the north central to south bay. This finding could be seen to be consistent with southward propagation of the diurnal rainfall pattern reported by earlier studies. Over the Arabian Sea, there is a spatially coherent pattern in the mode of the peak octet (1430 IST), in a region where it rains for more than 30% of the time. In the equatorial Indian Ocean, while most of the western part shows a late night/early morning peak, the eastern part does not show a spatially coherent pattern in the mode of the peak octet owing to the occurrence of a ual maxima (early morng and early/late afternoon). The imalayan foothills were found to have a mode of peak octet corresponding to 0230 IST, whereas over the Burmese mountains and the Western Ghats (west coast of India) the rainfall peaks during late afternoon/early evening (1430-1730 IST). This implies that the phase of the diurnal cycle over inland orography (e. g., Himalayas) is significantly different from coastal orography (e. g., Western Ghats). We also find that over the Gangetic plains, the peak octet is around 1430 IST, a few hours earlier compared to the typical early evening maxima over land.

Free and ATP-bound structures of Ap(4)A hydrolase from Aquifex aeolicus V5

Asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases degrade the metabolite Ap(4)A back into ATP and AMP. The three-dimensional crystal structure of Ap(4)A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 angstrom resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an alpha beta alpha-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap(4)A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.

Force-free equilibria of magnetized jets

Force-free equilibrium configurations of magnetic-pressure-dominated magnetized supersonic jets confined by slowly varying external pressure are investigated analytically. For the case where internal dissipation mechanisms are active, the lowest-energy field configuration is found to be the superposition of an axisymmetric mode and a helical mode with a wavelength equal to 5 times the jet radius, and the pressure below which the nonaxisymmetric mode becomes energetically favorable is given as 2700 times the product of the 4th power of the magnetic helicity per unit length and the -6th power of the magnetic flux. A model of the total and polarized emission of such a configuration is developed and applied to the extended well-collimated astronomically resolved jet NGC 6251. The model is shown to reproduce significant features such as transverse oscillations of the ridge line, width oscillations and emission knots, the projected magnetic-field configuration, oscillations of the degree of polarization, and the distribution of the Faraday rotation measure.

Magnetic energy dissipation in force-free jets

It is shown that a magnetic-pressure-dominated, supersonic jet which expands (or contracts) in response to variations in the confining external pressure can dissipate magnetic energy through field-line reconnection as it relaxes to a minimum-energy configuration. In order for a continuous dissipation to take place, the effective reconnection time must be a fraction ɛ ⪉ 1 of the expansion time. The amount of energy dissipation is calculated, and it is concluded that magnetic energy dissipation could, in principle, power the observed synchrotron emission in extragalactic radio jets such as NGC 6251. However, this mechanism is only viable if the reconnection time is substantially shorter than the nominal resistive tearing time in the jet.

Mechanism of failure in a free-standing Pt-aluminide bond coat during tensile testing at room temperature

The room temperature (RT) tensile behaviour of a free-standing high activity Pt-aluminide bond coat has been evaluated by microtensile testing technique. The coating had a typical three-layer microstructure. The stress-strain plot for the free-standing coating was linear, indicating the coating to be brittle at RT. Different fracture features were observed across the coating layers, namely quasi-cleavage in the outer layer and inner interdiffusion zone, and cleavage in the intermediate layer. By employing interrupted tensile test and observing the cross-sectional microstructure of the tested specimens, it was determined that failure of the microtensile samples occurred by the initiation of a single crack in the intermediate layer of the coating and its subsequent inside-out propagation. Such a mechanism of failure has been explained in terms of the fracture features observed across the sample thickness. This mechanism of failure is consistent with fracture toughness values of the individual coating layers. (C) 2009 Elsevier B.V. All rights reserved.

Nano-meter scale plasticity in KBr studied by nanoindenter and force microscopy

The early stages of plasticity in KBr single crystals have been studied by means of nano-meter-scale indentation in complementary experiments using both a nanoindenter and an atomic force microscope. Nanoindentafion experiments precisely correlate indentation depth and forces, while force microscopy provides high-resolution force measurements and images of the surface revealing dislocation activity. The two methods provide very similar results for the onset of plasticity in KBr. Upon loading we observe yield of the surface in atomic layer units which we attribute to the nucleation of single dislocations. Unloading is accompanied by plastic recovery as evident from a non-linear force distance unloading curve and delayed discrete plasticity events.