Conformational analysis and design of cross-strand disulfides in antiparallel beta-sheets

Cross-strand disulfides bridge two cysteines in a registered pair of antiparallel beta-strands. A nonredundant data set comprising 5025 polypeptides containing 2311 disulfides was used to study cross-strand disulfides. Seventy-six cross-strand disulfides were found of which 75 and 1 occurred at non-hydrogen-bonded (NHB) and hydrogen-bonded (HB) registered pairs, respectively. Conformational analysis and modeling studies demonstrated that disulfide formation at HB pairs necessarily requires an extremely rare and positive chi(1) value for at least one of the cysteine residues. Disulfides at HB positions also have more unfavorable steric repulsion with the main chain. Thirteen pairs of disulfides were introduced in NHB and HB pairs in four model proteins: leucine binding protein (LBP), leucine, isoleucine, valine binding protein (LIVBP), maltose binding protein (MBP), and Top7. All mutants LIVBP T247C V331C showed disulfide formation either on purification, or on treatment with oxidants. Protein stability in both oxidized and reduced states of all mutants was measured. Relative to wild type, LBP and MBP mutants were destabilized with respect to chemical denaturation, although the sole exposed NHB LBP mutant showed an increase of 3.1 degrees C in T-m. All Top7 mutants were characterized for stability through guanidinium thiocyanate chemical denaturation. Both exposed and two of the three buried NHB mutants were appreciably stabilized. All four HB Top7 mutants were destabilized (Delta Delta G(0) = -3.3 to -6.7 kcal/mol). The data demonstrate that introduction of cross-strand disulfides at exposed NHB pairs is a robust method of improving protein stability. All four exposed Top7 disulfide mutants showed mild redox activity. Proteins 2011; 79: 244-260. (C) 2010 Wiley-Liss, Inc.

Weighted subspace methods and spatial smoothing: analysis and comparison

The effect of using a spatially smoothed forward-backward covariance matrix on the performance of weighted eigen-based state space methods/ESPRIT, and weighted MUSIC for direction-of-arrival (DOA) estimation is analyzed. Expressions for the mean-squared error in the estimates of the signal zeros and the DOA estimates, along with some general properties of the estimates and optimal weighting matrices, are derived. A key result is that optimally weighted MUSIC and weighted state-space methods/ESPRIT have identical asymptotic performance. Moreover, by properly choosing the number of subarrays, the performance of unweighted state space methods can be significantly improved. It is also shown that the mean-squared error in the DOA estimates is independent of the exact distribution of the source amplitudes. This results in a unified framework for dealing with DOA estimation using a uniformly spaced linear sensor array and the time series frequency estimation problems.

Kinematic analysis and design of articulated manipulators with joint motion constraints

For an articulated manipulator with joint rotation constraints, we show that the maximum workspace is not necessarily obtained for equal link lengths but is also determined by the range and mean positions of the joint motions. We present expressions for sectional area, workspace volume, overlap volume and work area in terms of link ratios, mean positions and ranges of joint motion. We present a numerical procedure to obtain the maximum rectangular area that can be embedded in the workspace of an articulated manipulator with joint motion constraints. We demonstrate the use of analytical expressions and the numerical plots in the kinematic design of an articulated manipulator with joint rotation constraints.

The gasification of wood-char spheres in CO2---N2 mixtures: analysis and experiments

The gasification of charcoal spheres in an atmosphere of carbon-dioxide-nitrogen mixture involving diffusion and reactions in the pores is modelled and the results are compared with experiments of Standish and Tanjung and those performed in the laboratory on wood-char spheres to determine the effects of diameter, density, gas composition and flow. The results indicate that the conversion time, t(c) approximately d1.03 for large particles (> 5 mm), departing substantially from the t(c) approximately d2 law valid for diffusion limited conditions. The computational studies indicate that the kinetic limit for the particle is below 100 mum. The conversion time varies inversely as the initial char density as expected in the model. Predictions from the model show that there is no significant change in conversion time up to 60% N2 consistent with the CO2-N2 experiments. The variation of diameter and density with time are predicted. The peculiar dependence of conversion time on flow velocity in the experiments is sought to be explained by opposing free and forced convection heat transfer and the attempt is only partly successful. The studies also indicate that the dependence on the CO concentration with low CO2 is significant, indicating the need for multistep reaction mechanism against the generally accepted single-step reaction.

Pipelined ring algorithm for matrix multiplication on transputer networks: performance analysis and estimation

A parallel matrix multiplication algorithm is presented, and studies of its performance and estimation are discussed. The algorithm is implemented on a network of transputers connected in a ring topology. An efficient scheme for partitioning the input matrices is introduced which enables overlapping computation with communication. This makes the algorithm achieve near-ideal speed-up for reasonably large matrices. Analytical expressions for the execution time of the algorithm have been derived by analysing its computation and communication characteristics. These expressions are validated by comparing the theoretical results of the performance with the experimental values obtained on a four-transputer network for both square and irregular matrices. The analytical model is also used to estimate the performance of the algorithm for a varying number of transputers and varying problem sizes. Although the algorithm is implemented on transputers, the methodology and the partitioning scheme presented in this paper are quite general and can be implemented on other processors which have the capability of overlapping computation with communication. The equations for performance prediction can also be extended to other multiprocessor systems.

Origin of a trend in ECMWF wind analysis and its objective removal

The suitability of the European Centre for Medium Range Weather Forecasting (ECMWF) operational wind analysis for the period 1980-1991 for studying interannual variability is examined. The changes in the model and the analysis procedure are shown to give rise to a systematic and significant trend in the large scale circulation features. A new method of removing the systematic errors at all levels is presented using multivariate EOF analysis. Objectively detrended analysis of the three-dimensional wind field agrees well with independent Florida State University (FSU) wind analysis at the surface. It is shown that the interannual variations in the detrended surface analysis agree well in amplitude as well as spatial patterns with those of the FSU analysis. Therefore, the detrended analyses at other levels as well are expected to be useful for studies of variability and predictability at interannual time scales. It is demonstrated that this trend in the wind field is due to the shift in the climatologies from the period 1980-1985 to the period 1986-1991.

Optimum design of a helicopter rotor for low vibration using aeroelastic analysis and response surface methods

An aeroelastic analysis based on finite elements in space and time is used to model the helicopter rotor in forward flight. The rotor blade is represented as an elastic cantilever beam undergoing flap and lag bending, elastic torsion and axial deformations. The objective of the improved design is to reduce vibratory loads at the rotor hub that are the main source of helicopter vibration. Constraints are imposed on aeroelastic stability, and move limits are imposed on the blade elastic stiffness design variables. Using the aeroelastic analysis, response surface approximations are constructed for the objective function (vibratory hub loads). It is found that second order polynomial response surfaces constructed using the central composite design of the theory of design of experiments adequately represents the aeroelastic model in the vicinity of the baseline design. Optimization results show a reduction in the objective function of about 30 per cent. A key accomplishment of this paper is the decoupling of the analysis problem and the optimization problems using response surface methods, which should encourage the use of optimization methods by the helicopter industry. (C) 2002 Elsevier Science Ltd. All rights reserved.

Spatial Analysis and Characterisation of Lentic Ecosystems: A Case Study of Varthur Lake, Bangalore

Lentic ecosystems vital functions such as recycling of nutrients, purification of water, recharge of groundwater,augmenting and maintenance of stream flow and habitat provision for a wide variety of flora and fauna along with their recreation values necessitates their sustainable management through appropriate conservation mechanisms. Failure to restore these ecosystems will result in extinction of species or ecosystem types and cause permanent ecological damage. In Bangalore, lentic ecosystems (for example lakes) have played a prominent role serving the needs of agriculture and drinking water. But the burgeoning population accompanied by unplanned developmental activities has led to the drastic reduction in their numbers (from 262 in 1976 to 81). The existing water bodies are contaminated by residential, agricultural, commercial and industrial wastes/effluents. In order to restore the ecosystem, assessment of the level of contamination is crucial. This paper focuses on characterisation and restoration aspects of Varthur lake based on hydrological, morphometric, physical-chemical and socio-economic investigations for a period of six months covering post monsoon seasons. The results of the water quality analysis show that the lake is eutrophic with high concentrations of phosphorous and organic matter. The morphometric analysis indicates that the lake is shallow in relation to its surface area. Socio-economic analyses show dependence of local residents for irrigation, fodder, etc. These analyses highlight the need and urgency to restore the physical, chemical and biological integrity through viable restoration and sustainable watershed management strategies, which include pollution abatement, catchment treatment, desilting of the lake and educating all stakeholders on the conservation and restoration of lake ecosystems.

End-bearing capacity of driven piles in sand using the stress characteristics method: analysis and implementation

The method of stress characteristics has been employed to compute the end-bearing capacity of driven piles. The dependency of the soil internal friction angle on the stress level has been incorporated to achieve more realistic predictions for the end-bearing capacity of piles. The validity of the assumption of the superposition principle while using the bearing capacity equation based on soil plasticity concepts, when applied to deep foundations, has been examined. Fourteen pile case histories were compiled with cone penetration tests (CPT) performed in the vicinity of different pile locations. The end-bearing capacity of the piles was computed using different methods, namely, static analysis, effective stress approach, direct CPT, and the proposed approach. The comparison between predictions made by different methods and measured records shows that the stress-level-based method of stress characteristics compares better with experimental data. Finally, the end-bearing capacity of driven piles in sand was expressed in terms of a general expression with the addition of a new factor that accounts for different factors contributing to the bearing capacity. The influence of the soil nonassociative flow rule has also been included to achieve more realistic results.

Analysis and Synthesis of Reverberation for Parametric Stereo Audio

We propose a parametric stereo coding analysis and synthesis directly in the MDCT domain using an analysis by synthesis parameter estimation. The stereo signal is represented by an equalized sum signal and spatialization parameters. Equalized sum signal and the spatialization parameters are obtained by sub-band analysis in the MDCT domain. The de-correlated signal required for the stereo synthesis is also generated in the MDCT domain. Subjective evaluation test using MUSHRA shows that the synthesized stereo signal is perceptually satisfactory and comparable to the state of the art parametric coders.

Recent Advances in Low CTE and High Density System-on-a-Package (SOP) Substrate with Thin Film Component Integration

The Packaging Research Center has been developing next generation system-on-a-package (SOP) technology with digital, RF, optical, and sensor functions integrated in a single package/module. The goal of this effort is to develop a platform substrate technology providing very high wiring density and embedded thin film passive and active components using PWB compatible materials and processes. The latest SOP baseline process test vehicle has been fabricated on novel Si-matched CTE, high modulus C-SiC composite core substrates using 10mum thick BCB dielectric films with loss tangent of 0.0008 and dielectric constant of 2.65. A semi-additive plating process has been developed for multilayer microvia build-up using BCB without the use of any vacuum deposition or polishing/CMP processes. PWB and package substrate compatible processes such as plasma surface treatment/desmear and electroless/electrolytic pulse reverse plating was used. The smallest line width and space demonstrated in this paper is 6mum with microvia diameters in the 15-30mum range. This build-up process has also been developed on medium CTE organic laminates including MCL-E-679F from Hitachi Chemical and PTFE laminates with Cu-Invar-Cu core. Embedded decoupling capacitors with capacitance density of >500nF/cm2 have been integrated into the build-up layers using sol-gel synthesized BaTiO3 thin films (200-300nm film thickness) deposited on copper foils and integrated using vacuum lamination and subtractive etch processes. Thin metal alloy resistor films have been integrated into the SOP substrate using two methods: (a) NiCrAlSi thin films (25ohms per square) deposited on copper foils (Gould Electronics) laminated on the build-up layers and two step etch process for resistor definition, and (b) electroless plated Ni-W-P thin films (70 ohms to few Kohms per square) on the BCB dielectric by plasma surface treatment and activation. The electrical design and build-up layer structure along- - with key materials and processes used in the fabrication of the SOP4 test vehicle were presented in this paper. Initial results from the high density wiring and embedded thin film components were also presented. The focus of this paper is on integration of materials, processes and structures in a single package substrate for system-on-a-package (SOP) implementation