Deriving structural information from non-coding ribonucleic acids by mass spectrometry

The purpose of this study is to describe the development of application of mass spectrometry for the structural analyses of non-coding ribonucleic acids during past decade. Mass spectrometric methods are compared of traditional gel electrophoretic methods, the characteristics of performance of mass spectrometric, analyses are studied and the future trends of mass spectrometry of ribonucleic acids are discussed. Non-coding ribonucleic acids are short polymeric biomolecules which are not translated to proteins, but which may affect the gene expression in all organisms. Regulatory ribonucleic acids act through transient interactions with key molecules in signal transduction pathways. Interactions are mediated through specific secondary and tertiary structures. Posttranscriptional modifications in the structures of molecules may introduce new properties to the organism, such as adaptation to environmental changes or development of resistance to antibiotics. In the scope of this study, the structural studies include i) determination of the sequence of nucleobases in the polymer chain, ii) characterisation and localisation of posttranscriptional modifications in nucleobases and in the backbone structure, iii) identification of ribonucleic acid-binding molecules and iv) probing of higher order structures in the ribonucleic acid molecule. Bacteria, archaea, viruses and HeLa cancer cells have been used as target organisms. Synthesised ribonucleic acids consisting of structural regions of interest have been frequently used. Electrospray ionisation (ESI) and matrix-assisted laser desorption ionisation (MALDI) have been used for ionisation of ribonucleic analytes. Ammonium acetate and 2-propanol are common solvents for ESI. Trihydroxyacetophenone is the optimal MALDI matrix for ionisation of ribonucleic acids and peptides. Ammonium salts are used in ESI buffers and MALDI matrices as additives to remove cation adducts. Reverse phase high performance liquid chromatography has been used for desalting and fractionation of analytes either off-line of on-line, coupled with ESI source. Triethylamine and triethylammonium bicarbonate are used as ion pair reagents almost exclusively. Fourier transform ion cyclotron resonance analyser using ESI coupled with liquid chromatography is the platform of choice for all forms of structural analyses. Time-of-flight (TOF) analyser using MALDI may offer sensitive, easy-to-use and economical solution for simple sequencing of longer oligonucleotides and analyses of analyte mixtures without prior fractionation. Special analysis software is used for computer-aided interpretation of mass spectra. With mass spectrometry, sequences of 20-30 nucleotides of length may be determined unambiguously. Sequencing may be applied to quality control of short synthetic oligomers for analytical purposes. Sequencing in conjunction with other structural studies enables accurate localisation and characterisation of posttranscriptional modifications and identification of nucleobases and amino acids at the sites of interaction. High throughput screening methods for RNA-binding ligands have been developed. Probing of the higher order structures has provided supportive data for computer-generated three dimensional models of viral pseudoknots. In conclusion. mass spectrometric methods are well suited for structural analyses of small species of ribonucleic acids, such as short non-coding ribonucleic acids in the molecular size region of 20-30 nucleotides. Structural information not attainable with other methods of analyses, such as nuclear magnetic resonance and X-ray crystallography, may be obtained with the use of mass spectrometry. Sequencing may be applied to quality control of short synthetic oligomers for analytical purposes. Ligand screening may be used in the search of possible new therapeutic agents. Demanding assay design and challenging interpretation of data requires multidisclipinary knowledge. The implement of mass spectrometry to structural studies of ribonucleic acids is probably most efficiently conducted in specialist groups consisting of researchers from various fields of science.

Random vibration of a second order non-linear elastic system

A method is presented for obtaining, approximately, the response covariance and probability distribution of a non-linear oscillator under a Gaussian excitation. The method has similarities with the hierarchy closure and the equivalent linearization approaches, but is different. A Gaussianization technique is used to arrive at the output autocorrelation and the input-output cross-correlation. This along with an energy equivalence criterion is used to estimate the response distribution function. The method is applicable in both the transient and steady state response analysis under either stationary or non-stationary excitations. Good comparison has been observed between the predicted and the exact steady state probability distribution of a Duffing oscillator under a white noise input.

A numerical study of projectile impact on thin aluminium plates

This article deals with a simulation-based Study of the impact of projectiles on thin aluminium plates using LS-DYNA by modelling plates with shell elements and projectiles with solid elements. In order to establish the required modelling criterion in terms of element size for aluminium plates, a convergence Study of residual velocity has been carried Out by varying mesh density in the impact zone. Using the preferred material and meshing criteria arrived at here, extremely good prediction of test residual velocities and ballistic limits given by Gupta et al. (2001) for thin aluminium plates has been obtained. The simulation-based pattern of failure with localized bulging and jagged edge of perforation is similar to the perforation with petalling seen in tests. A number Of simulation-based parametric studies have been carried out and results consistent with published test data have been obtained. Despite the robust correlation achieved against published experimental results, it would be prudent to conduct one's own experiments, for a final correlation via the present modelling procedure and analysis with the explicit LS-DYNTA 970 solver. Hence, a sophisticated ballistic impact testing facility and a high-speed camera have been used to conduct additional tests on grade 1100 aluminium plates of 1 mm thickness with projectiles Of four different nose shapes. Finally, using the developed numerical simulation procedure, an excellent correlation of residual velocity and failure modes with the corresponding test results has been obtained.

Reliability analysis of torsional varactor

A torsional MEMS varactor with wide dynamic range, lower actuation voltage and isolation between actuation voltage and signal voltage has been proposed in C. Venkatesh et al. (2005). In this paper we address the effects of pull-in, residual stress and continuous cycling on the performance of torsional MEMS varactor.

Diagnostic Tests Based on Quantile Residuals for Nonlinear Time Series Models

This thesis studies quantile residuals and uses different methodologies to develop test statistics that are applicable in evaluating linear and nonlinear time series models based on continuous distributions. Models based on mixtures of distributions are of special interest because it turns out that for those models traditional residuals, often referred to as Pearson's residuals, are not appropriate. As such models have become more and more popular in practice, especially with financial time series data there is a need for reliable diagnostic tools that can be used to evaluate them. The aim of the thesis is to show how such diagnostic tools can be obtained and used in model evaluation. The quantile residuals considered here are defined in such a way that, when the model is correctly specified and its parameters are consistently estimated, they are approximately independent with standard normal distribution. All the tests derived in the thesis are pure significance type tests and are theoretically sound in that they properly take the uncertainty caused by parameter estimation into account. -- In Chapter 2 a general framework based on the likelihood function and smooth functions of univariate quantile residuals is derived that can be used to obtain misspecification tests for various purposes. Three easy-to-use tests aimed at detecting non-normality, autocorrelation, and conditional heteroscedasticity in quantile residuals are formulated. It also turns out that these tests can be interpreted as Lagrange Multiplier or score tests so that they are asymptotically optimal against local alternatives. Chapter 3 extends the concept of quantile residuals to multivariate models. The framework of Chapter 2 is generalized and tests aimed at detecting non-normality, serial correlation, and conditional heteroscedasticity in multivariate quantile residuals are derived based on it. Score test interpretations are obtained for the serial correlation and conditional heteroscedasticity tests and in a rather restricted special case for the normality test. In Chapter 4 the tests are constructed using the empirical distribution function of quantile residuals. So-called Khmaladze s martingale transformation is applied in order to eliminate the uncertainty caused by parameter estimation. Various test statistics are considered so that critical bounds for histogram type plots as well as Quantile-Quantile and Probability-Probability type plots of quantile residuals are obtained. Chapters 2, 3, and 4 contain simulations and empirical examples which illustrate the finite sample size and power properties of the derived tests and also how the tests and related graphical tools based on residuals are applied in practice.

Simulation of wavelength/time multiple-pulses-per-row fiber-optic CDMA network

Passive wavelength/time fiber-optic code division multiple access (WIT FO-CDMA) network is a viable option for highspeed access networks. Constructions of 2-D codes, suitable for incoherent WIT FO-CDMA, have been proposed to reduce the time spread of the 1-D sequences. The 2-D constructions can be broadly classified as 1) hybrid codes and 2) matrix codes. In our earlier work [141, we had proposed a new family of wavelength/time multiple-pulses-per-row (W/T MPR) matrix codes which have good cardinality, spectral efficiency and at the same time have the lowest off-peak autocorrelation and cross-correlation values equal to unity. In this paper we propose an architecture for a WIT MPR FO-CDAM network designed using the presently available devices and technology. A complete FO-CDMA network of ten users is simulated, for various number of simultaneous users and shown that 0 --> 1 errors can occur only when the number of interfering users is at least equal to the threshold value.

Quantum phase transition in capacitively coupled double quantum dots

We investigate two equivalent, capacitively coupled semiconducting quantum dots, each coupled to its own lead, in a regime where there are two electrons on the double dot. With increasing interdot coupling, a rich range of behavior is uncovered: first a crossover from spin- to charge-Kondo physics, via an intermediate SU(4) state with entangled spin and charge degrees of freedom, followed by a quantum phase transition of Kosterlitz-Thouless type to a non-Fermi-liquid "charge-ordered" phase with finite residual entropy and anomalous transport properties. Physical arguments and numerical renormalization group methods are employed to obtain a detailed understanding of the problem.

Comparison of ANN models for predicting water quality in distribution systems

Deterministic models have been widely used to predict water quality in distribution systems, but their calibration requires extensive and accurate data sets for numerous parameters. In this study, alternative data-driven modeling approaches based on artificial neural networks (ANNs) were used to predict temporal variations of two important characteristics of water quality chlorine residual and biomass concentrations. The authors considered three types of ANN algorithms. Of these, the Levenberg-Marquardt algorithm provided the best results in predicting residual chlorine and biomass with error-free and ``noisy'' data. The ANN models developed here can generate water quality scenarios of piped systems in real time to help utilities determine weak points of low chlorine residual and high biomass concentration and select optimum remedial strategies.

Studies of cryotreatment on the performance of integral diaphragm pressure transducers for space application

The integral diaphragm pressure transducers machined out of precipitation hardened martensite stainless steel (APX4) are widely used for propellant pressure measurements in space applications. These transducers are expected to exhibit dimensional stability and linearity for their entire useful life. These vital factors are very critical for the reliable performance and dependability of the pressure transducers. However, these transducers invariably develop internal stresses during various stages of machining. These stresses have an adverse effect on the performance of the transducers causing deviation from linearity. In order to eliminate these possibilities, it was planned to cryotreat the machined transducers to improve both the long-term linearity and dimensional stability. To study these effects, an experimental cryotreatment unit was designed and developed based on the concept of indirect cooling using the concept of cold nitrogen gas forced closed loop convection currents. The system has the capability of cryotreating large number of samples for varied rates of cooling, soaking and warm-up. After obtaining the initial levels of residual stress and retained austenite using X-ray diffraction techniques, the pressure transducers were cryotreated at 98 K for 36 h. Immediately after cryotreatment, the transducers were tempered at 510 degrees C for 3 h in vacuum furnace. Results after cryo treatment clearly indicated significant reduction in residual stress levels and conversion of retained austenite to martensite. These changes have brought in improvements in long term zero drift and dimensional stability. The cryotreated pressure transducers have been incorporated for actual space applications. (c) 2010 Published by Elsevier Ltd.

A numerical study of projectile impact on mild steel armour plates

The present article deals with the development of a finite element modelling approach for the prediction of residual velocities of hard core ogival-nose projectiles following normal impact on mild steel target plates causing perforation. The impact velocities for the cases analysed are in the range 818–866.3 m/s. Assessment of finite element modelling and analysis includes a comprehensive mesh convergence study using shell elements for representing target plates and solid elements for jacketed projectiles with a copper sheath and a rigid core. Dynamic analyses were carried out with the explicit contact-impact LS-DYNA 970 solver. It has been shown that proper choice of element size and strain rate-based material modelling of target plate are crucial for obtaining test-based residual velocity.The present modelling procedure also leads to realistic representation of target plate failure and projectile sheath erosion during perforation, and confirms earlier observations that thermal effects are not significant for impact problems within the ordnance range. To the best of our knowledge, any aspect of projectile failure or degradation obtained in simulation has not been reported earlier in the literature. The validated simulation approach was applied to compute the ballistic limits and to study the effects of plate thickness and projectile diameter on residual velocity, and trends consistent with experimental data for similar situations were obtained.

Autocalibration of dynamic bacterial growth model for water distribution system using GA

The presence of residual chlorine and organic matter govern the bacterial regrowth within a water distribution system. The bacterial growth model is essential to predict the spatial and temporal variation of all these substances throughout the system. The parameters governing the bacterial growth and biodegradable dissolved organic carbon (BDOC) utilization are difficult to determine by experimentation. In the present study, the estimation of these parameters is addressed by using simulation-optimization procedure. The optimal solution by genetic algorithm (GA) has indicated that the proper combination of parameter values are significant rather than correct individual values. The applicability of the model is illustrated using synthetic data generated by introducing noise in to the error-free measurements. The GA was found to be a potential tool in estimating the parameters controlling the bacterial growth and BDOC utilization. Further, the GA was also used for evaluating the sensitivity issues relating parameter values and objective function. It was observed that mu and k(cl) are more significant and dominating compared to the other parameters. But the magnitude of the parameters is also an important issue in deciding the dominance of a particular parameter. GA is found to be a useful tool in autocalibration of bacterial growth model and a sensitivity study of parameters.

A new parallel overlapped domain decomposition method for nonlinear dynamic finite element analysis

In this paper a new parallel algorithm for nonlinear transient dynamic analysis of large structures has been presented. An unconditionally stable Newmark-beta method (constant average acceleration technique) has been employed for time integration. The proposed parallel algorithm has been devised within the broad framework of domain decomposition techniques. However, unlike most of the existing parallel algorithms (devised for structural dynamic applications) which are basically derived using nonoverlapped domains, the proposed algorithm uses overlapped domains. The parallel overlapped domain decomposition algorithm proposed in this paper has been formulated by splitting the mass, damping and stiffness matrices arises out of finite element discretisation of a given structure. A predictor-corrector scheme has been formulated for iteratively improving the solution in each step. A computer program based on the proposed algorithm has been developed and implemented with message passing interface as software development environment. PARAM-10000 MIMD parallel computer has been used to evaluate the performances. Numerical experiments have been conducted to validate as well as to evaluate the performance of the proposed parallel algorithm. Comparisons have been made with the conventional nonoverlapped domain decomposition algorithms. Numerical studies indicate that the proposed algorithm is superior in performance to the conventional domain decomposition algorithms. (C) 2003 Elsevier Ltd. All rights reserved.

Accelerating Numerical Linear Algebra Kernels on a Scalable Run Time Reconfigurable Platform

Numerical Linear Algebra (NLA) kernels are at the heart of all computational problems. These kernels require hardware acceleration for increased throughput. NLA Solvers for dense and sparse matrices differ in the way the matrices are stored and operated upon although they exhibit similar computational properties. While ASIC solutions for NLA Solvers can deliver high performance, they are not scalable, and hence are not commercially viable. In this paper, we show how NLA kernels can be accelerated on REDEFINE, a scalable runtime reconfigurable hardware platform. Compared to a software implementation, Direct Solver (Modified Faddeev's algorithm) on REDEFINE shows a 29X improvement on an average and Iterative Solver (Conjugate Gradient algorithm) shows a 15-20% improvement. We further show that solution on REDEFINE is scalable over larger problem sizes without any notable degradation in performance.

Study of non-local wave properties of nanotubes with surface effects

In macroscopic and even microscopic structural elements, surface effects can be neglected and classical theories are sufficient. As the structural size decreases towards the nanoscale regime, the surface-to-bulk energy ratio increases and surface effects must be taken into account. In the present work, the terahertz wave dispersion characteristics of a nanotube are studied with consideration of the surface effects as well as the non-local small scale effects. Non-local elasticity theory is used to derive the general governing differential equation based on equilibrium approach to include those scale effects. Scale and surface property dependent wave characteristic equations are obtained via spectral analysis. For the present study the material properties of an anodic alumina nanotube with crystallographic of < 111 > direction are considered. The present analysis shows that the effect of surface properties (surface integrated residual stress and surface integrated modulus) on the flexural wave characteristics of anodic nanotubes are more significant. It has been found that the flexural wavenumbers with surface effects are high as compared to that without surface effects. It has also been shown that, with consideration of surface effects the flexural wavenumbers are under compressive nature. The effect of the small scale and the size of the nanotube on wave dispersion properties are also captured in the present work. (C) 2012 Elsevier B.V. All rights reserved.

Delamination Tolerance in Composites under Fatigue Loading

Delamination is one of the most commonly occurring defects in laminated composite structures. Under operating fatigue loads on the laminate this delamination could grow and totally delaminate certain number of layers from the base laminate. This will result in loss of both compressive residual strength and buckling margins available. In this paper, geometrically non-linear analysis and evaluation of Strain Energy Release Rates using MVCCI technique is presented. The problems of multiple delamination, effect of temperature exposure and delamination from pin loaded holes are addressed. Numerical results are presented to draw certain inferences of importance to design of high technology composite structures such as aircraft wing.