An algorithm to find similar internal sequence repeats

In recent years, identification of sequence patterns has been given immense importance to understand better their significance with respect to genomic organization and evolutionary processes. To this end, an algorithm has been derived to identify all similar sequence repeats present in a protein sequence. The proposed algorithm is useful to correlate the three-dimensional structure of various similar sequence repeats available in the Protein Data Bank against the same sequence repeats present in other databases like SWISS-PROT, PIR and Genome databases.

Time reversal technique for health monitoring of metallic structure using Lamb waves

Time reversal active sensing using Lamb waves is investigated for health monitoring of a metallic structure. Experiments were conducted on an aluminum plate to study the time reversal behavior of A(0) and S-0 Lamb wave modes under narrow band and broad band pulse excitation. Damage in the form of a notch was introduced in the plate to study the changes in the characteristics of the time reversed Lamb wave modes experimentally. Time-frequency analysis of the time reversed signal was carried out to extract the damage information. A measure of damage based on wavelet transform was derived to quantify the hidden damage information in the time reversed signal. It has been shown that time reversal can be used to achieve temporal recompression of Lamb waves under broadband signal excitation. Further, the broad band excitation can also improve the resolution of the technique in detecting closely located defects. This is demonstrated by picking up the reflection of waves from the edge of the plate, from a defect close to the edge of the plate and from defects located near to each other. This study shows the effectiveness of Lamb wave time reversal for temporal recompression of dispersive Lamb waves for damage detection in health monitoring applications. (C) 2009 Elsevier B.V. All rights reserved.

A semi-analytical particle filter for identification of nonlinear oscillators

Particle filters find important applications in the problems of state and parameter estimations of dynamical systems of engineering interest. Since a typical filtering algorithm involves Monte Carlo simulations of the process equations, sample variance of the estimator is inversely proportional to the number of particles. The sample variance may be reduced if one uses a Rao-Blackwell marginalization of states and performs analytical computations as much as possible. In this work, we propose a semi-analytical particle filter, requiring no Rao-Blackwell marginalization, for state and parameter estimations of nonlinear dynamical systems with additively Gaussian process/observation noises. Through local linearizations of the nonlinear drift fields in the process/observation equations via explicit Ito-Taylor expansions, the given nonlinear system is transformed into an ensemble of locally linearized systems. Using the most recent observation, conditionally Gaussian posterior density functions of the linearized systems are analytically obtained through the Kalman filter. This information is further exploited within the particle filter algorithm for obtaining samples from the optimal posterior density of the states. The potential of the method in state/parameter estimations is demonstrated through numerical illustrations for a few nonlinear oscillators. The proposed filter is found to yield estimates with reduced sample variance and improved accuracy vis-a-vis results from a form of sequential importance sampling filter.

Nonlinear secondary whirl of an overhung rotor

Gravity critical speeds of rotors have hitherto been studied using linear analysis, and ascribed to rotor stiffness asymmetry. Here, we study an idealized asymmetric nonlinear overhung rotor model of Crandall and Brosens, spinning close to its gravity critical speed.Nonlinearities arise from finite displacements, and the rotor's staticlateral deflection under gravity is taken as small. Assuming small asymmetry and damping, slow modulations of whirl amplitudes are studied using the method of multiple scales. Inertia asymmetry appears only at second order. More interestingly, even without stiffness asymmetry, the gravity-induced resonance survives through geometric nonlinearities. The gravity resonant forcing does not influence the resonant mode at leading order, unlike the typical resonant oscillations. Nevertheless,the usual phenomena of resonances, namely saddle-node bifurcations, jump phenomena and hysteresis, are all observed. An unanticipated periodic solution branch is found. In the three-dimensional space oftwo modal coefficients and a detuning parameter, the full set of periodic solutions is found to be an imperfect version of three mutually intersecting curves: a straight line,a parabola and an ellipse.

R1SVM: A randomised nonlinear approach to large-scale anomaly detection

The problem of unsupervised anomaly detection arises in a wide variety of practical applications. While one-class support vector machines have demonstrated their effectiveness as an anomaly detection technique, their ability to model large datasets is limited due to their memory and time complexity for training. To address this issue for supervised learning of kernel machines, there has been growing interest in random projection methods as an alternative to the computationally expensive problems of kernel matrix construction and sup-port vector optimisation. In this paper we leverage the theory of nonlinear random projections and propose the Randomised One-class SVM (R1SVM), which is an efficient and scalable anomaly detection technique that can be trained on large-scale datasets. Our empirical analysis on several real-life and synthetic datasets shows that our randomised 1SVM algorithm achieves comparable or better accuracy to deep auto encoder and traditional kernelised approaches for anomaly detection, while being approximately 100 times faster in training and testing.

Suppression of the zero-order term in off-axis digital holography through nonlinear filtering

We present experimental validation of a new reconstruction method for off-axis digital holographic microscopy (DHM). This method effectively suppresses the object autocorrelation,namely, the zero-order term,from holographic data,thereby improving the reconstruction bandwidth of complex wavefronts. The algorithm is based on nonlinear filtering and can be applied to standard DHM setups with realistic recording conditions.We study the robustness of the technique under different experimental configurations,and quantitatively demonstrate its enhancement capabilities on phase signals.

Transient response of nonlinear magneto-optic rotation in a paraffin-coated Rb vapor cell

We study resonant nonlinear magneto-optic rotation (NMOR) in a paraffin-coated Rb vapor cell as the magnetic field is swept. At low sweep rates, the nonlinear rotation appears as a narrow resonance signal with a linewidth of about ``300 mu G''(2 pi x 420 Hz). At high sweep rates, the signal shows transient response with an oscillatory decay. The decay time constant is of order 100 ms. The behavior is different for transitions starting from the lower or the upper hyperfine level of the ground state because of optical pumping effects.

A Nonlinear Approach for Re-entry Guidance of Reusable Launch Vehicles Using Model Predictive Static Programming

A nonlinear suboptimal guidance scheme is developed for the reentry phase of the reusable launch vehicles. A recently developed methodology, named as model predictive static programming (MPSP), is implemented which combines the philosophies of nonlinear model predictive control theory and approximate dynamic programming. This technique provides a finite time nonlinear suboptimal guidance law which leads to a rapid solution of the guidance history update. It does not have to suffer from computational difficulties and can be implemented online. The system dynamics is propagated through the flight corridor to the end of the reentry phase considering energy as independent variable and angle of attack as the active control variable. All the terminal constraints are satisfied. Among the path constraints, the normal load is found to be very constrictive. Hence, an extra effort has been made to keep the normal load within a specified limit and monitoring its sensitivity to the perturbation.

Boundary-layer effects on internal flow choking in dual-thrust solid rocket motors

Theoretical studies have been carried out to examine internal flow choking in the inert simulators of a dual-thrust motor. Using a two-dimensional k-omega turbulence model, detailed parametric studies have been carried out to examine aerodynamic choking and the existence of a fluid throat at the transition region during the startup transient of dual-thrust motors. This code solves standard k-omega turbulence equations with shear flow corrections using a coupled second-order-implicit unsteady formulation. In the numerical study, a fully implicit finite volume scheme of the compressible, Reynolds-averaged, Navier-Stokes equations is employed. It was observed that, at the subsonic inflow conditions, there is a possibility of the occurrence of internal flow choking in dual-thrust motors due to the formation of a fluid throat at the beginning of the transition region induced by area blockage caused by boundary-layer-displacement thickness. It has been observed that a 55% increase in the upstream port area of the dual-thrust motor contributes to a 25% reduction in blockage factor at the transition region, which could negate the internal How choking and supplement with an early choking of the dual-thrust motor nozzle. If the height of the upstream port relative to the motor length is too small, the developing boundary layers from either side of the port can interact, leading to a choked,flow. On the other hand, if the developing boundary layers are far enough apart, then choking does not occur. The blockage factor is greater in magnitude for the choked case than for the unchoked case. More tangible explanations are presented in this paper for the boundary-layer blockage and the internal flow choking in dual-thrust motors, which hitherto has been unexplored.

Composite scheme using localized relaxation with non-standard finite difference method for hyperbolic conservation laws

Non-standard finite difference methods (NSFDM) introduced by Mickens [Non-standard Finite Difference Models of Differential Equations, World Scientific, Singapore, 1994] are interesting alternatives to the traditional finite difference and finite volume methods. When applied to linear hyperbolic conservation laws, these methods reproduce exact solutions. In this paper, the NSFDM is first extended to hyperbolic systems of conservation laws, by a novel utilization of the decoupled equations using characteristic variables. In the second part of this paper, the NSFDM is studied for its efficacy in application to nonlinear scalar hyperbolic conservation laws. The original NSFDMs introduced by Mickens (1994) were not in conservation form, which is an important feature in capturing discontinuities at the right locations. Mickens [Construction and analysis of a non-standard finite difference scheme for the Burgers–Fisher equations, Journal of Sound and Vibration 257 (4) (2002) 791–797] recently introduced a NSFDM in conservative form. This method captures the shock waves exactly, without any numerical dissipation. In this paper, this algorithm is tested for the case of expansion waves with sonic points and is found to generate unphysical expansion shocks. As a remedy to this defect, we use the strategy of composite schemes [R. Liska, B. Wendroff, Composite schemes for conservation laws, SIAM Journal of Numerical Analysis 35 (6) (1998) 2250–2271] in which the accurate NSFDM is used as the basic scheme and localized relaxation NSFDM is used as the supporting scheme which acts like a filter. Relaxation schemes introduced by Jin and Xin [The relaxation schemes for systems of conservation laws in arbitrary space dimensions, Communications in Pure and Applied Mathematics 48 (1995) 235–276] are based on relaxation systems which replace the nonlinear hyperbolic conservation laws by a semi-linear system with a stiff relaxation term. The relaxation parameter (λ) is chosen locally on the three point stencil of grid which makes the proposed method more efficient. This composite scheme overcomes the problem of unphysical expansion shocks and captures the shock waves with an accuracy better than the upwind relaxation scheme, as demonstrated by the test cases, together with comparisons with popular numerical methods like Roe scheme and ENO schemes.

Long-term results of operative treatment for Hirschsprung's disease and internal anal sphincter achalasia

The aim of the study was to evaluate long-term results of operative treatment for Hirschsprung's disease(HD) and internal anal sphincter achalasia. Fecal continence and quality of life were evaluated by a questionnaire in 100 adult patients who had undergone surgery for HD, during 1950-75. Fecal continence was evaluated using a numerical scoring described by Holschneider. Fifty-four of the 100 patients underwent clinical examination, rigid sigmoidoscopy and manometric evaluation. In anorectal manometry basal resting pressure(BRP)and maximal squeeze pressure(MSP) were measured and voluntary sphincter force(VSF) was calculated by subtracting the BRP from MSP. The results of operative treatment for adult HD were compared with the results of the patients operated in childhood. In adult HD the symptoms are such mild that the patients attain adolescence or even adulthood. The patients with HD and cartilage-hair-hypoplasia were specifically evaluated. The outcome of the patients with internal anal sphincter achalasia operated on by myectomy was evaluated by a questionnaire and continence was evaluated using a numerical scoring described by Holschneider. Of the 100 patients operated on for HD 38 patients had completely normal bowel habits. A normal or good continence score was found in 91 our of 100 patients. Nine patients had fair continence. One of the patients with fair continence had Down's syndrome and two were mentally retarded for other reasons. Only one patient suffered from constipation. In anorectal manometry the difference in BRP between patients with normal and good continence was statistically significant, whereas the difference between good and fair continence groups was not statistically significant. The differences on MSP and VSF between patient groups with different continence outcome were not statistically significant. The differences between patient groups and normal controls were statistically significant in BRP and MSP. In VSF there was not statistically significant difference between the patients and the normal controls. The VSF reflects the working power of the muscles including external sphincter, levator ani and gluteal muscles. The patients operated at adult age had as good continence as patients operated in childhood. The patients with HD and cartilage-hair-hypoplasia had much more morbidity and mortality than non-cartilage-hair-hypoplasia HD patients. The mortality was as high as 38%. In patients with internal anal sphincter achalasia the constipation was cured or alleviated by myectomy whereas a significant number suffered from soiling-related social problems.

Laser damage studies in nonlinear optical crystal sodium p-nitrophenolate dihydrate

We report the surface laser damage threshold in sodium p-nitrophenolate dihydrate, a nonlinear optical crystal. The experiment is performed with a pulsed Nd:YAG laser in TEM00 mode. The single shot damage thresholds are 11.16 +/- 0.28GWcm(-2) and 1.25 +/- 0.02GWcm(-2) for 1064 nm and 532 nm laser wavelengths respectively. A close correlation between the laser damage threshold and mechanical hardness is observed. A possible mechanism of laser damage is discussed.

1H NMR study of internal motions and quantum rotational tunneling in (CH3)4NGeCl3

(CH3)4NGeCl3 is prepared, characterized and studied using 1H NMR spin lattice relaxation time and second moment to understand the internal motions and quantum rotational tunneling. Proton second moment is measured at 7 MHz as function of temperature in the range 300-77 K and spin lattice relaxation time (T1) is measured at two Larmor frequencies, as a function of temperature in the range 270-17 K employing a homemade wide-line/pulsed NMR spectrometers. T1 data are analyzed in two temperature regions using relevant theoretical models. The relaxation in the higher temperatures (270-115 K) is attributed to the hindered reorientations of symmetric groups (CH3 and (CH3)4N). Broad asymmetric T1 minima observed below 115 K down to 17 K are attributed to quantum rotational tunneling of the inequivalent methyl groups.