Applications of the dynamic mode decomposition

The decomposition of experimental data into dynamic modes using a data-based algorithm is applied to Schlieren snapshots of a helium jet and to time-resolved PIV-measurements of an unforced and harmonically forced jet. The algorithm relies on the reconstruction of a low-dimensional inter-snapshot map from the available flow field data. The spectral decomposition of this map results in an eigenvalue and eigenvector representation (referred to as dynamic modes) of the underlying fluid behavior contained in the processed flow fields. This dynamic mode decomposition allows the breakdown of a fluid process into dynamically revelant and coherent structures and thus aids in the characterization and quantification of physical mechanisms in fluid flow. © 2010 Springer-Verlag.

A species conserving genetic algorithm for multimodal function optimization

This paper introduces a new technique called species conservation for evolving parallel subpopulations. The technique is based on the concept of dividing the population into several species according to their similarity. Each of these species is built around a dominating individual called the species seed. Species seeds found in the current generation are saved (conserved) by moving them into the next generation. Our technique has proved to be very effective in finding multiple solutions of multimodal optimization problems. We demonstrate this by applying it to a set of test problems, including some problems known to be deceptive to genetic algorithms.

Mode I crack growth resistance of metallic foams

A Dugdale-type cohesive zone model is used to predict the mode I crack growth resistance (R-curve) of metallic foams, with the fracture process characterized by an idealized traction-separation law that relates the crack surface traction to crack opening displacement. A quadratic yield function, involving the von Mises effective stress and mean stress, is used to account for the plastic compressibility of metallic foams. Finite element calculations are performed for the crack growth resistance under small scale yielding and small scale bridging in plane strain, with K-field boundary conditions. The following effects upon the fracture process are quantified: material hardening, bridging strength, T-stress (the non-singular stress acting parallel to the crack plane), and the shape of yield surface. To study the failure behaviour and notch sensitivity of metallic foams in the presence of large scale yielding, a study is made for panels embedded with either a centre-crack or an open hole and subjected to tensile stressing. For the centre-cracked panel, a transition crack size is predicted for which the fracture response switches from net section yielding to elastic-brittle fracture. Likewise, for a panel containing a centre-hole, a transition hole diameter exists for which the fracture response switches from net section yielding to a local maximum stress criterion at the edge of the hole.

Performance of low density parity check codes as a function of actual and assumed noise levels

We investigate how sensitive Gallager's codes are, when decoded by the sum-product algorithm, to the assumed noise level. We have found a remarkably simple function that fits the empirical results as a function of the actual noise level at both high and low noise levels. © 2004 Elsevier B.V.

Performance of low density parity check codes as a function of actual and assumed noise levels

We investigate how sensitive Gallager's codes are, when decoded by the sum-product algorithm, to the assumed noise level. We have found a remarkably simple function that fits the empirical results as a function of the actual noise level at both high and low noise levels. ©2003 Published by Elsevier Science B. V.

Model-based control of a Rijke tube combustion instability

A Rijke tube is used to demonstrate model-based control of a combustion instability, where controller design is based on measurement of the unstable system. The Rijke tube used was of length 0.75m and had a grid-stabilised laminar flame in its lower half. A microphone was used as a sensor and a loudspeaker as an actuator for active control. The open loop transfer function (OLTF) required for controller design was that from the actuator to the sensor. This was measured experimentally by sending a signal with two components to the actuator. The first was a control component from an empirically designed controller, which was used to stabilise the system, thus eliminating the non-linear limit cycle. The second was a high bandwidth signal for identification of the OLTF. This approach to measuring the OLTF is generic and can be applied to large-scale combustors. The measured OLTF showed that only the fundamental mode of the tube was unstable; this was consistent with the OLTF predicted by a mathematical model of the tube, involving 1-D linear acoustic waves and a time delay heat release model. Based on the measured OLTF, a controller to stabilise the instability was designed using Nyquist techniques. This was implemented and was seen to result in an 80dB reduction in the microphone pressure spectrum. A robustness study was performed by adding an additional length to the top of the Rijke tobe. The controller was found to achieve control up to an increase in tube length of 19%. This compared favourably with the empirical controller, which lost control for an increase in tube length of less than 3%.

Gene function prediction from synthetic lethality networks via ranking on demand.

MOTIVATION: Synthetic lethal interactions represent pairs of genes whose individual mutations are not lethal, while the double mutation of both genes does incur lethality. Several studies have shown a correlation between functional similarity of genes and their distances in networks based on synthetic lethal interactions. However, there is a lack of algorithms for predicting gene function from synthetic lethality interaction networks. RESULTS: In this article, we present a novel technique called kernelROD for gene function prediction from synthetic lethal interaction networks based on kernel machines. We apply our novel algorithm to Gene Ontology functional annotation prediction in yeast. Our experiments show that our method leads to improved gene function prediction compared with state-of-the-art competitors and that combining genetic and congruence networks leads to a further improvement in prediction accuracy.

Protein functionalized ZnO thin film bulk acoustic resonator as an odorant biosensor

ZnO thin film bulk acoustic resonators (FBARs) with resonant frequency of ∼1.5 GHz have been fabricated to function as an odorant biosensor. Physical adsorption of an odorant binding protein (AaegOBP22 from Aedes aegypti) resulted in frequency down shift. N,N-diethyl-meta-toluamide (DEET) has been selected as a ligand to the odorant binding protein (OBP). Alternate exposure of the bare FBARs to nitrogen flow with and without DEET vapor did not cause any noticeable frequency change. However, frequency drop was detected when exposing the OBP loaded FBAR sensors to the nitrogen flow containing DEET vapor against nitrogen flow alone (control) and the extent of frequency shift was proportional to the amount of the protein immobilized on the FBAR surface, indicating a linear response to DEET binding. These findings demonstrate the potential of binding protein functionalized FBARs as odorant biosensors. © 2012 Elsevier B.V. All rights reserved.

Impact of mode localization on the motional resistance of coupled MEMS resonators

This paper investigates the effect of mode-localization that arises from structural asymmetry induced by manufacturing tolerances in mechanically coupled, electrically transduced Si MEMS resonators. We demonstrate that in the case of such mechanically coupled resonators, the achievable series motional resistance (R x) is dependent not only on the quality factor (Q) but also on the variations in the eigenvector of the chosen mode of vibration induced by mode localization due to manufacturing tolerances during the fabrication process. We study this effect of mode-localization both theoretically and experimentally in two pairs of coupled double-ended tuning fork resonators with different levels of initial structural asymmetry. The measured series R x is minimal when the system is close to perfect symmetry and any deviation from structural symmetry induced by fabrication tolerances leads to a degradation in the effective R x. Mechanical tuning experiments of the stiffness of one of the coupled resonators was also conducted to study variations in R x as a function of structural asymmetry within the system, the results of which demonstrated consistent variations in motional resistance with predictions. © 2012 IEEE.

On the applicability of the lognormal distribution in random dynamical systems

This paper is concerned with the probability density function of the energy of a random dynamical system subjected to harmonic excitation. It is shown that if the natural frequencies and mode shapes of the system conform to the Gaussian Orthogonal Ensemble, then under common types of loading the distribution of the energy of the response is approximately lognormal, providing the modal overlap factor is high (typically greater than two). In contrast, it is shown that the response of a system with Poisson natural frequencies is not approximately lognormal. Numerical simulations are conducted on a plate system to validate the theoretical findings and good agreement is obtained. Simulations are also conducted on a system made from two plates connected with rotational springs to demonstrate that the theoretical findings can be extended to a built-up system. The work provides a theoretical justification of the commonly used empirical practice of assuming that the energy response of a random system is lognormal.

Nonlinear phenomena in thermoacoustics: A comparison between single-mode and multi-mode methods

Nonlinear analysis of thermoacoustic instability is essential for prediction of frequencies and amplitudes of limit cycles. In frequency domain analyses, a quasi-linear transfer function between acoustic velocity and heat release rate perturbations, called the flame describing function (FDF), is obtained from a flame model or experiments. The FDF is a function of the frequency and amplitude of velocity perturbations but only contains the heat release response at the forcing frequency. While the gain and phase of the FDF provide insight into the nonlinear dynamics of the system, the accuracy of its predictions remains to be verified for different types of nonlinearity. In time domain analyses, the governing equations of the fully coupled problem are solved to find the time evolution of the system. One method is to discretize the governing equations using a suitable basis, such as the natural acoustic modes of the system. The number of modes used in the discretization alters the accuracy of the solution. In our previous work we have shown that predictions using the FDF are almost exactly the same as those obtained from the time-domain using only one mode for the discretization. We call this the single-mode method. In this paper we compare results from the single-mode and multi-mode methods, applied to a thermoacoustic system of a premixed flame in a tube. For some cases, the results differ greatly in both amplitude as well as frequency content. This study shows that the contribution from higher and subharmonics to the nonlinear dynamics can be significant and must be considered for an accurate and comprehensive analysis of thermoacoustic systems. Hence multi-mode simulations are necessary, and the single-mode method or the FDF may be insufficient to capture some of the complex nonlinear behaviour in fhermoacoustics.

Theory of high-power mode-locked lasers with a slow absorber

We develop an analytical theory of high-power passively mode-locked lasers with a slow absorber; the theory is valid at pulse energies well exceeding the saturation energy. We analyze the Haus modelocking master equation in the pulse-energy-domain representation, approximating the intensity profile function by a series in the vicinity of its peak value. We consider the high-power operation regime of subpicosecond blue-violet GaN mode-locked diode lasers, using the approach developed. © 2010 Springer Science+Business Media, Inc.