Mechanical Engineering - Research Publications
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ItemGene function prediction based on genomic context clustering and discriminative learning: an application to bacteriophages(BioMed Central, 2007-05-22)BACKGROUND: Existing methods for whole-genome comparisons require prior knowledge of related species and provide little automation in the function prediction process. Bacteriophage genomes are an example that cannot be easily analyzed by these methods. This work addresses these shortcomings and aims to provide an automated prediction system of gene function. RESULTS: We have developed a novel system called SynFPS to perform gene function prediction over completed genomes. The prediction system is initialized by clustering a large collection of weakly related genomes into groups based on their resemblance in gene distribution. From each individual group, data are then extracted and used to train a Support Vector Machine that makes gene function predictions. Experiments were conducted with 9 different gene functions over 296 bacteriophage genomes. Cross validation results gave an average prediction accuracy of ~80%, which is comparable to other genomic-context based prediction methods. Functional predictions are also made on 3 uncharacterized genes and 12 genes that cannot be identified by sequence alignment. The software is publicly available at http://www.synteny.net/. CONCLUSION: The proposed system employs genomic context to predict gene function and detect gene correspondence in whole-genome comparisons. Although our experimental focus is on bacteriophages, the method may be extended to other microbial genomes as they share a number of similar characteristics with phage genomes such as gene order conservation.
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ItemLarge-scale influences in near-wall turbulence(ROYAL SOC, 2007-03-15)Hot-wire data acquired in a high Reynolds number facility are used to illustrate the need for adequate scale separation when considering the coherent structure in wall-bounded turbulence. It is found that a large-scale motion in the log region becomes increasingly comparable in energy to the near-wall cycle as the Reynolds number increases. Through decomposition of fluctuating velocity signals, it is shown that this large-scale motion has a distinct modulating influence on the small-scale energy (akin to amplitude modulation). Reassessment of DNS data, in light of these results, shows similar trends, with the rate and intensity of production due to the near-wall cycle subject to a modulating influence from the largest-scale motions.
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ItemReynolds number invariance of the structure inclination angle in wall turbulence(AMER PHYSICAL SOC, 2007-09-14)Cross correlations of the fluctuating wall-shear stress and the streamwise velocity in the logarithmic region of turbulent boundary layers are reported over 3 orders of magnitude change in Reynolds number. These results are obtained using hot-film and hot-wire anemometry in a wind tunnel facility, and sonic anemometers and a purpose-built wall-shear stress sensor in the near-neutral atmospheric surface layer on the salt flats of Utah's western desert. The direct measurement of fluctuating wall-shear stress in the atmospheric surface layer has not been available before. Structure inclination angles are inferred from the cross correlation results and are found to be invariant over the large range of Reynolds number. The findings justify the prior use of low Reynolds number experiments for obtaining structure angles for near-wall models in the large-eddy simulation of atmospheric surface layer flows.
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ItemLaminar and turbulent comparisons for channel flow and flow control(CAMBRIDGE UNIV PRESS, 2007-01-10)A formula is derived that shows exactly how much the discrepancy between the volume flux in laminar and in turbulent flow at the same pressure gradient increases as the pressure gradient is increased. We compare laminar and turbulent flows in channels with and without flow control. For the related problem of a fixed bulk-Reynolds-number flow, we seek the theoretical lowest bound for skin-friction drag for control schemes that use surface blowing and suction with zero-net volume-flux addition. For one such case, using a crossflow approach, we show that sustained drag below that of the laminar-Poiseuille-flow case is not possible. For more general control strategies we derive a criterion for achieving sublaminar drag and use this to consider the implications for control strategy design and the limitations at high Reynolds numbers.
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ItemGene function prediction based on genomic context clustering and discriminative learning: an application to bacteriophages(BMC, 2007)BACKGROUND: Existing methods for whole-genome comparisons require prior knowledge of related species and provide little automation in the function prediction process. Bacteriophage genomes are an example that cannot be easily analyzed by these methods. This work addresses these shortcomings and aims to provide an automated prediction system of gene function. RESULTS: We have developed a novel system called SynFPS to perform gene function prediction over completed genomes. The prediction system is initialized by clustering a large collection of weakly related genomes into groups based on their resemblance in gene distribution. From each individual group, data are then extracted and used to train a Support Vector Machine that makes gene function predictions. Experiments were conducted with 9 different gene functions over 296 bacteriophage genomes. Cross validation results gave an average prediction accuracy of ~80%, which is comparable to other genomic-context based prediction methods. Functional predictions are also made on 3 uncharacterized genes and 12 genes that cannot be identified by sequence alignment. The software is publicly available at http://www.synteny.net/. CONCLUSION: The proposed system employs genomic context to predict gene function and detect gene correspondence in whole-genome comparisons. Although our experimental focus is on bacteriophages, the method may be extended to other microbial genomes as they share a number of similar characteristics with phage genomes such as gene order conservation.
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ItemOn-line scheduling with forbidden zones(TAYLOR & FRANCIS LTD, 2007-01)
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ItemRigorous analysis of numerical phase and group velocity bounds in Yee's FDTD grid(IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2007-08)
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ItemGabor wavelet similarity maps for optimising hierarchical road sign classifiers(ELSEVIER, 2007-01-15)
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ItemHierarchical and Interpretable Connectionist Structure Generation from Data(Research India Publications, 2007)
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ItemDo silica phytoliths really wear mammalian teeth?(ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, 2007-04)