On computing the physical sources of jet noise

We derive a closed system of equations that relates the acoustically radiating flow variables to the sources of sound for homentropic flows. We use radiating density, momentum density and modified pressure as the dependent variables which leads to simple source terms for the momentum equations. The source terms involve the non-radiating parts of the density and momentum density fields. These non-radiating components are obtained by removing the radiating wavenumbers in the Fourier domain. We demonstrate the usefulness of this new technique on an axi-symmetric jet solution of the Navier-Stokes equations, obtained by direct numerical simulation (DNS). The dominant source term is proportional to the square of the non-radiating part of the axial momentum density. We compare the sound sources to that obtained by an acoustic analogy and find that they have more realistic physical properties. Their frequency content and amplitudes are consistent with. We validate the sources by computing the radiating sound field and comparing it to the DNS solution. © 2010 by S. Sinayoko, A. Agarwal.

BarraCUDA - a fast short read sequence aligner using graphics processing units.

BACKGROUND: With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. FINDINGS: Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. CONCLUSIONS: BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology.BarraCUDA is currently available from http://seqbarracuda.sf.net.