High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP

This paper explores the pros and cons of reconfigurable computing in the form of FPGAs for high performance efficient computing. In particular, the paper presents the results of a comparative study between three different acceleration technologies, namely, Field Programmable Gate Arrays (FPGAs), Graphics Processor Units (GPUs), and IBM’s Cell Broadband Engine (Cell BE), in the design and implementation of the widely-used Smith-Waterman pairwise sequence alignment algorithm, with general purpose processors as a base reference implementation. Comparison criteria include speed, energy consumption, and purchase and development costs. The study shows that FPGAs largely outperform all other implementation platforms on performance per watt criterion and perform better than all other platforms on performance per dollar criterion, although by a much smaller margin. Cell BE and GPU come second and third, respectively, on both performance per watt and performance per dollar criteria. In general, in order to outperform other technologies on performance per dollar criterion (using currently available hardware and development tools), FPGAs need to achieve at least two orders of magnitude speed-up compared to general-purpose processors and one order of magnitude speed-up compared to domain-specific technologies such as GPUs

2-(4-Chloro-1H-indol-3-yl)acetonitrile

The title compound, C10H7ClN2, contains two approximately planar mol­ecules, A and B (r.m.s. deviations = 0.039 and 0.064 Å, respectively) in the asymmetric unit. In the crystal, N—H⋯N hydrogen bonds link the mol­ecules into C(7) chains of alternating A and B mol­ecules propagating along the a-axis direction. The crystal used for the data collection was found to be a racemic twin

Structural analysis and insight into novel MMP-13 inhibitors from natural chemiome as disease-modifying osteoarthritis drugs

Purpose: To identify natural chemiome that inhibits matrix-metalloproteinases (MMPs) with a view to discovering novel disease-modifying osteoarthritis drugs (DMOADs).Methods: Computer-aided drug design (CADD) with virtual screening, ADME/Tox, molecular docking, molecular dynamics simulation, and MM-PBSA calculations were used in search of novel natural compounds that inhibit MMPs.Results: From more than fifty thousand compounds, a single lead compound (IBS ID: 77312) was shortlisted using bias based on binding energy and drug-likeness. This lead compound synergistically bound to the S1 domain of MMP-13 protein through five hydrogen bonds. The interactions became stable within 100-nanosecond molecular dynamics simulation run. The in vitro data for the lead compound showed that its minimal non-lethal dose increased collagen content but decreased aggrecan level in chondrocytes.Conclusion: This study has identified a natural lead compound that may pave the way for a novel DMOAD of natural origin against OA.Keywords: Osteoarthritis, MMP-13, Natural chemiome, Disease-modifying osteoarthritis drug, Molecular dockin

A study on Fast Predicting the Washability Curve of Coal

AbstractA pure new MATLAB-based image recognition system was developed to compute the coal particle picture of same grain class through the digital image processing method, 13 image feature parameters was selected to be most representative image characteristic parameters. Take the above parameters as the input of RBF neural network, the density level of coal particles could be estimated, combined with the real ash content of each density level, the washability curve could be drawed. Experement show,the absolute error of the total ash is 2.375%,which is Slightly big in the China standards of coal preparation (GB/T477 -1998); the related coefficients of each indicator in both actual and predicted float-and-sink material are all close to 1, while the curves of λ, β, θ and δ are very similar and the deviation of ξ curve is relatively large

The Necessity of Hot Metal Desiliconization Process

AbstractThe technology of hot metal pretreatment had tremendous improvements in past decades and was widely used by the overwhelming majority of steelworks in Japan. While, since the first hot metal pretreatment station was established in Taiyuan Iron and Steel Co., Ltd in the later period of 1980s, this process began to be applied in domestic steel plants. And now 30 years have passed, the desilionization and dephosphorization process are still rarely seldom used in China except desulphurization process in most carbon steel plants. So in this paper, the metallurgical principles and effects of hot metal desiliconization were analyzed in great details. Meanwhile, the optimum silicon content of hot metal between iron-making and steelmaking process was summarized and calculated. The necessity of hot metal desiliconizaiton was discussed for the iron and steel companies in China