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Article
10-Million Atoms Simulation of First-Principle Package LS3DF
The growing demand for semiconductor devices simulation poses a big challenge for large-scale electronic structure calculations. Among various methods, the linearly scaling three-dimensional fragment (LS3DF) m...
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Article
PIM-Align: A Processing-in-Memory Architecture for FM-Index Search Algorithm
Genomic sequence alignment is the most critical and time-consuming step in genomic analysis. Alignment algorithms generally follow a seed-and-extend model. Acceleration of the extension phase for sequence alig...
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Article
Sediment Transport Capacity Under the River–Tide Interaction in the Changjiang Estuary
Sediment transport capacity is a fundamental parameter in sediment transport theory and its accurate calculation is important from both theoretical and engineering viewpoints. The capacity of sediment transpor...
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Article
Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine
Peptide identification in proteomics data is improved using an efficient open search engine.
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Article
Optimizing Parallel S n Sweeps on Unstructured Grids for Multi-Core Clusters
In particle transport simulations, radiation effects are often described by the discrete ordinates (S n ) form of Boltzmann equation. In each ordinate direction,...
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Article
Revisiting Multiple Pattern Matching Algorithms for Multi-Core Architecture
Due to the huge size of patterns to be searched, multiple pattern searching remains a challenge to several newly-arising applications like network intrusion detection. In this paper, we present an attempt to d...
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Article
Dawning Nebulae: A PetaFLOPS Supercomputer with a Heterogeneous Structure
Dawning Nebulae is a heterogeneous system composed of 9280 multi-core x86 CPUs and 4640 NVIDIA Fermi GPUs. With a Linpack performance of 1.271 petaFLOPS, it was ranked the second in the TOP500 List released in...
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Article
Experimental Study of Scour Rate in Consolidated Cohesive Sediment
The erosion process of a cohesive sediment after consolidation was studied experimentally in a closed conduit system. The test samples investigated in this study are mixtures of sand and clay with variable com...
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Article
Gate Regulation Speed and Transition Process of Unsteady Flow in Channel
The operation methods of channel and the speed of gate regulation have great influence on the transformation of flow in water conveyance channels. Based on characteristics method, a 1-D unsteady flow numerical...
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Article
One- and Two-Dimensional Coupled Hydrodynamics Model for Dam Break Flow
1-D and 2-D mathematical models for dam break flow were established and verified with the measured data in laboratory. The 1-D and 2-D models were then coupled, and used to simulate the dam break flow from the...
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Article
Horizontal 2-D Basic Equations and Simulation of Interchange Between Suspended Sediment and Bed Materials in Alluvial River
A set of new 2-D equations of interchange between suspended sediment and bed materials was serived by theoretical deduction based on the systematic summarization and assessment the previous studies of simulati...
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Article
Effects of Consolidation Time and Particle Size on Scour Rates of Cohesive Sediment
By means of flumes, experiments have been done in order to determine the effects of consolidation time and particle size on scour rates of cohesive sediment. Experimental results shown dry unit weight increase...
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Article
Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment
MegaBlast is one of the most important programs in NCBI BLAST (Basic Local Alignment Search Tool) toolkits. However, MegaBlast is computation and I/O intensive. It consumes a great deal of memory which is prop...
