972 resultados para high-performance computing, computational modelling, multi-scale simulation, Visible Cell, orthologue mapping, systems biology


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The authors present a VLSI circuit for implementing wave digital filter (WDF) two-port adaptors. Considerable speedups over conventional designs have been obtained using fine grained pipelining. This has been achieved through the use of most significant bit (MSB) first carry-save arithmetic, which allows systems to be designed in which latency L is small and independent of either coefficient or input data wordlength. L is determined by the online delay associated with the computation required at each node in the circuit (in this case a multiply/add plus two separate additions). This in turn means that pipelining can be used to considerably enhance the sampling rate of a recursive digital filter. The level of pipelining which will offer enhancement is determined by L and is fine-grained rather than bit level. In the case of the circuit considered, L = 3. For this reason pipeline delays (half latches) have been introduced between every two rows of cells to produce a system with a once every cycle sample rate.

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The design and VLSI implementation of two key components of the class-IV partial response maximum likelihood channel (PR-IV) the adaptive filter and the Viterbi decoder are described. These blocks are implemented using parameterised VHDL modules, from a library of common digital signal processing (DSP) and arithmetic functions. Design studies, based on 0.6 micron 3.3V standard cell processes, indicate that worst case sampling rates of 49 mega-samples per second are achievable for this system, with proportionally high sampling rates for full custom designs and smaller dimension processes. Significant increases in the sampling rate, from 49 MHz to approximately 180 MHz, can be achieved by operating four filter modules in parallel, and this implementation has 50% lower power consumption than a pipelined filter operating at the same speed.

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The design cycle for complex special-purpose computing systems is extremely costly and time-consuming. It involves a multiparametric design space exploration for optimization, followed by design verification. Designers of special purpose VLSI implementations often need to explore parameters, such as optimal bitwidth and data representation, through time-consuming Monte Carlo simulations. A prominent example of this simulation-based exploration process is the design of decoders for error correcting systems, such as the Low-Density Parity-Check (LDPC) codes adopted by modern communication standards, which involves thousands of Monte Carlo runs for each design point. Currently, high-performance computing offers a wide set of acceleration options that range from multicore CPUs to Graphics Processing Units (GPUs) and Field Programmable Gate Arrays (FPGAs). The exploitation of diverse target architectures is typically associated with developing multiple code versions, often using distinct programming paradigms. In this context, we evaluate the concept of retargeting a single OpenCL program to multiple platforms, thereby significantly reducing design time. A single OpenCL-based parallel kernel is used without modifications or code tuning on multicore CPUs, GPUs, and FPGAs. We use SOpenCL (Silicon to OpenCL), a tool that automatically converts OpenCL kernels to RTL in order to introduce FPGAs as a potential platform to efficiently execute simulations coded in OpenCL. We use LDPC decoding simulations as a case study. Experimental results were obtained by testing a variety of regular and irregular LDPC codes that range from short/medium (e.g., 8,000 bit) to long length (e.g., 64,800 bit) DVB-S2 codes. We observe that, depending on the design parameters to be simulated, on the dimension and phase of the design, the GPU or FPGA may suit different purposes more conveniently, thus providing different acceleration factors over conventional multicore CPUs.

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Traditional Chinese Medicines (TCMs) derived from animal horns are one of the most important types of Chinese medicine. In the present study, a fast and sensitive analytical method was established for qualitative and quantitative determination of 14 nucleosides and nucleobases in animal horns using hydrophilic interaction ultra-high performance liquid chromatography coupled with triple-quadruple tandem mass spectrometry (HILIC-UPLC-QQQ-MS/MS) in selective reaction monitoring (SRM) mode. The method was optimized and validated, and showed good linearity, precision, repeatability, and accuracy. The method was successfully used to determine contents of the 14 nucleosides and nucleobases in 25 animal horn samples. Hierarchical clustering analysis (HCA) and principal component analysis (PCA) were performed and the 25 samples were thereby divided into two groups, which agreed with taxonomy. The method may enable quick and effective search of substitutes for precious horns.

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The design of a high-performance IIR (infinite impulse response) digital filter is described. The chip architecture operates on 11-b parallel, two's complement input data with a 12-b parallel two's complement coefficient to produce a 14-b two's complement output. The chip is implemented in 1.5-µm, double-layer-metal CMOS technology, consumes 0.5 W, and can operate up to 15 Msample/s. The main component of the system is a fine-grained systolic array that internally is based on a signed binary number representation (SBNR). Issues addressed include testing, clock distribution, and circuitry for conversion between two's complement and SBNR.