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Kernel optimization for short-range molecular dynamics

COMPUTER PHYSICS COMMUNICATIONS 2017年 211卷 31-40页

作者： Hu Changjun Wang Xianmeng Li Jianjiang He Xinfu Li Shigang Feng Yangde Yang Shaofeng Bai He Univ Sci & Technol Beijing Beijing Peoples R China China Inst Atom Energy Beijing Peoples R China Chinese Acad Sci Inst Comp Technol State Key Lab Comp Syst & Architecture Beijing Peoples R China Chinese Acad Sci Comp Network Informat Ctr Beijing Peoples R China

To optimize short-range force computations in Molecular Dynamics (MD) simulations, multi-threading and SIMD optimizations are presented in this paper. With respect to multi-threading optimization, a Partition-and-Separate-Calculation (PSC) method is designed to avoid write conflicts caused by using Newton's third law. Serial bottlenecks are eliminated with no additional memory usage. The method is implemented by using the OpenMP model. Furthermore, the PSC method is employed on Intel Xeon Phi coprocessors in both native and offload models. We also evaluate the performance of the PSC method under different thread affinities on the MIC architecture. In the SIMD execution, we explain the performance influence in the PSC method, considering the "if-clause" of the cutoff radius check. The experiment results show that our PSC method is relatively more efficient compared to some traditional methods. In double precision, our 256-bit SIMD implementation is about 3 times faster than the scalar version. (C) 2016 Elsevier B.V. All rights reserved.

关键词： Molecular Dynamics OpenMP SIMD MIC

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Differences in the response of soil dehydrogenase activity to Cd contamination are determined by the different substrates used for its determination

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CHEMOSPHERE 2017年 169卷 324-332页

作者： Tan, Xiangping Liu, Yanju Yan, Kaihong Wang, Ziquan Lu, Guannan He, Yike He, Wenxiang Northwest A&F Univ Coll Nat Resources & Environm Key Lab Plant Nutr & Agroenvironm Northwest China Minist Agr Yangling 712100 Shaanxi Peoples R China Univ Newcastle Global Ctr Environm Res Fac Sci & Informat Technol Univ Dr Callaghan NSW 2308 Australia Cooperat Res Ctr Contaminat Assessment & Remediat Mawson Lakes SA 5095 Australia

Dehydrogenase activity (DHA) is an important indicator of heavy metal toxicity in contaminated soils. Different instances of DHA were determined using various substrates and which could affect the description of heavy metal toxicity. Currently, too few investigations have been done on selecting appropriate substrates. This study employed indoor simulation to determine soil DHA and its response to external cadmium (Cd) using two substrates (TTC and INT). Hormesis for DHA obtained using the TTC method (DHA-TTC) in low Cd concentration was observed which was quickly inhibited in high Cd concentration. While DHA obtained using the INT method (DHA-INT) decreased slowly when Cd concentration increased. The DHA-TTC and DHA-INT in soils at Cd concentration of 500 mg kg(-1) decreased 86% and 53%, respectively, compared to the control. The dose-response relationship of Cd to DHA can be well simulated using the logistic model (p < 0.01), which indicated DHA could be used to indicate soil Cd toxicity. Multiple stepwise regression analysis revealed that total organic matter (TOC) is the major factor influencing the toxicity of Cd to DHA-TTC, while TOC, pH and cation exchange capacity (CEC) are major factors influencing the toxicity of Cd to DHA-INT. The different responses of soil DHA-ITC and DHA-INT to Cd are due to the differences in electron transport chain characteristics between ITC and INT, as well as the influence of soil properties. Although both DHA-TTC and DHA-INT can monitor soil Cd contamination, DHA-INT is recommended as a superior bio-indicator to indicate and assess contamination of Cd in soil. (C) 2016 Elsevier Ltd. All rights reserved.

关键词： Dehydrogenase activity Ecological dose Cadmium Enzyme substrate Soil type

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LCS: An Efficient Data Eviction Strategy for Spark

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INTERNATIONAL JOURNAL OF PARALLEL programMING 2017年第6期45卷 1285-1297页

作者： Geng, Yuanzhen Shi, Xuanhua Pei, Cheng Jin, Hai Jiang, Wenbin Huazhong Univ Sci & Technol Sch Comp Sci & Technol Serv Comp Technol & Syst Lab Wuhan 430074 Peoples R China Huazhong Univ Sci & Technol Sch Comp Sci & Technol Cluster & Grid Comp Lab Wuhan 430074 Peoples R China Huazhong Univ Sci & Technol Sch Comp Sci & Technol Big Data Technol & Syst Lab Wuhan 430074 Peoples R China

As an in-memory distributed computing system, Spark is often used to speed up iterative applications. It caches intermediate data generated by previous iterations into memory, so there is no need to repeat the generation when reusing these data later. This sharing mechanism of caching data in memory makes Spark much faster than other systems. When memory used for caching data reaches the capacity limits, data eviction will be performed to supply space for new data, and the evicted data need to be recovered when they are used again. However, classical strategies do not aware of recovery cost, which could cause system performance degradation. This paper shows that the recovery costs have significant difference in Spark, thus a cost aware eviction strategy can obviously reduces the total recovery cost. To this end, a strategy named LCS is proposed, which gets dependencies information between cache data via analyzing application, and calculates the recovery cost during running. By predicting how many times cache data will be reused and using it to weight the recovery cost, LCS always evicts the data which lead to minimum recovery cost in future. Experimental results show that this approach can achieve better performance when memory space is not sufficient, and reduce 30-50% of the total execution time .

关键词： Spark Eviction strategy Cache management

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A Faraday laser lasing on Rb 1529 nm transition

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SCIENTIFIC REPORTS 2017年第1期7卷 1-8页

作者： Chang, Pengyuan Peng, Huanfa Zhang, Shengnan Chen, Zhangyuan Luo, Bin Chen, Jingbiao Guo, Hong Peking Univ Inst Quantum Elect Sch Elect Engn & Comp Sci State Key Lab Adv Optic Commun Syst & Network Beijing 100871 Peoples R China Beijing Univ Posts & Telecommun State Key Lab Informat Photon & Opt Commun Beijing 100876 Peoples R China

We present the design and performance characterization of a Faraday laser directly lasing on the Rb 1529 nm transition (Rb, 5P(3/2) - 4D(5/2)) with high stability, narrow spectral linewidth and low cost. This system does not need an additional frequency-stabilized pump laser as a prerequisite to preparing Rb atom from 5S to 5P excited state. Just by using a performance-improved electrodeless discharge lamp-based excited-state Faraday anomalous dispersion optical filter (LESFADOF), we realized a heterogeneously Faraday laser with the frequency corresponding to atomic transition, working stably over a range of laser diode (LD) current from 85 mA to 171 mA and the LD temperature from 11 degrees C to 32 degrees C, as well as the 24-hour long-term frequency fluctuation range of no more than 600 MHz. Both the laser linewidth and relative intensity noisy (RIN) are measured. The Faraday laser lasing on Rb 1529 nm transition (telecom C-band) can be applied to further research on metrology, microwave photonics and optical communication systems. Besides, since the transitions correspongding to the populated excited-states of alkali atoms within lamp are extraordinarily rich, this scheme can increase the flexibility for choosing proper wavelengths for Faraday laser and greatly expand the coverage of wavelength corresponding to atomic transmission for laser frequency stabilization.

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Phospholipase A1-Catalysed Synthesis of Docosahexaenoic Acid-Enriched Phosphatidylcholine in Reverse Micelles System

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APPLIED BIOCHEMISTRY AND BIOtechNOLOGY 2017年第3期182卷 1037-1052页

作者： Chen, Wuxi Guo, Wei Gao, Feng Chen, Limei Chen, Shulin Li, Demao Chinese Acad SciencesTianjin Tianjin Inst Ind Biotechnol Tianjin Key Lab Ind Biol Syst & Bioproc Engn 32 Xiqi RdTianjin Airport Econ Pk Tianjin 300308 Peoples R China

Phosphatidylcholine enriched with docosahexaenoic acid (DHA) was successfully produced by phospholipase A1-catalysed acidolysis. Reverse micelles were firstly selected as the reaction system to avoid the process of immobilization and to ensure the efficient catalysis of phospholipase A1. Parameters were optimized for a high incorporation of phosphatidylcholine enriched with DHA (DHA-PC). A response-surface design with four factors, including the water content, enzyme loading, pH and substrate-mass ratio were used to evaluate the influence of the major factors and to predict the optimal reaction conditions. The results indicated that the optimal reaction conditions for the production of DHA-PC were a water content of 0.4%, an enzyme loading of 40%, pH 6.92 and a substrate-mass ratio of 2.13. Under these optimized conditions, 20.90% of DHA content in DHA-PC was obtained.

关键词： Phosphatidylcholine Docosahexaenoic acid Phospholipase A1 Catalysed acidolysis Reverse micelles

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A tool for assessing the energy demand and efficiency of machining systems: Energy benchmarking

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ENERGY 2017年 138卷 332-347页

作者： Cai, Wei Liu, Fei Xie, Jun Liu, Peiji Tuo, Junbo Chongqing Univ State Key Lab Mech Transmiss Chongqing 400030 Peoples R China Chongqing Univ Technol Coll Mech Engn Chongqing 400050 Peoples R China

Energy benchmarking has been recognized as an effective analytical methodology and management tool to improve energy efficiency and performance. Many approaches to energy benchmarking have been applied in various fields. Machining systems, which are widely distributed and consume large amounts of energy with low efficiency, possess considerable potential for reductions in energy consumption. However, current research regarding the use of energy benchmarking for machining systems is insufficient due to the complexity and variety of energy consumption processes used in these systems. This paper proposes the use of energy benchmarking to strengthen the evaluation of energy demand and achieve efficiency improvements for machining systems. First, it analyses drivers for energy bench marking and their characteristics. Next, an energy benchmarking framework for machining systems is presented. Then the concepts of the static, dynamic, single-objective, multi-objective, product-based, and process-based energy benchmarking are discussed from three different perspectives: the motion, object and application level. This lays a theoretical foundation for further energy benchmarking research. Finally, methods for developing energy benchmarking are also addressed including the prediction method, statistical analysis and expert decision. The application of these methods to a real machining plant allows an analysis of the practicability of potentially saving energy through benchmarking. (C) 2017 Elsevier Ltd. All rights reserved.

关键词： Energy benchmarking Machining systems Energy assessments Energy demand Energy efficiency Energy consumption

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A novel MEMS inertial switch with a reinforcing rib structure and electrostatic power assist to prolong the contact time

A novel MEMS inertial switch with a reinforcing rib structur...

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19th Annual Conference and 8th International Conference of Chinese Society of Micro/Nano technology (CSMNT)

作者： Li, Jian Wang, Yan Yang, Zhuoqing Ding, Guifu Zhao, Xiaolin Wang, Hong Shanghai Jiao Tong Univ Shanghai 200240 Peoples R China

The MEMS inertial switch is widely used in various industries owing to its advantage of small size, high integration, low power consumption and low costs, especially in the timing of Internet of things, such as toys, handheld devices, accessories and vibration testing. This paper provided a novel inertial switch with a reinforcing rib structure and electrostatic power assist. The designed inertial switch can reduce the complexity of the post-processing circuit and broaden its application prospect. The continuous electrostatic force can extend the contact time of the designed inertia switch before the leakage of electricity ends. The moving electrode with a reinforcing rib structure can effectively restrain the bending of the lower surface of moving electrode caused by residual stress. The array-type fixed electrode can ensure stable contact between the electrodes when the device is sensitive to external shocks. The dynamic displacement-time curve can be simulated by the COMSOL finite element simulation software. The laminated plating process is used to produce the designed inertial switch and the drop hammer acceleration monitoring system is used to test the fabricated device. The results indicate that, compared with the traditional design, the bouncing phenomenon can be prevented and extend the contact time to 336 mu s.

关键词： Electrodes

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Soybean P34 Probable Thiol Protease Probably Has Proteolytic Activity on Oleosins

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JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017年第28期65卷 5741-5750页

作者： Zhao, Luping Kong, Xiangzhen Zhang, Caimeng Hua, Yufei Chen, Yeming Jiangnan Univ Sch Food Sci & Technol State Key Lab Food Sci & Technol 1800 Lihu Ave Wuxi 214122 Jiangsu Peoples R China

P34 probable thiol protease (P34) and Gly m Bd 30K (30K) show high relationship with the protease of 24 kDa oleosin of soybean oil bodies. In this study, 9 day germinated soybean was used to separate bioprocessed P34 (P32) from bioprocessed 30K (28K). Interestingly, P32 existed as dimer, whereas 28K existed as monomer;a P32 -rich sample had proteolytic activity and high cleavage site specificity (Lys-Thr of 24 kDa oleosin), whereas a 28K-rich sample showed low proteolytic activity;the P32 -rich sample contained one thiol protease. After mixing with purified oil bodies, all P32 dimers were dissociated and bound to 24 kDa oleosins to form P32-24 kDa oleosin complexes. By incubation, 24 kDa oleosin was preferentially hydrolyzed, and two hydrolyzed products (HPs;17 and 7 kDa) were confirmed. After most of 24 kDa oleosin was hydrolyzed, some P32 existed as dimer, and the other as P32-17 kDa HP. It was suggested that P32 was the protease.

关键词： oil bodies oleosins thiol protease P34 probable thiol protease Gly m Bd 30K

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A Small Calcium Beam Optical Frequency Standard with Fully-sealed Vacuum Tube

A Small Calcium Beam Optical Frequency Standard with Fully-s...

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Joint Conference of the European-Frequency-and-Time-Forum / IEEE International Frequency Control Symposium (EFTF/IFCS)

作者： Shang, Haosen Zhang, Xiaogang Zhang, Shengnan Chen, Jingbiao Chen, Haijun Peking Univ Sch Elect Engn & Comp Sci State Key Lab Adv Opt Commun Syst & Network Beijing 100871 Peoples R China Beijing Vacuum Elect Res Inst Natl Key Lab Sci & Technol Vacuum Elect Beijing 100015 Peoples R China

ISBN: (纸本)9781538629161

In this paper a small Calcium beam optical frequency standard utilizing fully-sealed Calcium beam vacuum tube owning smaller size compared with vacuum system with flanges is demonstrated. Adopting the electron shelving detection method, we detect the clock transition 657 nm saturation absorbing spectroscopy whose linewidth is 500 kHz. The instability of this small optical frequency standard is 6.8 x 10(-14) at 1 second and 1.8 x 10(-15) after 1000 seconds of averaging by comparing with another small Calcium beam optical frequency standard whose reported instability is 3.0 x 10(-14) at 1 second. The optical part of the whole system is specially designed for robustness and miniaturization.

关键词： small Calcium beam optical frequency standard fully-sealed Calcium beam vacuum tube electron-shelving detection method

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Airborne Near Infrared Three-Dimensional Ghost Imaging LiDAR via Sparsity Constraint

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REMotE SENSING 2018年第5期10卷

作者： Wang, Chenglong Mei, Xiaodong Pan, Long Wang, Pengwei Li, Wang Gao, Xin Bo, Zunwang Chen, Mingliang Gong, Wenlin Han, Shensheng Chinese Acad Sci Key Lab Quantum Opt Shanghai 201800 Peoples R China Chinese Acad Sci Shanghai Inst Opt & Fine Mech Ctr Cold Atom Phys Shanghai 201800 Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China

Three-dimensional ghost imaging LiDAR via sparsity constraint (3D GISC LiDAR), as a staring imaging method, can obtain both the range information and spatial distribution of a remote target with a single-pixel time-resolved detector. However, previous demonstrations mainly focused on the relatively static scene in visible light. Here we propose an airborne near infrared 3D GISC LiDAR system and airborne high-resolution imaging is implemented. Experimental results show that an image with 0.48 m horizontal resolution as well as 0.5 m range resolution at approximately 1.04 km height can be achieved. Some considerations on the improvement of this LiDAR system are also discussed.

关键词： ghost imaging LiDAR imaging system speckle

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