Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

▪ Abstract Plant responses to salinity stress are reviewed with emphasis on molecular mechanisms of signal transduction and on the physiological consequences of altered gene expression that affect biochemical reactions downstream of stress sensing. We make extensive use of comparisons with model organisms, halophytic plants, and yeast, which provide a paradigm for many responses to salinity exhibited by stress-sensitive plants. Among biochemical responses, we emphasize osmolyte biosynthesis and function, water flux control, and membrane transport of ions for maintenance and re-establishment of homeostasis. The advances in understanding the effectiveness of stress responses, and distinctions between pathology and adaptive advantage, are increasingly based on transgenic plant and mutant analyses, in particular the analysis of Arabidopsis mutants defective in elements of stress signal transduction pathways. We summarize evidence for plant stress signaling systems, some of which have components analogous to t...

Plant cellular and molecular responses to high salinity.

A fast-Fourier-transform method of topography and interferometry is proposed. By computer processing of a noncontour type of fringe pattern, automatic discrimination is achieved between elevation and depression of the object or wave-front form, which has not been possible by the fringe-contour-generation techniques. The method has advantages over moire topography and conventional fringe-contour interferometry in both accuracy and sensitivity. Unlike fringe-scanning techniques, the method is easy to apply because it uses no moving components.

Fourier-transform method of fringe-pattern analysis for computer-based topography and interferometry

Abiotic Stress Signaling and Responses in Plants

Nonpathogenic rhizobacteria can induce a systemic resistance in plants that is phenotypically similar to pathogen-induced systemic acquired resistance (SAR). Rhizobacteria-mediated induced systemic resistance (ISR) has been demonstrated against fungi, bacteria, and viruses in Arabidopsis, bean, carnation, cucumber, radish, tobacco, and tomato under conditions in which the inducing bacteria and the challenging pathogen remained spatially separated. Bacterial strains differ in their ability to induce resistance in different plant species, and plants show variation in the expression of ISR upon induction by specific bacterial strains. Bacterial determinants of ISR include lipopolysaccharides, siderophores, and salicylic acid (SA). Whereas some of the rhizobacteria induce resistance through the SA-dependent SAR pathway, others do not and require jasmonic acid and ethylene perception by the plant for ISR to develop. No consistent host plant alterations are associated with the induced state, but upon challenge inoculation, resistance responses are accelerated and enhanced. ISR is effective under field conditions and offers a natural mechanism for biological control of plant disease.

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Systemic resistance induced by rhizosphere bacteria

This paper describes a novel synchronous control system of high speed imaging, which combines a common path
interferometer system modulated by the space phase. The system can continuously grab multiple frame interferograms,
which contain transient flow field distortion. The study of this system will provide a fire-new means for the research of
aerodynamics. The light source of the system is Nd: YLF semiconductor pump solid pulsed laser of which wavelength is
1053 nanometers. The laser pulse width is less than 30 nanoseconds, far less than the exposure time of the camera
shutter. Thus the laser pulse can freeze the flow field within several dozen nanoseconds and catch the biggish change of
turbulent flow. The pulsed laser beam containing the information of turbulent flow enters a cyclical radial shearing
interferometer. The emergent lights, being respectively contracted and expanded, re-combine and form fringe pattern in
high space frequency, modulated with a definite carrier frequency. The fringe pattern is formed on the high speed CMOS
camera at last. An accurate short time delay circuit is provided for synchronization matching of the pulsed laser and
camera exposure. The speed of image acquisition in full pixels with 1280×1024 can reach 450 frames per second. This
interferogram acquisition system with compact configuration and strong anti-disturbance capability, has successfully
grabbed clear transient interferograms that provided reliable image information for follow-up image processing and flow
field density calculating.

Research of transient flow field real time interferogram acquisition system

Based on microscopic imaging and sub-aperture stitching technology, Surface defect detection system realizes the automatic quantitative detection of submicron defects on the macroscopic surface of optical components, and solves quality control problems of numerous large- aperture precision optical components in ICF (Inertial Confinement Fusion) system. In order to improve the testing efficiency and reduce the number of sub-aperture images, the large format CCD (charged-coupled device) camera is employed to expand the field of view of the system. Large format CCD cameras are usually mosaicked by multi-channel CCD chips, but the differences among the intensity-grayscale functions of different channels will lead to the obvious gray gap among different regions of image. It may cause the shortening and fracture of defects in the process of the image binarization , and thereby lead to the misjudgment of defects. This paper analyzes the different gray characteristics in unbalance images, establishes gray matrix mode of image pixels, and finally proposes a new method to correct the gray gap of CCD self-adaptively. Firstly, by solving the inflection point of the pixel level curve in the gray histogram of the original image, the background threshold is set, and then the background of the image is obtained; Secondly, pixels are sampled from the background and calculated to get the gray gap among different regions of the image; Ultimately, the gray gap is compensated. With this method, an experiment is carried out to adjust 96 dual-channel images from testing a fused silica sample with aperture 180mm×120mm. The results show that the gray gap of the images on different channel is reduced from 3.64 to 0.70 grayscale on average. This method can be also applied to other CCD mosaic camera.

Grayscale adjustment method for CCD mosaic camera in surface defect detection system

Effects of combustion chamber diameter on the performance and fuel–air mixing of a double swirl combustion system in a diesel engine

Aspheric design and fabrication have obtained great achievements with the fast developments of modern science and technology, especially computer science, while the test of aspherics has become a chief limitation of aspheric applications. Due to the arbitrary nature of aspherics, test of all aspherics with only one instrument seems impossible. This paper presents a non-null interferometric system that can be applied for general aspheric test. The systematic error of non-null aspheric test system is studied, according to which an error separating and correcting method is proposed then. Computer simulation shows the error correcting method can correct the systematic error of non-null aspheric test system effectively and efficiently. Experiments have been carried out with the proposed interferometric non-null aspheric test system and the results show the system can greatly increase the accuracy of the non-null aspheric test.

Non-null interferometric system for general aspheric test

The laser source with high peak power and high beam quality has important application in laser processing and other fields. A fiber laser with repetition of 50 kHz, pulse width of 3.9 ps, and average power of 10.9 mW is used as the seed source. After double-passing two-stage amplifiers, the average output power of 27.65 W with a peak power of 65 MW is obtained. The first stage is an end pumped Nd:YVO4 amplifier, and the second stage is a side pumped Nd:YAG amplifier. The beam quality is well preserved with M2 factor of 1.3 based on the method of spherical-aberration compensation and the optimizing of the beam filling factor.

Dong Liu

Papers

Research of transient flow field real time interferogram acquisition system

Grayscale adjustment method for CCD mosaic camera in surface defect detection system

Effects of combustion chamber diameter on the performance and fuel–air mixing of a double swirl combustion system in a diesel engine

Non-null interferometric system for general aspheric test

Fiber-solid hybrid amplification laser system with high peak power and high beam quality