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

Analysis and optimizationof the thermal performance ofmicrochannel heat sinks

The utility model discloses an infrared radiant energy signal based power plant boiler combustion optimized device, comprising two parts of hardware and software, wherein the hardware includes three parts: the first part includes near infrared radiant energy sensors arranged on four corners of the boiler, the near infrared radiant energy is transmitted to a photoelectric transformation element by an optical fiber, the photoelectric transformation element is connected with a lower computer data collection and transmission control module; the second part includes the lower computer data collection and transmission control module arranged on the boiler body; the third part includes an upper computer data analysis and control signal output module arranged inside an electric room; the software system is developed by the Labview programming software. The intensity information of the radiant energy in the boiler is detected by the near infrared radiant energy sensors, and the radiant energy deviation value is worked out by the artificial neural network optimization method, and then the deviation value is inputted in a DCS boiler fuel control module after the filtering treatment, thereby enhancing the coal feeding control logic, improving the load response speed of the machine set and guaranteeing the running stability of a turbine.

Infrared radiation signal based station boiler combustion optimizer

To overcome the retrieval problems in complex water, dual working wavelengths are required instead of a single wavelength in oceanic lidar. The wavelength optimization method of detecting chlorophyll a and Colored Dissolved Organic Matter (CDOM) absorption coefficient with a dual-wavelength lidar is studied in this paper. The inversion methods of chlorophyll a and CDOM absorption are developed based on the water absorption characteristics, which then lead to the inversion error equations. The effects of the wavelength on the inversion errors are studied. For the case in which λ1 and λ2 are both random, the errors are relatively small when λ1 is chosen between 420 and 560 nm and λ2 is selected under 420 nm. For the case in which λ1 is fixed at 532 nm, the errors generally decrease with decreasing λ2, with minimums around 300 and 356–360 nm under different water conditions. The wavelength optimization method discussed in this paper and the penetration depth criterion will be beneficial to the design of the dual-wavelength lidar.

Detection of Chlorophyll a and CDOM Absorption Coefficient with a Dual-Wavelength Oceanic Lidar: Wavelength Optimization Method

The distribution and transport of suspended sediment in the coastal areas has attracted more and more attention. Monitoring and modeling of the distribution and transport of suspended sediment is significant. The mutual promotion of remote sensing and numerical simulation plays an important role on the coastal water quality study. In this study, a method of coupling derived suspended sediment concentration (SSC) images with numerical model, based on GOCI and COHERENS (COupled Hydrodynamical-Ecological model for REgioNal and Shelf seas) model, is proposed to monitor the suspended sediment dynamics in the East China Sea. The retrieved SSC were extracted from GOCI images, to set as initial condition and employed to calibrate the parameters and validation for the hydrodynamic modeling and sediment transport modeling, respectively. The model is forced by considering tidal surface elevation at open sea boundary, river discharges, surface stress as a function of wind speed, air temperature, relative humidity and cloud coverage, bottom roughness and heat flux through sea surface. The model results are in accord with the in situ measurements. The results show that: (1) Numerical model which initialized with satellite-derived SSC data can quickly response to the changes of sediment concentration in real sense. (2) Remote sensing is helpful to calibrate and validate the model for simulating the suspended sediment concentration distribution. (3)The proposed approach can obtain reasonable simulated results in the East China Sea. (4) It is of great significance to combine remote sensing and numerical simulation together to study the water quality in the coastal areas.

Numerical simulation of suspended sediment transport merging with satellite derived data in coastal waters

Micropumps that can be directly integrated into microelectronic devices or microchannel heat sinks are of great interest due to performance, reliability, packaging and cost issues. One alternative is to generate the required flow directly in the microfluidic channels by inducing strong electromechanical forces in the fluid using integrated microelectrodes. In this work, a novel microfluidic pumping approach using traveling-wave dielectrophoresis (twDEP) of microparticles is presented. The dielectrophoretic motion of small particles arises when the suspended particles in a fluid medium are exposed to non-uniform electric fields causing interaction between the induced dipole on the particles and the fields. As the particles move, the surrounding fluid is dragged in the same direction due to viscous effects. The fluidic driving mechanisms due to the particle-fluid and particle-particle hydrodynamic interactions under twDEP are analyzed, and quantitative information on the induced flow field is obtained from numerical simulations. Experimental measurements of the flow velocity in a prototype DEP micropumping device using micro-particle image velocimetry show satisfactory agreement with the numerical predications. Results from this work indicate that the DEP-induced micropumping scheme holds promise for devising chip-integrated micropumping systems for thermal management.

http://www2.egr.uh.edu/~dli9/Publications/ITHERM%20DEP.pdf

Dong Liu

Papers

Analysis and optimizationof the thermal performance ofmicrochannel heat sinks

Infrared radiation signal based station boiler combustion optimizer

Detection of Chlorophyll a and CDOM Absorption Coefficient with a Dual-Wavelength Oceanic Lidar: Wavelength Optimization Method

Numerical simulation of suspended sediment transport merging with satellite derived data in coastal waters

Microfluidic pumping based on dielectrophoresis for thermal management of microelectronics