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.

/pdf/systemic-resistance-induced-by-rhizosphere-bacteria-13ehvnz7fj.pdf

Systemic resistance induced by rhizosphere bacteria


 Heat transfer to supercritical H2O/CO2 mixtures (24 MPa, 310 to 430 °C, and CO2 mass fractions up to 18.5%), the working fluids of a novel power generation system with coal gasified in supercritical water, was experimentally investigated for typical working conditions of this system. For these conditions, i.e., high mass velocities (above 1200 kg m−2 s−1) and low heat flux (below 300 kW m−2), the convection heat transfer coefficients (HTCs) of supercritical pure fluids usually increase with temperature, peak near the pseudo-critical point, i.e., heat transfer enhancement, and then decrease for higher temperatures. Here, we experimentally demonstrated a new heat transfer enhancement phenomenon for supercritical H2O/CO2 mixtures. A high-temperature and high-pressure apparatus was setup to measure the convection HTCs of the supercritical H2O/CO2 mixtures. Experimental results show that surprisingly two distinct peaks of convection HTCs appear, with one corresponding temperature being the pseudo-critical point of the H2O/CO2 mixture, i.e., the thermophysical property variation induced mechanism, and the other one being the critical miscible point of the mixture, i.e., the dissolution-induced mechanism. These results pave the way to efficient heat transfer devices that use supercritical mixtures as heat transfer fluids.

Anomalous Enhancement of Heat Transfer to H2O/CO2 Mixtures in Near-Critical Region

. A method is assessed which expands aerosol vertical
profiles inferred from nadir-pointing lidars to cross-track locations next
to nadir columns. This is achieved via matching of passive radiances at
off-nadir locations with their counterparts that are collocated with lidar
data. This spectral radiance matching (SRM) method is tested using profiles
inferred from Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) lidar observations and collocated Moderate Resolution Imaging
Spectroradiometer (MODIS) passive
imagery for the periods 10–25 April and 14–29 September 2015. CALIPSO
profiles are expanded out to 100 km on both sides of the daytime
ground track. Reliability of constructed profiles that are removed from the
ground track by number of kilometers are tested by requiring the algorithm to reconstruct
profiles using only profiles that are removed from it along track by more
than the number of kilometers. When sufficient numbers of pixels and columns are available, the SRM
method can correctly match ∼75  % and ∼68  %
of aerosol vertical structure at distances of 30 and 100 km from the
ground track, respectively. The construction algorithm is applied to the
eastern coast of Asia during spring 2015. Vertical distributions of different
aerosol subtypes indicate that the region was dominated by dust and polluted
dust transported from the continent. It is shown that atmospheric profiles
and aerosol optical depth (AOD) inferred from ground-based measurements
agree with those constructed by the SRM method. For profiles, the relative
errors between those measured by ground-based lidar and those constructed in
the surrounding area are similar to the relative errors between the ground-based
station and CALIPSO overpass at the closest distance. For AOD, the measurements
from the ground-based network agree with those inferred from constructed aerosol
structure better than direct observations from CALIPSO and close to those
inferred from MODIS radiances.

/pdf/analysis-of-global-three-dimensional-aerosol-structure-with-25kkp07rmd.pdf

Analysis of Global Three-Dimensional Aerosol Structure with Spectral Radiance Matching

The radial shearing interferometer that is immune to vibration and the spatial phase modulation technique that can retrieve the phase from a single interferogram can be used for precise measurement of aspheric surfaces. However, as a carrier is needed to be introduced in the system to keep the fringes open, the spatial phase modulation technique generally leads to a great increase in the density of the fringes. A novel method that uses just one frame of the interferogram and need not introduce any spatial carrier in the interferometer is proposed in the paper. To demodulate the closed interferograms generated in the system, a regularized phase-tracking technique that can be used for a single open or closed fringe pattern is employed to recover the phase map. Actually the presented method can also be applied in many other cases, for example flow visualization. Both computer simulation and experimental result have demonstrated the validity and efficiency of the proposed method.

Study on phase retrieval of a single closed fringe interferogram in radial shearing interferometer for aspheric test

A non-null annular subaperture stitching interferometry (NASSI), combining the subaperture stitching idea and non-null test method, is proposed for steep aspheric testing. Compared with standard annular subaperture stitching interferometry (ASSI), a partial null lens (PNL) is employed as an alternative to the transmission sphere, to generate different aspherical wavefronts as the references. The coverage subaperture number would thus be reduced greatly for the better performance of aspherical wavefronts in matching the local slope of aspheric surfaces. Instead of various mathematical stitching algorithms, a simultaneous reverse optimizing reconstruction (SROR) method based on system modeling and ray tracing is proposed for full aperture figure error reconstruction. All the subaperture measurements are simulated simultaneously with a multi-configuration model in a ray-tracing program, including the interferometric system modeling and subaperture misalignments modeling. With the multi-configuration model, full aperture figure error would be extracted in form of Zernike polynomials from subapertures wavefront data by the SROR method. This method concurrently accomplishes subaperture retrace error and misalignment correction, requiring neither complex mathematical algorithms nor subaperture overlaps. A numerical simulation exhibits the comparison of the performance of the NASSI and standard ASSI, which demonstrates the high accuracy of the NASSI in testing steep aspheric. Experimental results of NASSI are shown to be in good agreement with that of Zygo® Verifire TM Asphere interferometer.

Non-null annular subaperture stitching interferometry for aspheric test

Carrying out in-depth research on the formation characteristics and mechanisms of organic products in coal combustion will help to provide theoretical guidance for the emission reduction of coal-fired pollutants. Since the combustion of coal volatiles plays a vital role in the whole process of coal combustion, this work took coal pyrolysis gases as fuels and focused on the organic pollutants such as alkanes, olefins and aromatics in the combustion of coal pyrolysis gases. To explore the effects of three pyrolysis temperatures of 600 °C, 750 °C and 900 °C on the formation characteristics and mechanisms of hydrocarbon products during coal pyrolysis gases combustion, the online detection was carried out by gas chromatography (GC) and gas chromatography-mass spectrometer (GC-MS) on the counterflow diffusion flame platform, combined with chemical reaction kinetics simulations. The results showed that rising pyrolysis temperature had an inhibitory effect on the formation of light hydrocarbons and aromatic hydrocarbons, such as acetylene (C2H2), propyne (PC3H4), 1,3-butadiene (C4H6-13), vinylacetylene (C4H4), diacetylene (C4H2), benzene (C6H6), toluene (C6H5CH3) and naphthalene (C10H8), during the combustion of pyrolysis gases. Among three mechanisms used in this study, Creck mechanism was more accurate and applicable than KM2 mechanism and AramcoMech 3.0 mechanism. As the pyrolysis temperature rose, the rate of the reactions which dominated the formation of C2H2, propargyl (C3H3), C6H6 and C10H8 decreased continuously, because the decrease of CH3 concentration and the increase of H concentration inhibited the forward progress of these reactions. In addition, with rising pyrolysis temperature, less C3H3 was converted to butadiene (C4H6), C6H6 and Fulvene, and more inclined to its upstream reactants, allene (AC3H4) and PC3H4. The tendency of phenyl (C6H5) to form C6H6 was strengthened. Meanwhile, less C10H8 was generated from C4H4 and C6H5, but the dominant role of this reaction was still enhanced. 

Dong Liu

Papers

Anomalous Enhancement of Heat Transfer to H2O/CO2 Mixtures in Near-Critical Region

Analysis of Global Three-Dimensional Aerosol Structure with Spectral Radiance Matching

Study on phase retrieval of a single closed fringe interferogram in radial shearing interferometer for aspheric test

Non-null annular subaperture stitching interferometry for aspheric test

Assessment on combustion chemistry of coal volatiles for various pyrolysis temperatures