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

In the field of automatic optical inspection, it is imperative to measure the defects on spherical optical surfaces. So a novel spherical surface defect evaluation system is established in this paper to evaluate defects on optical spheres. In order to ensure the microscopic scattering dark-field imaging of optical spheres with different surface shape and radius of curvature, illumination with variable aperture angle is employed. In addition, the scanning path of subapertures along the parallels and meridians is planned to detect the large optical spheres. Since analysis shows that the spherical defect information could be lost in the optical imaging, the three-dimensional correction based on a pin-hole model is proposed to recover the actual spherical defects from the captured two-dimensional images. Given the difficulty of subaperture stitching and defect feature extraction in three-dimensional (3D) space after the correction, the 3D subapertures are transformed into a plane to be spliced through geometric projection. Then, methods of the surface integral and calibration are applied to quantitatively evaluate the spherical defects. Furthermore, the 3D panorama of defect distribution on the spherical optical components can be displayed through the inverse projective reconstruction. Finally, the evaluation results are compared with the OLYMPUS microscope, testifying to the micrometer resolution, and the detection error is less than 5%.

Defects evaluation system for spherical optical surfaces based on microscopic scattering dark-field imaging method.

As byproducts of the combustion process of hydrocarbon fuels, soot particles are difficult to remove, and they can greatly harm human health and pollute the environment. Therefore, the formation and growth processes of the soot particles has become a study focus of researchers. In this paper, the nanostructure and oxidation reactivity of carbonaceous particles collected from ethylene inverse diffusion flames with or without the additions of three pentanol isomers (1-pentanol, 3-methyl-1-butanol, and 2-methyl-1-butanol) were investigated in detail. The nanostructure and oxidation characteristics of nascent soot particles were characterized using high resolution transmission electron microscopy (HRTEM), X-ray diffractometry (XRD) and thermogravimetric analysis (TGA). It was found that the nascent soot cluster of pure ethylene flame had a loose structure, while the additions of pentanol isomers made the soot agglomerates more compact and delayed the growth of graphitic structures. The pentanol isomer additions also contributed to a higher disorder of the crystallite arrangement in the soot nanostructure. According to the TGA experiments, the results showed that the addition of pentanol isomers enhanced the oxidation reactivity of soot particles, which could help to reduce soot particle emissions.

https://www.mdpi.com/1996-1073/10/1/122/pdf

Nanostructure and Oxidation Reactivity of Nascent Soot Particles in Ethylene/Pentanol Flames

Plant architecture is an important agronomic trait and is useful for identification of plant species. The molecular basis of plant architecture, however, is largely unknown. Forward genetics was used to identify an Arabidopsis mutant with altered plant architecture. Using genetic and molecular approaches, we analyzed the roles of a mutated cyclophilin in the control of plant architecture. The Arabidopsis mutant roc1 has reduced stem elongation and increased shoot branching, and the mutant phenotypes are strongly affected by temperature and photoperiod. Map-based cloning and transgenic experiments demonstrated that the roc1 mutant phenotypes are caused by a gain-of-function mutation in a cyclophilin gene, ROC1. Besides, application of the plant hormone gibberellic acid (GA) further suppresses stem elongation in the mutant. GA treatment enhances the accumulation of mutated but not of wildtype (WT) ROC1 proteins. The roc1 mutation does not seem to interfere with GA biosynthesis or signaling. GA signaling, however, antagonizes the effect of the roc1 mutation on stem elongation. The altered plant architecture may result from the activation of an R gene by the roc1 protein. We also present a working model for the interaction between the roc1 mutation and GA signaling in regulating stem elongation.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.12056

A gain-of-function mutation in the ROC1 gene alters plant architecture in Arabidopsis

The achievement of perfect light absorption in ultrathin semiconductor materials is not only a long-standing goal, but also a critical challenge for solar energy applications, and thus requires a redesigned strategy. Here, a general strategy is demonstrated both theoretically and experimentally to create a planar metasurface absorber comprising a 1D ultrathin planar semiconductor film (replacing the 2D array of subwavelength elements in classical metasurfaces), a transparent spacer, and a metallic back reflector. Guided by derived formulisms, a new type of macroscopic planar metasurface absorber is experimentally demonstrated with light near-perfectly and exclusively absorbed by the ultrathin semiconductor film. To demonstrate the power and simplicity of this strategy, a prototype of a planar metasurface solar cell is experimentally demonstrated. Furthermore, the device model predicts that a colored planar metasurface perovskite solar cell can maintain 75% of the efficiency of its black counterpart despite the use of a perovskite film that is one order of magnitude thinner. The displayed cell colors have high purities comparable to those of state-of-the-art color filters, and are insensitive to viewing angles up to 60°. The general theoretical framework in conjunction with experimental demonstrations lays the foundation for designing miniaturized, planar, and multifunctional solar cells and optoelectronic devices.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/advs.201800836

Planar Metasurfaces Enable High-Efficiency Colored Perovskite Solar Cells.

The gene encoding osmotin, a tobacco pathogenesis-related protein, has been shown to be regulated by an array of hormonal and environmental signals. The osmotin promoter fragment −248 to −108 upstream of the transcription start site (fragment A), was sufficient to direct reporter gene expression when fused to a minimal CaMV 35S promoter in transient assays using microprojectile bombardment. This was consistent with previous 5′-deletion analyses of the osmotin promoter which showed that the promoter sequence from −248 to −108 is absolutely required for reporter gene activity. Nuclear protein factors from salt-adapted tobacco cells, ABA-treated unadapted cells, and young cultured tobacco leaves were shown to interact with fragment A by gel mobility-shift assays. DNase I footprinting revealed that three conserved promoter elements in fragment A interact specifically with nuclear factors. These elements are: (1) a cluster of G-box-like sequences (G sequence); (2) an AT-1 box-like sequence, 5′-AATTATTT-TATG-3′ (AT sequence); (3) a sequence highly conserved in ethylene-induced PR gene promoters, 5′-TAAGA/CGCCGCC-3′ (PR sequence). Transient expression assays performed with fragment A deletions fused to GUS indicated that osmotin promoter activity correlated with the presence of these elements. UV cross-linking analysis showed that the protein complex bound to fragment A consisted of at least four individual proteins with approximate molecular masses of 28, 29, 40 and 42 kDa. One component of this protein complex, which was associated with the G sequence, was a 14-3-3 like protein.

Dong Liu

Papers

Defects evaluation system for spherical optical surfaces based on microscopic scattering dark-field imaging method.

Nanostructure and Oxidation Reactivity of Nascent Soot Particles in Ethylene/Pentanol Flames

A gain-of-function mutation in the ROC1 gene alters plant architecture in Arabidopsis

Planar Metasurfaces Enable High-Efficiency Colored Perovskite Solar Cells.

Fine structure and function of the osmotin gene promoter