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

[i] An inventory of air pollutant emissions in Asia in the year 2000 is developed to support atmospheric modeling and analysis of observations taken during the TRACE-P experiment funded by the National Aeronautics and Space Administration (NASA) and the ACE-Asia experiment funded by the National Science Foundation (NSF) and the National Oceanic and Atmospheric Administration (NOAA). Emissions are estimated for all major anthropogenic sources, including biomass burning, in 64 regions of Asia. We estimate total Asian emissions as follows: 34.3 Tg SO 2 , 26.8 Tg NO x , 9870 Tg CO 2 , 279 Tg CO, 107 Tg CH 4 , 52.2 Tg NMVOC, 2.54 Tg black carbon (BC), 10.4 Tg organic carbon (OC), and 27.5 Tg NH 3 . In addition, NMVOC are speciated into 19 subcategories according to functional groups and reactivity. Thus we are able to identify the major source regions and types for many of the significant gaseous and particle emissions that influence pollutant concentrations in the vicinity of the TRACE-P and ACE-Asia field measurements. Emissions in China dominate the signature of pollutant concentrations in this region, so special emphasis has been placed on the development of emission estimates for China. China's emissions are determined to be as follows: 20.4 Tg SO 2 , 11.4 Tg NO x , 3820 Tg CO 2 , 116 Tg CO, 38.4 Tg CH 4 , 17.4 Tg NMVOC, 1.05 Tg BC, 3.4 Tg OC, and 13.6 Tg NH 3 . Emissions are gridded at a variety of spatial resolutions from 1° × 1° to 30 s x 30 s, using the exact locations of large point sources and surrogate GIS distributions of urban and rural population, road networks, landcover, ship lanes, etc. The gridded emission estimates have been used as inputs to atmospheric simulation models and have proven to be generally robust in comparison with field observations, though there is reason to think that emissions of CO and possibly BC may be underestimated. Monthly emission estimates for China are developed for each species to aid TRACE-P and ACE-Asia data interpretation. During the observation period of March/ April, emissions are roughly at their average values (one twelfth of annual). Uncertainties in the emission estimates, measured as 95% confidence intervals, range from a low of ±16% for SO 2 to a high of ±450% for OC.

An inventory of gaseous and primary aerosol emissions in Asia in the year 2000 : NASA global tropospheric experiment transport and chemical evolution over the pacific (TRACE-P): Measurements and analysis (TRACEP1)

Adsorption of dyes and heavy metal ions by chitosan composites: A review

http://sealight.persiangig.com/document/1.pdf

Use of iron oxide nanomaterials in wastewater treatment: a review.

A review on the adsorption of heavy metals by clay minerals, with special focus on the past decade

Transition metal-substituted magnetite minerals have attracted increasing attention for their wide application in industry and environmental protection. In this study, the valence and atomic environment of some substituting metals in magnetites (Fe3−x
 M
 x
 O4, M = V, Co, and Ni) were investigated using X-ray absorption fine structure spectroscopy. The results deduced from X-ray absorption near-edge structure spectroscopy indicated that the valences of V, Co, and Ni in Fe3−x
 M
 x
 O4 were +3, +2, and +2, respectively. The valences did not change as the substitution extent increased. Extended X-ray absorption fine structure spectroscopy suggested that the substituting cations occupied octahedral sites in the magnetite structure. The M–O and M–M/Fe distances were consistent with the Feoct–O and Feoct–Fe distances, respectively, in the magnetite (Fe3O4) structure. The occupancy of the substituting cations was assessed by crystal-field theory. We also considered the relationship between the chemical environment of substituting cations and their effects on the physicochemical properties of magnetite, including thermal stability, surface properties, and catalytic reactivity.

The oxidation state and microstructural environment of transition metals (V, Co, and Ni) in magnetite: an XAFS study

The enrichment of mercury in sphalerite plays an important role in the migration and accumulation of Hg in the earth system. Despite Fe being the most common foreign ion in natural sphalerite, the ...

Sequestration of Gaseous Hg0 by Sphalerite with Fe Substitution: Performance, Mechanism, and Structure–Activity Relationship

Two-line ferrihydrite (Fh) is an omnipresent iron oxyhydroxide nanomineral with high surface reactivity and weak crystallinity, and its phase transformation in nature has drawn significant concerns...

Effects of Fullerol and Graphene Oxide on the Phase Transformation of Two-Line Ferrihydrite

This chapter defines ‘organoclays’ (OC) and discusses their structure as well as the molecular environment of the loaded, or intercalated, organic modifiers. Major accomplishments in OC research over the last decades are presented, including where vibrational spectroscopy has been applied. This chapter also describes the factors used to control OC basal spacing and the molecular environment of the intercalated quaternary ammonium cation within interlayer space mainly based on X-ray diffraction (XRD) patterns and Fourier transform infrared (FTIR) spectra. These factors include alkyl chain length and number, packing density, temperature and water molecules. The FTIR spectral features of OC are introduced with assignments relating to the adsorbed organic modifiers and contaminants. The last section focuses on an outlook of the synthesis and characterization of OC.

Jianxi Zhu

Papers

The oxidation state and microstructural environment of transition metals (V, Co, and Ni) in magnetite: an XAFS study

Sequestration of Gaseous Hg0 by Sphalerite with Fe Substitution: Performance, Mechanism, and Structure–Activity Relationship

Effects of Fullerol and Graphene Oxide on the Phase Transformation of Two-Line Ferrihydrite

Analysis of Organoclays and Organic Adsorption by Clay Minerals

Calcined Mg/Al layered double hydroxides as efficient adsorbents for polyhydroxy fullerenes