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

The slope of the simple linear regression between log10 transformed mercury (Hg) concentration and stable nitrogen isotope values (δ15N), hereafter called trophic magnification slope (TMS), from several trophic levels in a food web can represent the overall degree of Hg biomagnification. We compiled data from 69 studies that determined total Hg (THg) or methyl Hg (MeHg) TMS values in 205 aquatic food webs worldwide. Hg TMS values were compared against physicochemical and biological factors hypothesized to affect Hg biomagnification in aquatic systems. Food webs ranged across 1.7 ± 0.7 (mean ± SD) and 1.8 ± 0.8 trophic levels (calculated using δ15N from baseline to top predator) for THg and MeHg, respectively. The average trophic level (based on δ15N) of the upper-trophic-level organisms in the food web was 3.7 ± 0.8 and 3.8 ± 0.8 for THg and MeHg food webs, respectively. For MeHg, the mean TMS value was 0.24 ± 0.08 but varied from 0.08 to 0.53 and was, on average, 1.5 times higher than that for THg with a...

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Biomagnification of Mercury in Aquatic Food Webs: A Worldwide Meta-Analysis

Salinization, a widespread threat to the structure and ecological functioning of inland and coastal wetlands, is currently occurring at an unprecedented rate and geographic scale. The causes of salinization are diverse and include alterations to freshwater flows, land-clearance, irrigation, disposal of wastewater effluent, sea level rise, storm surges, and applications of de-icing salts. Climate change and anthropogenic modifications to the hydrologic cycle are expected to further increase the extent and severity of wetland salinization. Salinization alters the fundamental physicochemical nature of the soil-water environment, increasing ionic concentrations and altering chemical equilibria and mineral solubility. Increased concentrations of solutes, especially sulfate, alter the biogeochemical cycling of major elements including carbon, nitrogen, phosphorus, sulfur, iron, and silica. The effects of salinization on wetland biogeochemistry typically include decreased inorganic nitrogen removal (with implica...

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A global perspective on wetland salinization: ecological consequences of a growing threat to freshwater wetlands

A review on chitosan-based flocculants and their applications in water treatment

Total concentrations and sources of heavy metal pollution in global river and lake water bodies from 1972 to 2017

Analyzing trophic transfer of heavy metals for food webs in the newly-formed wetlands of the Yellow River Delta, China.

Sediments were collected from the upper, middle and lower reaches of both urban and rural rivers in a typical urbanization zone of the Pearl River delta. Six heavy metals (Cd, Cr, Cu, Ni, Pb and Zn) were analyzed in all sediment samples, and their spatial distribution, pollution levels, toxicity and ecological risk levels were evaluated to compare the characteristics of heavy metal pollution between the two rivers. Our results indicated that the total contents of the six metals in all samples exceeded the soil background value in Guangdong province. Based on the soil quality thresholds of the China SEPA, Cd levels at all sites exceeded class III criteria, and other metals exhibited pollution levels exceeding class II or III criteria at both river sites. According to the sediment quality guidelines of the US EPA, all samples were moderately to heavily polluted by Cr, Cu, Ni, Pb and Zn. Compared to rural river sites, urban river sites exhibited heavier pollution. Almost all sediment samples from both rivers exhibited moderate to serious toxicity to the environment, with higher contributions from Cr and Ni. A "hot area" of heavy metal pollution being observed in the upper and middle reaches of the urban river area, whereas a "hot spot" was identified at a specific site in the middle reach of the rural river. Contrary metal distribution patterns were also observed along typical sediment profiles from urban and rural rivers. However, the potential ecological risk indices of rural river sediments in this study were equal to those of urban river sediments, implying that the ecological health issues of the rivers in the undeveloped rural area should also be addressed. Sediment organic matter and grain size might be important factors influencing the distribution profiles of these heavy metals.

Distribution and pollution, toxicity and risk assessment of heavy metals in sediments from urban and rural rivers of the Pearl River delta in southern China

The Pearl River Delta (PRD) region is one of the most industrialized areas in China, and the river water is increasingly deteriorated due to anthropogenic pollution from the rapid economic development. Principal component analysis (PCA) and cluster analysis (CA) were used to identify characteristics of water quality and to assess water quality spatial pattern in this region. The results of PCA for three regions showed that the first four components of PCA analysis showed 85.52% and 89.25% of the total variance in the data sets of North River region and West River region, respectively, the first three components showed 84.63% of variance for data set of East River region. Results of CA based on the station score of PCA were that stations of North River region, East River region and West River region were grouped into four, three and four clusters, respectively corresponding to severe pollution, moderate pollution, light pollution (except for East River region) and good water quality, which indicated the similarity and dissimilarity of the river water quality. Since, the results suggest that PCA and CA techniques are useful tools for assessment of water quality and management of water resources.

Assessment of river water quality in Pearl River Delta using multivariate statistical techniques

Samples collected from sites of 26 for water, soils and two native plants (Scirpus tripueter Linn. and Cyperus malaccensis Lam.) in riparian wetlands were analyzed to investigate the distribution of heavy metals (Cd, Cr, Cu, Ni, Pb and Zn) in Panyu-Nansha area of Pearl River estuary. The results indicated that concentrations of heavy metals among three compartments were in the order: soils > plants > water and no obvious correlations were found between in soils and water, water and plants. Pb is the only metal accumulated in both plants that correlated with its concentrations in soils. The weak or lack correlations among metals in water, soils and plants suggest that other factors existed influence the metal uptake and storage in plants other than absorbing from soils and water. The plants had the same trend in metal accumulation that was Cd > Zn > Cu > Ni > Cr > Pb. The translocation factors showed that metals accumulation was mostly occurred in roots for these two plants. Compared to the other heavy metals, Cd seemed to be much more hazardous. Principal Component analysis and Cluster analysis were used to analyze the relevance of different metals and identify the major sources. The results showed two factors dominated the metals variability (83.4% of total variance) that Cd and Pb, were dominated by PC1 whereas Cr, Cu and Ni charged by another factors and Zn was affected by both two components. Analysis of CA for the sampling sites showed that among all of anthropogenic pollutions, industrial wastewater was major sources of heavy metals especially for Cd, Cr, Cu and Zn in the PRE.

Honggang Zhang

Papers

Analyzing trophic transfer of heavy metals for food webs in the newly-formed wetlands of the Yellow River Delta, China.

Distribution and pollution, toxicity and risk assessment of heavy metals in sediments from urban and rural rivers of the Pearl River delta in southern China

Assessment of river water quality in Pearl River Delta using multivariate statistical techniques

Heavy metals in water, soils and plants in riparian wetlands in the Pearl River Estuary, South China

Combating hypoxia/anoxia at sediment-water interfaces: A preliminary study of oxygen nanobubble modified clay materials.