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

Transformation of Ordered Albite into Kaolinite: Implication for the “Booklet” Morphology

The catalytic process of poly-silicate-ferric (PSF) and generation mechanism of hydroxyl radical based on photo-Fenton system.

Abstract The formation of heteroaggregates is critical to controlling the stabilization and transformation of nanominerals and mineral nanoparticles (NMMNs) in nature, but the underlying mechanisms remain to be deciphered. In this work, we study the effect of surface interactions between ferrihydrite (Fh) and montmorillonite (Mnt) within their heteroaggregates on the transformation behaviors of Fh. A series of heteroaggregates composed of Fh and Mnt were synthesized by modulating their mass ratios and synthesis methods, i.e., directly complexing Fh with Mnt (Fh-Mnt) or in situ growing Fh on Mnt (Fh/Mnt). Structural characterization using XRD, TG-DSC, TEM, and FTIR indicated that Fh particles coated more evenly on the Mnt surface within the heteroaggregates synthesized by in situ growing Fh on Mnt and with lower Fh to Mnt ratio, and accordingly these heteroaggregates showed stronger surface interactions between Fh and Mnt. The phase transformation of Fh to hematite (Hem) on the heteroaggregates can be significantly affected during the heating treatment. Compared with that of pure Fh, the transformation of Fh on all of the heteroaggregates was retarded (e.g., slower transformation rate and smaller produced Hem particles), particularly for the samples with stronger surface interactions (e.g., Fh/Mnt with lower Fh to Mnt ratio). Noticeably, the heated heteroaggregates may simultaneously contain pristine Fh, intermediate maghemite, and transformed Hem, showing a heterogeneous transformation behavior of Fh. The strong interactions between Fh and Mnt will enhance the dispersion of Fh and restrict the structural rearrangement of Fh (particularly those at the interface) during the phase transformation process, resulting in retarded and heterogenous transformation of Fh on these heteroaggregates. These findings not only enrich our knowledge of the phase transformation characteristics of Fh but also advance our understanding of the important role of mineral surface interactions in stabilizing NMMNs in nature.

Heterogeneous and retarded phase transformation of ferrihydrite on montmorillonite surface: The important role of surface interactions

Nanoscale chemomechanical variations of montmorillonite induced by the specificity of counterions—An in situ XRD and AFM study

Abstract Aseismic slip is a stable fault slip, which allows strain to be relieved smoothly. Aseismic slip prevents the earthquake propagation, but it could nucleate an earthquake elsewhere. Understanding the mechanism of aseismic slip is promising in revealing the seismic cycle. Experimental evidence showed clay-rich fault gouge bears a low-friction strength, and the friction is strengthened with slip velocity (velocity-strengthening), which was thought to support aseismic slip. Clay minerals are comprised of platy crystalline layers with water intercalated between them, which may act as a lubricant. Sliding between clay layers was suspected to support aseismic slip but lacked a clarified mechanistic insight. We use non-equilibrium molecular dynamics simulations to show that shear-induced interlayer sliding is frictionally weak and velocity-strengthening, which evidences the role of clay minerals in aseismic slip. We find that interlayer water is a viscous fluid at most times, which explains the shear response of interlayer sliding. Depending on temperature and pressure conditions, intercalated water can be monolayer or bilayer, fluidic or ice like. Shear induces ice-like water to transform into fluidic water, which happens as a stick-slip phenomenon reflecting a first-order transition. Increased pore fluid pressure leads to the transformation from monolayer to bilayer intercalated water, resulting in a lower friction strength and enhanced velocity-strengthening behavior. Our work suggests that disclosing the hydration state of a clay mineral is preliminary when studying fault mechanics.

Jianxi Zhu

Papers

Transformation of Ordered Albite into Kaolinite: Implication for the “Booklet” Morphology

The catalytic process of poly-silicate-ferric (PSF) and generation mechanism of hydroxyl radical based on photo-Fenton system.

Heterogeneous and retarded phase transformation of ferrihydrite on montmorillonite surface: The important role of surface interactions

Nanoscale chemomechanical variations of montmorillonite induced by the specificity of counterions—An in situ XRD and AFM study

How clay delamination supports aseismic slip