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

Fluid pathway evolution and mass transfer during Mg-dominated mineral transformations

The Composition and Growth Mechanism of Coexisting 4M2 and 4A8 Biotite Polytypes from Rhyolite of Long Valley Caldera, California

The practical application of earth abundant pyrite (FeS2) in photovoltaic devices is extremely limited by the low open-circuit voltage (OCV) (∼200 mV) induced low efficiency (<3%) As such, finding out the causes for the low OCV and the corresponding solutions has been widely concerned Here, we report the hydration induced bandgap shift at the pyrite-water interface, which has been ignored in previous efforts The bandgap shift may be one of the reasons responsible for the low OCV Using ab initio calculations, we found that, compared to the pure pyrite surface in vacuum, the bandgap of the pyrite-water interfacial system possesses blue and red shifts at the water coverage of more and less than the mono-layer, respectively The bandgap shift of the interfacial system could be explained by the adsorption symmetry and charge transfer between water and the substrate These results reveal that the interfacial water could change the electronic structure of the pyrite surface, suggesting that hydration could be a highly probable stratagem to tune the photovoltage properties of pyrite-based materials

Hydration induced bandgap shift at pyrite-water interface

The different effects of sulfate on the adsorption of REEs on kaolinite and ferrihydrite

Nanoscale minerals (i.e., nanominerals and mineral nanoparticles) in terrestrial and extraterrestrial materials are difficult to characterize because of their small particle sizes, high surface energy, and/or poor crystallization. Transmission electron microscopy (TEM) is a powerful analytical platform for the characterization of minerals at the nano and even atomic scales, and it can determine their morphology through imaging, derive structural information using multiple electron-diffraction techniques, and investigate chemical compositions. Since the 1990s, the application of TEM to the characterization of nanoscale minerals has developed rapidly into a core technique in nanoscale Earth and planetary science (NEPS). This review introduces a brief history and the general principles of TEM, considers detailed methods of preparing specimens for nanoscale mineralogical characterization by TEM, and emphasizes the contributions of TEM to multiple NEPS research fields in recent decades. These contributions are considered from the perspective of nanoscale mineralogical studies of morphology, structure, and chemistry in complex geological materials. Finally, the work provides an outlook on current opportunities to apply TEM methods to nanoscale mineralogical study. This review aims to provide common and practical TEM methods to NEPS researchers and to support the use of TEM for a wide range of applications in nanoscale mineralogy to promote NEPS development. 

Jianxi Zhu

Papers

Fluid pathway evolution and mass transfer during Mg-dominated mineral transformations

The Composition and Growth Mechanism of Coexisting 4M2 and 4A8 Biotite Polytypes from Rhyolite of Long Valley Caldera, California

Hydration induced bandgap shift at pyrite-water interface

The different effects of sulfate on the adsorption of REEs on kaolinite and ferrihydrite

Nanoscale Mineralogical Characterization of Terrestrial and Extraterrestrial Samples by Transmission Electron Microscopy: A Review