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

Removal of heavy metal ions from wastewaters: A review

Controlled self-organization of nanoparticles can lead to new materials. The colloidal crystallization of non-spherical nanocrystals is a reaction channel in many crystallization reactions. With additives, self-organization can be stopped at an intermediary step-a mesocrystal-in which the primary units can still be identified. Mesocrystals were observed for various systems as kinetically metastable species or as intermediates in a crystallization reaction leading to single crystals with typical defects and inclusions. The control forces and mechanism of mesocrystal formation are largely unknown, but several mesocrystal properties are known. Mesocrystals are exiting examples of nonclassical crystallization, which does not proceed through ion-by-ion attachment, but by a modular nanobuilding-block route. This path makes crystallization more independent of ion products or molecular solubility, it occurs without pH or osmotic pressure changes, and opens new strategies for crystal morphogenesis.

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Mesocrystals: Inorganic superstructures made by highly parallel crystallization and controlled alignment

/pdf/processes-of-carbonate-precipitation-in-modern-microbial-176vfhaypi.pdf

Processes of carbonate precipitation in modern microbial mats

2.3. Amorphous Minerals 4354 3. Biological Routes to Controlling Morphology 4354 3.1. General Mechanisms 4356 3.1.1. Soluble and Insoluble Organic Molecules 4356 3.1.2. Control over Crystal Polymorph 4357 3.1.3. Control over Crystal Orientation 4359 3.2. Single-Crystal Biominerals 4359 3.2.1. Organic and Inorganic Soluble Additives 4360 3.2.2. Templating of Single-Crystal Morphologies 4361 3.3. Polycrystalline Biominerals 4366 3.3.1. Nacre Formation in Mollusks 4366 3.3.2. ForaminiferasA Biogenic Mesocrystal 4368 3.4. Amorphous Biominerals 4370 3.4.1. Silicification in Diatoms 4370 3.4.2. In Vitro Studies of Silicification in Diatoms 4371 4. Bioinspired Routes to Controlling Crystal Morphologies 4371

Controlling Mineral Morphologies and Structures in Biological and Synthetic Systems

Morphological development of calcite crystals is related to supersaturation conditions during growth. Crystallization of calcium carbonate (calcite and aragonite) as well as Mg-calcite was studied under controlled supersaturation conditions by the counter diffusion of Ca2+ and CO32- ions through a porous transport medium (a column of silica gel). Under our experimental conditions, where ion transport is constrained to be diffusion controlled, nucleation and growth take place under conditions of high supersaturation, the actual threshold value of the supersaturation depending on the supersaturation gradient. In the pure CaCO3 system, calcite grows at lower supersaturation than aragonite. The calcite develops relatively simple rhombohedra whil the aragonite grows as spherulites. Presence of Mg2+ in the interstitial fluid inhibits nucleation, increasing the threshold supersaturation at which crystallization begins. The resulting Mg-calcite crystals show a range of morphologies depending on the Mg content and the supersaturation at the point of crystallization. At high values of supersaturation, up to 15 mol % MgCO3 is incorporated into the calcite and the crystals form spheres. At lower supersaturations, Mg content decreases and morphologies change progressively through a well-defined and reproducible sequence from spheres to dumbbell-like forms to wheat-sheaf-like bundles and eventually single crystals with steep rhombohedral faces. The crystals are compositionally zoned, showing both sector and oscillatory zoning. The compositional evol tion is related to the supersaturation and interface roughness during crystal growth.

/pdf/the-role-of-magnesium-in-the-crystallization-of-calcite-and-lsv9svgsa6.pdf

The role of magnesium in the crystallization of calcite and aragonite in a porous medium

The relationship between the supersaturation at the point of crystallization and the rate at which supersaturation increases has been studied from nucleation experiments on barite BaSO4, strontianite SrCO3, witherite BaCO3 and gypsum CaSO4.2H2O. The crystallization experiments have been carried out by the counter-diifusion of cations and anions through a column of porous silica gel transport medium. Nucleation is suppressed in a finely-porous medium resulting in very high values of supersaturation before crystallization from the solution begins. This threshold supersaturation for nucleation depends on the solubility of the salt, the porosity of the medium and the supersaturation rate. Nucleation inhibitors were used to extend the range of supersaturation attainable. In all cases the experimental data fits the general expression: rate of change of supersaturation ∝ (threshold supersaturation)m. These results are compared to previous work from the field of chemical engineering on the relationship between supersaturation, volume and cooling rate in aqueous salt solutions. These experiments have important implications to supersaturation in natural fluids and subsequent crystallization in relation to geological problems including crystallization in low temperature sedimentary environments and fluid-rock ratios in hydrothermal mineral deposits.

Fluid supersaturation and crystallization in porous media

Experimental determination of the dissolution rates of calcite, aragonite, and bivalves

Nucleation, growth, and zoning phenomena in crystallizing (Ba,Sr)CO3, Ba(SO4,CrO4), (Ba,Sr)SO4, and (Cd,Ca)CO3 solid solutions from aqueous solutions

When two solutes crystallize simultaneously from an aqueous phase and have similar crystal structures, a solid solution is likely to form. Indeed, although often disregarded, solid solution-aqueous solution (SS-AS) effects are ubiquitous in both natural and industrial crystallization processes. In nature, and particularly on the Earth’s surface environments, the crystallization of minerals from multicomponent aqueous solutions provokes in most cases the formation of solids with more or less wide compositional ranges, i.e., solid solutions. Moreover, the interaction between existing minerals and water frequently leads to surface precipitation and dissolution-recrystallization processes, in which a number of substituting ions (major, minor, or trace) redistribute to adapt to the new conditions.

The study of SS-AS relationships between minerals and solutions can provide very valuable information about natural waters, contamination of soils and aquifers, and global element cycles. For instance, in diagenetic studies of sedimentary rocks, the minor and trace element concentrations are commonly used to infer the composition of the crystallizing fluids and have been demonstrated to play a major role in the dissolution-recrystallization processes that lead to the formation of authigenic minerals (e.g., Bottcher 1997b; Rimstidt et al. 1998; Kulik et al. 2000; Mucci 2004). Likewise, the concentrations of specific minor and trace elements in calcite and aragonite precipitated by marine organisms have been shown to correlate with various parameters of the growth environment, including temperature, salinity, nutrient levels, carbonate concentration, and water chemistry. These findings suggest that compositional signatures recorded in biogenic carbonates can be powerful tools in reconstruction of the past from the fossil record (e.g., Rosenthal et al. 1997; Stoll et al. 2002; Rickaby et al. 2002). Obviously, for these proxies to be effective, it is essential to rigorously investigate the underlying physical and chemical mechanisms both in the absence and in the presence …

Manuel Prieto

Papers

The role of magnesium in the crystallization of calcite and aragonite in a porous medium

Fluid supersaturation and crystallization in porous media

Experimental determination of the dissolution rates of calcite, aragonite, and bivalves

Nucleation, growth, and zoning phenomena in crystallizing (Ba,Sr)CO3, Ba(SO4,CrO4), (Ba,Sr)SO4, and (Cd,Ca)CO3 solid solutions from aqueous solutions

Thermodynamics of Solid Solution-Aqueous Solution Systems