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

Mechanical alloying (MA) is a solid-state powder processng technique involving repeated welding, fracturing, and rewelding of powder particles in a high-energy ball mill. Originally developed to produce oxide-dispersion strengthened (ODS) nickel- and iron-base superalloys for applications in the aerospace industry, MA has now been shown to be capable of synthesizing a variety of equilibrium and non-equilibrium alloy phases starting from blended elemental or prealloyed powders. The non-equilibrium phases synthesized include supersaturated solid solutions, metastable crystalline and quasicrystalline phases, nanostructures, and amorphous alloys. Recent advances in these areas and also on disordering of ordered intermetallics and mechanochemical synthesis of materials have been critically reviewed after discussing the process and process variables involved in MA. The often vexing problem of powder contamination has been analyzed and methods have been suggested to avoid/minimize it. The present understanding of the modeling of the MA process has also been discussed. The present and potential applications of MA are described. Wherever possible, comparisons have been made on the product phases obtained by MA with those of rapid solidification processing, another non-equilibrium processing technique.

Mechanical Alloying And Milling

5.1. Nanoalloys of Group 11 (Cu, Ag, Au) 865 5.1.1. Cu−Ag 866 5.1.2. Cu−Au 867 5.1.3. Ag−Au 870 5.1.4. Cu−Ag−Au 872 5.2. Nanoalloys of Group 10 (Ni, Pd, Pt) 872 5.2.1. Ni−Pd 872 * To whom correspondence should be addressed. Phone: +39010 3536214. Fax:+39010 311066. E-mail: ferrando@fisica.unige.it. † Universita di Genova. ‡ Argonne National Laboratory. § University of Birmingham. | As of October 1, 2007, Chemical Sciences and Engineering Division. Volume 108, Number 3

Nanoalloys: From Theory to Applications of Alloy Clusters and Nanoparticles

Nanostructured materials: basic concepts and microstructure☆

Metastasis, the dissemination and growth of neoplastic cells in an organ distinct from that in which they originated, is the most common cause of death in cancer patients. This is particularly true for pancreatic cancers, where most patients are diagnosed with metastatic disease and few show a sustained response to chemotherapy or radiation therapy. Whether the dismal prognosis of patients with pancreatic cancer compared to patients with other types of cancer is a result of late diagnosis or early dissemination of disease to distant organs is not known. Here we rely on data generated by sequencing the genomes of seven pancreatic cancer metastases to evaluate the clonal relationships among primary and metastatic cancers. We find that clonal populations that give rise to distant metastases are represented within the primary carcinoma, but these clones are genetically evolved from the original parental, non-metastatic clone. Thus, genetic heterogeneity of metastases reflects that within the primary carcinoma. A quantitative analysis of the timing of the genetic evolution of pancreatic cancer was performed, indicating at least a decade between the occurrence of the initiating mutation and the birth of the parental, non-metastatic founder cell. At least five more years are required for the acquisition of metastatic ability and patients die an average of two years thereafter. These data provide novel insights into the genetic features underlying pancreatic cancer progression and define a broad time window of opportunity for early detection to prevent deaths from metastatic disease.

SF-010-4 Distant metastasis occurs late during the genetic evolution of pancreatic cancer

We present the conceptual framework of atomistic simulations applied to the investigation of mechanical properties of materials. As a show-case application, we discuss a fracture event in bulk silicon carbide when a hard nanofiber inclusion of diamond is present in the neighborhood of a microcrack. We show that, for suitable distances between the two defects, the nanofiber inhibits the propagation of a fracture event from the microcrack tip. This result is consistent with the suggestion that fiber reinforcement could provide increased fracture thoughness in ceramic materials.

5048 - atomistic simulations on fracture events in nanostructured silicon carbide

Crack-tip stress shielding by a hard fiber in β-SiC: an atomistic study

This chapter delves into the mathematical toolbox of continuum mechanics, necessary to describe the mechanical deformation of biological materials. After being relegated for a long time to little more than the (useful, but quite uninspiring) role of providing healing and implants for broken body parts, the domain of biomechanics has been recently promoted to the highest level of attention. The modern view of biomaterials relies on connecting structures over multiple length-scales. Functional organisation is found at all levels, from the molecules, to fibrils and coils, to the carefully networked microstructures, up to the macroscopic scale. At odds with the variety of materials available in nature, just a small set of recurring molecule types, arranged in ever different structures, can give rise to such diverse tissues as skin, cartilage and bone, green stems, rose buds or wood. The secret is the hierarchical multi-level structure of biomaterials.

The Materials of the Living

Two-dimensional networks of ordered quantum dots beyond the percolation threshold are studied, as a typical example of conducting nanostructures with quenched random disorder. Theory predicts anomalous diffusion with stretched-exponential relaxation at short distances, and computer simulations on lattices of crossing, straight paths of random length confirm such a behavior. Anomalous diffusion is interpreted as resulting from the higher probability of taking straight, or ballistic, paths, when the traveled distance is comparable or shorter than the lattice characteristic length. Diffusion turns over to normal for longer traveled distances, whence all paths tend to become equiprobable. Such random lattice structures may represent a model for realistic quantum dot networks, with potential applications in optoelectronics, photovoltaics, or spintronics.

Ballistic to diffusive transition in a two-dimensional quantum dot lattice

Topological changes in microstructure are strictly related to the microscopic evolution of triple junctions (TJ). The three-sided grain disappearance, usually called T2 process, is here investigated via 3D-atomistic modeling. In particular the stability of a three-sided grain insertion in a triple junction in silicon is studied within the framework of Molecular Dynamics simulations. The Stillinger-Weber interatomic potential is adopted and constant-traction border conditions are considered to ensure a proper embedding of the atomistic region in a virtually infinite bulk continuum. Dealing with the T2-event, the critical radius below which the three- sided inner grain become unstable is evaluated to be three to four times the lattice constant of silicon. Moreover, we show that the instability sets in through the amorphization of the central shrinking grain.

Fabrizio Cleri

Papers

5048 - atomistic simulations on fracture events in nanostructured silicon carbide

Crack-tip stress shielding by a hard fiber in β-SiC: an atomistic study

The Materials of the Living

Ballistic to diffusive transition in a two-dimensional quantum dot lattice

A molecular dynamics investigation on grain disappearance at a triple junction in polycrystalline silicon