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 recent extensions of our stochastic microstructure evolution model including multiphase domain evolution and dislocation plasticity. The model was implemented by means of numerical simulations based on the velocity Monte Carlo algorithm. It describes the evolution of a two-dimensional microstructure by tracking the motion of triple junctions, i.e., the vertices where three grain boundaries (GBs) meet. GBs can be modeled as straight, curved, or discretized segments; the misorientation dependence of both grain-boundary energies and mobilities can be included to represent different textures.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0884291400066516

Multiphase microstructure evolution model including dislocation plasticity

Hydrogen storage in MgH2 matrices : a study of Mg-MgH2 interface using CPMD code on ENEA-GRID

We performed first-principles molecular dynamics calculations at finite temperature, to study the interacting conformations of Lewis-X (LeX) trisaccharides in the crystalline phase. The calculated cell parameters and detailed atomic structure of the LeX molecule compare well to the experimental data obtained by X-ray diffraction. We identify and characterize the hydrogen-bond network, responsible for the mutual interaction of the LeX pairs, whereas we find the intramolecular conformation and stability to be mainly assured by dispersion forces. The relative contributions to the crystallization energy of the hydrogen bonds and of the dispersion forces are defined and quantified. From this study, candidate configurations for the fully hydrated, in vivo structures of homotypic LeX-LeX interactions at cell surfaces can be proposed. We discuss how these configurations could also be relevant for the adhesion and self-assembly of nanostructures.

Interacting Lewis-X carbohydrates in condensed phase: a first-principles molecular dynamics study.

The behaviour of two different systems, NiZr2 and Cu3Au, submitted to a chemical disordering process under various thermodynamical conditions has been investigated by Molecular Dynamics simulations. The role played by volume expansion and elastic softening in the onset of the transition has been discussed in the framework of the percolation model (C.Massobrio and V.Pontikis, Phys.Rev.B 45 (1992) 2484), correlating the elastic instability with the percolation of the distorted regions which establishes in the lattice as a consequence of the external perturbations (introduction of defects, volume expansion, chemical disorder etc.).

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S1946427400524634

Atomistic Simulation of Crystal-to-Amorphous Transitions in the Intermetallic Alloys NiZr2 and Cu3Au

Tight-binding molecular dynamics simulations of typical high-energy grain boundaries in silicon show that the atomic structure of the interface in thermodynamic equilibrium is similar to that of bulk amorphous silicon and contains coordination defects. The corresponding electronic structure is also amorphous-like, displaying extra states in the forbidden gap mainly localized around the coordination defects, where large changes in the bond-hybridization character are observed. It is proposed that such coordination defects in disordered high-energy grain boundaries are responsible for the experimentally observed gap states in polycrystalline Si.

Fabrizio Cleri

Papers

Multiphase microstructure evolution model including dislocation plasticity

Hydrogen storage in MgH2 matrices : a study of Mg-MgH2 interface using CPMD code on ENEA-GRID

Interacting Lewis-X carbohydrates in condensed phase: a first-principles molecular dynamics study.

Atomistic Simulation of Crystal-to-Amorphous Transitions in the Intermetallic Alloys NiZr2 and Cu3Au

Structural Disorder and Localized Gap States in Silicon Grain Boundaries from a Tight-Binding Model