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

This paper reports a novel approach to scan with a high resolution the relative humidity around water in microsized environment. The humidity sensor is composed of a MEMS device, the Silicon Nano Tweezers (SNT) and a DNA bundle. The principle of the measurement is based on the relation between the electro-mechanical properties (conductance and stiffness) of a DNA bundle and the relative humidity. The system is developed to obtain precisely, quickly, and automatically the middle of the aperture of a microfluidic cavity for self-alignment purpose.

http://ieeexplore.ieee.org/iel7/7411154/7421533/07421613.pdf

3D humidity imager in micro environment based on DNA conductivity and rigidity measured by silicon nano tweezers

The mechanical behaviour of brittle materials is very sensitive to microstructure defects, like point or extended lattice imperfections, elastic inclusions, voids. Since the local stress conditions (i.e. the conditions nearby a defect) of such complex materials may largely differ from their average values, the prediction of the overall mechanical response to external loads results to be a though theoretical problem. This is, for instance, the case of the stress threshold at which a microcrack starts propagating, or the interaction features bewteen the defect and the incoming crack. In this work, we investigate at the proper nanoscale the interaction between a crack tip and elastic inclusions by combining a hierarchy of different computational tools, namely atomistic simulations (carried out at the molecular dynamics level) and statistical mechanics models (based on replica-symmetry breaking). The investigated material is silicon carbide, i.e. the prototypical example of brittle material with directional and covalent bonding.

/pdf/physical-modeling-of-fracture-mechanics-in-complex-materials-418acfxko6.pdf

Physical modeling of fracture mechanics in complex materials

Double strand breaks in the DNA backbone are the most lethal type of defect that can be induced in the cell nucleus by chemical and radiation treatments of cancer. However, little is known about the potentially large differences in the outcomes of damage between free and nucleosomal DNA, leading to corresponding differences in damage repair capability. We performed microsecond-length molecular dynamics computer simulations of nucleosomes including double-strand breaks (DSB) at various sites, to characterize the early stages of the evolution of this important DNA lesion right after its formation. We find that all DSB configurations tend to remain compact, with only the terminal bases interacting with histone proteins; the interacting molecular structures are studied by looking at the essential dynamics of the relevant DNA and histone fragments, and compared to the intact nucleosome, thus exposing key features of the interactions. Moreover, we show that the broken DNA ends at the DSB must overcome a free-energy barrier to detach from the nucleosome core, as measured by means of umbrella sampling of the potential of mean force. Finally, by using state-of-the-art calculation of the covariant mechanical stress at the molecular scale, we demonstrate that, depending on the DNA-core separation distance, the coupled bending and torsional stress stored in the detached DNA can force the free end to either stick back to the nucleosome core surface, or to open up straight, thus making it accessible to damage signalization proteins.

/pdf/mechanical-evolution-of-dna-double-strand-breaks-in-the-2206wgss7p.pdf

Mechanical evolution of DNA double-strand breaks in the nucleosome

The validity and predictive capability of continuum models of fracture rests on basic informations whose origin lies at the atomic scale. Examples of such crucial informations are, e.g., the explicit form of the cohesive law in the Barenblatt model and the shear-displacement relation in the Rice-Peierls-Nabarro model. Modem approaches to incorporate atomic-level information into fracture modelling require to increase the size of atomic-scale models up to millions of atoms and more; or to connect directly atomistic and macroscopic, e.g. finite-elements, models; or to pass information from atomistic to continuum models in the form of constitutive relations. A main drawback of the atomistic methods is the complexity of the simulation results, which can be rather difficult to rationalize in the framework of classical, continuum fracture mechanics. We critically discuss the main issues in the atomistic simulation of fracture problems (and dislocations, to some extent); our objective is to indicate how to set up atomistic simulations which represent well-posed problems also from the point of view of continuum mechanics, so as to ease the connection between atomistic information and macroscopic models of fracture.

Atomistic Aspects of Fracture Modelling in the Framework of Continuum Mechanics

The mathematical models of polymers and membranes are introduced, to describe the microscopic deformation of biological materials. The mechanical properties at the molecular scale are inherently statistical, and remain hidden below macroscopic averages. But we can now see and manipulate a single molecule, and follow its movements in real time. This is made possible thanks to the advent of revolutionary tools, such as the atomic-force microscope and the optical or magnetic tweezers, which allow to test the mechanics of biological materials with unprecedented quality and accuracy, down to the molecular scale. Today it is possible to measure the elasticity of a single molecule, of a piece of DNA, of a fragment of cell membrane, and from such strictly physical comparisons, a totally new wealth of information has started to invade the already flooded desk of the biologist.

Fabrizio Cleri

Papers

3D humidity imager in micro environment based on DNA conductivity and rigidity measured by silicon nano tweezers

Physical modeling of fracture mechanics in complex materials

Mechanical evolution of DNA double-strand breaks in the nucleosome

Atomistic Aspects of Fracture Modelling in the Framework of Continuum Mechanics

Molecular Mechanics of the Cell