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

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Mesure de la dégradation bio-mécanique d’une fibre d’ADN sous l’effet des rayons X thérapeutiques

Approach-to-Equilibrium Molecular Dynamics

Atomistic modelling of Materials Science problems often requires the simulation of systems with an irreducibly-large unit cell, such as amorphous materials, fullerites, or systems containing extended defects, such as dislocations, cracks or grain boundaries. Large-scale simulations with the Tight-Binding approach must face the computational obstacle represented by the O( N 3 )-scaling of the diagonalization of the Hamiltonian matrix. This bottleneck can be overcome by parallel computing techniques and/or the introduction of faster, O( N )-scaling algorithms. We report the activities performed in the frame of a collaboration among several research groups on the porting of TBMD codes on parallel computers. In particular, we describe the porting of a O( N 3 ) TBMD code on different MIMD computers, with either distributed or shared memory, by using appropriate software tools. Furthermore, preliminary results obtained in the porting of an O( N ) TBMD code on an experimental, hybrid MIMD-SIMD computer architecture are reported. The new perspective of using specialized platforms to deal with large-scale TBMD simulation is discussed.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S1946427400215388

Large Scale Atomistic Simulations using the Tight Binding Approach

Despite several demonstrations of electrochemical devices with limits of detection (LOD) of 1 cell/mL, the implementation of single-cell bioelectrochemical sensor arrays has remained elusive due to the challenges of scaling up. In this study, we show that the recently introduced nanopillar array technology combined with redox-labelled aptamers targeting epithelial cell adhesion molecule (EpCAM) is perfectly suited for such implementation. Combining nanopillar arrays with microwells determined for single cell trapping directly on the sensor surface, single target cells are successfully detected and analyzed. This first implementation of a single-cell electrochemical aptasensor array, based on Brownian-fluctuating redox species, opens new opportunities for large-scale implementation and statistical analysis of early cancer diagnosis and cancer therapy in clinical settings. For Table of Contents only

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Single-cell Electrochemical Aptasensor Array

We introduced 3D silicon electrodes to perform impedance cytometry on single cells without compromising practical integration with sensors measuring complementary properties, e.g., mechanical properties. Microfabricated from a highly-doped SOI wafer, some design modifications were made to improve their sensing performance. According to simulations, a trajectory-free measurement can be obtained by replacing the silicon backside under the sensing area with an insulating material. In addition, enlarging the distance between the electrodes and the surrounding silicon structure and filling them with some insulating material results experimentally in better signal quality and reduced parasitics. Combining these two device modifications improves the system frequency response and the signal quality at higher frequencies. The proposed process aims at creating silicon-based electrodes for impedance spectroscopy applications while providing opportunities to integrate them with MEMS sensors and actuators.

Fabrizio Cleri

Papers

Mesure de la dégradation bio-mécanique d’une fibre d’ADN sous l’effet des rayons X thérapeutiques

Approach-to-Equilibrium Molecular Dynamics

Large Scale Atomistic Simulations using the Tight Binding Approach

Single-cell Electrochemical Aptasensor Array

Silicon Compatible Process To Integrate Impedance Cytometry With Mechanical Characterization