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

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Bulk nanostructured materials from severe plastic deformation

Thank you very much for downloading table of integrals series and products. Maybe you have knowledge that, people have look hundreds times for their chosen books like this table of integrals series and products, but end up in harmful downloads. Rather than reading a good book with a cup of coffee in the afternoon, instead they cope with some harmful virus inside their laptop. table of integrals series and products is available in our book collection an online access to it is set as public so you can get it instantly. Our book servers saves in multiple locations, allowing you to get the most less latency time to download any of our books like this one. Merely said, the table of integrals series and products is universally compatible with any devices to read.

Table Of Integrals Series And Products

Mechanical properties of nanocrystalline materials

To specify a grain boundary at a macroscopic length scale requires the specification of five degrees of freedom. We use a specification in which three degrees of freedom associated with the boundary misorientation are in an orthogonal subspace from two associated with the mean boundary plane. By using Rodrigues vectors to describe rotations, we show how paths through these subspaces may be characterized. Some of these paths correspond to physical processes involving grain boundaries during microstructural evolution. Exploiting the orthogonality of the subspaces, a metric to measure ‘distance’ between two boundaries is defined in terms of the minimum set of rotations required to map one boundary on to the other. We compare our metric with others that have appeared. The existence of rotational symmetry in face-centred cubic crystals leads to as many as 2304 equivalent specifications of a boundary. We illustrate this multiplicity of descriptions for the (111) twin and a more general boundary. We present an algorithm to evaluate the geodesic distance between two boundaries, and apply it to identify the path along which the distance between these two boundaries is minimized. In general, the shortest path does not involve descriptions of boundary misorientations with the smallest misorientation angles.

/pdf/the-five-dimensional-parameter-space-of-grain-boundaries-4onq2tmlbv.pdf

The five-dimensional parameter space of grain boundaries

Despite numerous theoretical models and simulation results, a clear physical picture of dislocations traveling at velocities comparable to the speed of sound in the medium remains elusive. Using two complementary atomistic methods to model uniformly moving screw dislocations, lattice dynamics and molecular dynamics, the existence of mechanical instabilities in the system is shown. These instabilities are found at material-dependent velocities far below the speed of sound. We show that these are the onset of an atomistic kinematic generation mechanism, which ultimately results in an avalanche of further dislocations. This homogeneous nucleation mechanism, observed but never fully explained before, is relevant in moderate and high strain rate phenomena including adiabatic shear banding, dynamic fracture, and shock loading. In principle, these mechanical instabilities do not prevent supersonic motion of dislocations.

Instabilities of High Speed Dislocations.

We have modeled the decomposition of nonstoichiometric amorphous SiOx upon annealing into silicon and stoichiometric silica, using a new method based on mapping Metropolis Monte Carlo simulations onto rate equations. The concentrations of all oxidation states of silicon are derived as a function of time and found to attain steady-state values at long times dependent on temperature T and oxygen content x. The degree of phase separation and the sizes of Si particles are predicted as a function of T and x, enabling greater control over the size of silicon quantum dots in silica matrices.

/pdf/modeling-phase-separation-in-nonstoichiometric-silica-4mzwbzbvck.pdf

Modeling phase separation in nonstoichiometric silica.

Coarse-grained molecular dynamics simulations are used to elucidate molecular mechanisms responsible for different mechanical behaviours of elastomers containing spherical particles with different volume fractions We observe that different filler volume fractions result in qualitatively different responses of the polymer nanocomposite to tensile strain At relatively low filler volume fraction a yield drop appears in the stress-strain curve As the filler volume fraction increases there is a reduction in the rate of plastic hardening, becoming plastic softening at sufficiently high filler volume fraction We demonstrate that these behaviours are a result of the network formed by the polymer chains and filler particles We identify three distinct molecular structural motifs between polymer and filler particles whose relative prevalence varies with the filler volume fraction and as the system is dynamically strained We show how this evolution in molecular structure is directly linked to the observed mechanical response

/pdf/mechanisms-of-reinforcement-in-polymer-nanocomposites-27uoqs2fke.pdf

Mechanisms of reinforcement in polymer nanocomposites

Phase transformations in 2xxx series aluminium alloys (Al–Cu–Mg) are investigated with an off-lattice atomistic kinetic Monte Carlo simulation incorporating the effects of strai na round misfitting atoms and vacancies. Atomic interactions are modelled by Finnis–Sinclair potentials constructed for these simulations. Vacancy diffusion i sm odelled by comparing the energies of trial states, where the system is partially relaxed for each trial state. No special requirements are made about the description of atomic interactions, making our approach suitable for more fundamentally based models such as tight binding if sufficient computational resources are available. Only a limited precision is required for the energy of each trial state, determined by the value of kBT . Since the change in the relaxation displacement field caused by a vacancy hop decays as 1/r 3 ,i t is suff icient to determine the next move by relaxing only those atoms in a sphere of finite radius centred on the moving vacancy. However, once the next move has been selected, the entire system is relaxed. Simulations of the early stages of phase separation in Al–Cu with elastic relaxation show an enhanced rate of clustering compared to those performed on the same system with a rigid lattice. (Some figures in this article are in colour only in the electronic version)

http://iopscience.iop.org/article/10.1088/0953-8984/16/27/007/pdf

Adrian P. Sutton

Papers

The five-dimensional parameter space of grain boundaries

Instabilities of High Speed Dislocations.

Modeling phase separation in nonstoichiometric silica.

Mechanisms of reinforcement in polymer nanocomposites

Atomistic modelling of diffusional phase transformations with elastic strain