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

We measured the elastic properties and intrinsic breaking strength of free-standing monolayer graphene membranes by nanoindentation in an atomic force microscope. The force-displacement behavior is interpreted within a framework of nonlinear elastic stress-strain response, and yields second- and third-order elastic stiffnesses of 340 newtons per meter (N m(-1)) and -690 Nm(-1), respectively. The breaking strength is 42 N m(-1) and represents the intrinsic strength of a defect-free sheet. These quantities correspond to a Young's modulus of E = 1.0 terapascals, third-order elastic stiffness of D = -2.0 terapascals, and intrinsic strength of sigma(int) = 130 gigapascals for bulk graphite. These experiments establish graphene as the strongest material ever measured, and show that atomically perfect nanoscale materials can be mechanically tested to deformations well beyond the linear regime.

/pdf/measurement-of-the-elastic-properties-and-intrinsic-strength-27nythtm75.pdf

Measurement of the Elastic Properties and Intrinsic Strength of Monolayer Graphene

This article reviews the current status of lattice-dynamical calculations in crystals, using density-functional perturbation theory, with emphasis on the plane-wave pseudopotential method. Several specialized topics are treated, including the implementation for metals, the calculation of the response to macroscopic electric fields and their relevance to long-wavelength vibrations in polar materials, the response to strain deformations, and higher-order responses. The success of this methodology is demonstrated with a number of applications existing in the literature.

/pdf/phonons-and-related-crystal-properties-from-density-3mdybdn8w1.pdf

Phonons and related crystal properties from density-functional perturbation theory

The interest in nanoscale materials stems from the fact that new properties are acquired at this length scale and, equally important, that these properties * To whom correspondence should be addressed. Phone, 404-8940292; fax, 404-894-0294; e-mail, mostafa.el-sayed@ chemistry.gatech.edu. † Case Western Reserve UniversitysMillis 2258. ‡ Phone, 216-368-5918; fax, 216-368-3006; e-mail, burda@case.edu. § Georgia Institute of Technology. 1025 Chem. Rev. 2005, 105, 1025−1102

Chemistry and properties of nanocrystals of different shapes.

Carbon nanotubes subject to large deformations reversibly switch into different morphological patterns. Each shape change corresponds to an abrupt release of energy and a singularity in the stress-strain curve. These transformations, simulated using a realistic many-body potential, are explained by a continuum shell model. With properly chosen parameters, the model provides a remarkably accurate ``roadmap'' of nanotube behavior beyond Hooke's law.

/pdf/nanomechanics-of-carbon-tubes-instabilities-beyond-linear-c39bdv9fp7.pdf

Nanomechanics of carbon tubes: Instabilities beyond linear response.

High strain rate fracture and C-chain unraveling in carbon nanotubes

Large-scale molecular dynamics simulations were used to study the response of carbon nanotubes to a tensile load. Plastic or brittle behaviors can occur depending upon the external conditions and tube symmetry. All tubes are brittle at high strain and low temperature, while at low strain and high temperature armchair $(n,n)$ nanotubes can be completely or partially ductile. In zigzag $(n,0)$ tubes ductile behavior is expected for tubes with $nl14$, while larger tubes are completely brittle. In both cases the curvature determines the mechanical response.

/pdf/brittle-and-ductile-behavior-in-carbon-nanotubes-59o09a7esx.pdf

Brittle and Ductile Behavior in Carbon Nanotubes

The results of an extensive theoretical study of native defects in hexagonal GaN are presented. We have considered cation and anion vacancies, antisites, and interstitials. The computations were carried out using ab initio molecular dynamics in supercells containing 72 atoms. N vacancy introduces a shallow donor level, and may be responsible for the n-type character of as-grown GaN. Due to the wide gap of nitrides, self-compensation effects strongly reduce both n-type and p-type doping efficiencies due to the formation of gallium vacancy and interstitial Ga, respectively.

/pdf/native-defects-in-gallium-nitride-1vnot6um9k.pdf

Native defects in gallium nitride

We present a combined theoretical and experimental study of the ferromagnetic semiconductor (Ga,Mn)As which explains the remarkably large changes observed on low-temperature annealing. Careful control of the annealing conditions allows us to obtain samples with ferromagnetic transition temperatures up to 159 K. Ab initio calculations, in situ Auger spectroscopy, and resistivity measurements during annealing show that the observed changes are due to out diffusion of Mn interstitials towards the surface, governed by an energy barrier of 0.7-0.8 eV. Electric fields induced by Mn acceptors have a significant effect on the diffusion.

Jerry Bernholc

Papers

Nanomechanics of carbon tubes: Instabilities beyond linear response.

High strain rate fracture and C-chain unraveling in carbon nanotubes

Brittle and Ductile Behavior in Carbon Nanotubes

Native defects in gallium nitride

Mn interstitial diffusion in (ga,mn)as.