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

At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal.

Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs

A variety of two-dimensional materials have been reported in recent years, yet single-element systems such as graphene and black phosphorus have remained rare. Boron analogues have been predicted, as boron atoms possess a short covalent radius and the flexibility to adopt sp2 hybridization, features that favour the formation of two-dimensional allotropes, and one example of such a borophene material has been reported recently. Here, we present a parallel experimental work showing that two-dimensional boron sheets can be grown epitaxially on a Ag(111) substrate. Two types of boron sheet, a β12 sheet and a χ3 sheet, both exhibiting a triangular lattice but with different arrangements of periodic holes, are observed by scanning tunnelling microscopy. Density functional theory simulations agree well with experiments, and indicate that both sheets are planar without obvious vertical undulations. The boron sheets are quite inert to oxidization and interact only weakly with their substrate. We envisage that such boron sheets may find applications in electronic devices in the future. A variety of two-dimensional materials have been reported in the past few years, yet single-element systems—such as graphene and black phosphorus—have remained rare. 2D allotropes of boron have long been predicted and recently investigated. Two boron sheets have now been grown on a Ag(111) surface by molecule beam epitaxy that exhibit significant chemical stability against oxidation.

Experimental realization of two-dimensional boron sheets

Main-group analogues to fullerene-C60 have been predicted theoretically many times. Now, B40− has been observed using photoelectron spectroscopy and, with its neutral analogue, B40, confirmed computationally. In contrast to fullerene-C60, the all-boron fullerene (or borospherene) features triangles, hexagons and heptagons, bonded uniformly by delocalized σ and π bonds over the cage surface.

http://casey.brown.edu/chemistry/research/LSWang/publications/399.pdf

Observation of an all-boron fullerene.

Based on {ital ab initio} quantum-chemical methods, accurate calculations on small boron clusters B{sub n} (n=2{endash}14) were carried out to determine their electronic and geometric structures. The geometry optimization with a linear search of local minima on the potential-energy surface was performed using analytical gradients in the framework of the restricted Hartree-Fock self-consistent-field approach. Most of the final structures of the boron clusters (n{gt}9) are composed of two fundamental units: either of hexagonal or of pentagonal pyramids. Proposing an {open_quotes}Aufbau principle{close_quotes} one can easily construct various highly stable boron species. The resulting quasiplanar and convex structures can be considered as fragments of planar surfaces and as segments of nanotubes or hollow spheres, respectively. {copyright} {ital 1997} {ital The American Physical Society}

Systematic ab initio investigation of bare boron clusters:mDetermination of the geometryand electronic structures of B n (n=2–14)

Based on a series of ab initio studies we have pointed out the remarkable structural stability of nanotubular and quasiplanar boron clusters, and postulated the existence of novel layered, tubular, and quasicrystalline boron solids built from elemental subunits. The present study illustrates and predicts qualitative structural and electronic properties for various models of nanotubular and layered boron solids, and compares them to well-known tubular and layered forms of pure carbon and mixed boron compounds.

/pdf/new-boron-based-nanostructured-materials-1oivnl5tii.pdf

New boron based nanostructured materials

Solid α-B12 rhombohedral and γ-B28 orthorhombic boron as well as boron nanostructures in the form of spheres, sheets, and multirings beside a ring consisting of icosahedral B12 units were investigated using ab initio quantum chemical and density functional methods. The structure of the B100 fullerene exhibits unusual stability among all noninteracting free-standing clusters, and is more stable than the B120 cluster fragment of the γ-B28 solid, recently predicted and observed by Oganov et al. (Nature 2009, 457, 863). In addition, we compared the stability of the multirings and reported the structural transition from double-ring to triple-ring systems. This structural transition occurs between B52 and B54 clusters. We confirm that the noninteracting free-standing triangular buckled-sheet is more stable than the γ-sheet, assembled in this work, and than the α-sheet, proposed by Tang and Ismail-Beigi (Phys. Rev. Lett. 2007, 99, 115501). In contrast, however, when these sheets are considered as infinite period...

The Unusually Stable B100 Fullerene, Structural Transitions in Boron Nanostructures, and a Comparative Study of α- and γ-Boron and Sheets

Using ab initio quantum-chemical and density functional methods we have determined novel structures of bare boron clusters. In addition to previously reported quasi-planar, convex and spherical cluster forms, boron nanotubules seem to be highly stable as well. These novel nanotubular structures are composed of hexagonal pyramids only and can be considered as segments of extended pipes. Applying a previously reported "Aufbau Principle", one can easily construct stable boron structures besides the new nanotubular clusters described below. Thus the Aufbau principle should help in illuminating the chemical and physical nature of new boron materials based on boron nanotubules.

https://iopscience.iop.org/article/10.1209/epl/i1997-00388-9/pdf

Ihsan Boustani

Papers

Systematic ab initio investigation of bare boron clusters:mDetermination of the geometryand electronic structures of B n (n=2–14)

New boron based nanostructured materials

The Unusually Stable B100 Fullerene, Structural Transitions in Boron Nanostructures, and a Comparative Study of α- and γ-Boron and Sheets

Nanotubules of bare boron clusters: Ab initio and density functional study

Structure and stability of small boron clusters. A density functional theoretical study