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

Diamond-like carbon (DLC) is a metastable form of amorphous carbon with significant sp3 bonding. DLC is a semiconductor with a high mechanical hardness, chemical inertness, and optical transparency. This review will describe the deposition methods, deposition mechanisms, characterisation methods, electronic structure, gap states, defects, doping, luminescence, field emission, mechanical properties and some applications of DLCs. The films have widespread applications as protective coatings in areas, such as magnetic storage disks, optical windows and micro-electromechanical devices (MEMs).

/pdf/diamond-like-amorphous-carbon-3pczopr0z7.pdf

Diamond-like amorphous carbon

The electronic ground state of a periodic system is usually described in terms of extended Bloch orbitals, but an alternative representation in terms of localized "Wannier functions" was introduced by Gregory Wannier in 1937. The connection between the Bloch and Wannier representations is realized by families of transformations in a continuous space of unitary matrices, carrying a large degree of arbitrariness. Since 1997, methods have been developed that allow one to iteratively transform the extended Bloch orbitals of a first-principles calculation into a unique set of maximally localized Wannier functions, accomplishing the solid-state equivalent of constructing localized molecular orbitals, or "Boys orbitals" as previously known from the chemistry literature. These developments are reviewed here, and a survey of the applications of these methods is presented. This latter includes a description of their use in analyzing the nature of chemical bonding, or as a local probe of phenomena related to electric polarization and orbital magnetization. Wannier interpolation schemes are also reviewed, by which quantities computed on a coarse reciprocal-space mesh can be used to interpolate onto much finer meshes at low cost, and applications in which Wannier functions are used as efficient basis functions are discussed. Finally the construction and use of Wannier functions outside the context of electronic-structure theory is presented, for cases that include phonon excitations, photonic crystals, and cold-atom optical lattices.

Maximally-localized Wannier Functions: Theory and Applications

LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

A transferable empirical potential for carbon is developed by extending the environment-dependent interaction potential proposed for silicon Generalized coordination functions, parametrized using ab initio data, describe dihedral rotation, nonbonded $\ensuremath{\pi}$-repulsion and fractional coordination Elastic constants agree well with experiment, and simulations of liquid carbon compare very favorably with Car-Parrinello calculations Amorphous networks generated by liquid quench have properties superior to those of the Tersoff, Brenner, and orthogonal tight-binding methods

Generalizing the environment-dependent interaction potential for carbon

Graphitization of amorphous carbons: A comparative study of interatomic potentials

The thermally induced transformation of kaolinite to metakaolin is simulated using molecular dynamics through a step-wise dehydroxylation approach. The simulation shows that the removal of structural water through dehydroxylation produces a distortion or buckling effect in the 1 : 1 Al–Si layers, which is due to the migration of the aluminium into vacant sites provided by the inter-layer spacing. The structural change is characterized by a loss of crystallinity and a concomitant change in aluminium coordination from octahedral to tetrahedral, with this study confirming the presence of 5-fold aluminium within the metakaolin structure. The degree and probability of Al migration are proportional to the amount of local disorder within the structure, which is governed by the degree of local hydroxyl group loss. This results in the formation of aluminium clusters within the layers. This study proposes that instead of a uniform structure, metakaolin exhibits regions of differing aluminium concentrations, which can have major effects in the reaction chemistry at those sites.

/pdf/dehydroxylation-of-kaolinite-to-metakaolin-a-molecular-4hvvphnc1x.pdf

Dehydroxylation of Kaolinite to Metakaolin - A Molecular Dynamics Study

Amorphous carbon networks are used to test various levels of theoretical approaches to molecular dynamics simulations. The density-functional theory as implemented in the Car-Parrinello method, nonorthogonal tight-binding method, the environment-dependent interaction potential (EDIP), and the Brenner potential are compared directly in liquid quench simulations containing 125 atoms at four densities. We find that at low densities the predictions of the Brenner potential are in agreement with those from density-functional theory, while structures produced by nonorthogonal tight-binding method compare well with density-functional theory at all densities. The tight-binding method does, however, find a slightly lower ${\mathrm{sp}}^{3}$ fraction at high densities and the presence of singly coordinated atoms at low densities. The frequency of three-membered rings are underpredicted by the tight-binding and EDIP methods due to an overestimate of strain energy relative to density- functional theory and experiment. Aside from the small rings, and a slight underestimate in ${\mathrm{sp}}^{3}$ fraction at the highest densities, the EDIP simulations are in very good agreement with density-functional theory. The EDIP method is also used to quantify the statistical variability of liquid quenching, and comparisons with film growth simulations verify that liquid quenching is a good representation of bulk amorphous carbon.

http://phelafel.technion.ac.il/~yoelk/files/118094project/articles/Comparison%20of%20density-functional,%20tight-binding,%20and%20empirical%20methods%20for%20the%20simulation%20of%20amorphous%20carbon.pdf

Comparison of density-functional, tight-binding, and empirical methods for the simulation of amorphous carbon

The molecular-dynamics technique involving the rapid cooling of a liquid to simulate an amorphous solid has been used for several years. Despite the success of the technique, the method has lacked a physical justification, and the cooling rates have been assumed to be too fast. In this paper an analysis of thermal spike cooling times in tetrahedral amorphous carbon shows that the method is reasonable and that rapid cooling rates are appropriate. Using three independent methods it is found that the thermal spike cools in less than a picosecond, considerably faster than previously recognized. An algorithm suitable for estimating cooling times in materials other than tetrahedral amorphous carbon is also presented.

Nigel A. Marks

Papers

Generalizing the environment-dependent interaction potential for carbon

Graphitization of amorphous carbons: A comparative study of interatomic potentials

Dehydroxylation of Kaolinite to Metakaolin - A Molecular Dynamics Study

Comparison of density-functional, tight-binding, and empirical methods for the simulation of amorphous carbon

Evidence for subpicosecond thermal spikes in the formation of tetrahedral amorphous carbon