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

Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software

/pdf/advanced-capabilities-for-materials-modelling-with-quantum-40poaosrve.pdf

Advanced capabilities for materials modelling with Quantum ESPRESSO.

Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

/pdf/advanced-capabilities-for-materials-modelling-with-quantum-1mm65lmkt8.pdf

Advanced capabilities for materials modelling with Quantum ESPRESSO

Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.

/pdf/advances-in-methods-and-algorithms-in-a-modern-quantum-29c5vso11m.pdf

Advances in methods and algorithms in a modern quantum chemistry program package

Quantum-mechanical integral and differential cross-sections have been calculated for the title reaction at the two collision energies (Ecoll=1.35 and 1.98 kcal mol-1) studied in the 1985 molecular beam experiment of Lee and co-workers, using the new abinitio potential-energy surface of Stark and Werner. The DF+H product channel is found to behave essentially classically: the present quantum-mechanical angular distributions for this channel are in good agreement with both the earlier quasi-classical trajectory results of Aoiz and co-workers on the same potential-energy surface and the results of the molecular beam experiment. However, the HF+D product channel in which the light H atom is transferred between two heavier atoms is inherently more quantum-mechanical: our computed angular distributions for this channel differ significantly from the quasi-classical trajectory results and agree better with the results of the experiment (especially at the higher of the two experimental collision energies). The main quantum-mechanical effect that is identified in the calculations is a reactive scattering resonance that gives rise to a pronounced forward-scattering peak in the calculated F+HD(v=0, j=0)→HF(v′=3)+D differential cross-section. The influence of this resonance on the reaction dynamics is discussed in some detail, together with the implications of our results at the lower of the two collision energies for an improvement to the Stark–Werner potential-energy surface.

Quantum mechanical angular distributions for the F+HD reaction

How to observe the elusive resonances in F + H2 reactive scattering

A leapfrog carbon cluster can be constructed geometrically by omnicapping and dualising a polyhedral parent cluster with one third the number of carbon atoms. In this paper the Huckel molecular orbital energy levels of leapfrog fullerenes, and other related leapfrog carbon clusters, are investigated analytically using graph theory. It is proved in particular that all trivalent leapfrog clusters have antibonding lowest unoccupied molecular orbitals (LUMOs), and that all trivalent leapfrog clusters containing at least one ring of r≠ 3k atoms have bonding highest occupied molecular orbitals (HOMOs). More generally, all trivalent leapfrog clusters have bonding or non-bonding HOMOs. A chemically significant corollary is that all trivalent leapfrog clusters, irespective of their ring counts, are closed shell.

David E. Manolopoulos

Papers

Quantum mechanical angular distributions for the F+HD reaction

How to observe the elusive resonances in F + H2 reactive scattering

Electronic stability of fullerenes: eigenvalue theorems for leapfrog carbon clusters

Structural proposals for endohedral metal—fullerene complexes

Possible symmetries of fullerene structures