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

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

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QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials

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

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

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Scalable molecular dynamics with NAMD

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Scalable Molecular Dynamics with NAMD

Graphene, a newly discovered material with unusual electrical and optical properties, has attracted interest for a number of potential applications. One of the most actively pursued applications is using graphene as a transparent conducting electrode for use in solar cells, displays or touch screens. In this work, two studies are pursued in parallel to explore the electrical and optical properties of graphene. Graphene was prepared on copper by the standard chemical vapor deposition (CVD) method [1], the preparation procedure and conditions are described in [2]. The effect of chemical p-type doping on graphene stacks was studied in order to reduce the sheet resistance of graphene. The doping decreases the sheet resistance by a factor of 3, yielding films comprised of eight stacked layers with a sheet resistance of 90 Ω/ at a transmittance of 80% [2]. A theoretical model that accurately describes the stacked graphene film system as a resistor network was also developed [2]. The experimental data shows a linear increase in conductivity with the number of graphene layers, indicating that each layer provides an additional transport channel, in good agreement with the theoretical model (Fig. 1).

Electrical and optical properties of graphene mono- and multi-layers; towards graphene-based optoelectronics

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The doping mechanism in graphene

The Grand Challenge problem presented by simulation of perpendicular magnetic recording requires an algorithm scaling close to linearly with the number of elements in the simulation cell. We derive an appropriate algorithm based on 2D FFT's of field and magnetization in the disk plane, combined with a novel treatment of field propagation in the z-direction. The near-linear scaling of the algorithm with number of elements is demonstrated by computer experiments. Although the computation contains a strong dataparallel element, in that an ensemble of 20 members is required in order to achieve statistics, some parallelization is desirable. Adequate parallelization is achieved on an SP machine. On an Intel cluster, speed-up saturation is observed, and is understood in terms of bandwidth limitations.

Performance of a novel algorithm for perpendicular magnetic recording simulation

Es werden eine Vorrichtung, ein System und ein Verfahren zum Zerschneiden eines linearen geladenen Polymers innerhalb einer Nanopore bereitgestellt. There are provided a nanopore within a device, a system and a method of cutting a linear charged polymer. Es wird eine erste Spannung angelegt, um ein elektrisches Feld in einer ersten Richtung zu erzeugen. There is applied a first voltage to generate an electric field in a first direction. Es wird eine zweite Spannung angelegt, um ein elektrisches Feld in einer zweiten Richtung zu erzeugen, und die erste Richtung ist der zweiten Richtung entgegengesetzt. There is applied a second voltage to generate an electric field in a second direction and the first direction is opposite the second direction. Wenn das elektrische Feld in der ersten Richtung und das elektrische Feld in der zweiten Richtung an ein lineares geladenes Polymer innerhalb einer Nanopore angelegt werden, wird das lineare geladene Polymer an einer Stelle mit einer vorgegebenen Genauigkeit zerschnitten. When the electric field in the first direction and the electric field can be applied in the second direction to a linear charged polymer within a nanopore, the linear charged polymer is cut at a point with a given accuracy.

Nanoporeneinheit zum Zerschneiden langer DNS-Moleküle in Fragmente Nanopores unit for cutting long DNA molecules into fragments

Eine Nanorohren-Graphen-Hybriddunnschicht und ein Verfahren zum Ausbilden einer gereinigten Nanorohren-Graphen-Hybriddunnschicht. Das Verfahren beinhaltet ein Abscheiden einer Nanorohren-Dunnschicht uber einem Substrat, um eine Schicht einer Nanorohren-Dunnschicht zu erzeugen, ein Entfernen von Verunreinigungen von einer Oberflache der Schicht der Nanorohren-Dunnschicht, die das Substrat nicht beruhrt, um eine gereinigte Schicht einer Nanorohren-Dunnschicht zu erzeugen, ein Abscheiden einer Schicht Graphen uber der gereinigten Schicht der Nanorohren-Dunnschicht, um eine Nanorohren-Graphen-Hybriddunnschicht zu erzeugen, und ein Entfernen von Verunreinigungen von einer Oberflache der Nanorohren-Graphen-Hybriddunnschicht, um eine gereinigte Nanorohren-Graphen-Hybriddunnschicht zu erzeugen, wobei die Hybriddunnschicht eine verbesserte elektrische Leistungsfahigkeit aufweist. Ein weiteres Verfahren beinhaltet ein Abscheiden einer Nanorohren-Dunnschicht uber einer Metallfolie, um eine Schicht einer Nanorohren-Dunnschicht zu erzeugen, ein Platzieren der Metallfolie mit der abgeschiedenen Nanorohren-Dunnschicht in einem Ofen fur chemische Gasphasenabscheidung, um Graphen auf der Nanorohren-Dunnschicht aufzuwachsen, um eine Nanorohren-Graphen-Hybriddunnschicht auszubilden, und ein Ubertragen der Nanorohren-Graphen-Hybriddunnschicht uber ein Substrat.

Glenn J. Martyna

Papers

Electrical and optical properties of graphene mono- and multi-layers; towards graphene-based optoelectronics

The doping mechanism in graphene

Performance of a novel algorithm for perpendicular magnetic recording simulation

Nanoporeneinheit zum Zerschneiden langer DNS-Moleküle in Fragmente Nanopores unit for cutting long DNA molecules into fragments

Transparenter Kohlenstoff-Nanoröhren-Graphen-Hybridleiter und Feldeffekttransistor