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

A doped, passivated graphene nanomesh includes a graphene nanomesh, a plurality of nanoholes formed in a graphene sheet, and a plurality of carbon atoms which are formed adjacent to the plurality of nanoholes; a passivating element bonded to the plurality of carbon atoms; and a dopant bonded to the passivating element, the dopant comprising one of an electron-donating element for making the graphene nanomesh an n-doped graphene nanomesh, and an electron-accepting element for making the graphene nanomesh a p-doped graphene nanomesh.

Doped, passivated graphene nanomesh, method of making the doped, passivated graphene nanomesh, and semiconductor device including the doped, passivated graphene nanomesh

A nanodevice includes a reservoir filled with a conductive fluid and a membrane separating the reservoir. The membrane includes an insulating layer. A nanopore is formed through the membrane, and an organic coating is provided on the insulating layer to form a transient bond to a DNA molecule in the nanopore. The transient bond is stronger than thermal motion, such that the transient bond can hold the DNA molecule against the thermal motion. When a voltage is applied across the membrane, the voltage will break the transient bond to move the DNA molecule through the nanopore in a controllable state.

Dna motion control based on nanopore with organic coating forming transient bonding to dna

A fine grained parallel smooth particle mesh Ewald algorithm for biophysical simulation studies: Application to the 6-D torus QCDOC supercomputer

The Piezoelectronic Transistor (PET) has been proposed as a post-CMOS device for fast, low-power switching. In this device, the piezoresistive channel is metalized via the expansion of a relaxor piezoelectric element to turn the device on. The mixed-valence compound SmSe is a good choice of PET channel material because of its isostructural pressure-induced continuous metal insulator transition, which is well characterized in bulk single crystals. Prediction and optimization of the performance of a realistic, nano-scaled PET based on SmSe requires the understanding of quantum confinement, tunneling, and the effect of metal interface. In this work, a computationally efficient empirical tight binding (ETB) model is developed for SmSe to study quantum transport in these systems and the scaling limit of PET channel lengths. Modulation of the SmSe band gap under pressure is successfully captured by ETB, and ballistic conductance shows orders of magnitude change under hydrostatic strain, supporting operability of the PET device at nanoscale.

Electron transport in nano-scaled piezoelectronic devices

The potentials and forces that govern the interaction of atoms and molecules with each other, and with their environment, are crucial for understanding and simulating complex condensed matter systems. At the same time, they are complicated and hard to describe at a microscopic level. This review gives a pedagogical introduction to a method for treating these interactions in an effective manner that can be used for simulations of noble gas fluids and solids, as well as water, and has potential for applications to more complicated systems.

Glenn J. Martyna

Papers

Doped, passivated graphene nanomesh, method of making the doped, passivated graphene nanomesh, and semiconductor device including the doped, passivated graphene nanomesh

Dna motion control based on nanopore with organic coating forming transient bonding to dna

A fine grained parallel smooth particle mesh Ewald algorithm for biophysical simulation studies: Application to the 6-D torus QCDOC supercomputer

Electron transport in nano-scaled piezoelectronic devices

Electronic coarse graining: Predictive atomistic modeling of condensed matter