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

If they could be easily exfoliated, layered materials would become a diverse source of two-dimensional crystals whose properties would be useful in applications ranging from electronics to energy storage. We show that layered compounds such as MoS2, WS2, MoSe2, MoTe2, TaSe2, NbSe2, NiTe2, BN, and Bi2Te3 can be efficiently dispersed in common solvents and can be deposited as individual flakes or formed into films. Electron microscopy strongly suggests that the material is exfoliated into individual layers. By blending this material with suspensions of other nanomaterials or polymer solutions, we can prepare hybrid dispersions or composites, which can be cast into films. We show that WS2 and MoS2 effectively reinforce polymers, whereas WS2/carbon nanotube hybrid films have high conductivity, leading to promising thermoelectric properties.

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Two-Dimensional Nanosheets Produced by Liquid Exfoliation of Layered Materials

Recent years have seen a rapid growth of interest by the scientific and engineering communities in the thermal properties of materials. Heat removal has become a crucial issue for continuing progress in the electronic industry, and thermal conduction in low-dimensional structures has revealed truly intriguing features. Carbon allotropes and their derivatives occupy a unique place in terms of their ability to conduct heat. The room-temperature thermal conductivity of carbon materials span an extraordinary large range--of over five orders of magnitude--from the lowest in amorphous carbons to the highest in graphene and carbon nanotubes. Here, I review the thermal properties of carbon materials focusing on recent results for graphene, carbon nanotubes and nanostructured carbon materials with different degrees of disorder. Special attention is given to the unusual size dependence of heat conduction in two-dimensional crystals and, specifically, in graphene. I also describe the prospects of applications of graphene and carbon materials for thermal management of electronics.

Thermal properties of graphene and nanostructured carbon materials

Thermoelectric materials are solid-state energy converters whose combination of thermal, electrical, and semiconducting properties allows them to be used to convert waste heat into electricity or electrical power directly into cooling and heating. These materials can be competitive with fluid-based systems, such as two-phase air-conditioning compressors or heat pumps, or used in smaller-scale applications such as in automobile seats, night-vision systems, and electrical-enclosure cooling. More widespread use of thermoelectrics requires not only improving the intrinsic energy-conversion efficiency of the materials but also implementing recent advancements in system architecture. These principles are illustrated with several proven and potential applications of thermoelectrics.

http://engin1000.pbworks.com/f/TE_rev.pdf

Cooling, heating, generating power, and recovering waste heat with thermoelectric systems.

The ab-initio theory of charge transport in semiconductors typically employs the lowest-order perturbation theory in which electrons interact with one phonon (1ph). This theory is accepted to be adequate to explain the low-field mobility of non-polar semiconductors but has not been tested extensively beyond the low-field regime. Here, we report first-principles calculations of the electric field-dependence of the electron mobility of Si as described by the warm electron coefficient, $\beta$. Although the 1ph theory overestimates the low-field mobility by only around 20%, it overestimates $\beta$ by over a factor of two over a range of temperatures and crystallographic axes. We show that the discrepancy in $\beta$ is reconciled by inclusion of on-shell iterated 2-phonon (2ph) scattering processes, indicating that scattering from higher-order electron-phonon interactions is non-negligible even in non-polar semiconductors. Further, a ~20% underestimate of the low-field mobility with 2ph scattering suggests that non-trivial cancellations may occur in the perturbative expansion of the electron-phonon interaction.

Two-phonon scattering in nonpolar semiconductors: A first-principles study of warm electron transport in Si

High electron mobility transistors are widely used as microwave amplifiers owing to their low microwave noise figure. Electronic noise in these devices is typically modeled by noise sources at the gate and drain. While consensus exists regarding the origin of the gate noise, that of drain noise is a topic of debate. Here, we report a theory of drain noise as a type of partition noise arising from real-space transfer of hot electrons from the channel to the barrier. The theory accounts for the magnitude and dependencies of the drain temperature and suggests strategies to realize devices with lower noise figure.

Theory of drain noise in high electron mobility transistors based on real-space transfer.

Transient grating (TG) spectroscopy is an important experimental technique to measure mean free path (MFP) spectra using observations of quasiballistic heat conduction. To obtain MFP spectra, the measurements must be interpreted within the framework of the frequency-dependent Boltzmann transport equation (BTE), but previous solutions have restricted validity due to simplifying assumptions. Here, we analyze heat conduction in TG using a new analytical solution of the frequency-dependent BTE that accurately describes thermal transport from the diffusive to ballistic regimes. We demonstrate that our result enables a more accurate measurement of MFP spectra and thus will lead to an improved understanding of heat conduction in solids.

Quasiballistc Heat Conduction in Transient Grating Spectroscopy

Scientific Reports 7: Article number: 44254; published online: 14 March 2017; updated: 02 May 2017 This Article contains errors in Figures 3, 4 and 5 where the graphs were labelled incorrectly. The correct Figures 3, 4 and 5 appear below as Figures 1, 2 and 3 respectively.

/pdf/corrigendum-thermal-transport-in-nanocrystalline-si-and-sige-43b56qveea.pdf

Corrigendum: Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation.

Which sizes of nanoparticles embedded in a crystalline solid yield the lowest thermal conductivity? Nanoparticles have long been demonstrated to reduce the thermal conductivity of crystals by scattering phonons, but most previous works assumed the nanoparticles to have a single size. Here, we use optimization methods to show that the best nanoparticle size distribution to scatter the broad thermal phonon spectrum is not a similarly broad distribution but rather several discrete peaks at well-chosen nanoparticle radii. For SiGe, the best size distribution yields a thermal conductivity below that of amorphous silicon. Further, we demonstrate that a simplified distribution yields nearly the same low thermal conductivity and can be readily fabricated. Our work provides important insights into how to manipulate the full spectrum of phonons and will guide the design of more efficient thermoelectric materials.

Austin J. Minnich

Papers

Two-phonon scattering in nonpolar semiconductors: A first-principles study of warm electron transport in Si

Theory of drain noise in high electron mobility transistors based on real-space transfer.

Quasiballistc Heat Conduction in Transient Grating Spectroscopy

Corrigendum: Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation.

The Best Nanoparticle Size Distribution for Minimum Thermal Conductivity