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.

/pdf/two-dimensional-nanosheets-produced-by-liquid-exfoliation-of-4215j2k2b1.pdf

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.

This paper presents thermal characterization results for three high-power THz Schottky frequency multipliers in the temperature range of 20–380 K. All measured multipliers have different substrates: a 5- $\mu\hbox{m}$ -thick GaAs membrane, a 40- $\mu\hbox{m}$ -thick GaAs substrate, and a 5- $\mu\hbox{m}$ -thick GaAs membrane glued to a 20- $\mu\hbox{m}$ -thick CVD diamond substrate with polymer bonding agent. The thermal characterization results include such parameters as the maximum average junction temperature of the anodes, device total thermal resistance, and device cooling (or heating) times. The results enable designers to better optimize their devices for the maximum power level and temperature range and system engineers to better predict the overall performance of the system in an environment, where the ambient conditions might change. For example, from the thermal resistance point of view the GaAs membrane on diamond substrate clearly outperforms the device on GaAs membrane alone at room temperature or above. However, perhaps surprisingly, at temperatures below 125 K, the GaAs membrane is on par, or even has lower thermal resistance than the membrane on diamond.

Thermal Characterization of Substrate Options for High-Power THz Multipliers Over a Broad Temperature Range

Spontaneously formed natural nanostructures are responsible for a glass-like thermal conductivity in a perfectly crystalline semiconductor

Thermal transport: Naturally glassy crystals

We describe a coupled cluster framework for coupled systems of electrons and phonons. Neutral and charged excitations are accessed via the equation-of-motion version of the theory. Benchmarks on the Hubbard-Holstein model allow us to assess the strengths and weaknesses of different coupled cluster approximations which generally perform well for weak to moderate coupling. Finally, we report progress towards an implementation for {\it ab initio} calculations on solids, and present some preliminary results on finite-size models of diamond. We also report the implementation of electron-phonon coupling matrix elements from crystalline Gaussian type orbitals (cGTO) within the PySCF program package.

/pdf/a-coupled-cluster-framework-for-electrons-and-phonons-2yw4e5wo37.pdf

A coupled cluster framework for electrons and phonons

Recently, we proposed an active thermal extraction (ATX) scheme that enables thermally populated surface phonon polaritons to escape into the far-field. The concept is based on a fluorescence upconversion process that also occurs in laser cooling of solids (LCS). Here, we present a generalized analysis of our scheme using the theoretical framework for LCS. We show that both LCS and ATX can be described with the same mathematical formalism by replacing the electron-phonon coupling parameter in LCS with the electron-photon coupling parameter in ATX. Using this framework, we compare the ideal efficiency and power extracted for the two schemes and examine the parasitic loss mechanisms. This work advances the application of ATX to manipulate near-field thermal radiation for applications such as temperature sensing and active radiative cooling.

/pdf/active-thermal-extraction-and-temperature-sensing-of-near-4ck59icr4v.pdf

Active Thermal Extraction and Temperature Sensing of Near-field Thermal Radiation

The fundamental limits of the microwave noise performance of high electron-mobility transistors (HEMTs) are of scientific and practical interest for applications in radio astronomy and quantum computing. Self-heating at cryogenic temperatures has been reported to be a limiting mechanism for the noise, but cryogenic cooling strategies to mitigate it, for instance, using liquid cryogens, have not been evaluated. Here, we report microwave noise measurements of a packaged two-stage amplifier with GaAs metamorphic HEMTs immersed in normal and superfluid [Formula: see text]He baths and in vacuum from 1.6 to 80 K. We find that these liquid cryogens are unable to mitigate the thermal noise associated with self-heating. Considering this finding, we examine the implications for the lower bounds of cryogenic noise performance in HEMTs. Our analysis supports the general design principle for cryogenic HEMTs of maximizing gain at the lowest possible power.

/pdf/self-heating-of-cryogenic-high-electron-mobility-transistor-3vlwoomo.pdf

Austin J. Minnich

Papers

Thermal Characterization of Substrate Options for High-Power THz Multipliers Over a Broad Temperature Range

Thermal transport: Naturally glassy crystals

A coupled cluster framework for electrons and phonons

Active Thermal Extraction and Temperature Sensing of Near-field Thermal Radiation

Self-heating of cryogenic high electron-mobility transistor amplifiers and the limits of microwave noise performance