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.

Materials that possess low density, low thermal conductivity, and high stiffness are desirable for engineering applications, but most materials cannot realize these properties simultaneously due to the coupling between them. Nanotrusses, which consist of hollow nanoscale beams architected into a periodic truss structure, can potentially break these couplings due to their lattice architecture and nanoscale features. In this work, we study heat conduction in the exact nanotruss geometry by solving the frequency-dependent Boltzmann transport equation using a variance-reduced Monte Carlo algorithm. We show that their thermal conductivity can be described with only two parameters, solid fraction and wall thickness. Our simulations predict that nanotrusses can realize unique combinations of mechanical and thermal properties that are challenging to achieve in typical materials.

Heat conduction in multifunctional nanotrusses studied using Boltzmann transport equation

Simulating complex molecules and materials is an anticipated application of quantum devices. With strong quantum advantage demonstrated in artiﬁcial tasks, we examine how such advantage translates into modeling physical problems of correlated electronic structure. We simulate static and dynamical electronic structure on a superconducting quantum processor derived from Google’s Sycamore architecture for two representative correlated electron problems: the nitrogenase iron-sulfur molecular clusters, and α -ruthenium trichloride, a proximate spin-liquid material. To do so, we simplify the electronic structure into low-energy spin models that ﬁt on the device. With exten-sive error mitigation and assistance from classically simulated data, we achieve quantitatively meaningful results deploying about 1/5 of the gate resources used in artiﬁcial quantum advantage experiments on a similar architecture. gate a the Our serves to convert measures of into a physically

Simulating challenging correlated molecules and materials on the Sycamore quantum processor

Radiative heat transport between materials supporting surface-phonon polaritons is greatly enhanced when the materials are placed at subwavelength separation as a result of the contribution of near-field surface modes. However, the enhancement is limited to small separations due to the evanescent decay of the surface waves. In this work, we propose and numerically demonstrate an active scheme to extract these modes to the far field. Our approach exploits the monochromatic nature of near-field thermal radiation to drive a transition in a laser gain medium, which, when coupled with external optical pumping, allows the resonant surface mode to be emitted into the far field. Our study demonstrates an approach to manipulate thermal radiation that could find applications in thermal management.

Active thermal extraction of near-field thermal radiation

The heat-carrying acoustic excitations of amorphous silicon are of interest because their mean free paths may approach micron scales at room temperature. Despite extensive investigation, the origin of the weak acoustic damping in the heat-carrying frequencies remains a topic of debate. Here, we report measurements of the thermal conductivity mean free path accumulation function in amorphous silicon thin films from 60 - 315 K using transient grating spectroscopy. With additional picosecond acoustics measurements and considering the known frequency-dependencies of damping mechanisms in glasses, we reconstruct the mean free paths from $\sim 0.1-3$ THz. The mean free paths are independent of temperature and exhibit a Rayleigh scattering trend over most of this frequency range. The observed trend is inconsistent with the predictions of numerical studies based on normal mode analysis but agrees with diverse measurements on other glasses. The micron-scale MFPs in amorphous Si arise from the absence of anharmonic or two-level system damping in the sub-THz frequencies, leading to heat-carrying acoustic excitations with room-temperature damping comparable to that of other glasses at cryogenic temperatures.

/pdf/origin-of-micron-scale-propagation-lengths-of-heat-carrying-1ftnex0xa5.pdf

Origin of micron-scale propagation lengths of heat-carrying acoustic excitations in amorphous silicon

Molybdenum disulfide (MoS2), a member of transition-metal dichalcogenide family, is of intense interest due to its unique electronic and thermoelectric properties. However, reports of its in-plane thermal conductivity vary due to the difficulty of in-plane thermal conductivity measurements on thin films, and an experimental measurement of the in-plane sound velocity has not been reported. Here, we use time-resolved transient grating spectroscopy to simultaneously measure the in-plane elastic and thermal properties of free-standing MoS2 membranes at room temperature. We obtain a longitudinal acoustic phonon velocity of 7000 ± 40 m s−1 and an in-plane thermal conductivity of 74 ± 21 W m−1K−1. Our measurements provide useful insights into the elastic and thermal properties of MoS2 and demonstrate the capability of transient grating spectroscopy to investigate the in-plane vibrational properties of van der Waals materials that are challenging to characterize with conventional methods.

Austin J. Minnich

Papers

Heat conduction in multifunctional nanotrusses studied using Boltzmann transport equation

Simulating challenging correlated molecules and materials on the Sycamore quantum processor

Active thermal extraction of near-field thermal radiation

Origin of micron-scale propagation lengths of heat-carrying acoustic excitations in amorphous silicon

In-plane Elastic and thermal properties of free-standing Molybdenum Disulfide Membranes measured using Ultrafast Transient Grating Spectroscopy