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

New materials capable of storing hydrogen at high gravimetric and volumetric densities are required if hydrogen is to be widely employed as a clean alternative to hydrocarbon fuels in cars and other mobile applications. With exceptionally high surface areas and chemically-tunable structures, microporous metal–organic frameworks have recently emerged as some of the most promising candidate materials. In this critical review we provide an overview of the current status of hydrogen storage within such compounds. Particular emphasis is given to the relationships between structural features and the enthalpy of hydrogen adsorption, spectroscopic methods for probing framework–H2 interactions, and strategies for improving storage capacity (188 references).

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Hydrogen storage in metal–organic frameworks

Hydrogen Storage in Metal–Organic Frameworks

Natural gas hydrates are solid, non-stoichiometric compounds of small gas molecules and water. They form when the constituents come into contact at low temperature and high pressure. The physical properties of these compounds, most notably that they are non-flowing crystalline solids that are denser than typical fluid hydrocarbons and that the gas molecules they contain are effectively compressed, give rise to numerous applications in the broad areas of energy and climate effects. In particular, they have an important bearing on flow assurance and safety issues in oil and gas pipelines, they offer a largely unexploited means of energy recovery and transportation, and they could play a significant role in past and future climate change.

Fundamental principles and applications of natural gas hydrates

High-pressure Raman, infrared, x-ray, and neutron studies show that H2 and H2O mixtures crystallize into the sII clathrate structure with an approximate H2/H2O molar ratio of 1:2. The clathrate cages are multiply occupied, with a cluster of two H2 molecules in the small cage and four in the large cage. Substantial softening and splitting of hydrogen vibrons indicate increased intermolecular interactions. The quenched clathrate is stable up to 145 kelvin at ambient pressure. Retention of hydrogen at such high temperatures could help its condensation in planetary nebulae and may play a key role in the evolution of icy bodies.

https://science.sciencemag.org/content/sci/297/5590/2247.full.pdf

Hydrogen clusters in clathrate hydrate.

Compressed under ambient temperature, graphite undergoes a transition at ∼17 gigapascals. The near K-edge spectroscopy of carbon using synchrotron x-ray inelastic scattering reveals that half of the π-bonds between graphite layers convert to σ-bonds, whereas the other half remain as π-bonds in the high-pressure form. The x-ray diffraction pattern of the high-pressure form is consistent with a distorted graphite structure in which bridging carbon atoms between graphite layers pair and form σ-bonds, whereas the nonbridging carbon atoms remain unpaired with π-bonds. The high-pressure form is superhard, capable of indenting cubic-diamond single crystals.

https://science.sciencemag.org/content/sci/302/5644/425.full.pdf

Bonding Changes in Compressed Superhard Graphite

At low temperature (T) and high pressure (P), gas molecules can be held in ice cages to form crystalline molecular compounds that may have application for energy storage. We synthesized a hydrogen clathrate hydrate, H2(H2O)2, that holds 50 g/liter hydrogen by volume or 5.3 wt %. The clathrate, synthesized at 200–300 MPa and 240–249 K, can be preserved to ambient P at 77 K. The stored hydrogen is released when the clathrate is warmed to 140 K at ambient P. Low T also stabilizes other molecular compounds containing large amounts of molecular hydrogen, although not to ambient P, e.g., the stability field for H2(H2O) filled ice (11.2 wt % molecular hydrogen) is extended from 2,300 MPa at 300 K to 600 MPa at 190 K, and that for (H2)4CH4 (33.4 wt % molecular hydrogen) is extended from 5,000 MPa at 300 K to 200 MPa at 77 K. These unique characteristics show the potential of developing low-T molecular crystalline compounds as a new means for hydrogen storage.

https://www.pnas.org/content/pnas/101/3/708.full.pdf

Hydrogen storage in molecular compounds.

3. Experimental Probes 4142 3.1. Neutron Scattering 4142 3.1.1. Structure 4142 3.1.2. Phonon Density of States 4143 3.2. Raman Scattering 4144 3.2.1. Internal ModessCrystal Field 4144 3.2.2. Rotational and Translational Modes 4145 3.3. Nuclear Magnetic Resonance 4145 3.4. Thermal Conductivity and Heat Capacity 4146 4. Theoretical Developments 4147 4.1. Semiempirical Models 4147 4.1.1. Extensions of van der Waals−Platteeuw Theory 4147

Hydrogen storage in molecular clathrates.

Evidence of life on Earth is manifestly preserved in the rock record. However, the microfossil record only extends to ∼3.5 billion years (Ga), the chemofossil record arguably to ∼3.8 Ga, and the rock record to 4.0 Ga. Detrital zircons from Jack Hills, Western Australia range in age up to nearly 4.4 Ga. From a population of over 10,000 Jack Hills zircons, we identified one >3.8-Ga zircon that contains primary graphite inclusions. Here, we report carbon isotopic measurements on these inclusions in a concordant, 4.10 ± 0.01-Ga zircon. We interpret these inclusions as primary due to their enclosure in a crack-free host as shown by transmission X-ray microscopy and their crystal habit. Their δ13CPDB of −24 ± 5‰ is consistent with a biogenic origin and may be evidence that a terrestrial biosphere had emerged by 4.1 Ga, or ∼300 My earlier than has been previously proposed.

https://www.pnas.org/content/pnas/early/2015/10/14/1517557112.full.pdf

Wendy L. Mao

Papers

Hydrogen clusters in clathrate hydrate.

Bonding Changes in Compressed Superhard Graphite

Hydrogen storage in molecular compounds.

Hydrogen storage in molecular clathrates.

Potentially Biogenic Carbon Preserved in a 4.1 Billion-Year-Old Zircon