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

Dopant defects in semiconductors can trap charge carriers or ionize to produce charge carriers─playing a critical role in electronic transport. Halide perovskites are a technologically important semiconductor family with a large pressure response. Yet, to our knowledge, the effect of high pressures on defects in halide perovskites has not been experimentally investigated. Here, we study the structural, optical, and electronic consequences of compressing the small-bandgap double perovskites Cs2AgTlX6 (X = Cl or Br) up to 56 GPa. Mild compression to 1.7 GPa increases the conductivity of Cs2AgTlBr6 by ca. 1 order of magnitude and decreases its bandgap from 0.94 to 0.7 eV. Subsequent compression yields complex optoelectronic behavior: the bandgap varies by 1.2 eV and conductivity ranges by a factor of 104. These conductivity changes cannot be explained by the evolving bandgap. Instead, they can be understood as tuning of the bromine vacancy defect with pressure─varying between a delocalized shallow defect state with a small ionization energy and a localized deep defect state with a large ionization energy. Activation energy measurements reveal that the shallow-to-deep defect transition occurs near 1.5 GPa, well before the cubic-to-tetragonal phase transition. An analysis of the orbital interactions in Cs2AgTlBr6 illustrates how the bromine vacancy weakens the adjacent Tl s-Br p antibonding interaction, driving the shallow-to-deep defect transition. Our orbital analysis leads us to propose that halogen vacancies are most likely to be shallow donors in halide double perovskites that have a conduction band derived from the octahedral metal's s orbitals.

Tuning Defects in a Halide Double Perovskite with Pressure.

Natural kamacite samples (Fe92.5Ni7.5) from a fragment of the Gibeon meteorite were studied as a proxy material for terrestrial cores to examine phase transition kinetics under shock compression for a range of different pressures up to 140 GPa. In situ time-resolved X-ray diffraction (XRD) data were collected of a body-centered cubic (bcc) kamacite section that transforms to the high-pressure hexagonal close-packed (hcp) phase with sub-nanosecond temporal resolution. The coarse-grained crystal of kamacite rapidly transformed to highly oriented crystallites of the hcp phase at maximum compression. The hcp phase persisted for as long as 9.5 ns following shock release. Comparing the c/a ratio with previous static and dynamic work on Fe and Fe-rich Fe-Ni alloys, it was found that some shots exhibit a larger than ideal c/a ratio, up to nearly 1.65. This work represents the first time-resolved laser shock compression structural study of a natural iron meteorite, relevant for understanding the dynamic material properties of metallic planetary bodies during impact events and Earth’s core elasticity.

https://www.mdpi.com/2075-163X/11/6/567/pdf

Ultrafast X-ray Diffraction Study of a Shock-Compressed Iron Meteorite above 100 GPa

Elasticity of iron-rich silicate in Earth’s D″ layer

Polyamorphism discovered in lanthanide-rich metallic glasses (MGs) has been attributed to the electronic transition of the lanthanide element as a solvent element. In this work, we report that pressure-induced polyamorphism still exists in a Ce-poor Al93Ce7 binary MG where the 4f electron element serves as a solute and solute–solute avoidance is expected. The polyamorphic transition, observed by in situ high-pressure synchrotron x-ray diffraction, is accompanied by a volume collapse of ∼0.78% and occurs over a narrow pressure range from ∼0.8 to ∼1.8 GPa. Further synchrotron Ce L3-edge x-ray absorption spectroscopy measurements reveal that pressure-induced 4f electron delocalization underlies the polyamorphic transition. Molecular dynamics simulations confirm that the Ce atoms in the MG are completely isolated by the solvent Al atoms. This result demonstrates that 4f element-bearing alloys with extremely dilute concentrations can also exhibit polyamorphic states originating from electronic transitions, extending the compositional space of polyamorphism of MGs into very dilute regions. Our work suggests that tunable properties under compressive stress could be achieved in MGs by even minor doping of elements prone to electronic transitions.

Polyamorphism in a solute-lean Al–Ce metallic glass

Mn$_3$O$_4$ is a spin frustrated magnet that adopts a tetragonally distorted spinel structure at ambient conditions and a CaMn$_2$O$_4$-type postspinel structure at high pressure. We conducted both optical measurements and \emph{ab} \emph{initio} calculations, and systematically studied the electronic band structures of both the spinel and postspinel Mn$_3$O$_4$ phases. For both phases, theoretical electronic structures are consistent with the optical absorption spectra, and display characteristic band-splitting of the conduction band. The band gap obtained from the absorption spectra is 1.91(6) eV for the spinel phase, and 0.94(2) eV for the postspinel phase. Both phases are charge-transfer type insulators. The Mn 3\emph{d} $t_2$$_g$ and O 2\emph{p} form antibonding orbitals situated at the conduction band with higher energy.

Wendy L. Mao

Papers

Tuning Defects in a Halide Double Perovskite with Pressure.

Ultrafast X-ray Diffraction Study of a Shock-Compressed Iron Meteorite above 100 GPa

Elasticity of iron-rich silicate in Earth’s D″ layer

Polyamorphism in a solute-lean Al–Ce metallic glass

Electronic structure of spin frustrated magnets: Mn$_3$O$_4$ spinel and postspinel