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

The use of individual molecules as functional electronic devices was first proposed in the 1970s (ref 1) Since then, molecular electronics2,3 has attracted much interest, particularly because it could lead to conceptually new miniaturization strategies in the electronics and computer industry The realization of single-molecule devices has remained challenging, largely owing to difficulties in achieving electrical contact to individual molecules Recent advances in nanotechnology, however, have resulted in electrical measurements on single molecules4,5,6,7 Here we report the fabrication of a field-effect transistor—a three-terminal switching device—that consists of one semiconducting8,9,10 single-wall carbon nanotube11,12 connected to two metal electrodes By applying a voltage to a gate electrode, the nanotube can be switched from a conducting to an insulating state We have previously reported5 similar behaviour for a metallic single-wall carbon nanotube operated at extremely low temperatures The present device, in contrast, operates at room temperature, thereby meeting an important requirement for potential practical applications Electrical measurements on the nanotube transistor indicate that its operation characteristics can be qualitatively described by the semiclassical band-bending models currently used for traditional semiconductor devices The fabrication of the three-terminal switching device at the level of a single molecule represents an important step towards molecular electronics

Room-temperature transistor based on a single carbon nanotube

Ionization of highly compressed ammonia has previously been predicted by computation. Here, the authors provide experimental evidence for this autoionization process at high pressures, showing the transformation of molecular ammonia into ammonium amide.

/pdf/ammonia-as-a-case-study-for-the-spontaneous-ionization-of-a-43dukoq5c2.pdf

Ammonia as a case study for the spontaneous ionization of a simple hydrogen-bonded compound

We have developed an efficient and reliable methodology for crystal structure prediction, merging ab initio total-energy calculations and a specifically devised evolutionary algorithm. This method allows one to predict the most stable crystal structure and a number of low-energy metastable structures for a given compound at any P-T conditions without requiring any experimental input. Extremely high (nearly 100%) success rate has been observed in a few tens of tests done so far, including ionic, covalent, metallic, and molecular structures with up to 40 atoms in the unit cell. We have been able to resolve some important problems in high-pressure crystallography and report a number of new high-pressure crystal structures (stable phases: epsilon-oxygen, new phase of sulphur, new metastable phases of carbon, sulphur and nitrogen, stable and metastable phases of CaCO3). Physical reasons for the success of this methodology are discussed.

Crystal structure prediction using ab initio evolutionary techniques: principles and applications.

Our ability to interpret seismic observations including the seismic discontinuities and the density and velocity profiles in the earth's interior is critically dependent on the accuracy of pressure measurements up to 364 GPa at high temperature. Pressure scales based on the reduced shock-wave equations of state alone may predict pressure variations up to 7% in the megabar pressure range at room temperature and even higher percentage at high temperature, leading to large uncertainties in understanding the nature of the seismic discontinuities and chemical composition of the earth's interior. Here, we report compression data of gold (Au), platinum (Pt), the NaCl-B2 phase, and solid neon (Ne) at 300 K and high temperatures up to megabar pressures. Combined with existing experimental data, the compression data were used to establish internally consistent thermal equations of state of Au, Pt, NaCl-B2, and solid Ne. The internally consistent pressure scales provide a tractable, accurate baseline for comparing high pressure-temperature experimental data with theoretical calculations and the seismic observations, thereby advancing our understanding fundamental high-pressure phenomena and the chemistry and physics of the earth's interior.

https://www.pnas.org/content/pnas/104/22/9182.full.pdf

Toward an internally consistent pressure scale.

High-pressure melting, phase transitions and structures of iron have been studied to 84 GPa and 3500 K with an improved laser heated diamond anvil cell technique and in situ high P-T x-ray diffraction. At pressures below 60 GPa, the lower bound on the melting curve is close to those measured by Boehler [1993] and Saxena et al. [1993]; however, at pressures above 60 GPa our data indicate melting at higher temperatures than these studies, but still lower than the melting curve of Williams et al [1990]. The e-γ-1 triple point is 60(±5) GPa and 2800(±200) K, based on our data of the e-γ phase transition and the observation of melting by in situ x-ray diffraction. No solid phases other than e-Fe and γ-Fe were observed in situ at high temperatures (>1000 K) and pressures to 84 GPa. However, the diffraction patterns of temperature quenched products at high pressure can be fit to other structures such as dhcp.

https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/97GL03776

Melting and crystal structure of iron at high pressures and temperatures

We report phonon densities of states (DOS) of iron measured by nuclear resonant inelastic x-ray scattering to 153 gigapascals and calculated from ab initio theory. Qualitatively, they are in agreement, but the theory predicts density at higher energies. From the DOS, we derive elastic and thermodynamic parameters of iron, including shear modulus, compressional and shear velocities, heat capacity, entropy, kinetic energy, zero-point energy, and Debye temperature. In comparison to the compressional and shear velocities from the preliminary reference Earth model (PREM) seismic model, our results suggest that Earth's inner core has a mean atomic number equal to or higher than pure iron, which is consistent with an iron-nickel alloy.

/pdf/phonon-density-of-states-of-iron-up-to-153-gigapascals-4k4yykszs3.pdf

Phonon Density of States of Iron up to 153 Gigapascals

We describe a laser heated diamond anvil cell system at the GeoSoilEnviroCARS sector at the Advanced Photon Source. The system can be used for in situ x-ray measurements at simultaneously ultrahigh pressures (to >150 GPa) and ultrahigh temperatures (to >4000 K). Design goals of the laser heating system include generation of a large heating volume compared to the x-ray beam size, minimization of the sample temperature gradients both radially and axially in the diamond anvil cell, and maximization of heating stability. The system is based on double-sided laser heating technique and consists of two Nd:YLF lasers with one operating in TEM00 mode and the other in TEM01* mode, optics to heat the sample from both sides, and two spectroradiometric systems for temperature measurements on both sides. When combined with an x-ray microbeam (3–10 μm) technique, a temperature variation of less than 50 K can be achieved within an x-ray sampled region for longer than 10 min. The system has been used to obtain in situ str...

Guoyin Shen

Papers

Toward an internally consistent pressure scale.

Melting and crystal structure of iron at high pressures and temperatures

Phonon Density of States of Iron up to 153 Gigapascals

Laser heated diamond cell system at the Advanced Photon Source for in situ x-ray measurements at high pressure and temperature

Thermodynamic Data on Oxides and Silicates