There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

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

VASPKIT: A user-friendly interface facilitating high-throughput computing and analysis using VASP code

IN two previous notes1, Prof. Max Born and I have shown that one can obtain a theory of superconductivity by taking account of the fact that the interaction of the electrons with the ionic lattice is appreciable only near the boundaries of Brillouin zones, and particularly strong near the corners of these. This leads to the criterion that the metal should be superconductive if a set of corners of a Brillouin zone is lying very near the Fermi surface, considered as a sphere, which limits the region in the momentum space completely filled with electrons.

On the theory of superconductivity

Recent discovery of high-temperature superconductivity (Tc = 190 K) in sulfur hydrides at megabar pressures breaks the traditional belief on the Tc limit of 40 K for conventional superconductors, and open up the doors in searching new high-temperature superconductors in compounds made up of light elements. Selenium is a sister and isoelectronic element of sulfur, with a larger core and a weaker electronegativity. Whether selenium hydrides share similar high-temperature superconductivity remain elusive, but it is a subject of considerable interest. First-principles swarm structure predictions are performed in an effort to seek for energetically stable and metallic selenium hydrides at high pressures. We find the stable phase diagram of selenium hydrides is different from its sulfur analogy. Three stable and metallic species with stoichiometries of HSe2, HSe and H3Se are identified above ~120 GPa and they all exhibit superconductive behaviors, of which the hydrogen-rich HSe and H3Se phases show high Tc in the range of 40-106 K. Our simulations established the high-temperature superconductive nature of selenium hydrides and provided useful route for experimental verification.

Phase Diagram and High-Temperature Superconductivity of Selenium Hydrides at High Pressures

Alloy-induced reduction and anisotropy change of lattice thermal conductivity in Ruddlesden–Popper phase halide perovskites

Surface charge transfer doping (SCTD) is an alternative approach to achieving n-type doped diamonds since the n-type bulk doping of diamonds remains a challenge, but so far efficient diamond n-type SCTD has not been achieved. Here we provide a comprehensive study of the n-type SCTD of the diamond by using first-principles calculations based on the density functional theory. Taking the principle that ionization potentials of the dopants must be higher than those of the diamond, we screened a series of molecules that may be suitable for diamond n-type SCTD doping. Methyl viologen and benzyl viologen provide the largest amount of transfer electron among the common n-type SCTD dopants for the oxygen and fluorine terminated (100) surface diamond, with the electron areal densities of 2.60×1013cm−2 and 9.20×1012cm−2, respectively. It is indicated that the transferred electron amount is positively correlated with the difference between the ionization potentials of the dopants and the electron affinity of the diamond, while the density of dopants also has a positive impact with a decreasing trend. The present work provides a useful understanding of the physical mechanism for the n-type SCTD of diamonds, and benefits the development of n-type SCTD diamond materials.

First-principles screening of surface-charge-transfer molecular dopants for n-type diamond


 Flow-type landslide is one type of landslide that generally exhibits characteristics of high flow velocities, long jump distances, and poor predictability. Simulation of it facilitates propagation analysis and provides solutions for risk assessment and mitigation design. The smoothed particle hydrodynamics (SPH) method has been successfully applied to the simulation of two-dimensional (2D) and three-dimensional (3D) flow-like landslides. However, the influence of boundary resistance on the whole process of landslide failure is rarely discussed. In this study, a boundary algorithm considering the friction is proposed, and integrated into the boundary condition of the SPH method, and its accuracy is verified. Moreover, the Navier-Stokes equation combined with the non-Newtonian fluid rheology model was utilized to solve the dynamic behavior of the flow-like landslide. To verify its performance, the Shuicheng landslide event, which occurred in Guizhou, China, was taken as a case study. In the 2D simulation, a sensitivity analysis was conducted, and the results showed that the shearing strength parameters have more influence on the computation accuracy in comparison with the coefficient of viscosity. Afterwards, the dynamic characteristics of the landslide, such as the velocity and the impact area, were analyzed in the 3D simulation. The simulation results are in good agreement with the field investigations. The simulation results demonstrate that the SPH method performs well in reproducing the landslide process, and facilitates the analysis of landslide characteristics as well as the affected areas, which provides a scientific basis for conducting the risk assessment and disaster mitigation design.

/pdf/application-of-smoothed-particle-hydrodynamics-sph-for-the-2ihfheyi.pdf

Application of Smoothed Particle Hydrodynamics (SPH) for the Simulation of Flow-like Landslides on 3D Terrains

Properties of ${\text{ThCr}}_{2}{\text{Si}}_{2}$-structure ${\text{CsFe}}_{2}{\text{Sb}}_{2}$ and its alloy with Co are investigated using first principles calculations. ${\text{CsFe}}_{2}{\text{Sb}}_{2}$ is an antiferromagnetic metal at the density functional level. The electronic structure is closely related to the Fe-based superconductors. Results are discussed in relation to the Fe-based superconductors.

Electronic structure of CsFe 2 Sb 2 and its alloy with cobalt: A magnetic compound related to the iron superconductors

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