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

In this review we intend to provide a relatively comprehensive summary of the work of supramolecular hydrogelators after 2004 and to put emphasis particularly on the applications of supramolecular hydrogels/hydrogelators as molecular biomaterials. After a brief introduction of methods for generating supramolecular hydrogels, we discuss supramolecular hydrogelators on the basis of their categories, such as small organic molecules, coordination complexes, peptides, nucleobases, and saccharides. Following molecular design, we focus on various potential applications of supramolecular hydrogels as molecular biomaterials, classified by their applications in cell cultures, tissue engineering, cell behavior, imaging, and unique applications of hydrogelators. Particularly, we discuss the applications of supramolecular hydrogelators after they form supramolecular assemblies but prior to reaching the critical gelation concentration because this subject is less explored but may hold equally great promise for helping ...

Supramolecular Hydrogelators and Hydrogels: From Soft Matter to Molecular Biomaterials

Journal of Physics Condensed Matter: Preface

Optimum structure with homogeneous optimum truss-like material

The transport behavior of water molecules inside a model carbon nanotube is investigated by using nonequilibrium molecular dynamcis (NMED) simulations. The shearing stress between the nanotube wall and the water molecules is identified as a key factor in determining the nanofluidic properties. Due to the effect of nanoscale confinement, the effective shearing stress is not only size sensitive but also strongly dependent on the fluid flow rate. Consequently, the nominal viscosity of the confined water decreases rapidly as the tube radius is reduced or when a faster flow rate is maintained. An infiltration experiment on a nanoporous carbon is performed to qualitatively validate these findings.

/pdf/nanoscale-fluid-transport-size-and-rate-effects-3oijypthoy.pdf

Nanoscale Fluid Transport: Size and Rate Effects

Because of its ultrahigh specific capacity, lithium metal holds great promise for revolutionizing current rechargeable battery technologies. Nevertheless, the unavoidable formation of dendritic Li, as well as the resulting safety hazards and poor cycling stability, have significantly hindered its practical applications. A mainstream strategy to solve this problem is introducing porous media, such as solid electrolytes, modified separators, or artificial protection layers, to block Li dendrite penetration. However, the scientific foundation of this strategy has not yet been elucidated. Herein, using experiments and simulation we analyze the role of the porous media in suppressing dendritic Li growth and probe the underlying fundamental mechanisms. It is found that the tortuous pores of the porous media, which drastically reduce the local flux of Li+ moving toward the anode and effectively extend the physical path of dendrite growth, are the key to achieving the nondendritic Li growth. On the basis of the t...

Suppressing Dendritic Lithium Formation Using Porous Media in Lithium Metal-Based Batteries.

In the current study, we analyze the motion of pressurized water molecules in nanopores of a well-crystallized, hydrophobic zeolite using both experiment and molecular dynamics simulation. It is discovered that, contradictory to the prediction of the classic Laplace-Young equation, the required infiltration pressure is highly dependent on the infiltration volume. A modified Laplace-Young equation is developed to take into consideration the effective solid-liquid interfacial tension, the thermal energy exchange, as well as the variation in configuration of confined liquid molecules. The last two factors are significant only when the nanopore diameter is comparable with the liquid molecule size. It is also remarkable that the infiltrated liquid molecules, when confined in the nanoenvironment, could transform from a single-chain conformation to a double-helical structure as the pressure increases, accompanied by an abrupt system free energy change that leads to different pressure-induced transport behaviors.

/pdf/pressurized-liquid-in-nanopores-a-modified-laplace-young-4vvp9rfxco.pdf

Pressurized Liquid in Nanopores: A Modified Laplace-Young Equation

Reducing the thermal conductivity of nanowires may enhance their already exciting efficiency of thermoelectric energy conversion. Using molecular dynamics simulations, we demonstrate that the thermal conductivity of silicon nanowires could be significantly decreased by patterning (or etching) induced roughness of the nanowire surfaces. The type, amplitude, and wavelength of the surface roughness all have profound effects, and the thermal conductivity could be reduced more when the wavelength is smaller or the amplitude is larger. Such an effect of roughness on the thermal conductivity is furthermore found to be coupled with the effects of nanowire cross-sectional size and length. Typically, the roughness effect is more prominent in longer and larger nanowires.

Ling Liu

Papers

Optimum structure with homogeneous optimum truss-like material

Nanoscale Fluid Transport: Size and Rate Effects

Suppressing Dendritic Lithium Formation Using Porous Media in Lithium Metal-Based Batteries.

Pressurized Liquid in Nanopores: A Modified Laplace-Young Equation

Effect of surface roughness on thermal conductivity of silicon nanowires