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

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

J. Appl. Cryst.の発刊に際して

We show that, for a two level system, the non-equilibrium (glassy state) entropy and the statistical (Gibbs) entropy – as defined by Takada et al. – are mathematically equivalent and therefore the equality between these two entropies shown by Takada et al. using simulations does not imply any new physics. In addition, we point out that the free energy of a glass, in the Takada et al. treatment, becomes less than the free energy of the liquid for all temperatures below the fictive temperature of the glass, a result that is clearly unphysical.

Comment on ``Residual entropy and structural disorder in glass: A two level model and a review of spatial and ensemble vs. temporal sampling'' by A. Takada, R. Conradt, and P. Richet [J. Non-Cryst. Solids, 360, 13 (2013)]

Disordered systems like liquids, gels, glasses, or granular materials are not only ubiquitous in daily life and in industrial applications but they are also crucial for the mechanical stability of cells or the transport of chemical and biological agents in living organisms [1-3]. Despite the importance of these systems, their microscopic structure is understood only on a rudimentary level, thus in stark contrast to the case of gases and crystals [1,4]. Experimental and theoretical investigations indicate that disordered systems have a structural order on the length scale of a few particle diameters but which then quickly vanishes at larger distances [5]. This conclusion is, however, based mainly on the behavior of two-point correlation functions such as the static structure factor or the radial distribution function [5.6]. Whether or not disordered systems have an order that extents to larger length scales is therefore a highly important question that is still open [7-10]. Here we use computer simulations to show that liquids have an intricate structural order given by alternating layers with icosahedral and dodecahedral symmetries and which extends to surprisingly large distances. We show that the temperature dependence of the corresponding length scale can be detected in the static structure factor, making it directly accessible to scattering experiments. These results, obtained by a novel type of four point correlation function that probes directly the particle density in three dimensions, show that liquids are far more ordered than envisaged so far but that this structural information is encoded in non-standard correlation functions.

On the Structure of Liquids: More order than expected

A recent breakthrough in glass science has been the synthesis of ultrastable glasses via physical vapor deposition techniques. These samples display enhanced thermodynamic, kinetic and mechanical stability, with important implications for fundamental science and technological applications. However, the vapor deposition technique is limited to atomic, polymer and organic glass-formers and is only able to produce thin film samples. Here, we propose a novel approach to generate ultrastable glassy configurations in the bulk, via random particle bonding, and using computer simulations we show that this method does indeed allow for the production of ultrastable glasses. Our technique is in principle applicable to any molecular or soft matter system, such as colloidal particles with tunable bonding interactions, thus opening the way to the design of a large class of ultrastable glasses. 

/pdf/creating-bulk-ultrastable-glasses-by-random-particle-bonding-k6nmsofs.pdf

Creating bulk ultrastable glasses by random particle bonding

In this article we review results of computer simulation of glasses carried out using first principles approaches, notably density functional theory. We start with a brief introduction to this method and compare the pros and cons of this approach with the ones of simulations with classical potentials. This is followed by a discussion of simulation results of various glass-forming systems that have been obtained via ab initio simulations and that demonstrate the usefulness of this approach to understand the properties of glasses on the microscopic level.

First-principles simulations of glass-formers

The structure of surfaces and interfaces of silica (SiO2) is investigated by large scale molecular dynamics computer simulations. In the case of a free silica surface, the results of a classical molecular dynamics simulation are compared to those of an ab initio method, the Car—Parrinello molecular dynamics. This comparative study allows to check the accuracy of the model potential that underlies the classical simulation. By means of a pure classical MD, the interface between amorphous and crystalline SiO2 is investigated, and as a third example the structure of a silica melt between walls is studied in equilibrium and under shear. We show that in the latter three examples important structural information such as ring size distributions can be gained from the computer simulation that is not accessible in experiments.

https://arxiv.org/pdf/cond-mat/0308151.pdf

Walter Kob

Papers

Comment on ``Residual entropy and structural disorder in glass: A two level model and a review of spatial and ensemble vs. temporal sampling'' by A. Takada, R. Conradt, and P. Richet [J. Non-Cryst. Solids, 360, 13 (2013)]

On the Structure of Liquids: More order than expected

Creating bulk ultrastable glasses by random particle bonding

First-principles simulations of glass-formers

Amorphous Silica at Surfaces and Interfaces: Simulation Studies