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 use molecular dynamics computer simulations to study the equilibrium properties of the surface of amorphous silica. Two types of geometries are investigated: (i) clusters with different diameters (13.5, 19, and 26.5 A) and (ii) a thin film with thickness 29 A. We find that the shape of the clusters is independent of temperature and that it becomes more spherical with increasing size. The surface energy is in qualitative agreement with the experimental value for the surface tension. The density distribution function shows a small peak just below the surface, the origin of which is traced back to a local chemical ordering at the surface. Close to the surface the partial radial distribution functions as well as the distributions of the bond–bond angles show features which are not observed in the interior of the systems. By calculating the distribution of the length of the Si–O rings we can show that these additional features are related to the presence of two-membered rings at the surface. The surface den...

Structure and dynamics of amorphous silica surfaces

Using molecular dynamics computer simulations we investigate how the relaxation dynamics of a simple supercooled liquid with Newtonian dynamics differs from the one with a stochastic dynamics. We find that, apart from the early $\ensuremath{\beta}$-relaxation regime, the two dynamics give rise to the same relaxation behavior. The increase of the relaxation times of the system upon cooling, the details of the $\ensuremath{\alpha}$ relaxation, as well as the wave-vector dependence of the Edwards-Anderson parameters, are independent of the microscopic dynamics.

How Does the Relaxation of a Supercooled Liquid Depend on Its Microscopic Dynamics

Using molecular dynamics simulations we study the out of equilibrium dynamic correlations in a model glass-forming liquid. The system is quenched from a high temperature to a temperature below its glass transition temperature and the decay of the two-time intermediate scattering function $C({t}_{w}{,t+t}_{w})$ is monitored for several values of the waiting time ${t}_{w}$ after the quench. We find that $C({t}_{w}{,t+t}_{w})$ shows a strong dependence on the waiting time, i.e., aging, depends on the temperature before the quench, and, similar to the case of spin glasses, can be scaled onto a master curve.

Aging Effects in a Lennard-Jones Glass

We study in detail the predictions of various theoretical approaches, in particular, mode-coupling theory (MCT) and kinetically constrained models (KCMs), concerning the time, temperature, and wave vector dependence of multipoint correlation functions that quantify the strength of both induced and spontaneous dynamical fluctuations. We also discuss the precise predictions of MCT concerning the statistical ensemble and microscopic dynamics dependence of these multipoint correlation functions. These predictions are compared to simulations of model fragile and strong glass-forming liquids. Overall, MCT fares quite well in the fragile case, in particular, explaining the observed crucial role of the statistical ensemble and microscopic dynamics, while MCT predictions do not seem to hold in the strong case. KCMs provide a simplified framework for understanding how these multipoint correlation functions may encode dynamic correlations in glassy materials. However, our analysis highlights important unresolved questions concerning the application of KCMs to supercooled liquids.

Spontaneous and induced dynamic correlations in glass formers. II. Model calculations and comparison to numerical simulations

We analyze static point-to-set correlations in glass-forming liquids. The generic idea is to freeze the position of a set of particles in an equilibrium configuration and to perform sampling in the presence of this additional constraint. Qualitatively different geometries for the confining set of particles are considered and a detailed comparison of resulting static and dynamic correlation functions is performed. Our results reveal the existence of static spatial correlations not detected by conventional two-body correlators, which appear to be decoupled from, and shorter-ranged than, dynamical length scales characterizing dynamic heterogeneity. We find that the dynamics slows down dramatically under confinement, which suggests new ways to investigate the glass transition. Our results indicate that the geometry in which particles are randomly pinned is the best candidate to study static correlations.

Walter Kob

Papers

Structure and dynamics of amorphous silica surfaces

How Does the Relaxation of a Supercooled Liquid Depend on Its Microscopic Dynamics

Aging Effects in a Lennard-Jones Glass

Spontaneous and induced dynamic correlations in glass formers. II. Model calculations and comparison to numerical simulations

Static point-to-set correlations in glass-forming liquids