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

Using large-scale molecular dynamics simulations, we investigate the surface properties of lithium, sodium, and potassium silicate glasses containing 25 mol % of alkali oxide. The comparison of two types of surfaces, a melt-formed surface (MS) and a fracture surface (FS), demonstrates that the influence of the alkali modifier on the surface properties depends strongly on the nature of the surface. The FS exhibits a monotonic increase of modifier concentration with increasing alkali size while the MS shows a saturation of alkali concentration when going from Na to K glasses, indicating the presence of competing mechanisms that influence the properties of a MS. For the FS, we find that larger alkali ions reduce the concentration of under-coordinated Si atoms and increase the fraction of two-membered rings, implying an enhanced chemical reactivity of the surface. For both types of surfaces, the roughness is found to increase with alkali size, with the effect being more pronounced for the FS than for the MS. The height-height correlation functions of the surfaces show a scaling behavior that is independent of the alkali species considered: The ones for the MS are compatible with the prediction of the frozen capillary wave theory while the ones for the FS show a logarithmic growth, i.e., on the nanoscale these surfaces are not self-affine fractals. The influence of the modifier on the surface properties are rationalized in terms of the interplay between multiple factors involving the size of the ions, bond strength, and charge balance on the surface.

https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0155497/18016529/244504_1_5.0155497.pdf

Surface properties of alkali silicate glasses: Influence of the modifiers.

Granular materials such as sand, powders, and grains are omnipresent in daily life, industrial applications, and earth-science [1]. When unperturbed, they form stable structures that resemble the ones of other amorphous solids like metallic and colloidal glasses [2]. It is commonly conjectured that all these amorphous materials show a universal mechanical response when sheared slowly, i.e., to have an elastic regime, followed by yielding [3]. Here we use X-ray tomography to determine the microscopic dynamics of a cyclically sheared granular system in three dimensions. Independent of the shear amplitude Γ, the sample shows a cross-over from creep to diffusive dynamics, indicating that granular materials have no elastic response and always yield, in stark contrast to other glasses. The overlap function [4] reveals that at large Γ yielding is a simple cross-over phenomenon, while for small Γ it shows features of a first order transition with a critical point at Γ ≈ 0.1 at which one finds a pronounced slowing down and dynamical heterogeneity. Our findings are directly related to the surface roughness of granular particles which induces a micro-corrugation to the potential energy landscape, thus creating relaxation channels that are absent in simple glasses. These processes must be understood for reaching an understanding of the complex relaxation dynamics of granular systems. Introduction Yielding of amorphous materials is ubiquitous, governing a wide range of phenomena like mechanical failure of metallic glasses [5], complex rheologies of soft glasses [6], or geophysical catastrophes [7]. A typical amorphous solid under quasistatic simple shear will deform elastically at small strain and flow plastically beyond the yielding strain. Depending on whether the material is brittle or ductile, the stress-strain curve shows a drop or a smooth crossover to a plateau, respectively. On the particle level, yielding is a cooperative phenomenon of local plastic events [8, 9], and computer simulations hint that this phenomenon shares many aspects with a first order phase transition [4, 10, 11]. However, for real systems the precise nature of this transition has not yet been clarified since such experiments are very challenging. In contrast to standard glasses, for granular systems there is at present no satisfactory understanding of yielding on the level of the particles. It has been suggested that sheared granular solids are marginally stable, i.e., contacts between particles will change irreversibly even under a tiny applied strain, which implies that such systems have no elastic regime [12]. This view seems to be at odds with experimental results which found that the stress-strain curve of granular solids under simple shear does in fact resemble the one for a glass [13]. One possibility to resolve this discrepancy is to consider a different type of driving, i.e., cyclic shear, since it allows to probe directly the reversibility of the particle trajectories and hence the presence of elasticity in the system. A number of computational studies have ∗ walter.kob@umontpellier.fr † yujiewang@sjtu.edu.cn

From creep to flow: Granular materials under cyclic shear

Using molecular dynamics computer simulations we investigate the aging dynamics of a gel We start from a fractal structure generated by the DLCA-DEF algorithm, onto which we then impose an interaction potential consisiting of a short-range attraction as well as a long-range repulsion After relaxing the system at T = 0, we let it evolve at a fixed finite temperature Depending on the temperature T we find different scenarios for the aging behavior For T & 02 the fractal structure is unstable and breaks up into small clusters which relax to equilibrium For T  02 the structure is stable and the dynamics slows down with increasing waiting time At intermediate and low T the mean squared displacement scales as t 2/3 and we discuss several mechanisms for this anomalous time dependence For intermediate T, the self-intermediate scattering function is given by a compressed exponential at small wave-vectors and by a stretched exponential at large wave-vectors In contrast, for low T it is a stretched exponential for all wave-vectors This behavior can be traced back to a subtle interplay between elastic rearrangements, fluctuations of chain-like filaments, and heterogeneity

Aging Dynamics of a Fractal Model Gel

Silica is known as the archetypal strong liquid, exhibiting an Arrhenius viscosity curve with a high glass transition temperature and constant activation energy. However, given the ideally isostatic nature of the silica network, the presence of even a small concentration of defects can lead to a significant decrease in both the glass transition temperature and activation energy for viscous flow. To understand the impact of trace level dopants on the viscosity of silica, we measure the viscosity-temperature curves for seven silica glass samples having different impurities, including four natural and three synthetic samples. Depending on the type of dopant, the glass transition temperature can vary by nearly 300 K. A common crossover is found for all viscosity curves around ~2200-2500 K, which we attribute to a change of the transport mechanism in the melt from being dominated by intrinsic defects at high temperature to dopant-induced defects at low temperatures.

Viscosity of Silica and Doped Silica Melts: Evidence for a Crossover Temperature

We present molecular dynamics simulations of the motion of a single rod in a two-dimensional random static array of disks. For long rods the mean-squared displacement of the center-of-mass shows a cage effect similar to that observed in supercooled liquids or dense colloidal systems. We have determined the time-dependence of the non-Gaussian parameter for different rod lengths. It is found that the long-time regime is strongly non-Gaussian even at length scales of the order of 10-15 times the rod length, thus showing the heterogeneity of the dynamics at such length scales.

https://arxiv.org/pdf/cond-mat/0303510.pdf

Walter Kob

Papers

Surface properties of alkali silicate glasses: Influence of the modifiers.

From creep to flow: Granular materials under cyclic shear

Aging Dynamics of a Fractal Model Gel

Viscosity of Silica and Doped Silica Melts: Evidence for a Crossover Temperature

Dynamics of a rod in a random static environment: non-Gaussianity at large length scales