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

This review summarizes theoretical progress in the field of active matter, placing it in the context of recent experiments. This approach offers a unified framework for the mechanical and statistical properties of living matter: biofilaments and molecular motors in vitro or in vivo, collections of motile microorganisms, animal flocks, and chemical or mechanical imitations. A major goal of this review is to integrate several approaches proposed in the literature, from semimicroscopic to phenomenological. In particular, first considered are ``dry'' systems, defined as those where momentum is not conserved due to friction with a substrate or an embedding porous medium. The differences and similarities between two types of orientationally ordered states, the nematic and the polar, are clarified. Next, the active hydrodynamics of suspensions or ``wet'' systems is discussed and the relation with and difference from the dry case, as well as various large-scale instabilities of these nonequilibrium states of matter, are highlighted. Further highlighted are various large-scale instabilities of these nonequilibrium states of matter. Various semimicroscopic derivations of the continuum theory are discussed and connected, highlighting the unifying and generic nature of the continuum model. Throughout the review, the experimental relevance of these theories for describing bacterial swarms and suspensions, the cytoskeleton of living cells, and vibrated granular material is discussed. Promising extensions toward greater realism in specific contexts from cell biology to animal behavior are suggested, and remarks are given on some exotic active-matter analogs. Last, the outlook for a quantitative understanding of active matter, through the interplay of detailed theory with controlled experiments on simplified systems, with living or artificial constituents, is summarized.

Hydrodynamics of soft active matter

A revolution in novel nanoparticles and colloidal building blocks has been enabled by recent breakthroughs in particle synthesis These new particles are poised to become the ‘atoms’ and ‘molecules’ of tomorrow’s materials if they can be successfully assembled into useful structures Here, we discuss the recent progress made in the synthesis of nanocrystals and colloidal particles and draw analogies between these new particulate building blocks and better-studied molecules and supramolecular objects We argue for a conceptual framework for these new building blocks based on anisotropy attributes and discuss the prognosis for future progress in exploiting anisotropy for materials design and assembly

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Anisotropy of building blocks and their assembly into complex structures

Differently from passive Brownian particles, active particles, also known as self-propelled Brownian particles or microswimmers and nanoswimmers, are capable of taking up energy from their environment and converting it into directed motion. Because of this constant flow of energy, their behavior can be explained and understood only within the framework of nonequilibrium physics. In the biological realm, many cells perform directed motion, for example, as a way to browse for nutrients or to avoid toxins. Inspired by these motile microorganisms, researchers have been developing artificial particles that feature similar swimming behaviors based on different mechanisms. These man-made micromachines and nanomachines hold a great potential as autonomous agents for health care, sustainability, and security applications. With a focus on the basic physical features of the interactions of self-propelled Brownian particles with a crowded and complex environment, this comprehensive review will provide a guided tour through its basic principles, the development of artificial self-propelling microparticles and nanoparticles, and their application to the study of nonequilibrium phenomena, as well as the open challenges that the field is currently facing.

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Active Particles in Complex and Crowded Environments

We describe experimental investigations of the structure of two-dimensional spherical crystals. The crystals, formed by beads self-assembled on water droplets in oil, serve as model systems for exploring very general theories about the minimum-energy configurations of particles with arbitrary repulsive interactions on curved surfaces. Above a critical system size we find that crystals develop distinctive high-angle grain boundaries, or scars, not found in planar crystals. The number of excess defects in a scar is shown to grow linearly with the dimensionless system size. The observed slope is expected to be universal, independent of the microscopic potential.

https://arxiv.org/pdf/cond-mat/0303289.pdf

Grain Boundary Scars and Spherical Crystallography

The addition of small 'seed' particles to a supersaturated solution can greatly increase the rate at which crystals nucleate. This process is understood, at least qualitatively, when the seed has the same structure as the crystal that it spawns. However, the microscopic mechanism of seeding by a 'foreign' substance is not well understood. Here we report numerical simulations of colloidal crystallization seeded by foreign objects. We perform Monte Carlo simulations to study how smooth spherical seeds of various sizes affect crystallization in a suspension of hard colloidal particles. We compute the free-energy barrier associated with crystal nucleation. A low barrier implies that nucleation is easy. We find that to be effective crystallization promoters, the seed particles need to exceed a well-defined minimum size. Just above this size, seed particles act as crystallization 'catalysts' as newly formed crystallites detach from the seed. In contrast, larger seed particles remain covered by the crystallites that they spawn. This phenomenon should be experimentally observable and can have important consequences for the control of the resulting crystal size distribution.

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Onset of heterogeneous crystal nucleation in colloidal suspensions

We study the assembly of spherical particles with opposite electric charge on both hemispheres, in the case that the particle diameter exceeds the electrostatic screening length. Clusters result, not strings. The cluster shapes are analyzed by combined epifluorescence microscopy and Monte Carlo computer simulations with excellent agreement, indicating that the particles assemble in aqueous suspension to form equilibrated aggregates. The simulations show that charge asymmetry of individual Janus particles is preserved in the clusters.

Clusters of Charged Janus Spheres

Adding a nonadsorbing polymer to passive colloids induces an attraction between the particles via the “depletion” mechanism. High enough polymer concentrations lead to phase separation. We combine experiments, theory, and simulations to demonstrate that using active colloids (such as motile bacteria) dramatically changes the physics of such mixtures. First, significantly stronger interparticle attraction is needed to cause phase separation. Secondly, the finite size aggregates formed at lower interparticle attraction show unidirectional rotation. These micro-rotors demonstrate the self-assembly of functional structures using active particles. The angular speed of the rotating clusters scales approximately as the inverse of their size, which may be understood theoretically by assuming that the torques exerted by the outermost bacteria in a cluster add up randomly. Our simulations suggest that both the suppression of phase separation and the self-assembly of rotors are generic features of aggregating swimmers and should therefore occur in a variety of biological and synthetic active particle systems.

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Phase separation and rotor self-assembly in active particle suspensions

Orientation-dependent interactions can drive unusual self-assembly of colloidal particles. This study, based on combined epifluorescence microscopy and Monte Carlo simulations, shows that amphiphilic colloidal spheres, hydrophobic on one hemisphere and charged on the other, assemble in water into extended structures not formed by spheres of uniform surface chemical makeup. Small, compact clusters each comprised of less than 10 of these Janus spheres link up, as increasing salt concentration enhances electrostatic screening, into wormlike strings.

Angelo Cacciuto

Papers

Grain Boundary Scars and Spherical Crystallography

Onset of heterogeneous crystal nucleation in colloidal suspensions

Clusters of Charged Janus Spheres

Phase separation and rotor self-assembly in active particle suspensions

Clusters of amphiphilic colloidal spheres.