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

1980 Preface * 1999 Preface * 1999 Acknowledgements * Introduction * 1 Circular Logic * 2 Phase Singularities (Screwy Results of Circular Logic) * 3 The Rules of the Ring * 4 Ring Populations * 5 Getting Off the Ring * 6 Attracting Cycles and Isochrons * 7 Measuring the Trajectories of a Circadian Clock * 8 Populations of Attractor Cycle Oscillators * 9 Excitable Kinetics and Excitable Media * 10 The Varieties of Phaseless Experience: In Which the Geometrical Orderliness of Rhythmic Organization Breaks Down in Diverse Ways * 11 The Firefly Machine 12 Energy Metabolism in Cells * 13 The Malonic Acid Reagent ('Sodium Geometrate') * 14 Electrical Rhythmicity and Excitability in Cell Membranes * 15 The Aggregation of Slime Mold Amoebae * 16 Numerical Organizing Centers * 17 Electrical Singular Filaments in the Heart Wall * 18 Pattern Formation in the Fungi * 19 Circadian Rhythms in General * 20 The Circadian Clocks of Insect Eclosion * 21 The Flower of Kalanchoe * 22 The Cell Mitotic Cycle * 23 The Female Cycle * References * Index of Names * Index of Subjects

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/596B270197FE27DE5FABB598B6210622/S0025557200150892a.pdf/div-class-title-span-class-italic-the-geometry-of-biological-time-span-by-a-t-winfree-pp-544-dm68-corrected-second-printing-1990-isbn-3-540-52528-9-springer-div.pdf

The geometry of biological time , by A. T. Winfree. Pp 544. DM68. Corrected Second Printing 1990. ISBN 3-540-52528-9 (Springer)

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

The motion of an artificial microscale swimmer that uses a chemical reaction catalyzed on its own surface to achieve autonomous propulsion is fully characterized experimentally. It is shown that at short times it has a substantial component of directed motion, with a velocity that depends on the concentration of fuel molecules. At longer times, the motion reverts to a random walk with a substantially enhanced diffusion coefficient. Our results suggest strategies for designing artificial chemotactic systems.

/pdf/self-motile-colloidal-particles-from-directed-propulsion-to-s5m3ihlmcr.pdf

Self-motile colloidal particles: from directed propulsion to random walk.

A simple model for the reaction-driven propulsion of a small device is proposed as a model for (part of) a molecular machine in aqueous media. The motion of the device is driven by an asymmetric distribution of reaction products. The propulsive velocity of the device is calculated as well as the scale of the velocity fluctuations. The effects of hydrodynamic flow as well as a number of different scenarios for the kinetics of the reaction are addressed.

https://arxiv.org/pdf/cond-mat/0701169.pdf

Propulsion of a Molecular Machine by Asymmetric Distribution of Reaction Products

Small objects can swim by generating around them fields or gradients which in turn induce fluid motion past their surface by phoretic surface effects. We quantify for arbitrary swimmer shapes and surface patterns, how efficient swimming requires both surface 'activity' to generate the fields, and surface 'phoretic mobility.' We show in particular that (i) swimming requires symmetry breaking in either or both of the patterns of 'activity' and 'mobility,' and (ii) for a given geometrical shape and surface pattern, the swimming velocity is size-independent. In addition, for given available surface properties, our calculation framework provides a guide for optimizing the design of swimmers.

https://iopscience.iop.org/article/10.1088/1367-2630/9/5/126/pdf

Designing phoretic micro- and nano-swimmers

We propose a very simple one-dimensional swimmer consisting of three spheres that are linked by rigid rods whose lengths can change between two values. With a periodic motion in a nonreciprocal fashion, which breaks the time-reversal symmetry as well as the translational symmetry, we show that the model device can swim at low Reynolds number. This model system could be used in constructing molecular-sized machines.

https://arxiv.org/pdf/cond-mat/0402070.pdf

Simple swimmer at low Reynolds number: Three linked spheres

The static Casimir effect describes an attractive force between two conducting plates, due to quantum fluctuations of the electromagnetic (EM) field in the intervening space. Thermal fluctuations of correlated fluids (such as critical mixtures, super-fluids, liquid crystals, or electrolytes) are also modified by the boundaries, resulting in finite-size corrections at criticality, and additional forces that affect wetting and layering phenomena. Modified fluctuations of the EM field can also account for the ``van der Waals'' interaction between conducting spheres, and have analogs in the fluctuation-induced interactions between inclusions on a membrane. We employ a path integral formalism to study these phenomena for boundaries of arbitrary shape. This allows us to examine the many unexpected phenomena of the dynamic Casimir effect due to moving boundaries. With the inclusion of quantum fluctuations, the EM vacuum behaves essentially as a complex fluid, and modifies the motion of objects through it. In particular, from the mechanical response function of the EM vacuum, we extract a plethora of interesting results, the most notable being: (i) The effective mass of a plate depends on its shape, and becomes anisotropic. (ii) There is dissipation and damping of the motion, again dependent upon shape and direction of motion, due to emission of photons. (iii) There is a continuous spectrum of resonant cavity modes that can be excited by the motion of the (neutral) boundaries.

Ramin Golestanian

Papers

Self-motile colloidal particles: from directed propulsion to random walk.

Propulsion of a Molecular Machine by Asymmetric Distribution of Reaction Products

Designing phoretic micro- and nano-swimmers

Simple swimmer at low Reynolds number: Three linked spheres

The `Friction' of Vacuum, and other Fluctuation-Induced Forces