Journal Article•
Rheology of Active-Particle Suspensions
TL;DR: The phenomena of cytoplasmic streaming, elastotaxis, and active mechanosensing find natural explanations within the model of hydrodynamic velocity, concentration, and stress fields in a suspension of active, energy-dissipating particles.
Abstract: We study the interplay of activity, order, and flow through a set of coarse-grained equations governing the hydrodynamic velocity, concentration, and stress fields in a suspension of active, energy-dissipating particles. We make several predictions for the rheology of such systems, which can be tested on bacterial suspensions, cell extracts with motors and filaments, or artificial machines in a fluid. The phenomena of cytoplasmic streaming, elastotaxis, and active mechanosensing find natural explanations within our model.
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28 Jul 2005
TL;DR: PfPMP1）与感染红细胞、树突状组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�ly.
Abstract: 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。
18,940 citations
Posted Content•
TL;DR: This review will describe two recently developed classes of active matter systems, in which simple building blocks-self-propelled colloidal particles or extensile rod-like particles- self-organize to form macroscopic structures with features not possible in equilibrium systems.
Abstract: Biological systems exhibit large-scale self-organized dynamics and structures which enable organisms to perform the functions of life. The field of active matter strives to develop and understand microscopically-driven nonequilibrium materials, with emergent properties comparable to those of living systems. This review will describe two recently developed classes of active matter systems, in which simple building blocks --- self-propelled colloidal particles or extensile rod-like particles --- self-organize to form macroscopic structures with features not possible in equilibrium systems. We summarize the recent experimental and theoretical progress on each of these systems, and we present simple descriptions of the physics underlying their emergent behaviors.
40 citations
TL;DR: It is concluded that bottom heaviness is not a prerequisite for the increase of viscosity and that the effect of gravity on the rheology of the strain of Chlamydomonas reinhardtii is negligible.
Abstract: Active microswimmers are known to affect the macroscopic viscosity of suspensions in a more complex manner than passive particles. For puller-like microswimmers an increase in the viscosity has been observed. It has been suggested that the persistence of the orientation of the microswimmers hinders the rotation that is normally caused by the vorticity. It was previously shown that some sorts of algaes are bottom-heavy swimmers, i.e. their centre of mass is not located in the centre of the body. In this way, the algae affects the vorticity of the flow when it is perpendicular oriented to the axis of gravity. This orientation of gravity to vorticity is given in a rheometer that is equipped with a cone-plate geometry. Here we present measurements of the viscosity both in a cone-plate and a Taylor-Couette cell. The two set-ups yielded the same increase in viscosity although the axis of gravitation in the Taylor-Couette cell is parallel to the direction of vorticity. In a complementary experiment we tested the orientation of the direction of swimming through microscopic observation of single \textit{Chlamydomonas reinhardtii} and could not identify a preferred orientation, i. e. our specific strain of \textit{Chlamydomonas reinhardtii} are not bottom-heavy swimmers. We thus conclude that bottom heaviness is not a prerequisite for the increase of viscosity and that the effect of gravity on the rheology of our strain of \textit{Chlamydomonas reinhardtii} is negligible. This finding reopens the question of whether origin of persistence in the orientation of cells is actually responsible for the increased viscosity of the suspension.
32 citations
Journal Article•
TL;DR: This work investigates the geometrical and mechanical properties of a bacterial colony growing on a substrate with free boundary, and demonstrates that such an expanding colony self-organizes into a "mosaic" of micro-domains consisting of highly aligned cells.
Abstract: Bacterial colonies are abundant on living and non-living surfaces and are known to mediate a broad range of processes in ecology, medicine and industry. Although extensively researched, from single cells to demographic scales, a comprehensive biomechanical picture, highlighting the cell-to-colony dynamics, is still lacking. Here, using molecular dynamics simulations and continuous modelling, we investigate the geometrical and mechanical properties of a bacterial colony growing on a substrate with free boundary, and demonstrate that such an expanding colony self-organizes into a \"mosaic\" of micro-domains consisting of highly aligned cells. The emergence of micro-domains is mediated by two competing forces: the steric forces between neighboring cells which favour cell alignment, and the extensile stresses due to cell growth that tend to reduce the local orientational order, and thereby distort the system. This interplay results into an exponential distribution of the domain areas, and sets a characteristic length scale proportional to the square root of the ratio between the system orientational stiffness and the magnitude of the extensile active stress. Finally, our examination of the internal stresses reveal that, in addition to biochemical pathways, the spatiotemporal organization in microbial colonies is significantly affected by the mechanical forces exerted and experienced by the growing cells.
22 citations
TL;DR: In this paper , the authors report on the progress in bacterial active matter from the physics viewpoint, and provide a critical assessment of major theoretical approaches, and address the effects of visco-elasticity, liquid crystallinity, and external confinement on collective behavior in bacterial suspensions.
Abstract: Bacteria are among the oldest and most abundant species on Earth. Bacteria successfully colonize diverse habitats and play a significant role in the oxygen, carbon, and nitrogen cycles. They also form human and animal microbiota and may become sources of pathogens and a cause of many infectious diseases. Suspensions of motile bacteria constitute one of the most studied examples of active matter: a broad class of non-equilibrium systems converting energy from the environment (e.g., chemical energy of the nutrient) into mechanical motion. Concentrated bacterial suspensions, often termed active fluids, exhibit complex collective behavior, such as large-scale turbulent-like motion (so-called bacterial turbulence) and swarming. The activity of bacteria also affects the effective viscosity and diffusivity of the suspension. This work reports on the progress in bacterial active matter from the physics viewpoint. It covers the key experimental results, provides a critical assessment of major theoretical approaches, and addresses the effects of visco-elasticity, liquid crystallinity, and external confinement on collective behavior in bacterial suspensions.
17 citations
References
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28 Jul 2005
TL;DR: PfPMP1）与感染红细胞、树突状组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�ly.
Abstract: 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。
18,940 citations
TL;DR: The renormalization group theory has been applied to a variety of dynamic critical phenomena, such as the phase separation of a symmetric binary fluid as mentioned in this paper, and it has been shown that it can explain available experimental data at the critical point of pure fluids, and binary mixtures, and at many magnetic phase transitions.
Abstract: An introductory review of the central ideas in the modern theory of dynamic critical phenomena is followed by a more detailed account of recent developments in the field. The concepts of the conventional theory, mode-coupling, scaling, universality, and the renormalization group are introduced and are illustrated in the context of a simple example---the phase separation of a symmetric binary fluid. The renormalization group is then developed in some detail, and applied to a variety of systems. The main dynamic universality classes are identified and characterized. It is found that the mode-coupling and renormalization group theories successfully explain available experimental data at the critical point of pure fluids, and binary mixtures, and at many magnetic phase transitions, but that a number of discrepancies exist with data at the superfluid transition of $^{4}\mathrm{He}$.
4,980 citations
TL;DR: This review summarizes theoretical progress in the field of active matter, placing it in the context of recent experiments, and highlights the experimental relevance of various semimicroscopic derivations of the continuum theory for describing bacterial swarms and suspensions, the cytoskeleton of living cells, and vibrated granular material.
Abstract: 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.
3,314 citations
TL;DR: The biophysical and mechanical principles of locomotion at the small scales relevant to cell swimming, tens of micrometers and below are reviewed, with emphasis on the simple physical picture and fundamental flow physics phenomena in this regime.
Abstract: Cell motility in viscous fluids is ubiquitous and affects many biological processes, including reproduction, infection and the marine life ecosystem. Here we review the biophysical and mechanical principles of locomotion at the small scales relevant to cell swimming, tens of micrometers and below. At this scale, inertia is unimportant and the Reynolds number is small. Our emphasis is on the simple physical picture and fundamental flow physics phenomena in this regime. We first give a brief overview of the mechanisms for swimming motility, and of the basic properties of flows at low Reynolds number, paying special attention to aspects most relevant for swimming such as resistance matrices for solid bodies, flow singularities and kinematic requirements for net translation. Then we review classical theoretical work on cell motility, in particular early calculations of swimming kinematics with prescribed stroke and the application of resistive force theory and slender-body theory to flagellar locomotion. After examining the physical means by which flagella are actuated, we outline areas of active research, including hydrodynamic interactions, biological locomotion in complex fluids, the design of small-scale artificial swimmers and the optimization of locomotion strategies. (Some figures in this article are in colour only in the electronic version) This article was invited by Christoph Schmidt.
2,274 citations
TL;DR: In this paper, a unified view of the many kinds of active matter is presented, encompassing not only living systems but inanimate analogs, including all living organisms and their motile constituents such as molecular motors.
Abstract: Active particles contain internal degrees of freedom with the ability to take in and dissipate energy and, in the process, execute systematic movement. Examples include all living organisms and their motile constituents such as molecular motors. This article reviews recent progress in applying the principles of nonequilibrium statistical mechanics and hydrodynamics to form a systematic theory of the behavior of collections of active particles–active matter–with only minimal regard to microscopic details. A unified view of the many kinds of active matter is presented, encompassing not only living systems but inanimate analogs. Theory and experiment are discussed side by side.
1,546 citations