Phase separation and rotor self-assembly in active particle suspensions

114

163

Secretion of extracellular polymeric substances (EPSs) by growing bacteria is an integral part of forming biofilm-like structures. In such dense systems, mechanical interactions among the structural components can be expected to significantly contribute to morphological properties. Here, we use a particle-based modeling approach to study the self-organization of nonmotile rod-shaped bacterial cells growing on a solid substrate in the presence of selfproduced EPSs. In our simulation, all of the components interact mechanically via repulsive forces, occurring as the bacterial cells grow and divide (via consuming diffusing nutrient) and produce EPSs. Based on our simulation, we show that mechanical interactions control the collective behavior of the system. In particular, we find that the presence of nonadsorbing EPSs can lead to spontaneous aggregation of bacterial cells by a depletion attraction and thereby generates phase separated patterns in the nonequilibrium growing colony. Both repulsive interactions between cell and EPSs and the overall concentration of EPSs are important factors in the self-organization in a nonequilibrium growing colony. Furthermore, we investigate the interplay of mechanics with the nutrient diffusion and consumption by bacterial cells and observe that suppression of branch formation occurs due to EPSs compared with the case where no EPS is produced.A common underlying theme of biophysics of living matter is the quest to understand how local interactions of individual components lead to collective behavior and formation of highly self-organized systems (1-6). In this regard, bacterial systems are an especially interesting example. Bacteria are known to selforganize into multicellular communities, commonly known as biofilms, in which microbial cells live in close association with a solid surface or liquid-air interface and are embedded in a self-produced extracellular matrix. Extracellular polymeric substances (EPSs) play an important role in determining the structural and mechanical architecture of a biofilm (7-12). Generally, the collective dynamics of bacterial colony involves a complex interplay of various physical, chemical, and biological mechanisms, such as growth and differentiation of cells, production of EPSs, the collective movement of cells determined by interacting physical forces and chemical cues, e.g., chemotaxis, motility, cellcell signaling, adhesion, and gene regulation (13)(14)(15)(16)(17)(18)(19). At low density, communication among cells occurs mainly through chemical signals (20). However, at a higher density, as bacteria aggregate and form dense communities, direct mechanical interaction becomes increasingly relevant in the self-organization (21-23). In this regard, microfluidics-based experiments coupled with continuum modeling of cellular dynamics by Volfson et al.(24) was a pioneering study emphasizing the role of cell-cell mechanical interaction in the growth of a highly organized bacterial colony. As a significant extension, Farrell and coworkers (25, 26) hav...

mentioning

confidence: 91%

Mechanically-driven phase separation in a growing bacterial colony

Ghosh

Mondal

Ben‐Jacob

et al. 2015

114

163

“…4D. This scheme is significantly simpler than the previous examples because the active colloids simply rotate about the micropillars, and there are many ways to get colloids to actively rotate (7,(25)(26)(27)(28)(29). Despite the simplicity of the motion of the individual active particles, the combination is sufficient to create a braid, further demonstrating the robustness of active particles as an assembly machine.…”

Section: Physicsmentioning

confidence: 99%

“…This has led to the growth of the field of active matter, which aims to design, control, and understand self-propelled particles (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12). These active particles provide significant yet untapped potential: by combining this mechanism for energy input with controllable interactions, it becomes possible to imagine the creation of colloidal-scale machines that can do work and perform tasks.…”

mentioning

confidence: 99%

Using active colloids as machines to weave and braid on the micrometer scale

Goodrich

Brenner

2016

Controlling motion at the microscopic scale is a fundamental goal in the development of biologically inspired systems. We show that the motion of active, self-propelled colloids can be sufficiently controlled for use as a tool to assemble complex structures such as braids and weaves out of microscopic filaments. Unlike typical self-assembly paradigms, these structures are held together by geometric constraints rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves precisely controlling the 2D motion of active colloids so that their path has a nontrivial topology. We demonstrate with proof-ofprinciple Brownian dynamics simulations that, when the colloids are attached to long semiflexible filaments, this motion causes the filaments to braid. The ability of the active particles to provide sufficient force necessary to bend the filaments into a braid depends on a number of factors, including the self-propulsion mechanism, the properties of the filament, and the maximum curvature in the braid. Our work demonstrates that nonequilibrium assembly pathways can be designed using active particles.colloidal machines | active colloids | self-assembly | braids and weaves B iology has long been known to use a combination of programmable interactions with specific energy input through small molecules (ATP) to create remarkable machines. Because we have not yet developed the ability to emulate these machines artificially, understanding assembly pathways at the microscopic scale is a fundamental challenge in both biology and nanotechnology (1). However, recently there have been major advances in colloidal science, making it possible to program interactions between individual units. This has led to robust assembly of complex structures, approaching the complexity of biological systems. But biological systems also use specific energy input of small molecules to create machines. How can we do this with soft materials?A parallel recent development has been to use chemical reactions on the surface of colloids to create motility mechanisms. This has led to the growth of the field of active matter, which aims to design, control, and understand self-propelled particles (2-12). These active particles provide significant yet untapped potential: by combining this mechanism for energy input with controllable interactions, it becomes possible to imagine the creation of colloidal-scale machines that can do work and perform tasks.Here we present a proof-of-principle demonstration of how this could work. We show one way in which active colloids can be harnessed to drive the assembly of weaves and braids, turning long filaments into complex structures, using only active forces [e.g., hydrogen peroxide-propelled colloids (2-4)] and nonspecific short-range attractive forces (e.g., depletion forces). The typical self-assembly paradigm encodes information through the specific interactions between building blocks that in turn promote assembly. For example, a given amino acid sequence consistently folds into a specific pro...

“…There has been a considerable amount of work on swimmers that can propel themselves by cyclically changing their shapes (14). Interactions between such swimmers and their collective flows have been analyzed (15)(16)(17)(18)(19)(20)(21). Also, interactions between active hydrodynamic dipoles have been investigated theoretically (22,23) and experimentally (24,25).…”

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confidence: 99%

Hydrodynamic collective effects of active protein machines in solution and lipid bilayers

Mikhailov

Kapral

2015

100

113

The cytoplasm and biomembranes in biological cells contain large numbers of proteins that cyclically change their shapes. They are molecular machines that can function as molecular motors or carry out various other tasks in the cell. Many enzymes also undergo conformational changes within their turnover cycles. We analyze the advection effects that nonthermal fluctuating hydrodynamic flows induced by active proteins have on other passive molecules in solution or membranes. We show that the diffusion constants of passive particles are enhanced substantially. Furthermore, when gradients of active proteins are present, a chemotaxis-like drift of passive particles takes place. In lipid bilayers, the effects are strongly nonlocal, so that active inclusions in the entire membrane contribute to local diffusion enhancement and the drift. All active proteins in a biological cell or in a membrane contribute to such effects and all passive particles, and the proteins themselves, will be subject to them