Behavior Of Active Matter Research Articles

Kinetic Asymmetry versus Dissipation in the Evolution of Chemical Systems as Exemplified by Single Enzyme Chemotaxis.

Single enzyme chemotaxis is a phenomenon by which a nonequilibrium spatial distribution of an enzyme is created and maintained by concentration gradients of the substrate and product of the catalyzed reaction. These gradients can arise either naturally through metabolism or experimentally, e.g., by flow of materials through microfluidic channels or by use of diffusion chambers with semipermeable membranes. Numerous hypotheses regarding the mechanism of this phenomenon have been proposed. Here, we discuss a mechanism based solely on diffusion and chemical reaction and show that kinetic asymmetry, a difference in the transition state energies for dissociation/association of substrate and product, and diffusion asymmetry, a difference in the diffusivities of the bound and free forms of the enzyme, are the determinates of the direction of chemotaxis and can result in either positive or negative chemotaxis, both of which have been demonstrated experimentally. Exploration of these fundamental symmetries that govern nonequilibrium behavior helps to distinguish between possible mechanisms for the evolution of a chemical system from initial to the steady state and whether the principle that determines the direction a system shifts when exposed to an external energy source is based on thermodynamics or on kinetics with the latter being supported by the results of the present paper. Our results show that, while dissipation ineluctably accompanies nonequilibrium phenomena, including chemotaxis, systems do not evolve to maximize or minimize dissipation but rather to attain greater kinetic stability and accumulate in regions where their effective diffusion coefficient is as small as possible. The chemotactic response to the chemical gradients formed by other enzymes participating in a catalytic cascade provides a mechanism for forming loose associations known as metabolons. Significantly, the direction of the effective force due to these gradients depends on the kinetic asymmetry of the enzyme and so can be nonreciprocal, where one enzyme is attracted to another enzyme, but the other enzyme is repelled by the one, in seeming contradiction to Newtons third law. This nonreciprocity is an important ingredient in the behavior of active matter.

Phase separation phenomenon in mixed system composed of low- and high-inertia active particles

Active matter refers to a class of substance capable of autonomously moving by harnessing energy from its surrounding environment. The substance exhibits unique non-equilibrium phenomenon, and hence has attracted great attention in the scientific community. Many active matters, such as bacteria, cells, micro-swimmers, and self-propelled colloidal particles, operate in viscous environments and their motions are described usually by using overdamped models. Examples include overdamped active Brownian particle (ABP) model for self-propelled colloidal particles in solution and run-and-tumble (RTP) model for swimming bacteria. In recent years, increasing studies focus on the influence of inertia on the behavior of active matter. Vibrating robots, runners, flying insects, and micro-fliers are typical of active systems under the underdamped condition. The motions of these active matters can be modelled by underdamped Langevin equation, known as the active inertial particle (AIP) model. Previous studies have demonstrated that like the scenarios in ABP systems, motility-induced phase separation (MIPS) phenomena also happen in AIP systems under certain density conditions. However, due to the strong collision-and-rebound effect, aggregation of AIP particles and hence the MIPS are impeded. In complex living/application environments, mixture of different active agents is often seen. Some studies on mixed systems of active matter show that the composition is an important quantity, which influences the phase separation phenomena. In this paper, we study the phase separation phenomena in a mixed system composed of low- and high-inertia active particles by underdamped Langevin dynamics simulations. We find that compared with single-component system, the mixed system is unexpectedly favorable for the occurrence of phase separation at a moderate overall concentration and a certain range of component fraction, while unfavorable for phase separation at a high overall concentration. The underlying mechanism is that the presence of a small number of the high-inertia particles could accelerate the motion of the low-inertia particles, thus facilitating their aggregation and promoting the phase separation. However, when the fraction of the high-inertia particles is large, frequent elastic collisions would disturb the aggregation of the low-inertia particles and suppress the occurrence of phase separation. Our results provide a new insight into the collective behavior of active materials and also a reference for their design and applications.

Spontaneous self-propulsion and nonequilibrium shape fluctuations of a droplet enclosing active particles

Active particles, such as swimming bacteria or self-propelled colloids, spontaneously assemble into large-scale dynamic structures. Geometric boundaries often enforce different spatio-temporal patterns compared to unconfined environment and thus provide a platform to control the behavior of active matter. Here, we report collective dynamics of active particles enclosed by soft, deformable boundary, that is responsive to the particles’ activity. We reveal that a quasi two-dimensional fluid droplet enclosing motile colloids powered by the Quincke effect (Quincke rollers) exhibits strong shape fluctuations with a power spectrum consistent with active fluctuations driven by particle-interface collisions. A broken detailed balance confirms the nonequilibrium nature of the shape dynamics. We further find that rollers self-organize into a single drop-spanning vortex, which can undergo a spontaneous symmetry breaking and vortex splitting. The droplet acquires motility while the vortex doublet exists. Our findings provide insights into the complex collective behavior of active colloidal suspensions in soft confinement.

Stability analysis of flow of active extensile fibers in confined domains.

In this article, we study shear flow of active extensile filaments confined in a narrow channel. They behave as nematic liquid crystals that we assumed are governed by the Ericksen-Leslie equations of balance of linear and angular momentum. The addition of an activity source term in the Leslie stress captures the role of the biofuel prompting the dynamics. The dimensionless form of the governing system includes the Ericksen, activity, and Reynolds numbers together with the aspect ratio of the channel as the main driving parameters affecting the stability of the system. The active system that guides our analysis is composed of microtubules concentrated in bundles, hundreds of microns long, placed in a narrow channel domain, of aspect ratios in the range between 10-2 and 10-3 dimensionless units, which are able to align due to the combination of adenosine triphosphate-supplied energy and confinement effects. Specifically, this work aims at studying the role of confinement on the behavior of active matter. It is experimentally observed that, at an appropriately low activity and channel width, the active flow is laminar, with the linear velocity profile and the angle of alignment analogous to those in passive shear, developing defects and becoming chaotic, at a large activity and a channel aspect ratio. The present work addresses the laminar regime, where defect formation does not play a role. We perform a normal mode stability analysis of the base shear flow. A comprehensive description of the stability properties is obtained in terms of the driving parameters of the system. Our main finding, in addition to the geometry and magnitude of the flow profiles, and also consistent with the experimental observations, is that the transition to instability of the uniformly aligned shear flow occurs at a threshold value of the activity parameter, with the transition also being affected by the channel aspect ratio. The role of the parameters on the vorticity and angular profiles of the perturbing flow is also analyzed and found to agree with the experimentally observed transition to turbulent regimes. A spectral method based on Chebyshev polynomials is used to solve the generalized eigenvalue problems arising in the stability analysis.

Confinement and activity regulate bacterial motion in porous media.

Understanding how bacteria move in porous media is critical to applications in healthcare, agriculture, environmental remediation, and chemical sensing. Recent work has demonstrated that E. coli, which moves by run-and-tumble dynamics in a homogeneous medium, exhibits a new form of motility when confined in a disordered porous medium: hopping-and-trapping motility, in which cells perform rapid, directed hops punctuated by intervals of slow, undirected trapping. Here, we use direct visualization to shed light on how these processes depend on pore-scale confinement and cellular activity. We find that hopping is determined by pore-scale confinement, and is independent of cellular activity; by contrast, trapping is determined by the competition between pore-scale confinement and cellular activity, as predicted by an entropic trapping model. These results thus help to elucidate the factors that regulate bacterial motion in porous media, and could help aid the development of new models of motility in heterogeneous environments.