1
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Nakul U, Gopalakrishnan M. Stationary states of an active Brownian particle in a harmonic trap. Phys Rev E 2023; 108:024121. [PMID: 37723685 DOI: 10.1103/physreve.108.024121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 07/14/2023] [Indexed: 09/20/2023]
Abstract
We study the stationary states of an overdamped active Brownian particle (ABP) in a harmonic trap in two dimensions via mathematical calculations and numerical simulations. In addition to translational diffusion, the ABP self-propels with a certain velocity, whose magnitude is constant, but its direction is subject to Brownian rotation. In the limit where translational diffusion is negligible, the stationary distribution of the particle's position shows a transition between two different shapes, one with maximum and the other with minimum density at the center, as the trap stiffness is increased. We show that this nonintuitive behavior is captured by the relevant Fokker-Planck equation, which, under minimal assumptions, predicts a continuous phase transition-like change between the two different shapes. As the translational diffusion coefficient is increased, both these distributions converge into the equilibrium, Boltzmann form. Our simulations support the analytical predictions and also show that the probability distribution of the orientation angle of the self-propulsion velocity undergoes a transition from unimodal to bimodal forms in this limit. We also extend our simulations to a three-dimensional trap and find similar behavior.
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Affiliation(s)
- Urvashi Nakul
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
| | - Manoj Gopalakrishnan
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
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2
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Dutta S. Most probable paths for active Ornstein-Uhlenbeck particles. Phys Rev E 2023; 107:054130. [PMID: 37329007 DOI: 10.1103/physreve.107.054130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 05/05/2023] [Indexed: 06/18/2023]
Abstract
Fluctuations play an important role in the dynamics of stochastic systems. In particular, for small systems, the most probable thermodynamic quantities differ from their averages because of the fluctuations. Using the Onsager Machlup variational formalism we analyze the most probable paths for nonequilibrium systems, in particular, active Ornstein-Uhlenbeck particles, and investigate how the entropy production along these paths differs from the average entropy production. We investigate how much information about their nonequilibrium nature can be obtained from their extremum paths and how these paths depend on the persistence time and their swim velocities. We also look at how the entropy production along the most probable paths varies with the active noise and how it differs from the average entropy production. This study would be useful to design artificial active systems with certain target trajectories.
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Affiliation(s)
- Sandipan Dutta
- Department of Physics, Birla Institute of Technology and Science, Pilani, Rajasthan, 333031, India
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3
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Zheng H, Yan N, Feng W, Liu Y, Luo H, Jing G. Swimming of Buoyant Bacteria in Quiescent Medium and Shear Flows. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4224-4232. [PMID: 36926901 DOI: 10.1021/acs.langmuir.2c03088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Gravity has an unavoidable effect on all living organisms inhabiting fluidic surroundings. To investigate the spatial distribution of bacteria in quiescent fluids and their rheotactic behavior in shear flows under buoyancy, we adjust the buoyant force to regulate bacterial swimming in a microfluidic channel. It is found that swimming bacteria of Escherichia coli exhibit an obvious vertical separation when exposed to a medium with high density and gradually gather close to the up wall within minutes. The bacterial population presents a net upward number flux, which enhances the trapping of motile bacteria onto the up surface as a result of buoyancy force apart from the hydrodynamic and kinematic interactions in quiescent fluids. When flow is imposed into the channel, the buoyancy effect is however significantly suppressed. Additionally, the drift velocity perpendicular to the buoyancy vector as a result of chirality-induced transverse swimming decreases with buoyancy force. However, this transverse drift capability is recovered after excluding the intrinsic swimming motility in a quiescent medium. Failing to escape from the trapping as a result of buoyant force allows for a facile separation of bacteria along the vertical direction. The findings also offer a controllable way to redisperse and homogenize the bacteria distribution close to walls by imposing a weak shear flow.
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Affiliation(s)
- Huan Zheng
- School of Physics, Northwest University, Xi'an, Shaanxi 710069, People's Republic of China
| | - Ningzhe Yan
- School of Physics, Northwest University, Xi'an, Shaanxi 710069, People's Republic of China
| | - Wei Feng
- School of Physics, Northwest University, Xi'an, Shaanxi 710069, People's Republic of China
| | - Yanan Liu
- School of Physics, Northwest University, Xi'an, Shaanxi 710069, People's Republic of China
| | - Hao Luo
- School of Physics, Northwest University, Xi'an, Shaanxi 710069, People's Republic of China
| | - Guangyin Jing
- School of Physics, Northwest University, Xi'an, Shaanxi 710069, People's Republic of China
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4
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Venkatareddy N, Lin ST, Maiti PK. Phase behavior of active and passive dumbbells. Phys Rev E 2023; 107:034607. [PMID: 37073042 DOI: 10.1103/physreve.107.034607] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 03/08/2023] [Indexed: 04/20/2023]
Abstract
We report phase separation in a mixture of "hot" and "cold" three-dimensional dumbbells which interact by Lennard-Jones potential. We also have studied the effect of asymmetry of dumbbells and the variation of ratio of "hot" and "cold" dumbbells on their phase separation. The ratio of the temperature difference between hot and cold dumbbells to the temperature of cold dumbbells is a measure of the activity χ of the system. From constant density simulations of symmetric dumbbells, we observe that the "hot" and "cold" dumbbells phase separate at higher activity ratio (χ>5.80) compared to that of a mixture of hot and cold Lennard-Jones monomers (χ>3.44). We find that, in the phase-separated system, the hot dumbbells have high effective volume and hence high entropy which is calculated by two-phase thermodynamic method. The high kinetic pressure of hot dumbbells forces the cold dumbbells to form dense clusters such that at the interface the high kinetic pressure of hot dumbbells is balanced by the virial pressure of cold dumbbells. We find that phase separation pushes the cluster of cold dumbbells to have solidlike ordering. Bond orientation order parameters reveal that the cold dumbbells form solidlike ordering consisting of predominantly face-centered cubic and hexagonal-close packing packing, but the individual dumbbells have random orientations. The simulation of the nonequilibrium system of symmetric dumbbells at different ratios of number of hot dumbbells to cold dumbbells reveals that the critical activity of phase separation decreases with increase in fraction of hot dumbbells. The simulation of equal mixture of hot and cold asymmetric dumbbells revealed that the critical activity of phase separation was independent of the asymmetry of dumbbells. We also observed that the clusters of cold asymmetric dumbbells showed both crystalline and noncrystalline order depending on the asymmetry of dumbbells.
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Affiliation(s)
- Nayana Venkatareddy
- Department of Physics, Indian Institute of Science, C. V. Raman Ave,Bengaluru 560012, India
| | - Shiang-Tai Lin
- Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan 10617
| | - Prabal K Maiti
- Department of Physics, Indian Institute of Science, C. V. Raman Ave,Bengaluru 560012, India
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5
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Chepizhko O, Franosch T. Resonant Diffusion of a Gravitactic Circle Swimmer. PHYSICAL REVIEW LETTERS 2022; 129:228003. [PMID: 36493425 DOI: 10.1103/physrevlett.129.228003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/16/2022] [Accepted: 10/07/2022] [Indexed: 06/17/2023]
Abstract
We investigate the dynamics of a single chiral active particle subject to an external torque due to the presence of a gravitational field. Our computer simulations reveal an arbitrarily strong increase of the long-time diffusivity of the gravitactic agent when the external torque approaches the intrinsic angular drift. We provide analytic expressions for the mean-square displacement in terms of eigenfunctions and eigenvalues of the noisy-driven-pendulum problem. The pronounced maximum in the diffusivity is then rationalized by the vanishing of the lowest eigenvalues of the Fokker-Planck equation for the angular motion as the rotational diffusion decreases and the underlying classical bifurcation is approached. A simple harmonic-oscillator picture for the barrier-dominated motion provides a quantitative description for the onset of the resonance while its range of validity is determined by the crossover to a critical-fluctuation-dominated regime.
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Affiliation(s)
- Oleksandr Chepizhko
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Thomas Franosch
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
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6
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Tucci G, Gambassi A, Majumdar SN, Schehr G. First-passage time of run-and-tumble particles with noninstantaneous resetting. Phys Rev E 2022; 106:044127. [PMID: 36397533 DOI: 10.1103/physreve.106.044127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
We study the statistics of the first-passage time of a single run-and-tumble particle (RTP) in one spatial dimension, with or without resetting, to a fixed target located at L>0. First, we compute the first-passage time distribution of a free RTP, without resetting or in a confining potential, but averaged over the initial position drawn from an arbitrary distribution p(x). Recent experiments used a noninstantaneous resetting protocol that motivated us to study in particular the case where p(x) corresponds to the stationary non-Boltzmann distribution of an RTP in the presence of a harmonic trap. This distribution p(x) is characterized by a parameter ν>0, which depends on the microscopic parameters of the RTP dynamics. We show that the first-passage time distribution of the free RTP, drawn from this initial distribution, develops interesting singular behaviors, depending on the value of ν. We then switch on resetting, mimicked by relaxation of the RTP in the presence of a harmonic trap. Resetting leads to a finite mean first-passage time and we study this as a function of the resetting rate for different values of the parameters ν and b=L/c, where c is the position of the right edge of the initial distribution p(x). In the diffusive limit of the RTP dynamics, we find a rich phase diagram in the (b,ν) plane, with an interesting reentrance phase transition. Away from the diffusive limit, qualitatively similar rich behaviors emerge for the full RTP dynamics.
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Affiliation(s)
- Gennaro Tucci
- SISSA-International School for Advanced Studies and INFN, via Bonomea 265, I-34136 Trieste, Italy
| | - Andrea Gambassi
- SISSA-International School for Advanced Studies and INFN, via Bonomea 265, I-34136 Trieste, Italy
| | - Satya N Majumdar
- LPTMS, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Grégory Schehr
- Sorbonne Université, Laboratoire de Physique Théorique et Hautes Energies, CNRS UMR 7589, 4 Place Jussieu, 75252 Paris Cedex 05, France
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7
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Thiffeault JL, Guo J. Anisotropic active Brownian particle with a fluctuating propulsion force. Phys Rev E 2022; 106:L012603. [PMID: 35974529 DOI: 10.1103/physreve.106.l012603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
The active Brownian particle (ABP) model describes a swimmer, synthetic or living, whose direction of swimming is a Brownian motion. The swimming is due to a propulsion force, and the fluctuations are typically thermal in origin. We present a two-dimensional model where the fluctuations arise from nonthermal noise in a propelling force acting at a single point, such as that due to a flagellum. We take the overdamped limit and find several modifications to the traditional ABP model. Since the fluctuating force causes a fluctuating torque, the diffusion tensor describing the process has a coupling between translational and rotational degrees of freedom. An anisotropic particle also exhibits a mass-dependent noise-induced drift, which does not disappear in the overdamped limit. We show that these effects have measurable consequences for the long-time diffusivity of active particles, in particular adding a contribution that is independent of where the force acts.
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Affiliation(s)
- Jean-Luc Thiffeault
- Department of Mathematics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jiajia Guo
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan 48109, USA
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8
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Aranson IS. Bacterial active matter. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:076601. [PMID: 35605446 DOI: 10.1088/1361-6633/ac723d] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
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.
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Affiliation(s)
- Igor S Aranson
- Departments of Biomedical Engineering, Chemistry, and Mathematics, Pennsylvania State University, University Park, PA 16802, United States of America
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9
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Spatial patterns in ecological systems: from microbial colonies to landscapes. Emerg Top Life Sci 2022; 6:245-258. [PMID: 35678374 DOI: 10.1042/etls20210282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/17/2022]
Abstract
Self-organized spatial patterns are ubiquitous in ecological systems and allow populations to adopt non-trivial spatial distributions starting from disordered configurations. These patterns form due to diverse nonlinear interactions among organisms and between organisms and their environment, and lead to the emergence of new (eco)system-level properties unique to self-organized systems. Such pattern consequences include higher resilience and resistance to environmental changes, abrupt ecosystem collapse, hysteresis loops, and reversal of competitive exclusion. Here, we review ecological systems exhibiting self-organized patterns. We establish two broad pattern categories depending on whether the self-organizing process is primarily driven by nonlinear density-dependent demographic rates or by nonlinear density-dependent movement. Using this organization, we examine a wide range of observational scales, from microbial colonies to whole ecosystems, and discuss the mechanisms hypothesized to underlie observed patterns and their system-level consequences. For each example, we review both the empirical evidence and the existing theoretical frameworks developed to identify the causes and consequences of patterning. Finally, we trace qualitative similarities across systems and propose possible ways of developing a more quantitative understanding of how self-organization operates across systems and observational scales in ecology.
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10
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Scagliarini A, Pagonabarraga I. Hydrodynamic and geometric effects in the sedimentation of model run-and-tumble microswimmers. SOFT MATTER 2022; 18:2407-2413. [PMID: 35266484 PMCID: PMC9904398 DOI: 10.1039/d1sm01594j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
The sedimentation process in an active suspension is the result of the competition between gravity and the autonomous motion of particles. We carry out simulations of run-and-tumble squirmers that move in a fluid medium, focusing on the dependence of the non-equilibrium steady state on the swimming properties. We find that for large enough activity, the density profiles are no longer simple exponentials; we recover the numerical results through the introduction of a local effective temperature, suggesting that the breakdown of the Perrin-like exponential form is a collective effect due to fluid-mediated dynamic correlations among particles. We show that analogous concepts can also fit the case of active non-motile particles, for which we report the first study of this kind. Moreover, we provide evidence of scenarios where the solvent hydrodynamics induces non-local effects which require the full three-dimensional dynamics to be taken into account in order to understand sedimentation in active suspensions. Finally, analyzing the statistics of the orientations of microswimmers, the emergence of a height-dependent polar order in the system is discussed.
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Affiliation(s)
- Andrea Scagliarini
- IAC-CNR, Istituto per le Applicazioni del Calcolo "Mauro Picone", Via dei Taurini 19, 00185 Rome, Italy.
- INFN, Sezione Roma "Tor Vergata", Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Ignacio Pagonabarraga
- CECAM, Centre Européen de Calcul Atomique et Moléculaire, Ecole Polytechnique Fédérale de Lausanne, Batochimie, Avenue Forel 2, 1015 Lausanne, Switzerland
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Carrer de Martí i Franquès 1, 08028 Barcelona, Spain
- Universitat de Barcelona, Institute of Complex Systems (UBICS), Universitat de Barcelona, 08028 Barcelona, Spain
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11
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Rühle F, Zantop AW, Stark H. Gyrotactic cluster formation of bottom-heavy squirmers. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2022; 45:26. [PMID: 35304659 PMCID: PMC8933315 DOI: 10.1140/epje/s10189-022-00183-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Squirmers that are bottom-heavy experience a torque that aligns them along the vertical so that they swim upwards. In a suspension of many squirmers, they also interact hydrodynamically via flow fields that are initiated by their swimming motion and by gravity. Swimming under the combined action of flow field vorticity and gravitational torque is called gyrotaxis. Using the method of multi-particle collision dynamics, we perform hydrodynamic simulations of a many-squirmer system floating above the bottom surface. Due to gyrotaxis they exhibit pronounced cluster formation with increasing gravitational torque. The clusters are more volatile at low values but compactify to smaller clusters at larger torques. The mean distance between clusters is mainly controlled by the gravitational torque and not the global density. Furthermore, we observe that neutral squirmers form clusters more easily, whereas pullers require larger gravitational torques due to their additional force-dipole flow fields. We do not observe clustering for pusher squirmers. Adding a rotlet dipole to the squirmer flow field induces swirling clusters. At high gravitational strengths, the hydrodynamic interactions with the no-slip boundary create an additional vertical alignment for neutral squirmers, which also supports cluster formation.
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Affiliation(s)
- Felix Rühle
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, D-10623, Berlin, Germany.
| | - Arne W Zantop
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, D-10623, Berlin, Germany
| | - Holger Stark
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, D-10623, Berlin, Germany
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12
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Khatri N, Burada PS. Diffusion of chiral active particles in a Poiseuille flow. Phys Rev E 2022; 105:024604. [PMID: 35291080 DOI: 10.1103/physreve.105.024604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
We study the diffusive behavior of chiral active (self-propelled) Brownian particles in a two-dimensional microchannel with a Poiseuille flow. Using numerical simulations, we show that the behavior of the transport coefficients of particles, for example, the average velocity v and the effective diffusion coefficient D_{eff}, strongly depends on flow strength u_{0}, translational diffusion constant D_{0}, rotational diffusion rate D_{θ}, and chirality of the active particles Ω. It is demonstrated that the particles can exhibit upstream drift, resulting in a negative v, for the optimal parameter values of u_{0}, D_{θ}, and Ω. Interestingly, the direction of v can be controlled by tuning these parameters. We observe that for some optimal values of u_{0} and Ω, the chiral particles aggregate near a channel wall and the corresponding D_{eff} are enhanced. However, for the nonchiral particles (Ω=0), D_{eff} is suppressed by the presence of Poiseuille flow. It is expected that these findings have a great potential for developing microfluidic and lab-on-a-chip devices for separating the active particles.
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Affiliation(s)
- Narender Khatri
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - P S Burada
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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13
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Chakraborty R, Maiti A, Sharma N, Dey KK. Active matter dynamics in confined microfluidic environments. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 186:245-265. [PMID: 35033287 DOI: 10.1016/bs.pmbts.2021.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The field of active matter is a nascent area of research in soft condensed matter physics, which is drawing on the expertise of researchers from diverse disciplines. Small scale active particles-both inorganic and biological-display non-trivial emergent dynamics and interactions that could help us understand complex biological processes and phenomena. Recently, using microfluidic technologies, several research groups have performed important experimental and theoretical studies to understand the behavior of self-propelled particles and molecular active matter within confined environments-to glean a fundamental understanding of the cellular processes occurring under ultra-low Reynolds number conditions. In this chapter, we would like to review applications of microfluidics in active matter research, highlighting a few important theoretical and experimental investigations. We will conclude the discussion with a note on the future of this field mentioning a few open questions that are at the forefront of our minds.
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Affiliation(s)
- Rik Chakraborty
- Discipline of Physics, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India
| | - Arnab Maiti
- Discipline of Physics, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India
| | - Nikita Sharma
- Discipline of Physics, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India
| | - Krishna Kanti Dey
- Discipline of Physics, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India.
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14
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Choudhary A, Stark H. On the cross-streamline lift of microswimmers in viscoelastic flows. SOFT MATTER 2021; 18:48-52. [PMID: 34878484 DOI: 10.1039/d1sm01339d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The current work studies the dynamics of a microswimmer in pressure-driven flow of a weakly viscoelastic fluid. Employing a second-order fluid model, we show that a self-propelling swimmer experiences a viscoelastic swimming lift in addition to the well-known passive lift that arises from its resistance to shear flow. Using the reciprocal theorem, we evaluate analytical expressions for the swimming lift experienced by neutral and pusher/puller-type swimmers and show that they depend on the hydrodynamic signature associated with the swimming mechanism. We find that, in comparison to passive particles, the focusing of neutral swimmers towards the centerline can be significantly accelerated, while for force-dipole swimmers no net modification in cross-streamline migration occurs.
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Affiliation(s)
- Akash Choudhary
- Institute of Theoretical Physics, Technische Universität Berlin, 10623 Berlin, Germany.
| | - Holger Stark
- Institute of Theoretical Physics, Technische Universität Berlin, 10623 Berlin, Germany.
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15
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Liebchen B, Mukhopadhyay AK. Interactions in active colloids. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 34:083002. [PMID: 34788232 DOI: 10.1088/1361-648x/ac3a86] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
The past two decades have seen a remarkable progress in the development of synthetic colloidal agents which are capable of creating directed motion in an unbiased environment at the microscale. These self-propelling particles are often praised for their enormous potential to self-organize into dynamic nonequilibrium structures such as living clusters, synchronized super-rotor structures or self-propelling molecules featuring a complexity which is rarely found outside of the living world. However, the precise mechanisms underlying the formation and dynamics of many of these structures are still barely understood, which is likely to hinge on the gaps in our understanding of how active colloids interact. In particular, besides showing comparatively short-ranged interactions which are well known from passive colloids (Van der Waals, electrostatic etc), active colloids show novel hydrodynamic interactions as well as phoretic and substrate-mediated 'osmotic' cross-interactions which hinge on the action of the phoretic field gradients which are induced by the colloids on other colloids in the system. The present article discusses the complexity and the intriguing properties of these interactions which in general are long-ranged, non-instantaneous, non-pairwise and non-reciprocal and which may serve as key ingredients for the design of future nonequilibrium colloidal materials. Besides providing a brief overview on the state of the art of our understanding of these interactions a key aim of this review is to emphasize open key questions and corresponding open challenges.
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Affiliation(s)
- Benno Liebchen
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Aritra K Mukhopadhyay
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
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16
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Singh J, Patteson AE, Torres Maldonado BO, Purohit PK, Arratia PE. Bacterial activity hinders particle sedimentation. SOFT MATTER 2021; 17:4151-4160. [PMID: 33881035 DOI: 10.1039/d0sm02115f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Sedimentation in active fluids has come into focus due to the ubiquity of swimming micro-organisms in natural and industrial processes. Here, we investigate sedimentation dynamics of passive particles in a fluid as a function of bacteria E. coli concentration. Results show that the presence of swimming bacteria significantly reduces the speed of the sedimentation front even in the dilute regime, in which the sedimentation speed is expected to be independent of particle concentration. Furthermore, bacteria increase the dispersion of the passive particles, which determines the width of the sedimentation front. For short times, particle sedimentation speed has a linear dependence on bacterial concentration. Mean square displacement data shows, however, that bacterial activity decays over long experimental (sedimentation) times. An advection-diffusion equation coupled to bacteria population dynamics seems to capture concentration profiles relatively well. A single parameter, the ratio of single particle speed to the bacteria flow speed can be used to predict front sedimentation speed.
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Affiliation(s)
- Jaspreet Singh
- Department of Mechanical Engineering & Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | | | - Bryan O Torres Maldonado
- Department of Mechanical Engineering & Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Prashant K Purohit
- Department of Mechanical Engineering & Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Paulo E Arratia
- Department of Mechanical Engineering & Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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17
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Fazli Z, Naji A. Active particles with polar alignment in ring-shaped confinement. Phys Rev E 2021; 103:022601. [PMID: 33736018 DOI: 10.1103/physreve.103.022601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/13/2021] [Indexed: 12/17/2022]
Abstract
We study steady-state properties of active, nonchiral and chiral Brownian particles with polar alignment and steric interactions confined within a ring-shaped confinement (annulus) in two dimensions. Exploring possible interplays between polar interparticle alignment, geometric confinement and the surface curvature, being incorporated here on minimal levels, we report a surface-population reversal effect, whereby active particles migrate from the outer concave boundary of the annulus to accumulate on its inner convex boundary. This contrasts the conventional picture, implying stronger accumulation of active particles on concave boundaries relative to the convex ones. The population reversal is caused by both particle alignment and surface curvature, disappearing when either of these factors is absent. We explore the ensuing consequences for the chirality-induced current and swim pressure of active particles and analyze possible roles of system parameters, such as the mean number density of particles and particle self-propulsion, chirality, and alignment strengths.
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Affiliation(s)
- Zahra Fazli
- School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran
| | - Ali Naji
- School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran.,School of Nano Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran
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18
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Ravoni A, Angelani L. Lattice model for active flows in microchannels. Phys Rev E 2021; 102:062602. [PMID: 33465978 DOI: 10.1103/physreve.102.062602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/10/2020] [Indexed: 11/07/2022]
Abstract
We introduce a one-dimensional lattice model to study active particles in narrow channel connecting finite reservoirs. The model describes interacting run-and-tumble swimmers exerting pushing forces on neighboring particles, allowing the formation of long active clusters inside the channel. Our model is able to reproduce the emerging oscillatory dynamics observed in full molecular dynamics simulations of self-propelled bacteria [Paoluzzi et al., Phys. Rev. Lett. 115, 188303 (2015)PRLTAO0031-900710.1103/PhysRevLett.115.188303] and allows us to extend in a simple way the analysis to a wide range of system parameters (box length, number of swimmers), taking into account different physical conditions (presence or absence of tumbling, different forms of the entrance probability into the channel). We find that the oscillatory behavior is suppressed for short channels length L<L^{*} and for high tumbling rates λ>λ^{*}, with threshold values L^{*} and λ^{*} which in general depend on physical parameters. Moreover, we find that oscillations persist by using different entrance probabilities, which, however, affect the oscillation properties and the filling dynamics of reservoirs.
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Affiliation(s)
- Alessandro Ravoni
- Department of Mathematics and Physics, Roma Tre University, 00146 Rome, Italy
| | - Luca Angelani
- ISC-CNR, Institute for Complex Systems, and Dipartimento di Fisica, Università Sapienza, I-00185 Rome, Italy
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19
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Zarif M, Naji A. Confinement-induced alternating interactions between inclusions in an active fluid. Phys Rev E 2020; 102:032613. [PMID: 33075886 DOI: 10.1103/physreve.102.032613] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 09/08/2020] [Indexed: 11/07/2022]
Abstract
In a system of colloidal inclusions suspended in an equilibrium bath of smaller particles, the particulate bath engenders effective, short-ranged, primarily attractive interactions between the inclusions, known as depletion interactions, that originate from the steric depletion of bath particles from the immediate vicinity of the inclusions. In a bath of active (self-propelled) particles, the nature of such bath-mediated interactions can qualitatively change from attraction to repulsion, and they become stronger in magnitude and range of action as compared with typical equilibrium depletion interactions, especially as the bath activity (particle self-propulsion) is increased. We study effective interactions mediated by a bath of active Brownian particles between two fixed, impenetrable, and disk-shaped inclusions in a planar (channel) confinement in two dimensions. Confinement is found to strongly influence the effective interaction between the inclusions, specifically by producing alternating interaction profiles with possible attractive and repulsive regions in sufficiently narrow channels. We study the dependence of the ensuing interactions on different system parameters and the orientational (parallel versus perpendicular) configuration of the inclusion pair relative to the channel walls. The confinement effects are largely regulated by the layering of active particles next to the surface boundaries, both of the inclusions and the channel walls that counteract one another in accumulating the active particles in their own proximities. In narrow channels, the combined effects due to the channel walls and the inclusions lead to peculiar structuring of active particles (reminiscent of wavelike interference patterns) within the channel.
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Affiliation(s)
- Mahdi Zarif
- Department of Physical and Computational Chemistry, Shahid Beheshti University, Tehran 19839-9411, Iran
| | - Ali Naji
- School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran.,School of Nano Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran
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20
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Peng YS, Sheng YJ, Tsao HK. Partition of nanoswimmers between two immiscible phases: a soft and penetrable boundary. SOFT MATTER 2020; 16:5054-5061. [PMID: 32452505 DOI: 10.1039/d0sm00298d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The behavior of run-and-tumble nanoswimmers which can self-propel in two immiscible liquids such as water-oil systems and are able to cross the interface is investigated by dissipative particle dynamics. At the steady-state, the partition ratio (φ) of nanoswimmers between the two immiscible liquids is obtained, and it depends on the active force (Fa), run time (τ), and swimmer-solvent interactions. The partition ratio φ is found to grow generally with increasing Fa2τ. At sufficiently large Fa, it is surprising to find that hydrophilic nanoswimmers prefer to stay in the oil phase rather than in the water phase. The partition ratio is also influenced by the hydrophobicity of swimmers in the oil phase. Two simple models are proposed to describe the partition ratio, including a near-equilibrium model and a kinetic model. Surface accumulation appearing at an impenetrable interface is also observed at the fluid-fluid interface for small Fa but it vanishes for sufficiently large Fa.
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Affiliation(s)
- Ying-Shuo Peng
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan.
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21
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Shabanniya MR, Naji A. Active dipolar spheroids in shear flow and transverse field: Population splitting, cross-stream migration, and orientational pinning. J Chem Phys 2020; 152:204903. [PMID: 32486664 DOI: 10.1063/5.0002757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We study the steady-state behavior of active, dipolar, Brownian spheroids in a planar channel subjected to an imposed Couette flow and an external transverse field, applied in the "downward" normal-to-flow direction. The field-induced torque on active spheroids (swimmers) is taken to be of magnetic form by assuming that they have a permanent magnetic dipole moment, pointing along their self-propulsion (swim) direction. Using a continuum approach, we show that a host of behaviors emerges over the parameter space spanned by the particle aspect ratio, self-propulsion and shear/field strengths, and the channel width. The cross-stream migration of the model swimmers is shown to involve a regime of linear response (quantified by a linear-response factor) in weak fields. For prolate swimmers, the weak-field behavior crosses over to a regime of full swimmer migration to the bottom half of the channel in strong fields. For oblate swimmers, a counterintuitive regime of reverse migration arises in intermediate fields, where a macroscopic fraction of swimmers reorient and swim to the top channel half at an acute "upward" angle relative to the field axis. The diverse behaviors reported here are analyzed based on the shear-induced population splitting (bimodality) of the swim orientation, giving two distinct, oppositely polarized, swimmer subpopulations (albeit very differently for prolate/oblate swimmers) in each channel half. In strong fields, swimmers of both types exhibit net upstream currents relative to the laboratory frame. The onsets of full migration and net upstream current depend on the aspect ratio, enabling efficient particle separation strategies in microfluidic setups.
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Affiliation(s)
- Mohammad Reza Shabanniya
- School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran
| | - Ali Naji
- School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran
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22
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Rühle F, Stark H. Emergent collective dynamics of bottom-heavy squirmers under gravity. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2020; 43:26. [PMID: 32445113 DOI: 10.1140/epje/i2020-11949-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/17/2020] [Indexed: 05/26/2023]
Abstract
We present the results of hydrodynamic simulations using the method of multi-particle collision dynamics for a system of squirmer microswimmers moving under the influence of gravity at low Reynolds numbers. In addition, the squirmers are bottom-heavy so that they experience a torque which aligns them along the vertical. The squirmers interact hydrodynamically by the flow fields of a stokeslet and rotlet, which are initiated by the acting gravitational force and torque, respectively, and by their own flow fields. By varying the ratio of swimming to bulk sedimentation velocity and the torque, we determine state diagrams for the emergent collective dynamics of neutral squirmers as well as strong pushers and pullers. For low swimming velocity and torque we observe conventional sedimentation, while the sedimentation profile becomes inverted when their values are increased. For neutral squirmers we discover convective rolls of circulating squirmers between both sedimentation states, which sit at the bottom of the system and are fed by plumes made of collectively sinking squirmers. At larger torques porous clusters occur that spawn single squirmers. The two latter states can also occur transiently starting from a uniform squirmer distribution and then disappear in the long-time limit. For strong pushers and pullers only weak plume formation is observed.
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Affiliation(s)
- Felix Rühle
- Technische Universität Berlin, Institut für Theoretische Physik, Hardenbergstr. 36, D-10623, Berlin, Germany.
| | - Holger Stark
- Technische Universität Berlin, Institut für Theoretische Physik, Hardenbergstr. 36, D-10623, Berlin, Germany
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23
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Bolitho A, Singh R, Adhikari R. Periodic Orbits of Active Particles Induced by Hydrodynamic Monopoles. PHYSICAL REVIEW LETTERS 2020; 124:088003. [PMID: 32167321 DOI: 10.1103/physrevlett.124.088003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/05/2020] [Indexed: 06/10/2023]
Abstract
Terrestrial experiments on active particles, such as Volvox, involve gravitational forces, torques and accompanying monopolar fluid flows. Taking these into account, we analyze the dynamics of a pair of self-propelling, self-spinning active particles between widely separated parallel planes. Neglecting flow reflected by the planes, the dynamics of orientation and horizontal separation is symplectic, with a Hamiltonian exactly determining limit cycle oscillations. Near the bottom plane, gravitational torque damps and reflected flow excites this oscillator, sustaining a second limit cycle that can be perturbatively related to the first. Our work provides a theory for dancing Volvox and highlights the importance of monopolar flow in active matter.
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Affiliation(s)
- Austen Bolitho
- DAMTP, Centre for Mathematical Sciences, University of Cambridge, Cambridge CB3 0WA, United Kingdom
| | - Rajesh Singh
- DAMTP, Centre for Mathematical Sciences, University of Cambridge, Cambridge CB3 0WA, United Kingdom
| | - R Adhikari
- DAMTP, Centre for Mathematical Sciences, University of Cambridge, Cambridge CB3 0WA, United Kingdom
- The Institute of Mathematical Sciences-HBNI, CIT Campus, Chennai 600113, India
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24
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Kolb T, Klotsa D. Active binary mixtures of fast and slow hard spheres. SOFT MATTER 2020; 16:1967-1978. [PMID: 31859309 DOI: 10.1039/c9sm01799b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We computationally studied the phase behavior and dynamics of binary mixtures of active particles, where each species had distinct activities leading to distinct velocities, fast and slow. We obtained phase diagrams demonstrating motility-induced phase separation (MIPS) upon varying the activity and concentration of each species, and extended current kinetic theory of active/passive mixtures to active/active mixtures. We discovered two regimes of behavior quantified through the participation of each species in the dense phase compared to their monodisperse counterparts. In regime I (active/passive and active/weakly-active), we found that the dense phase was segregated by particle type into domains of fast and slow particles. Moreover, fast particles were suppressed from entering the dense phase while slow particles were enhanced entering the dense phase, compared to monodisperse systems of all-fast or all-slow particles. These effects decayed asymptotically as the activity of the slow species increased, approaching the activity of the fast species until they were negligible (regime II). In regime II, the dense phase was homogeneously mixed and each species participated in the dense phase as if it were it a monodisperse system (i.e. not mixed at all). Finally, we showed that a weighted average of constituent particle activities, which we term the net activity, defines a binodal for the MIPS transition in active/active binary mixtures. We examined the critical point of the transition and found a critical exponent (β = 0.45) in agreement with similar studies on monodisperse systems, and distinct from equilibrium systems.
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Affiliation(s)
- Thomas Kolb
- Department of Chemistry, University of North Carolina at Chapel Hill, USA and Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, USA.
| | - Daphne Klotsa
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, USA.
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25
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Rana S, Samsuzzaman M, Saha A. Tuning the self-organization of confined active particles by the steepness of the trap. SOFT MATTER 2019; 15:8865-8878. [PMID: 31616877 DOI: 10.1039/c9sm01691k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We consider the collective dynamics of self-propelling particles in two dimensions. They can align themselves according to the direction of propulsion of their neighbours, together with small rotational fluctuations. They also interact with each other via soft, isotropic, repulsive potentials. The particles are confined in a circular trap. The steepness of the trap is tuneable. The average packing fraction of the particles is low. When the trap is steep, particles flock along its boundary. They form a polar cluster that spreads over the boundary. The cluster is not spatially ordered. We show that when the steepness is decreased beyond a threshold value, the cluster becomes round and compact and eventually spatial order (hexagonal) emerges in addition to the pre-established polar order. We investigate the kinetics of such ordering. We find that while rotating around the centre of the trap along its circular boundary, the cluster needs to roll around its centre of mass to be spatially ordered. We have studied the stability of the order when the trap is suddenly switched off. We find that for the particles with velocity alignment interaction, the decay of the spatial order is much slower than the particles without the alignment interaction.
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Affiliation(s)
- Shubhashis Rana
- S. N. Bose National Centre For Basic Sciences, Kolkata, 700098, India.
| | - Md Samsuzzaman
- Department of Physics, Savitribai Phule Pune University, Pune, 411007, India.
| | - Arnab Saha
- Department of Physics, Savitribai Phule Pune University, Pune, 411007, India.
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26
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Caprini L, Hernández-García E, López C, Marini Bettolo Marconi U. A comparative study between two models of active cluster crystals. Sci Rep 2019; 9:16687. [PMID: 31723160 PMCID: PMC6853940 DOI: 10.1038/s41598-019-52420-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/19/2019] [Indexed: 12/28/2022] Open
Abstract
We study a system of active particles with soft repulsive interactions that lead to an active cluster-crystal phase in two dimensions. We use two different modelizations of the active force - Active Brownian particles (ABP) and Ornstein-Uhlenbeck particles (AOUP) - and focus on analogies and differences between them. We study the different phases appearing in the system, in particular, the formation of ordered patterns drifting in space without being altered. We develop an effective description which captures some properties of the stable clusters for both ABP and AOUP. As an additional point, we confine such a system in a large channel, in order to study the interplay between the cluster crystal phase and the well-known accumulation near the walls, a phenomenology typical of active particles. For small activities, we find clusters attached to the walls and deformed, while for large values of the active force they collapse in stripes parallel to the walls.
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Affiliation(s)
- Lorenzo Caprini
- Gran Sasso Science Institute (GSSI), Via. F. Crispi 7, 67100, L'Aquila, Italy.
| | - Emilio Hernández-García
- IFISC (CSIC-UIB), Instituto de Física Interdisciplinar y Sistemas Complejos, Campus Universitat de les Illes Balears, E-07122, Palma de Mallorca, Spain
| | - Cristóbal López
- IFISC (CSIC-UIB), Instituto de Física Interdisciplinar y Sistemas Complejos, Campus Universitat de les Illes Balears, E-07122, Palma de Mallorca, Spain
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27
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Bárdfalvy D, Nordanger H, Nardini C, Morozov A, Stenhammar J. Particle-resolved lattice Boltzmann simulations of 3-dimensional active turbulence. SOFT MATTER 2019; 15:7747-7756. [PMID: 31393504 DOI: 10.1039/c9sm00774a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Collective behaviour in suspensions of microswimmers is often dominated by the impact of long-ranged hydrodynamic interactions. These phenomena include active turbulence, where suspensions of pusher bacteria at sufficient densities exhibit large-scale, chaotic flows. To study this collective phenomenon, we use large-scale (up to N = 3 × 106) particle-resolved lattice Boltzmann simulations of model microswimmers described by extended stresslets. Such system sizes enable us to obtain quantitative information about both the transition to active turbulence and characteristic features of the turbulent state itself. In the dilute limit, we test analytical predictions for a number of static and dynamic properties against our simulation results. For higher swimmer densities, where swimmer-swimmer interactions become significant, we numerically show that the length- and timescales of the turbulent flows increase steeply near the predicted finite-system transition density.
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Affiliation(s)
- Dóra Bárdfalvy
- Division of Physical Chemistry, Lund University, Box 124, S-221 00 Lund, Sweden.
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28
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Peng YS, Wang Z, Chu KC, Sheng YJ, Tsao HK. Favorable partition of nanoswimmers toward a confined slit. Phys Rev E 2019; 100:042604. [PMID: 31770970 DOI: 10.1103/physreve.100.042604] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Indexed: 06/10/2023]
Abstract
The partition of nanoswimmers between a narrow channel and a reservoir is explored by dissipative particle dynamics. In contrast to passive colloids, nanoswimmers prefer to stay in the slit rather than in the reservoir for sufficiently large active force (F_{a}) or run time (τ). The partition ratio (φ) increases with F_{a} and τ. Interestingly, as the slit height decreases, φ grows accordingly until the confinement effect dominates. Three types of the concentration profile in the slit are identified as a consequence of the competition between surface accumulation and entropic barrier.
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Affiliation(s)
- Ying-Shuo Peng
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Zhengjia Wang
- Condensed Matter Science and Technology Institute, School of Science, Harbin Institute of Technology, Harbin 150080, People's Republic of China
| | - Kang-Ching Chu
- Department of Chemical and Materials Engineering, Department of Physics, National Central University, Jhongli 320, Taiwan
| | - Yu-Jane Sheng
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Heng-Kwong Tsao
- Department of Chemical and Materials Engineering, Department of Physics, National Central University, Jhongli 320, Taiwan
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29
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Hoell C, Löwen H, Menzel AM. Multi-species dynamical density functional theory for microswimmers: Derivation, orientational ordering, trapping potentials, and shear cells. J Chem Phys 2019. [DOI: 10.1063/1.5099554] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Christian Hoell
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Andreas M. Menzel
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany
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30
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Mathijssen AJTM, Figueroa-Morales N, Junot G, Clément É, Lindner A, Zöttl A. Oscillatory surface rheotaxis of swimming E. coli bacteria. Nat Commun 2019; 10:3434. [PMID: 31366920 PMCID: PMC6668461 DOI: 10.1038/s41467-019-11360-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 07/08/2019] [Indexed: 11/19/2022] Open
Abstract
Bacterial contamination of biological channels, catheters or water resources is a major threat to public health, which can be amplified by the ability of bacteria to swim upstream. The mechanisms of this 'rheotaxis', the reorientation with respect to flow gradients, are still poorly understood. Here, we follow individual E. coli bacteria swimming at surfaces under shear flow using 3D Lagrangian tracking and fluorescent flagellar labelling. Three transitions are identified with increasing shear rate: Above a first critical shear rate, bacteria shift to swimming upstream. After a second threshold, we report the discovery of an oscillatory rheotaxis. Beyond a third transition, we further observe coexistence of rheotaxis along the positive and negative vorticity directions. A theoretical analysis explains these rheotaxis regimes and predicts the corresponding critical shear rates. Our results shed light on bacterial transport and reveal strategies for contamination prevention, rheotactic cell sorting, and microswimmer navigation in complex flow environments.
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Affiliation(s)
- Arnold J T M Mathijssen
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA, 94305, USA
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, 1 Keble Road, OX1 3NP, UK
| | - Nuris Figueroa-Morales
- PMMH, UMR 7636 CNRS-ESPCI-PSL Research University, Sorbonne University, University Paris Diderot, 7-9 quai Saint-Bernard, 75005, Paris, France
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Gaspard Junot
- PMMH, UMR 7636 CNRS-ESPCI-PSL Research University, Sorbonne University, University Paris Diderot, 7-9 quai Saint-Bernard, 75005, Paris, France
| | - Éric Clément
- PMMH, UMR 7636 CNRS-ESPCI-PSL Research University, Sorbonne University, University Paris Diderot, 7-9 quai Saint-Bernard, 75005, Paris, France
| | - Anke Lindner
- PMMH, UMR 7636 CNRS-ESPCI-PSL Research University, Sorbonne University, University Paris Diderot, 7-9 quai Saint-Bernard, 75005, Paris, France.
| | - Andreas Zöttl
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, 1 Keble Road, OX1 3NP, UK.
- PMMH, UMR 7636 CNRS-ESPCI-PSL Research University, Sorbonne University, University Paris Diderot, 7-9 quai Saint-Bernard, 75005, Paris, France.
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10, Wien, Austria.
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31
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Kuhr JT, Rühle F, Stark H. Collective dynamics in a monolayer of squirmers confined to a boundary by gravity. SOFT MATTER 2019; 15:5685-5694. [PMID: 31246219 DOI: 10.1039/c9sm00889f] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We present a hydrodynamic study of a monolayer of squirmer model microswimmers confined to a boundary by strong gravity using the simulation method of multi-particle collision dynamics. The squirmers interact with each other via their self-generated hydrodynamic flow fields and thereby form a variety of fascinating dynamic states when density and squirmer type are varied. Weak pushers, neutral squirmers, and pullers have an upright orientation. With their flow fields they push neighbors away and thereby form a hydrodynamic Wigner fluid at lower densities. Furthermore, states of fluctuating chains and trimers, of kissing, and at large densities a global cluster exist. Finally, pushers at all densities can tilt against the wall normal and their in-plane velocities align to show swarming. It turns into chaotic swarming for strong pushers at high densities. We characterize all these states quantitatively.
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Affiliation(s)
- Jan-Timm Kuhr
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
| | - Felix Rühle
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
| | - Holger Stark
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
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32
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Stürmer J, Seyrich M, Stark H. Chemotaxis in a binary mixture of active and passive particles. J Chem Phys 2019; 150:214901. [DOI: 10.1063/1.5080543] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Julian Stürmer
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Maximilian Seyrich
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Holger Stark
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
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33
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Fily Y. Self-propelled particle in a nonconvex external potential: Persistent limit in one dimension. J Chem Phys 2019; 150:174906. [PMID: 31067874 DOI: 10.1063/1.5085759] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Equilibrium mapping techniques for nonaligning self-propelled particles have made it possible to predict the density profile of an active ideal gas in a wide variety of external potentials. However, they fail when the self-propulsion is very persistent and the potential is nonconvex, which is precisely when the most uniquely active phenomena occur. Here, we show how to predict the density profile of a 1D active Ornstein-Uhlenbeck particle in an arbitrary external potential in the persistent limit and discuss the consequences of the potential's nonconvexity on the structure of the solution, including the central role of the potential's inflection points and the nonlocal dependence of the density profile on the potential.
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Affiliation(s)
- Yaouen Fily
- Wilkes Honors College, Florida Atlantic University, Jupiter, Florida 33458, USA
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34
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Caprini L, Cecconi F, Marini Bettolo Marconi U. Transport of active particles in an open-wedge channel. J Chem Phys 2019; 150:144903. [DOI: 10.1063/1.5090104] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lorenzo Caprini
- Gran Sasso Science Institute (GSSI), Via F.Crispi 7, I-67100 L’Aquila, Italy
| | - Fabio Cecconi
- Istituto dei Sistemi Complessi (CNR), Via Taurini 19, I-00185 Roma, Italy
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35
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Caprini L, Marini Bettolo Marconi U, Puglisi A. Activity induced delocalization and freezing in self-propelled systems. Sci Rep 2019; 9:1386. [PMID: 30718579 PMCID: PMC6361910 DOI: 10.1038/s41598-018-36824-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/23/2018] [Indexed: 11/08/2022] Open
Abstract
We study a system of interacting active particles, propelled by colored noises, characterized by an activity time τ, and confined by a single-well anharmonic potential. We assume pair-wise repulsive forces among particles, modelling the steric interactions among microswimmers. This system has been experimentally studied in the case of a dilute suspension of Janus particles confined through acoustic traps. We observe that already in the dilute regime - when inter-particle interactions are negligible - increasing the persistent time, τ, pushes the particles away from the potential minimum, until a saturation distance is reached. We compute the phase diagram (activity versus interaction length), showing that the interaction does not suppress this delocalization phenomenon but induces a liquid- or solid-like structure in the densest regions. Interestingly a reentrant behavior is observed: a first increase of τ from small values acts as an effective warming, favouring fluidization; at higher values, when the delocalization occurs, a further increase of τ induces freezing inside the densest regions. An approximate analytical scheme gives fair predictions for the density profiles in the weakly interacting case. The analysis of non-equilibrium heat fluxes reveals that in the region of largest particle concentration equilibrium is restored in several aspects.
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Affiliation(s)
- Lorenzo Caprini
- Gran Sasso Science Institute (GSSI), Via. F. Crispi 7, 67100, L'Aquila, Italy.
| | | | - Andrea Puglisi
- Istituto dei Sistemi Complessi - CNR and Dipartimento di Fisica, Università di Roma Sapienza, P.le Aldo Moro 2, 00185, Rome, Italy
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36
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Vachier J, Mazza MG. Dynamics of sedimenting active Brownian particles. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:11. [PMID: 30687883 DOI: 10.1140/epje/i2019-11770-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 01/04/2019] [Indexed: 06/09/2023]
Abstract
We investigate the stochastic dynamics of one sedimenting active Brownian particle in three dimensions under the influence of gravity and passive fluctuations in the translational and rotational motion. We present an analytical solution of the Fokker-Planck equation for the stochastic process which allows us to describe the dynamics of one active Brownian particle in three dimensions. We address the time evolution of the density, the polarization, and the steady-state solution. We also perform Brownian dynamics simulations and study the effect of the activity of the particles on their collective motion. These results qualitatively agree with our model. Finally, we compare our results with experiments (J. Palacci et al., Phys. Rev. Lett. 105, 088304 (2010)) and find very good agreement.
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Affiliation(s)
- Jérémy Vachier
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077, Göttingen, Germany
| | - Marco G Mazza
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077, Göttingen, Germany.
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, LE11 3TU, Loughborough, Leicestershire, UK.
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37
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Rodenburg J, Paliwal S, de Jager M, Bolhuis PG, Dijkstra M, van Roij R. Ratchet-induced variations in bulk states of an active ideal gas. J Chem Phys 2018; 149:174910. [DOI: 10.1063/1.5048698] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jeroen Rodenburg
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Siddharth Paliwal
- Soft Condensed Matter Group, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Marjolein de Jager
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Peter G. Bolhuis
- Van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Marjolein Dijkstra
- Soft Condensed Matter Group, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - René van Roij
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
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38
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Mirzakhanloo M, Alam MR. Flow characteristics of Chlamydomonas result in purely hydrodynamic scattering. Phys Rev E 2018; 98:012603. [PMID: 30110819 DOI: 10.1103/physreve.98.012603] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Indexed: 11/07/2022]
Abstract
It has long been believed that eukaryotic flagellated swimming cells feel solid boundaries through direct ciliary contact. Specifically, based on observations of behavior of green alga Chlamydomonas reinhardtii it has been reported that it is their "flagella [that] prevent the cell body from touching the surface" [Kantsler et al., Proc. Natl. Acad. Sci. USA 110, 1187 (2013)PNASA60027-842410.1073/pnas.1210548110]. Here, via investigation of a model swimmer whose flow field closely resembles that of C. reinhardtii, we show that the scattering from a wall can be purely hydrodynamic and that no mechanical or flagellar force is needed for sensing and escaping the boundary.
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Affiliation(s)
- Mehdi Mirzakhanloo
- Department of Mechanical Engineering, University of California, Berkeley, California 94720, USA
| | - Mohammad-Reza Alam
- Department of Mechanical Engineering, University of California, Berkeley, California 94720, USA
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39
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Pessot G, Löwen H, Menzel AM. Binary pusher–puller mixtures of active microswimmers and their collective behaviour. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1496291] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Giorgio Pessot
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Andreas M. Menzel
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
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40
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Chen YF, Wang Z, Chu KC, Chen HY, Sheng YJ, Tsao HK. Hydrodynamic interaction induced breakdown of the state properties of active fluids. SOFT MATTER 2018; 14:5319-5326. [PMID: 29900446 DOI: 10.1039/c8sm00881g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The mechanical pressure of active fluids in which swimmers are modeled by soft run-and-tumble spheres is investigated by dissipative particle dynamics simulations. The incremental pressure (Π) with respect to the system pressure with inactive swimmers comprises the direct contribution of the swimmers (π) and the indirect contribution of fluids associated with hydrodynamic interactions (HIs). The pressure can be determined from the bulk and confining wall and the former is always less than the latter. The π of dilute active dispersions is proportional to their active diffusivity while Π grows generally with propulsive force and run time. However, Π is always substantially less than π because of negative contributions to pressure by HIs. The wall pressure depends on the swimmer-wall interactions, verifying that pressure is not a state function for active spheres due to the HIs. Owing to the distinct flow patterns, Π varies with the swim-type (pusher and puller) subject to the same run-and-tumble parameters at high concentrations.
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Affiliation(s)
- Yen-Fu Chen
- Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan 106, Republic of China.
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41
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Schwarzendahl FJ, Mazza MG. Maximum in density heterogeneities of active swimmers. SOFT MATTER 2018; 14:4666-4678. [PMID: 29717736 DOI: 10.1039/c7sm02301d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Suspensions of unicellular microswimmers such as flagellated bacteria or motile algae can exhibit spontaneous density heterogeneities at large enough concentrations. We introduce a novel model for biological microswimmers that creates the flow field of the corresponding microswimmers, and takes into account the shape anisotropy of the swimmer's body and stroke-averaged flagella. By employing multiparticle collision dynamics, we directly couple the swimmer's dynamics to the fluid's. We characterize the nonequilibrium phase diagram, as the filling fraction and Péclet number are varied, and find density heterogeneities in the distribution of both pullers and pushers, due to hydrodynamic instabilities. We find a maximum degree of clustering at intermediate filling fractions and at large Péclet numbers resulting from a competition of hydrodynamic and steric interactions between the swimmers. We develop an analytical theory that supports these results. This maximum might represent an optimum for the microorganisms' colonization of their environment.
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Affiliation(s)
- Fabian Jan Schwarzendahl
- Max-Planck-Institute for Dynamics and Self-Organization, Am Fassberg 17, 37077 Göttingen, Germany.
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42
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Gutiérrez-Ramos S, Hoyos M, Ruiz-Suárez JC. Induced clustering of Escherichia coli by acoustic fields. Sci Rep 2018; 8:4668. [PMID: 29549342 PMCID: PMC5856742 DOI: 10.1038/s41598-018-22960-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 02/26/2018] [Indexed: 11/21/2022] Open
Abstract
Brownian or self-propelled particles in aqueous suspensions can be trapped by acoustic fields generated by piezoelectric transducers usually at frequencies in the megahertz. The obtained confinement allows the study of rich collective behaviours like clustering or spreading dynamics in microgravity-like conditions. The acoustic field induces the levitation of self-propelled particles and provides secondary lateral forces to capture them at nodal planes. Here, we give a step forward in the field of confined active matter, reporting levitation experiments of bacterial suspensions of Escherichia coli. Clustering of living bacteria is monitored as a function of time, where different behaviours are clearly distinguished. Upon the removal of the acoustic signal, bacteria rapidly spread, impelled by their own swimming. Nevertheless, long periods of confinement result in irreversible bacteria entanglements that could act as seeds for levitating bacterial aggregates.
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Affiliation(s)
- Salomé Gutiérrez-Ramos
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes (PMMH UMR 7636) CNRS, ESPCI Paris, PSL Research University, Sorbonne Université, Université Paris Diderot, 10 rue Vauquelin, 75005 Paris, France.,Centro de Investigación y de Estudios Avanzados, Unidad Monterrey, PIIT Autopista al Aeropuerto Km. 9.5, Apodaca, Nuevo León, 66600, Mexico
| | - Mauricio Hoyos
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes (PMMH UMR 7636) CNRS, ESPCI Paris, PSL Research University, Sorbonne Université, Université Paris Diderot, 10 rue Vauquelin, 75005 Paris, France
| | - J C Ruiz-Suárez
- Centro de Investigación y de Estudios Avanzados, Unidad Monterrey, PIIT Autopista al Aeropuerto Km. 9.5, Apodaca, Nuevo León, 66600, Mexico.
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43
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Härtel A, Richard D, Speck T. Three-body correlations and conditional forces in suspensions of active hard disks. Phys Rev E 2018; 97:012606. [PMID: 29448434 DOI: 10.1103/physreve.97.012606] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Indexed: 06/08/2023]
Abstract
Self-propelled Brownian particles show rich out-of-equilibrium physics, for instance, the motility-induced phase separation (MIPS). While decades of studying the structure of liquids have established a deep understanding of passive systems, not much is known about correlations in active suspensions. In this work we derive an approximate analytic theory for three-body correlations and forces in systems of active Brownian disks starting from the many-body Smoluchowski equation. We use our theory to predict the conditional forces that act on a tagged particle and their dependence on the propulsion speed of self-propelled disks. We identify preferred directions of these forces in relation to the direction of propulsion and the positions of the surrounding particles. We further relate our theory to the effective swimming speed of the active disks, which is relevant for the physics of MIPS. To test and validate our theory, we additionally run particle-resolved computer simulations, for which we explicitly calculate the three-body forces. In this context, we discuss the modeling of active Brownian swimmers with nearly hard interaction potentials. We find very good agreement between our simulations and numerical solutions of our theory, especially for the nonequilibrium pair-distribution function. For our analytical results, we carefully discuss their range of validity in the context of the different levels of approximation we applied. This discussion allows us to study the individual contribution of particles to three-body forces and to the emerging structure. Thus, our work sheds light on the collective behavior, provides the basis for further studies of correlations in active suspensions, and makes a step towards an emerging liquid state theory.
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Affiliation(s)
- Andreas Härtel
- Institute of Physics, University of Freiburg, Hermann-Herder-Straße 3, 79104 Freiburg, Germany
| | - David Richard
- Institute of Physics, Johannes Gutenberg-University Mainz, Staudinger Weg 9, 55128 Mainz, Germany
| | - Thomas Speck
- Institute of Physics, Johannes Gutenberg-University Mainz, Staudinger Weg 9, 55128 Mainz, Germany
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44
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Zaeifi Yamchi M, Naji A. Effective interactions between inclusions in an active bath. J Chem Phys 2017; 147:194901. [DOI: 10.1063/1.5001505] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Mahdi Zaeifi Yamchi
- School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran
| | - Ali Naji
- School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran
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45
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Adhyapak TC, Jabbari-Farouji S. Flow properties and hydrodynamic interactions of rigid spherical microswimmers. Phys Rev E 2017; 96:052608. [PMID: 29347781 DOI: 10.1103/physreve.96.052608] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Indexed: 06/07/2023]
Abstract
We analyze a minimal model for a rigid spherical microswimmer and explore the consequences of its extended surface on the interplay between its self-propulsion and flow properties. The model is the first order representation of microswimmers, such as bacteria and algae, with rigid bodies and flexible propelling appendages. The flow field of such a microswimmer at finite distances significantly differs from that of a point-force (Stokeslet) dipole. For a suspension of microswimmers, we derive the grand mobility matrix that connects the motion of an individual swimmer to the active and passive forces and torques acting on all the swimmers. Our investigation of the mobility tensors reveals that hydrodynamic interactions among rigid-bodied microswimmers differ considerably from those among the corresponding point-force dipoles. Our results are relevant for the study of collective behavior of hydrodynamically interacting microswimmers by means of Stokesian dynamics simulations at moderate concentrations.
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Affiliation(s)
- Tapan Chandra Adhyapak
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
| | - Sara Jabbari-Farouji
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 7-9, 55128 Mainz, Germany
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46
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Kuhr JT, Blaschke J, Rühle F, Stark H. Collective sedimentation of squirmers under gravity. SOFT MATTER 2017; 13:7548-7555. [PMID: 28967939 DOI: 10.1039/c7sm01180f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Active particles, which interact hydrodynamically, display a remarkable variety of emergent collective phenomena. We use squirmers to model spherical microswimmers and explore the collective behavior of thousands of them under the influence of strong gravity using the method of multi-particle collision dynamics for simulating fluid flow. The sedimentation profile depends on the ratio of swimming to sedimentation velocity as well as on the squirmer type. It shows closely packed squirmer layers at the bottom and a highly dynamic region with exponential density dependence towards the top. The mean vertical orientation of the squirmers strongly depends on height. For swimming velocities larger than the sedimentation velocity, squirmers show strong convection in the exponential region. We quantify the strength of convection and the extent of convection cells by the vertical current density and its current dipole, which are large for neutral squirmers as well as for weak pushers and pullers.
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Affiliation(s)
- Jan-Timm Kuhr
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstr. 36, 10623 Berlin, Germany.
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47
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Guccione G, Pimponi D, Gualtieri P, Chinappi M. Diffusivity of E. coli-like microswimmers in confined geometries: The role of the tumbling rate. Phys Rev E 2017; 96:042603. [PMID: 29347505 DOI: 10.1103/physreve.96.042603] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Indexed: 11/07/2022]
Abstract
We analyzed the effect of confinement on the effective diffusion of a run-and-tumble E. coli-like flagellated microswimmer. We used a simulation protocol where the run phases are obtained via a fully resolved swimming problem, i.e., Stokes equations for the fluid coupled with rigid-body dynamics for the microorganism, while tumbles and collisions with the walls are modeled as random reorientation of the microswimmer. For weak confinement, the swimmer is trapped in circular orbits close to the solid walls. In this case, optimal diffusivity is observed when the tumbling frequency is comparable with the angular velocity of the stable orbits. For strong confinement, stable circular orbits disappear and the diffusion coefficient monotonically decreases with the tumbling rate. Our findings are generic and can be potentially applied to other natural or artificial chiral microswimmers that follow circular trajectories close to an interface or in confined geometries.
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Affiliation(s)
- Giorgia Guccione
- Dipartimento di Fisica, Università di Roma Tor Vergata, via della Ricerca Scientifica 1, 00133 Roma, Italia
| | - Daniela Pimponi
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, via Eudossiana 18, 00184 Roma, Italia
| | - Paolo Gualtieri
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, via Eudossiana 18, 00184 Roma, Italia
| | - Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, via del Politecnico 1, 00133 Roma, Italia
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48
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Ishimoto K. Guidance of microswimmers by wall and flow: Thigmotaxis and rheotaxis of unsteady squirmers in two and three dimensions. Phys Rev E 2017; 96:043103. [PMID: 29347500 DOI: 10.1103/physreve.96.043103] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Indexed: 06/07/2023]
Abstract
The motions of an unsteady circular-disk squirmer and a spherical squirmer have been investigated in the presence of a no-slip infinite wall and a background shear flow in order to clarify the similarities and differences between two- and three-dimensional motions. Despite the similar bifurcation structure of the dynamical system, the stability of the fixed points differs due to the Hamiltonian structure of the disk squirmer. Once the unsteady oscillating surface velocity profile is considered, the disk squirmer can behave in a chaotic manner and cease to be confined in a near-wall region. In contrast, in an unsteady spherical squirmer, the dynamics is well attracted by a stable fixed point. Additional wall contact interactions lead to stable fixed points for the disk squirmer, and, in turn, the surface entrapment of the disk squirmer can be stabilized, regardless of the existence of the background flow. Finally, we consider spherical motion under a background flow. The separated time scales of the surface entrapment (thigmotaxis) and the turning toward the flow direction (rheotaxis) enable us to reduce the dynamics to two-dimensional phase space, and simple weather-vane mechanics can predict squirmer rheotaxis. The analogous structure of the phase plane with the wall contact in two and three dimensions implies that the two-dimensional disk swimmer successfully captures the nonlinear interactions, and thus two-dimensional approximation could be useful in designing microfluidic devices for the guidance of microswimmers and for clarifying the locomotions in a complex geometry.
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Affiliation(s)
- Kenta Ishimoto
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG, United Kingdom; The Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8501, Japan; and Research Institute for Mathematical Sciences, Kyoto University, Kyoto 606-8502, Japan
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49
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Stenhammar J, Nardini C, Nash RW, Marenduzzo D, Morozov A. Role of Correlations in the Collective Behavior of Microswimmer Suspensions. PHYSICAL REVIEW LETTERS 2017; 119:028005. [PMID: 28753351 DOI: 10.1103/physrevlett.119.028005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Indexed: 06/07/2023]
Abstract
In this Letter, we study the collective behavior of a large number of self-propelled microswimmers immersed in a fluid. Using unprecedentedly large-scale lattice Boltzmann simulations, we reproduce the transition to bacterial turbulence. We show that, even well below the transition, swimmers move in a correlated fashion that cannot be described by a mean-field approach. We develop a novel kinetic theory that captures these correlations and is nonperturbative in the swimmer density. To provide an experimentally accessible measure of correlations, we calculate the diffusivity of passive tracers and reveal its nontrivial density dependence. The theory is in quantitative agreement with the lattice Boltzmann simulations and captures the asymmetry between pusher and puller swimmers below the transition to turbulence.
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Affiliation(s)
- Joakim Stenhammar
- Division of Physical Chemistry, Lund University, P.O. Box 124, S-221 00 Lund, Sweden
| | - Cesare Nardini
- DAMTP, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
- Service de Physique de l'État Condensé, CNRS UMR 3680, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - Rupert W Nash
- EPCC, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Alexander Morozov
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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50
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Nili H, Kheyri M, Abazari J, Fahimniya A, Naji A. Population splitting of rodlike swimmers in Couette flow. SOFT MATTER 2017; 13:4494-4506. [PMID: 28584884 DOI: 10.1039/c7sm00293a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a quantitative analysis on the response of a dilute active suspension of self-propelled rods (swimmers) in a planar channel subjected to an imposed shear flow. To best capture the salient features of the shear-induced effects, we consider the case of an imposed Couette flow, providing a constant shear rate across the channel. We argue that the steady-state behavior of swimmers can be understood in the light of a population splitting phenomenon, occurring as the shear rate exceeds a certain threshold, initiating the reversal of the swimming direction for a finite fraction of swimmers from down- to upstream or vice versa, depending on the swimmer position within the channel. Swimmers thus split into two distinct, statistically significant and oppositely swimming majority and minority populations. The onset of population splitting translates into a transition from a self-propulsion-dominated regime to a shear-dominated regime, corresponding to a unimodal-to-bimodal change in the probability distribution function of the swimmer orientation. We present a phase diagram in terms of the swim and flow Péclet numbers showing the separation of these two regimes by a discontinuous transition line. Our results shed further light on the behavior of swimmers in a shear flow and provide an explanation for the previously reported non-monotonic behavior of the mean, near-wall, parallel-to-flow orientation of swimmers with increasing shear strength.
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Affiliation(s)
- Hossein Nili
- School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran.
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