1
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Frydel D. Statistical mechanics of passive Brownian particles in a fluctuating harmonic trap. Phys Rev E 2024; 110:024613. [PMID: 39294941 DOI: 10.1103/physreve.110.024613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 08/15/2024] [Indexed: 09/21/2024]
Abstract
We consider passive Brownian particles trapped in an "imperfect" harmonic trap. The trap is imperfect because it is randomly turned off and on, and as a result particles fail to equilibrate. Another way to think about this is to say that a harmonic trap is time dependent on account of its strength evolving stochastically in time. Particles in such a system are passive and activity arises through external control of a trapping potential, thus, no internal energy is used to power particle motion. A stationary Fokker-Planck equation of this system can be represented as a third-order differential equation, and its solution, a stationary distribution, can be represented as a superposition of Gaussian distributions for different strengths of a harmonic trap. This permits us to interpret a stationary system as a system in equilibrium with quenched disorder.
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2
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Mangeat M, Chakraborty S, Wysocki A, Rieger H. Stationary particle currents in sedimenting active matter wetting a wall. Phys Rev E 2024; 109:014616. [PMID: 38366426 DOI: 10.1103/physreve.109.014616] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/02/2024] [Indexed: 02/18/2024]
Abstract
Recently it was predicted, on the basis of a lattice gas model, that scalar active matter in a gravitational field would rise against gravity up a confining wall or inside a thin capillary-in spite of repulsive particle-wall interactions [Phys. Rev. Lett. 124, 048001 (2020)0031-900710.1103/PhysRevLett.124.048001]. In this paper we confirm this prediction with sedimenting active Brownian particles (ABPs) in a box numerically and elucidate the mechanism leading to the formation of a meniscus rising above the bulk of the sedimentation region. The height of the meniscus increases with the activity of the system, algebraically with the Péclet number. The formation of the meniscus is determined by a stationary circular particle current, a vortex, centered at the base of the meniscus, whose size and strength increase with the ABP activity. The origin of these vortices can be traced back to the confinement of the ABPs in a box: already the stationary state of ideal (noninteracting) ABPs without gravitation displays circular currents that arrange in a highly symmetric way in the eight octants of the box. Gravitation distorts this vortex configuration downward, leaving two major vortices at the two side walls, with a strong downward flow along the walls. Repulsive interactions between the ABPs change this situation only as soon as motility induced phase separation (MIPS) sets in and forms a dense, sedimented liquid region at the bottom, which pushes the center of the vortex upwards towards the liquid-gas interface. Self-propelled particles therefore represent an impressive realization of scalar active matter that forms stationary particle currents being able to perform visible work against gravity or any other external field, which we predict to be observable experimentally in active colloids under gravitation.
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Affiliation(s)
- Matthieu Mangeat
- Center for Biophysics & Department for Theoretical Physics, Saarland University, D-66123 Saarbrücken, Germany
| | - Shauri Chakraborty
- Center for Biophysics & Department for Theoretical Physics, Saarland University, D-66123 Saarbrücken, Germany
| | - Adam Wysocki
- Center for Biophysics & Department for Theoretical Physics, Saarland University, D-66123 Saarbrücken, Germany
| | - Heiko Rieger
- Center for Biophysics & Department for Theoretical Physics, Saarland University, D-66123 Saarbrücken, Germany
- INM - Leibniz Institute for New Materials, Campus D2 2, D-66123 Saarbrücken, Germany
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3
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He X, Zhang W, Feng P, Mai Z, Gong X, Zhang G. Role of Surface Coverage of Sessile Probiotics in Their Interplay with Pathogen Bacteria Investigated by Digital Holographic Microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:17308-17317. [PMID: 37974298 DOI: 10.1021/acs.langmuir.3c02436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The adhesion of probiotics plays an important role in the gastrointestinal tract. Understanding the effect of the coverage of colonized probiotics on enteric pathogens is critical for the design of effective probiotic therapies. In the present work, we have investigated the adaptive behaviors of the intestinal pathogenic bacteria Enterobacter sakazakii (ES) near the surfaces coated with a probiotic─Lactobacillus rhamnosus GG (LGG) as a function of surface coverage ratio (CRLGG) by using a home-setup digital holographic microscopy. It shows that ES cells can adaptively sense LGG within a distance of 4.2 μm, even at CRLGG values as low as 0.05%. The growth inhibition of ES cells slightly varies with CRLGG, but the near-surface acceleration and accumulation of ES cells have much dependence on CRLGG. As CRLGG increases from 0.05 to 24.6%, the percentage of actively swimming ES, the motion bias, the acceleration, and the interplay duration do not linearly vary with CRLGG. Instead, each of them shows an extreme at CRLGG of 13.4%, corresponding to the chemotaxis behaviors of ES cells induced by diffusing stimuli (organic acids, bacteriocins, etc.) released from LGG, which showed an extreme concentration gradient at CRLGG = 13.4% by simulations. Our study clearly demonstrates that surface coverage of sessile probiotics profoundly influences their interplay with pathogen bacteria, which should be taken into account in designing probiotic therapies.
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Affiliation(s)
- Xintong He
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Weixiong Zhang
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Pu Feng
- School of Civil Engineering and Transportation, South China University of Technology, Guangzhou 510641, P. R. China
| | - Zhihui Mai
- Department of Stomatology, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou 510630, P. R. China
| | - Xiangjun Gong
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, P. R. China
- Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates (South China University of Technology), Guangzhou 510640, P. R. China
| | - Guangzhao Zhang
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, P. R. China
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4
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Ning L, Lou X, Ma Q, Yang Y, Luo N, Chen K, Meng F, Zhou X, Yang M, Peng Y. Hydrodynamics-Induced Long-Range Attraction between Plates in Bacterial Suspensions. PHYSICAL REVIEW LETTERS 2023; 131:158301. [PMID: 37897752 DOI: 10.1103/physrevlett.131.158301] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/23/2023] [Indexed: 10/30/2023]
Abstract
We perform optical-tweezers experiments and mesoscale fluid simulations to study the effective interactions between two parallel plates immersed in bacterial suspensions. The plates are found to experience a long-range attraction, which increases linearly with bacterial density and decreases with plate separation. The higher bacterial density and orientation order between plates observed in the experiments imply that the long-range effective attraction mainly arises from the bacterial flow field, instead of the direct bacterium-plate collisions, which is confirmed by the simulations. Furthermore, the hydrodynamic contribution is inversely proportional to the squared interplate separation in the far field. Our findings highlight the importance of hydrodynamics on the effective forces between passive objects in active baths, providing new possibilities to control activity-directed assembly.
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Affiliation(s)
- Luhui Ning
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Xin Lou
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Qili Ma
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Yaochen Yang
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory for Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Nan Luo
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Chen
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Fanlong Meng
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
- CAS Key Laboratory for Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Xin Zhou
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Mingcheng Yang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Yi Peng
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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5
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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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6
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Forgács P, Libál A, Reichhardt C, Reichhardt CJO. Active matter shepherding and clustering in inhomogeneous environments. Phys Rev E 2021; 104:044613. [PMID: 34781504 DOI: 10.1103/physreve.104.044613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/08/2021] [Indexed: 11/07/2022]
Abstract
We consider a mixture of active and passive run-and-tumble disks in an inhomogeneous environment where only half of the sample contains quenched disorder or pinning. The disks are initialized in a fully mixed state of uniform density. We identify several distinct dynamical phases as a function of motor force and pinning density. At high pinning densities and high motor forces, there is a two-step process initiated by a rapid accumulation of both active and passive disks in the pinned region, which produces a large density gradient in the system. This is followed by a slower species phase separation process where the inactive disks are shepherded by the active disks into the pin-free region, forming a nonclustered fluid and producing a more uniform density with species phase separation. For higher pinning densities and low motor forces, the dynamics becomes very slow and the system maintains a strong density gradient. For weaker pinning and large motor forces, a floating clustered state appears, and the time-averaged density of the system is uniform. We illustrate the appearance of these phases in a dynamic phase diagram.
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Affiliation(s)
- P Forgács
- Mathematics and Computer Science Department, Babeş-Bolya University, Cluj 400084, Romania
| | - A Libál
- Mathematics and Computer Science Department, Babeş-Bolya University, Cluj 400084, Romania
| | - C Reichhardt
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - C J O Reichhardt
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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7
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Singh C. Guided run-and-tumble active particles: wall accumulation and preferential deposition. SOFT MATTER 2021; 17:8858-8866. [PMID: 34541594 DOI: 10.1039/d1sm00775k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial biofilms cost an enormous amount of resources in the health, medical, and industrial sectors. To understand early biofilm formation, beginning from planktonic states of active suspensions (such as Escherichia coli) to micro-colonization, it is vital to study the mechanics of cell accumulation near surfaces and subsequent deposition. Variability in bacterial motion strategies and the presence of taxis fields make the problem even more multifaceted. In this study, analytical expressions for the density and angular distributions, mean orientation, and deposition rates in such bacterial suspensions are derived, with and without the effects of external guiding or taxis fields. The derived results are closely verified by simulations of confined active particles using run-and-tumble statistics from multiple past experiments and utilizing a preferential sticking probability model for deposition. The behavioral changes in cell running strategies are modeled by varying the run-time distribution from an exponential to a heavy-tailed one. It is found that the deposition rates can be altered significantly by a guiding torque but are less affected by a change in the cell running behavior. However, both the mechanisms alter the pair correlation function of the deposited structures. The factor behind the changes in the architecture of deposited biomass under a torque generating guiding field turns out to be an asymmetrical rotational drift of planktonic cells, which can be an important physical mechanism behind the organization in confined active particle suspensions.
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Affiliation(s)
- Chamkor Singh
- Department of Physics, Central University of Punjab, Bathinda 151401, India.
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
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8
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Coppola S, Kantsler V. Curved ratchets improve bacteria rectification in microfluidic devices. Phys Rev E 2021; 104:014602. [PMID: 34412208 DOI: 10.1103/physreve.104.014602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/16/2021] [Indexed: 11/07/2022]
Abstract
We study how bacteria rectification in microfluidics devices can be optimized by performing experiments with eight ratchets of different shape and size. Results show that curved ratchets perform best and that their radius of curvature influences how well they perform, as it affects the time bacteria spend on the ratchet surface. We find that the optimal bacterial ratchet is a 60μm radius semicircle witch 15μm concavities. We also show that the angle at which bacteria leave the ratchets can play an important role in their efficiency. Lastly, we reproduce our experimental conditions in a simple numerical simulation to confirm our findings.
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Affiliation(s)
- Simone Coppola
- Physics Department, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Vasily Kantsler
- Physics Department, University of Warwick, Coventry CV4 7AL, United Kingdom
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9
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Frydel D. Kuramoto model with run-and-tumble dynamics. Phys Rev E 2021; 104:024203. [PMID: 34525604 DOI: 10.1103/physreve.104.024203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
This work considers an extension of the Kuramoto model with run-and-tumble dynamics-a type of self-propelled motion. The difference between the extended and the original model is that in the extended version angular velocity of individual particles is no longer fixed but can change sporadically with a new velocity drawn from a distribution g(ω). Because the Kuramoto model undergoes phase transition, it offers a simple case study for investigating phase transition for a system with self-propelled particles.
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Affiliation(s)
- Derek Frydel
- Department of Chemistry, Universidad Técnica Federico Santa María, Campus San Joaquin, Santiago, Chile
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10
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Zhang J, Chinappi M, Biferale L. Base flow decomposition for complex moving objects in linear hydrodynamics: Application to helix-shaped flagellated microswimmers. Phys Rev E 2021; 103:023109. [PMID: 33736027 DOI: 10.1103/physreve.103.023109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
The motion of microswimmers in complex flows is ruled by the interplay between swimmer propulsion and the dynamics induced by the fluid velocity field. Here we study the motion of a chiral microswimmer whose propulsion is provided by the spinning of a helical tail with respect to its body in a simple shear flow. Thanks to an efficient computational strategy that allowed us to simulate thousands of different trajectories, we show that the tail shape dramatically affects the swimmer's motion. In the shear dominated regime, the swimmers carrying an elliptical helical tail show several different Jeffery-like (tumbling) trajectories depending on their initial configuration. As the propulsion torque increases, a progressive regularization of the motion is observed until, in the propulsion dominated regime, the swimmers converge to the same final trajectory independently on the initial configuration. Overall, our results show that elliptical helix swimmer presents a much richer variety of trajectories with respect to the usually studied circular helix tails.
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Affiliation(s)
- Ji Zhang
- Beijing Computational Science Research Center, Beijing 100193, China
| | - Mauro Chinappi
- Department of Industrial Engineering, University of Rome, Tor Vergata, Via del Politecnico 1, 00133 Roma, Italy
| | - Luca Biferale
- Department of Physics, INFN, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133 Roma, Italy
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11
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Smith ND, Swift MR, Smith MI. Collision-enhanced friction of a bouncing ball on a rough vibrating surface. Sci Rep 2021; 11:442. [PMID: 33432078 PMCID: PMC7801373 DOI: 10.1038/s41598-020-80067-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/15/2020] [Indexed: 11/30/2022] Open
Abstract
We describe experiments and simulations to investigate the dynamics of a ball bouncing on a rough vibrating surface. Directly measuring the impulse due to each bounce we find that the frictional interaction with the surface is strongly enhanced near to the side wall. The enhanced dissipation arises as a consequence of the coupling between the collision, rotation and surface friction. This dissipation, which for our experimental conditions was estimated to be up to three times larger than the more obvious inelastic collision, can result in an enhanced probability density near boundaries and particle–particle spatial correlations. Our findings imply that the effective particle collision properties cannot be considered independently of the surface’s frictional properties.
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Affiliation(s)
- N D Smith
- School of Physics and Astronomy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - M R Swift
- School of Physics and Astronomy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - M I Smith
- School of Physics and Astronomy, University of Nottingham, Nottingham, NG7 2RD, UK.
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12
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Telezki V, Klumpp S. Simulations of structure formation by confined dipolar active particles. SOFT MATTER 2020; 16:10537-10547. [PMID: 33078178 DOI: 10.1039/d0sm00926a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Dipolar active particles describe a class of self-propelled, biological or artificial particles equipped with an internal (typically magnetic) dipole moment. Because of the interplay between self-propulsion and dipole-dipole interactions, complex collective behavior is expected to emerge in systems of such particles. Here, we use Brownian dynamics simulations to explore this collective behavior. We focus on the structures that form in small systems in spatial confinement. We quantify the type of structures that emerge and how they depend on the self-propulsion speed and the dipolar (magnetic) strength of the particles. We observe that the dipolar active particles self-assemble into chains and rings. The dominant configuration is quantified with an order parameter for chain and ring formation and shown to depend on the self-propulsion speed and the dipolar magnetic strength of the particles. In addition, we show that the structural configurations are also affected by the confining walls. To that end, we compare different confining geometries and study the impact of a reorienting 'wall torque' upon collisions of a particle with a wall. Our results indicate that dipolar interactions can further enhance the already rich variety of collective behaviors of active particles.
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Affiliation(s)
- Vitali Telezki
- Institute for the Dynamics of Complex Systems, Georg August University Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.
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13
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Aldana M, Fuentes-Cabrera M, Zumaya M. Self-Propulsion Enhances Polymerization. ENTROPY 2020; 22:e22020251. [PMID: 33286025 PMCID: PMC7516688 DOI: 10.3390/e22020251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 11/28/2022]
Abstract
Self-assembly is a spontaneous process through which macroscopic structures are formed from basic microscopic constituents (e.g., molecules or colloids). By contrast, the formation of large biological molecules inside the cell (such as proteins or nucleic acids) is a process more akin to self-organization than to self-assembly, as it requires a constant supply of external energy. Recent studies have tried to merge self-assembly with self-organization by analyzing the assembly of self-propelled (or active) colloid-like particles whose motion is driven by a permanent source of energy. Here we present evidence that points to the fact that self-propulsion considerably enhances the assembly of polymers: self-propelled molecules are found to assemble faster into polymer-like structures than non self-propelled ones. The average polymer length increases towards a maximum as the self-propulsion force increases. Beyond this maximum, the average polymer length decreases due to the competition between bonding energy and disruptive forces that result from collisions. The assembly of active molecules might have promoted the formation of large pre-biotic polymers that could be the precursors of the informational polymers we observe nowadays.
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Affiliation(s)
- Maximino Aldana
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Colonia Chamilpa, Cuernavaca 62210, Morelos, Mexico;
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Coyoacán 04510, Mexico City, Mexico
- Correspondence: ; Tel.: +52-777-329-1787
| | - Miguel Fuentes-Cabrera
- Oak Ridge National Laboratory, Center for Nanophase Materials Sciences, Oak Ridge, TN 37831, USA;
- Oak Ridge National Laboratory, Computational Sciences and Engineering Division, Oak Ridge, TN 37831, USA
| | - Martín Zumaya
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Colonia Chamilpa, Cuernavaca 62210, Morelos, Mexico;
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Coyoacán 04510, Mexico City, Mexico
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14
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Desai N, Ardekani AM. Biofilms at interfaces: microbial distribution in floating films. SOFT MATTER 2020; 16:1731-1750. [PMID: 31976509 DOI: 10.1039/c9sm02038a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cellular motility is a key function guiding microbial adhesion to interfaces, which is the first step in the formation of biofilms. The close association of biofilms and bioremediation has prompted extensive research aimed at comprehending the physics of microbial locomotion near interfaces. We study the dynamics and statistics of microorganisms in a 'floating biofilm', i.e., a confinement with an air-liquid interface on one side and a liquid-liquid interface on the other. We use a very general mathematical model, based on a multipole representation and probabilistic simulations, to ascertain the spatial distribution of microorganisms in films of different viscosities. Our results reveal that microorganisms can be distributed symmetrically or asymmetrically across the height of the film, depending on their morphology and the ratio of the film's viscosity to that of the fluid substrate. Long-flagellated, elongated bacteria exhibit stable swimming parallel to the liquid-liquid interface when the bacterial film is less viscous than the underlying fluid. Bacteria with shorter flagella on the other hand, swim away from the liquid-liquid interface and accumulate at the free surface. We also analyze microorganism dynamics in a flowing film and show how a microorganism's ability to resist 'flow-induced-erosion' from interfaces is affected by its elongation and mode of propulsion. Our study generalizes past efforts on understanding microorganism dynamics under confinement by interfaces and provides key insights on biofilm initiation at liquid-liquid interfaces.
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Affiliation(s)
- Nikhil Desai
- School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, USA.
| | - Arezoo M Ardekani
- School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, USA.
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15
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Colloid Transport in Porous Media: A Review of Classical Mechanisms and Emerging Topics. Transp Porous Media 2019. [DOI: 10.1007/s11242-019-01270-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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16
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Sevilla FJ, Arzola AV, Cital EP. Stationary superstatistics distributions of trapped run-and-tumble particles. Phys Rev E 2019; 99:012145. [PMID: 30780275 DOI: 10.1103/physreve.99.012145] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Indexed: 06/09/2023]
Abstract
We present an analysis of the stationary distributions of run-and-tumble particles trapped in external potentials in terms of a thermophoretic potential that emerges when trapped active motion is mapped to trapped passive Brownian motion in a fictitious inhomogeneous thermal bath. We elaborate on the meaning of the non-Boltzmann-Gibbs stationary distributions that emerge as a consequence of the persistent motion of active particles. These stationary distributions are interpreted as a class of distributions in nonequilibrium statistical mechanics known as superstatistics. Our analysis provides an original insight on the link between the intrinsic nonequilibrium nature of active motion and the well-known concept of local equilibrium used in nonequilibrium statistical mechanics and contributes to the understanding of the validity of the concept of effective temperature. Particular cases of interest, regarding specific trapping potentials used in other theoretical or experimental studies, are discussed. We point out as an unprecedented effect, the emergence of new modes of the stationary distribution as a consequence of the coupling of persistent motion in a trapping potential that varies highly enough with position.
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Affiliation(s)
- Francisco J Sevilla
- Instituto de Física, Universidad Nacional Autónoma de México, Apdo. Postal 20-364, 01000 Ciudad de México, Mexico
| | - Alejandro V Arzola
- Instituto de Física, Universidad Nacional Autónoma de México, Apdo. Postal 20-364, 01000 Ciudad de México, Mexico
| | - Enrique Puga Cital
- Instituto de Física, Universidad Nacional Autónoma de México, Apdo. Postal 20-364, 01000 Ciudad de México, Mexico
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Miño GL, Baabour M, Chertcoff R, Gutkind G, Clément E, Auradou H, Ippolito I. <i>E coli</i> Accumulation behind an Obstacle. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/aim.2018.86030] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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