1
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Janzen G, Matoz-Fernandez DA. Density and inertia effects on two-dimensional active semiflexible filament suspensions. SOFT MATTER 2024; 20:6618-6626. [PMID: 39108173 DOI: 10.1039/d4sm00572d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
We examine the influence of density on the transition between chain and spiral structures in planar assemblies of active semiflexible filaments, utilizing detailed numerical simulations. We focus on how increased density, and higher Péclet numbers, affect the activity-induced transition spiral state in a semiflexible, self-avoiding active chain. Our findings show that increasing the density causes the spiral state to break up, reverting to a motile chain-like shape. This results in a density-dependent reentrant phase transition from spirals back to open chains. We attribute this phenomenon to an inertial effect observed at the single polymer level, where increased persistence length due to inertia has been shown in recent three-dimensional studies to cause polymers to open up. Our two-dimensional simulations further reveal that a reduction in the damping coefficient leads to partial unwinding of the spirals, forming longer arms. In suspension, interactions among these extended arms can trigger a complete unwinding of the spirals, driven by the combined effects of density and inertia.
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Affiliation(s)
- Giulia Janzen
- Department of Theoretical Physics, Complutense University of Madrid, 28040 Madrid, Spain.
| | - D A Matoz-Fernandez
- Department of Theoretical Physics, Complutense University of Madrid, 28040 Madrid, Spain.
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2
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Xu TL, Qin CR, Tang B, Gao JC, Zhou J, Chen K, Zhang TH, Tian WD. Constrained motion of self-propelling eccentric disks linked by a spring. J Chem Phys 2024; 161:064905. [PMID: 39140446 DOI: 10.1063/5.0217158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/10/2024] [Indexed: 08/15/2024] Open
Abstract
It has been supposed that the interplay of elasticity and activity plays a key role in triggering the non-equilibrium behaviors in biological systems. However, the experimental model system is missing to investigate the spatiotemporally dynamical phenomena. Here, a model system of an active chain, where active eccentric-disks are linked by a spring, is designed to study the interplay of activity, elasticity, and friction. Individual active chain exhibits longitudinal and transverse motions; however, it starts to self-rotate when pinning one end and self-beat when clamping one end. In addition, our eccentric-disk model can qualitatively reproduce such behaviors and explain the unusual self-rotation of the first disk around its geometric center. Furthermore, the structure and dynamics of long chains were studied via simulations without steric interactions. It was found that a hairpin conformation emerges in free motion, while in the constrained motions, the rotational and beating frequencies scale with the flexure number (the ratio of self-propelling force to bending rigidity), χ, as ∼(χ)4/3. Scaling analysis suggests that it results from the balance between activity and energy dissipation. Our findings show that topological constraints play a vital role in non-equilibrium synergy behaviors.
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Affiliation(s)
- Tian-Liang Xu
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Chao-Ran Qin
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Bin Tang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Jin-Cheng Gao
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Jiankang Zhou
- School of Optoelectronic Science and Engineering, Soochow University, Suzhou 215006, China
| | - Kang Chen
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Tian Hui Zhang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
| | - Wen-de Tian
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
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3
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Karan C, Chaudhuri A, Chaudhuri D. Inertia and activity: spiral transitions in semi-flexible, self-avoiding polymers. SOFT MATTER 2024; 20:6221-6230. [PMID: 39049672 DOI: 10.1039/d4sm00511b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
We consider a two-dimensional, tangentially active, semi-flexible, self-avoiding polymer to find a dynamical re-entrant transition between motile open chains and spinning achiral spirals with increasing activity. Utilizing probability distributions of the turning number, we ascertain the comparative stability of the spiral structure and present a detailed phase diagram within the activity inertia plane. The onset of spiral formation at low activity levels is governed by a torque balance and is independent of inertia. At higher activities, however, inertial effects lead to spiral destabilization, an effect absent in the overdamped limit. We further delineate alterations in size and shape by analyzing the end-to-end distance distribution and the radius of gyration tensor. The Kullback-Leibler divergence from equilibrium distributions exhibits a non-monotonic relationship with activity, reaching a peak at the most compact spirals characterized by the most persistent spinning. As inertia increases, this divergence from equilibrium diminishes.
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Affiliation(s)
- Chitrak Karan
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Abhishek Chaudhuri
- Department of Physical Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, Knowledge City, S. A. S. Nagar, Manauli, PO 140306, India.
| | - Debasish Chaudhuri
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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4
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Wu-Zhang B, Fedosov DA, Gompper G. Collective behavior of squirmers in thin films. SOFT MATTER 2024; 20:5687-5702. [PMID: 38639062 DOI: 10.1039/d4sm00075g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Bacteria in biofilms form complex structures and can collectively migrate within mobile aggregates, which is referred to as swarming. This behavior is influenced by a combination of various factors, including morphological characteristics and propulsive forces of swimmers, their volume fraction within a confined environment, and hydrodynamic and steric interactions between them. In our study, we employ the squirmer model for microswimmers and the dissipative particle dynamics method for fluid modeling to investigate the collective motion of swimmers in thin films. The film thickness permits a free orientation of non-spherical squirmers, but constraints them to form a two-layered structure at maximum. Structural and dynamic properties of squirmer suspensions confined within the slit are analyzed for different volume fractions of swimmers, motility types (e.g., pusher, neutral squirmer, puller), and the presence of a rotlet dipolar flow field, which mimics the counter-rotating flow generated by flagellated bacteria. Different states are characterized, including a gas-like phase, swarming, and motility-induced phase separation, as a function of increasing volume fraction. Our study highlights the importance of an anisotropic swimmer shape, hydrodynamic interactions between squirmers, and their interaction with the walls for the emergence of different collective behaviors. Interestingly, the formation of collective structures may not be symmetric with respect to the two walls. Furthermore, the presence of a rotlet dipole significantly mitigates differences in the collective behavior between various swimmer types. These results contribute to a better understanding of the formation of bacterial biofilms and the emergence of collective states in confined active matter.
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Affiliation(s)
- Bohan Wu-Zhang
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany.
| | - Dmitry A Fedosov
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany.
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany.
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5
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Kurjahn M, Deka A, Girot A, Abbaspour L, Klumpp S, Lorenz M, Bäumchen O, Karpitschka S. Quantifying gliding forces of filamentous cyanobacteria by self-buckling. eLife 2024; 12:RP87450. [PMID: 38864737 PMCID: PMC11178357 DOI: 10.7554/elife.87450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024] Open
Abstract
Filamentous cyanobacteria are one of the oldest and today still most abundant lifeforms on earth, with manifold implications in ecology and economics. Their flexible filaments, often several hundred cells long, exhibit gliding motility in contact with solid surfaces. The underlying force generating mechanism is not yet understood. Here, we demonstrate that propulsion forces and friction coefficients are strongly coupled in the gliding motility of filamentous cyanobacteria. We directly measure their bending moduli using micropipette force sensors, and quantify propulsion and friction forces by analyzing their self-buckling behavior, complemented with analytical theory and simulations. The results indicate that slime extrusion unlikely generates the gliding forces, but support adhesion-based hypotheses, similar to the better-studied single-celled myxobacteria. The critical self-buckling lengths align well with the peaks of natural length distributions, indicating the importance of self-buckling for the organization of their collective in natural and artificial settings.
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Affiliation(s)
- Maximilian Kurjahn
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS)GöttingenGermany
| | - Antaran Deka
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS)GöttingenGermany
| | - Antoine Girot
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS)GöttingenGermany
- Experimental Physics V, University of BayreuthBayreuthGermany
| | - Leila Abbaspour
- Max Planck School Matter to Life, University of GöttingenGöttingenGermany
- Institute for Dynamics of Complex Systems, University of GöttingenGöttingenGermany
| | - Stefan Klumpp
- Max Planck School Matter to Life, University of GöttingenGöttingenGermany
- Institute for Dynamics of Complex Systems, University of GöttingenGöttingenGermany
| | - Maike Lorenz
- Department of Experimental Phycology and SAG Culture Collection of Algae Albrecht-von-Haller Institute for Plant Science, University of GöttingenGöttingenGermany
| | - Oliver Bäumchen
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS)GöttingenGermany
- Experimental Physics V, University of BayreuthBayreuthGermany
| | - Stefan Karpitschka
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS)GöttingenGermany
- Fachbereich Physik, University of KonstanzKonstanzGermany
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6
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Lamura A. Excluded volume effects on tangentially driven active ring polymers. Phys Rev E 2024; 109:054611. [PMID: 38907431 DOI: 10.1103/physreve.109.054611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/08/2024] [Indexed: 06/24/2024]
Abstract
The conformational and dynamical properties of active ring polymers are studied by numerical simulations. The two-dimensionally confined polymer is modeled as a closed bead-spring chain, driven by tangential forces, put in contact with a heat bath described by the Brownian multiparticle collision dynamics. Both phantom polymers and chains comprising excluded volume interactions are considered for different bending rigidities. The size and shape are found to be dependent on persistence length, driving force, and bead mutual exclusion. The lack of excluded volume interactions is responsible for a shrinkage of active rings when increasing driving force in the flexible limit, while the presence induces a moderate swelling of chains. The internal dynamics of flexible phantom active rings shows activity-enhanced diffusive behavior at large activity values while, in the case of self-avoiding active chains, it is characterized by active ballistic motion not depending on stiffness. The long-time dynamics of active rings is marked by rotational motion whose period scales as the inverse of the applied tangential force, irrespective of persistence length and beads' self-exclusion.
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Affiliation(s)
- A Lamura
- Istituto Applicazioni Calcolo, Consiglio Nazionale delle Ricerche (CNR), Via Amendola 122/D, 70126 Bari, Italy
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7
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Zhu G, Gao L, Sun Y, Wei W, Yan LT. Non-equilibrium structural and dynamic behaviors of active polymers in complex and crowded environments. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 87:054601. [PMID: 38608453 DOI: 10.1088/1361-6633/ad3e11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/12/2024] [Indexed: 04/14/2024]
Abstract
Active matter systems, which convert internal chemical energy or energy from the environment into directed motion, are ubiquitous in nature and exhibit a range of emerging non-equilibrium behaviors. However, most of the current works on active matter have been devoted to particles, and the study of active polymers has only recently come into the spotlight due to their prevalence within living organisms. The intricate interplay between activity and conformational degrees of freedom gives rise to novel structural and dynamical behaviors of active polymers. Research in active polymers remarkably broadens diverse concepts of polymer physics, such as molecular architecture, dynamics, scaling and so on, which is of significant importance for the development of new polymer materials with unique performance. Furthermore, active polymers are often found in strongly interacting and crowded systems and in complex environments, so that the understanding of this behavior is essential for future developments of novel polymer-based biomaterials. This review thereby focuses on the study of active polymers in complex and crowded environments, and aims to provide insights into the fundamental physics underlying the adaptive and collective behaviors far from equilibrium, as well as the open challenges that the field is currently facing.
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Affiliation(s)
- Guolong Zhu
- School of Physics and Electronics, Hunan University, Changsha 410082, People's Republic of China
| | - Lijuan Gao
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yihang Sun
- School of Physics and Electronics, Hunan University, Changsha 410082, People's Republic of China
| | - Wenjie Wei
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Li-Tang Yan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
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8
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Yan R, Zhao C, Zhao N. Attractive crowding effect on passive and active polymer looping kinetics. J Chem Phys 2024; 160:134902. [PMID: 38568946 DOI: 10.1063/5.0199023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024] Open
Abstract
Loop formation in complex environments is crucially important to many biological processes in life. In the present work, we adopt three-dimensional Langevin dynamics simulations to investigate passive and active polymer looping kinetics in crowded media featuring polymer-crowder attraction. We find polymers undergo a remarkable coil-globule-coil transition, highlighted by a marked change in the Flory scaling exponent of the gyration radius. Meanwhile, looping time as a function of the crowder's volume fraction demonstrates an apparent non-monotonic alteration. A small number of crowders induce a compact structure, which largely facilitates the looping process. While a large number of crowders heavily impede end-to-end diffusion, looping kinetics is greatly inhibited. For a self-propelled chain, we find that the attractive crowding triggers an unusual activity effect on looping kinetics. Once a globular state is formed, activity takes an effort to open the chain from the compact structure, leading to an unexpected activity-induced inhibition of looping. If the chain maintains a coil state, the dominant role of activity is to enhance diffusivity and, thus, speed up looping kinetics. The novel conformational change and looping kinetics of both passive and active polymers in the presence of attractive crowding highlight a rather distinct scenario that has no analogy in a repulsive crowding counterpart. The underlying mechanism enriches our understanding of the crucial role of attractive interactions in modulating polymer structure and dynamics.
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Affiliation(s)
- Ran Yan
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Chaonan Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China
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9
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Vatin M, Kundu S, Locatelli E. Conformation and dynamics of partially active linear polymers. SOFT MATTER 2024; 20:1892-1904. [PMID: 38323323 DOI: 10.1039/d3sm01162c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
We perform numerical simulations of isolated, partially active polymers, driven out-of-equilibrium by a fraction of their monomers. We show that, if the active beads are all gathered in a contiguous block, the position of the section along the chain determines the conformational and dynamical properties of the system. Notably, one can modulate the diffusion coefficient of the polymer from active-like to passive-like just by changing the position of the active block. Further, we show that a slight modification of the self-propulsion rule may give rise to an enhancement of diffusion under certain conditions, despite a decrease of the overall polymer activity. Our findings may help in the modelisation of active biophysical systems, such as filamentous bacteria or worms.
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Affiliation(s)
- Marin Vatin
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy.
- INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - Sumanta Kundu
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy.
- INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
- International School for Advanced Studies (SISSA), 34136, Trieste, Italy
| | - Emanuele Locatelli
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy.
- INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
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10
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Bera P, Wasim A, Ghosh P. Interplay of cell motility and self-secreted extracellular polymeric substance induced depletion effects on spatial patterning in a growing microbial colony. SOFT MATTER 2023; 19:8136-8149. [PMID: 37847026 DOI: 10.1039/d3sm01144e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Reproducing bacteria self-organize to develop patterned biofilms in various conditions. Various factors contribute to the shaping of a multicellular bacterial organization. Here we investigate how motility force and self-secreted extracellular polymeric substances (EPS) influence bacterial cell aggregation, leading to phase-separated colonies using a particle-based/individual-based model. Our findings highlight the critical role of the interplay between motility force and depletion effects in regulating phase separation within a growing colony under far-from-equilibrium conditions. We observe that increased motility force hinders depletion-induced cell aggregation and phase segregation, necessitating a higher depletion effect for highly motile bacteria to undergo phase separation within a growing biofilm. We present a phase diagram illustrating the systematic variation of motility force and repulsive mechanical force, shedding light on the combined contributions of these two factors: self-propulsive motion and aggregation due to the depletion effect, resulting in the presence of small to large bacterial aggregates. Furthermore, our study reveals the dynamic nature of clustering, marked by changes in cluster size over time. Additionally, our findings suggest that differential dispersion among the components can lead to the localization of EPS at the periphery of a growing colony. Our study enhances the understanding of the collective dynamics of motile bacterial cells within a growing colony, particularly in the presence of a self-secreted polymer-driven depletion effect.
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Affiliation(s)
- Palash Bera
- Tata Institute of Fundamental Research Hyderabad, Telangana 500046, India
| | - Abdul Wasim
- Tata Institute of Fundamental Research Hyderabad, Telangana 500046, India
| | - Pushpita Ghosh
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala, 695551, India.
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11
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Faluweki MK, Cammann J, Mazza MG, Goehring L. Active Spaghetti: Collective Organization in Cyanobacteria. PHYSICAL REVIEW LETTERS 2023; 131:158303. [PMID: 37897773 DOI: 10.1103/physrevlett.131.158303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 08/30/2023] [Indexed: 10/30/2023]
Abstract
Filamentous cyanobacteria can show fascinating examples of nonequilibrium self-organization, which, however, are not well understood from a physical perspective. We investigate the motility and collective organization of colonies of these simple multicellular lifeforms. As their area density increases, linear chains of cells gliding on a substrate show a transition from an isotropic distribution to bundles of filaments arranged in a reticulate pattern. Based on our experimental observations of individual behavior and pairwise interactions, we introduce a nonreciprocal model accounting for the filaments' large aspect ratio, fluctuations in curvature, motility, and nematic interactions. This minimal model of active filaments recapitulates the observations, and rationalizes the appearance of a characteristic length scale in the system, based on the Péclet number of the cyanobacteria filaments.
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Affiliation(s)
- Mixon K Faluweki
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom
- Malawi Institute of Technology, Malawi University of Science and Technology, S150 Road, Thyolo 310105, Malawi
| | - Jan Cammann
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom
| | - Marco G Mazza
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Am Faßberg 17, 37077 Göttingen, Germany
| | - Lucas Goehring
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom
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12
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Deblais A, Prathyusha KR, Sinaasappel R, Tuazon H, Tiwari I, Patil VP, Bhamla MS. Worm blobs as entangled living polymers: from topological active matter to flexible soft robot collectives. SOFT MATTER 2023; 19:7057-7069. [PMID: 37706563 PMCID: PMC10523214 DOI: 10.1039/d3sm00542a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023]
Abstract
Recently, the study of long, slender living worms has gained attention due to their unique ability to form highly entangled physical structures, exhibiting emergent behaviors. These organisms can assemble into an active three-dimensional soft entity referred to as the "blob", which exhibits both solid-like and liquid-like properties. This blob can respond to external stimuli such as light, to move or change shape. In this perspective article, we acknowledge the extensive and rich history of polymer physics, while illustrating how these living worms provide a fascinating experimental platform for investigating the physics of active, polymer-like entities. The combination of activity, long aspect ratio, and entanglement in these worms gives rise to a diverse range of emergent behaviors. By understanding the intricate dynamics of the worm blob, we could potentially stimulate further research into the behavior of entangled active polymers, and guide the advancement of synthetic topological active matter and bioinspired tangling soft robot collectives.
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Affiliation(s)
- Antoine Deblais
- van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - K R Prathyusha
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Rosa Sinaasappel
- van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Harry Tuazon
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Ishant Tiwari
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - Vishal P Patil
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - M Saad Bhamla
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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13
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Yan R, Tan F, Wang J, Zhao N. Conformation and dynamics of an active filament in crowded media. J Chem Phys 2023; 158:114905. [PMID: 36948796 DOI: 10.1063/5.0142559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
Abstract
The structural and dynamical properties of active filamentous objects under macromolecular crowding have a great relevance in biology. By means of Brownian dynamics simulations, we perform a comparative study for the conformational change and diffusion dynamics of an active chain in pure solvents and in crowded media. Our result shows a robust compaction-to-swelling conformational change with the augment of the Péclet number. The presence of crowding facilitates self-trapping of monomers and, thus, reinforces the activity mediated compaction. In addition, the efficient collisions between the self-propelled monomers and crowders induce a coil-to-globulelike transition, indicated by a marked change of the Flory scaling exponent of the gyration radius. Moreover, the diffusion dynamics of the active chain in crowded solutions demonstrates activity-enhanced subdiffusion. The center of mass diffusion manifests rather new scaling relations with respect to both the chain length and Péclet number. The interplay of chain activity and medium crowding provides a new mechanism to understand the non-trivial properties of active filaments in complex environments.
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Affiliation(s)
- Ran Yan
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Fei Tan
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Jingli Wang
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China
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14
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Bera P, Wasim A, Ghosh P. A mechanistic understanding of microcolony morphogenesis: coexistence of mobile and sessile aggregates. SOFT MATTER 2023; 19:1034-1045. [PMID: 36648295 DOI: 10.1039/d2sm01365g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Most bacteria in the natural environment self-organize into collective phases such as cell clusters, swarms, patterned colonies, or biofilms. Several intrinsic and extrinsic factors, such as growth, motion, and physicochemical interactions, govern the occurrence of different phases and their coexistence. Hence, predicting the conditions under which a collective phase emerges due to individual-level interactions is crucial. Here we develop a particle-based biophysical model of bacterial cells and self-secreted extracellular polymeric substances (EPS) to decipher the interplay of growth, motility-mediated dispersal, and mechanical interactions during microcolony morphogenesis. We show that the microcolony dynamics and architecture significantly vary depending upon the heterogeneous EPS production. In particular, microcolony shows the coexistence of both motile and sessile aggregates rendering a transition towards biofilm formation. We identified that the interplay of differential dispersion and the mechanical interactions among the components of the colony determines the fate of the colony morphology. Our results provide a significant understanding of the mechano-self-regulation during biofilm morphogenesis and open up possibilities of designing experiments to test the predictions.
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Affiliation(s)
- Palash Bera
- Tata Institute of Fundamental Research Hyderabad, Telangana, 500046, India
| | - Abdul Wasim
- Tata Institute of Fundamental Research Hyderabad, Telangana, 500046, India
| | - Pushpita Ghosh
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala, 695551, India.
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15
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Wen H, Zhu Y, Peng C, Kumar PBS, Laradji M. Collective vortical motion and vorticity reversals of self-propelled particles on circularly patterned substrates. Phys Rev E 2023; 107:024606. [PMID: 36932499 DOI: 10.1103/physreve.107.024606] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
The collective behavior of self-propelled particles (SPPs) under the combined effects of a circularly patterned substrate and circular confinement is investigated through coarse-grained molecular dynamics simulations of polarized and disjoint ring polymers. The study is performed over a wide range of values of the SPPs packing fraction ϕ[over ¯], motility force F_{D}, and area fraction of the patterned region. At low packing fractions, the SPPs are excluded from the system's center and exhibit a vortical motion that is dominated by the substrate at intermediate values of F_{D}. This exclusion zone is due to the coupling between the driving force and torque induced by the substrate, which induces an outward spiral motion of the SPPs. For high values of F_{D}, the SPPs exclusion from the center is dominated by the confining boundary. At high values of ϕ[over ¯], the substrate pattern leads to reversals in the vorticity, which become quasiperiodic with increasing ϕ[over ¯]. We also found that the substrate pattern is able to separate SPPs based on their motilities.
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Affiliation(s)
- Haosheng Wen
- Department of Physics and Materials Science, The University of Memphis, Memphis, Tennessee 38152, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yu Zhu
- Department of Physics and Materials Science, The University of Memphis, Memphis, Tennessee 38152, USA
| | - Chenhui Peng
- Department of Physics and Materials Science, The University of Memphis, Memphis, Tennessee 38152, USA
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - P B Sunil Kumar
- Department of Physics, Indian Institute of Technology Palakkad, Palakkad 668557, Kerala, India
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India
| | - Mohamed Laradji
- Department of Physics and Materials Science, The University of Memphis, Memphis, Tennessee 38152, USA
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16
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Tejedor AR, Carracedo R, Ramírez J. Molecular dynamics simulations of active entangled polymers reptating through a passive mesh. POLYMER 2023. [DOI: 10.1016/j.polymer.2023.125677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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17
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Zhou H, Jung W, Farhana TI, Fujimoto K, Kim T, Yokokawa R. Durability of Aligned Microtubules Dependent on Persistence Length Determines Phase Transition and Pattern Formation in Collective Motion. ACS NANO 2022; 16:14765-14778. [PMID: 36098647 DOI: 10.1021/acsnano.2c05593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Collective motion is a ubiquitous phenomenon in nature. The collective motion of cytoskeleton filaments results mainly from dynamic collisions and alignments; however, the detailed mechanism of pattern formation still needs to be clarified. In particular, the influence of persistence length, which is a measure of filament flexibility, on collective motion is still unclear and lacks experimental verifications although it is likely to directly affect the orientational flexibility of filaments. Here, we investigated the collective motion of microtubules with different persistence lengths using a microtubule-kinesin motility system. We showed that local interactions between microtubules significantly vary depending on their persistence length. We demonstrated that the bundling of microtubules is enhanced by more durable alignment, rather than by greater likelihood of alignment. An agent-based computational model confirmed that the rigidity-dependent durability of microtubule alignment dominates their collective behavior.
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Affiliation(s)
- Hang Zhou
- Department of Micro Engineering, Kyoto University, Kyoto daigaku-katsura, Nishikyo-ku, Kyoto 615-8540, Japan
| | - Wonyeong Jung
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Tamanna Ishrat Farhana
- Department of Micro Engineering, Kyoto University, Kyoto daigaku-katsura, Nishikyo-ku, Kyoto 615-8540, Japan
| | - Kazuya Fujimoto
- Department of Micro Engineering, Kyoto University, Kyoto daigaku-katsura, Nishikyo-ku, Kyoto 615-8540, Japan
| | - Taeyoon Kim
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ryuji Yokokawa
- Department of Micro Engineering, Kyoto University, Kyoto daigaku-katsura, Nishikyo-ku, Kyoto 615-8540, Japan
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18
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Wang Y, Gao YW, Tian WD, Chen K. Obstacle-induced giant jammed aggregation of active semiflexible filaments. Phys Chem Chem Phys 2022; 24:23779-23789. [PMID: 36156612 DOI: 10.1039/d2cp02819k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Filaments driven by bound motor proteins and chains of self-propelled colloidal particles are a typical example of active polymers (APs). Due to deformability, APs exhibit very rich dynamic behaviors and collective assembling structures. Here, we are concerned with a basic question: how APs behave near a single obstacle? We find that, in the presence of a big single obstacle, the assembly of APs becomes a two-state system, i.e. APs either gather nearly completely together into a giant jammed aggregate (GJA) on the surface of the obstacle or distribute freely in space. No partial aggregation is observed. Such a complete aggregation/collection is unexpected since it happens on a smooth convex surface instead of, e.g., a concave wedge. We find that the formation of a GJA experiences a process of nucleation and the curves of the transition between the GJA and the non-aggregate state form hysteresis-like loops. Statistical analysis of massive data on the growing time, chirality and angular velocity of both the GJAs and the corresponding nuclei shows the strong random nature of the phenomenon. Our results provide new insights into the behavior of APs in contact with porous media and also a reference for the design and application of polymeric active materials.
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Affiliation(s)
- Ying Wang
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
| | - Yi-Wen Gao
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
| | - Wen-de Tian
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
| | - Kang Chen
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China. .,School of Physics and Information Engineering, Shanxi Normal University, Linfen 041004, China.
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19
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Zantop AW, Stark H. Emergent collective dynamics of pusher and puller squirmer rods: swarming, clustering, and turbulence. SOFT MATTER 2022; 18:6179-6191. [PMID: 35822601 DOI: 10.1039/d2sm00449f] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We study the interplay of steric and hydrodynamic interactions in suspensions of elongated microswimmers by simulating the full hydrodynamics of squirmer rods in the quasi two-dimensional geometry of a Hele-Shaw cell. To create pusher or puller-type squirmer rods, we concentrate the surface slip-velocity field more to the back or to the front of the rod and thereby are able to tune the rod's force-dipole strength. We study a wide range of aspect ratios and area fractions and provide corresponding state diagrams. The flow field of pusher-type squirmer rods destabilizes ordered structures and favors the disordered state at small area fractions and aspect ratios. Only when steric interactions become relevant, we observe a turbulent and dynamic cluster state, while for large aspect ratios a single swarm and jammed cluster occurs. The power spectrum of the turbulent state shows two distinct energy cascades at small and large wave numbers with power-law scaling and non-universal exponents. Pullers show a strong tendency to form swarms instead of the disordered state found for neutral and pusher rods. At large area fractions a dynamic cluster is observed and at larger aspect ratio a single swarm or jammed cluster occurs.
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Affiliation(s)
- Arne W Zantop
- 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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20
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Prathyusha KR, Ziebert F, Golestanian R. Emergent conformational properties of end-tailored transversely propelling polymers. SOFT MATTER 2022; 18:2928-2935. [PMID: 35348175 DOI: 10.1039/d2sm00237j] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We study the dynamics and conformations of a single active semiflexible polymer whose monomers experience a propulsion force perpendicular to the local tangent, with the end beads being different from the inner beads ("end-tailored"). Using Langevin simulations, we demonstrate that, apart from sideways motion, the relative propulsion strength between the end beads and the polymer backbone significantly changes the conformational properties of the polymers as a function of bending stiffness, end-tailoring and propulsion force. Expectedly, for slower ends the polymer curves away from the moving direction, while faster ends lead to opposite curving, in both cases slightly reducing the center of mass velocity compared to a straight fiber. Interestingly, for faster end beads there is a rich and dynamic morphology diagram: the polymer ends may get folded together to 2D loops or hairpin-like conformations that rotate due to their asymmetry in shape and periodic flapping motion around a rather straight state during full propulsion is also possible. We rationalize the simulations using scaling and kinematic arguments and present the state diagram of the conformations. Sideways propelled fibers comprise a rather unexplored and versatile class of self-propellers, and their study will open novel ways for designing, e.g. motile actuators or mixers in soft robotics.
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Affiliation(s)
- K R Prathyusha
- Max Planck Institute for Dynamics and Self-Organization, D-37077 Göttingen, Germany.
- Center for Softmatter Physics and its Applications, University of Beihang, Beijing, China
| | - Falko Ziebert
- Institute for Theoretical Physics, Heidelberg University, D-69120 Heidelberg, Germany.
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization, D-37077 Göttingen, Germany.
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, UK.
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21
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Paul S, Majumder S, Das SK, Janke W. Effects of alignment activity on the collapse kinetics of a flexible polymer. SOFT MATTER 2022; 18:1978-1990. [PMID: 35023525 DOI: 10.1039/d1sm01055g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The dynamics of various biological filaments can be understood within the framework of active polymer models. Here we consider a bead-spring model for a flexible polymer chain in which the active interaction among the beads is introduced via an alignment rule adapted from the Vicsek model. Following quenching from the high-temperature coil phase to a low-temperature state point, we study the coarsening kinetics via molecular dynamics (MD) simulations using the Langevin thermostat. For the passive polymer case the low-temperature equilibrium state is a compact globule. The results from our MD simulations reveal that though the globular state is also the typical final state in the active case, the nonequilibrium pathways to arrive at such a state differ from the picture for the passive case due to the alignment interaction among the beads. We notice that deviations from the intermediate "pearl-necklace"-like arrangement, which is observed in the passive case, and the formation of more elongated dumbbell-like structures increase with increasing activity. Furthermore, it appears that while a small active force on the beads certainly makes the coarsening process much faster, there exists a nonmonotonic dependence of the collapse time on the strength of active interaction. We quantify these observations by comparing the scaling laws for the collapse time and growth of pearls with the passive case.
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Affiliation(s)
- Subhajit Paul
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany.
| | - Suman Majumder
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany.
| | - Subir K Das
- Theoretical Sciences Unit and School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore-560064, India.
| | - Wolfhard Janke
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany.
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22
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Wen H, Zhu Y, Peng C, Kumar PBS, Laradji M. Collective motion of cells modeled as ring polymers. SOFT MATTER 2022; 18:1228-1238. [PMID: 35043821 DOI: 10.1039/d1sm01640g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In this article, we use a coarse-grained model of disjoint semi-flexible ring polymers to investigate computationally the spatiotemporal collective behavior of cell colonies. A ring polymer in this model is self-propelled by a motility force along the cell's polarity, which depends on its historical kinetics. Despite the repulsive interaction between the cells, a collective behavior sets in as a result of cells pushing against each other. This cooperative motion emerges as the amplitude of the motility force is increased and/or their areal density is increased. The degree of collectivity, characterized by the average cluster size, the velocity field order parameter, and the polarity field nematic order parameter, is found to increase with increasing the amplitude of the motility force and area coverage of the cells. Furthermore, the degree of alignment exhibited by the cell velocity field within a cluster is found to be stronger than that exhibited by the cell polarity. Comparison between the collective behavior of elongated cells and that of circular cells, at the same area coverage and motility force, shows that elongated cells exhibit a stronger collective behavior than circular cells, in agreement with earlier studies of self-propelled anisotropic particles. An investigation of two-cell collisions shows that while two clustered cells move in tandem, their polarities are misaligned. As such the cells push against each other while moving coherently.
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Affiliation(s)
- Haosheng Wen
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - Yu Zhu
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - Chenhui Peng
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
| | - P B Sunil Kumar
- Department of Physics, Indian Institute of Technology Palakkad, Palakkad-668557, Kerala, India
| | - Mohamed Laradji
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN 38152, USA.
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23
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Peterson MSE, Baskaran A, Hagan MF. Vesicle shape transformations driven by confined active filaments. Nat Commun 2021; 12:7247. [PMID: 34903731 PMCID: PMC8668962 DOI: 10.1038/s41467-021-27310-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 11/12/2021] [Indexed: 12/02/2022] Open
Abstract
In active matter systems, deformable boundaries provide a mechanism to organize internal active stresses. To study a minimal model of such a system, we perform particle-based simulations of an elastic vesicle containing a collection of polar active filaments. The interplay between the active stress organization due to interparticle interactions and that due to the deformability of the confinement leads to a variety of filament spatiotemporal organizations that have not been observed in bulk systems or under rigid confinement, including highly-aligned rings and caps. In turn, these filament assemblies drive dramatic and tunable transformations of the vesicle shape and its dynamics. We present simple scaling models that reveal the mechanisms underlying these emergent behaviors and yield design principles for engineering active materials with targeted shape dynamics.
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Affiliation(s)
- Matthew S E Peterson
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA, 02453, United States
| | - Aparna Baskaran
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA, 02453, United States.
| | - Michael F Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA, 02453, United States.
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24
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Pirhadi E, Cheng X, Yong X. Dependency of active pressure and equation of state on stiffness of wall. Sci Rep 2021; 11:22204. [PMID: 34773049 PMCID: PMC8590019 DOI: 10.1038/s41598-021-01605-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/01/2021] [Indexed: 11/09/2022] Open
Abstract
Autonomous motion and motility are hallmarks of active matter. Active agents, such as biological cells and synthetic colloidal particles, consume internal energy or extract energy from the environment to generate self-propulsion and locomotion. These systems are persistently out of equilibrium due to continuous energy consumption. It is known that pressure is not always a state function for generic active matter. Torque interaction between active constituents and confinement renders the pressure of the system a boundary-dependent property. The mechanical pressure of anisotropic active particles depends on their microscopic interactions with a solid wall. Using self-propelled dumbbells confined by solid walls as a model system, we perform numerical simulations to explore how variations in the wall stiffness influence the mechanical pressure of dry active matter. In contrast to previous findings, we find that mechanical pressure can be independent of the interaction of anisotropic active particles with walls, even in the presence of intrinsic torque interaction. Particularly, the dependency of pressure on the wall stiffness vanishes when the stiffness is above a critical level. In such a limit, the dynamics of dumbbells near the walls are randomized due to the large torque experienced by the dumbbells, leading to the recovery of pressure as a state variable of density.
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Affiliation(s)
- Emad Pirhadi
- grid.264260.40000 0001 2164 4508Department of Mechanical Engineering, Binghamton University, Binghamton, NY 13902 USA
| | - Xiang Cheng
- grid.17635.360000000419368657Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455 USA
| | - Xin Yong
- Department of Mechanical Engineering, Binghamton University, Binghamton, NY, 13902, USA.
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25
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Zantop AW, Stark H. Multi-particle collision dynamics with a non-ideal equation of state. II. Collective dynamics of elongated squirmer rods. J Chem Phys 2021; 155:134904. [PMID: 34624984 DOI: 10.1063/5.0064558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Simulations of flow fields around microscopic objects typically require methods that both solve the Navier-Stokes equations and also include thermal fluctuations. One such method popular in the field of soft-matter physics is the particle-based simulation method of multi-particle collision dynamics (MPCD). However, in contrast to the typically incompressible real fluid, the fluid of the traditional MPCD methods obeys the ideal-gas equation of state. This can be problematic because most fluid properties strongly depend on the fluid density. In a recent article, we proposed an extended MPCD algorithm and derived its non-ideal equation of state and an expression for the viscosity. In the present work, we demonstrate its accuracy and efficiency for the simulations of the flow fields of single squirmers and of the collective dynamics of squirmer rods. We use two exemplary squirmer-rod systems for which we compare the outcome of the extended MPCD method to the well-established MPCD version with an Andersen thermostat. First, we explicitly demonstrate the reduced compressibility of the MPCD fluid in a cluster of squirmer rods. Second, for shorter rods, we show the interesting result that in simulations with the extended MPCD method, dynamic swarms are more pronounced and have a higher polar order. Finally, we present a thorough study of the state diagram of squirmer rods moving in the center plane of a Hele-Shaw geometry. From a small to large aspect ratio and density, we observe a disordered state, dynamic swarms, a single swarm, and a jammed cluster, which we characterize accordingly.
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Affiliation(s)
- Arne W Zantop
- Institute of Theoretical Physics, Technische Universität Berlin, Hardenbergstraße 36, 10623 Berlin, Germany
| | - Holger Stark
- Institute of Theoretical Physics, Technische Universität Berlin, Hardenbergstraße 36, 10623 Berlin, Germany
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26
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Teixeira EF, Fernandes HCM, Brunnet LG. A single active ring model with velocity self-alignment. SOFT MATTER 2021; 17:5991-6000. [PMID: 34048522 DOI: 10.1039/d1sm00080b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cellular tissue behavior is a multiscale problem. At the cell level, out of equilibrium, biochemical reactions drive physical cell-cell interactions in a typical active matter process. Cell modeling computer simulations are a robust tool to explore countless possibilities and test hypotheses. Here, we introduce a two-dimensional, extended active matter model for biological cells. A ring of interconnected self-propelled particles represents the cell. Neighboring particles are subject to harmonic and bending potentials. Within a characteristic time, each particle's self-velocity tends to align with its scattering velocity after an interaction. Translational modes, rotational modes, and mixtures of these appear as collective states. Using analytical results derived from active Brownian particles, we identify effective characteristic time scales for ballistic and diffusive movements. Finite-size scale investigation shows that the ring diffusion increases linearly with its size when in collective movement. A study on the ring shape reveals that all collective states are present even when bending forces are weak. In that case, when in a translational mode, the collective velocity aligns with the largest ring's direction in a spontaneous polarization emergence.
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Affiliation(s)
- Emanuel F Teixeira
- Instituto de Física, Universidade Federal do Rio Grande do Sul, CP 15051, CEP 91501-970 Porto Alegre - RS, Brazil.
| | - Heitor C M Fernandes
- Instituto de Física, Universidade Federal do Rio Grande do Sul, CP 15051, CEP 91501-970 Porto Alegre - RS, Brazil.
| | - Leonardo G Brunnet
- Instituto de Física, Universidade Federal do Rio Grande do Sul, CP 15051, CEP 91501-970 Porto Alegre - RS, Brazil.
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27
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Abstract
Pattern formation processes in active systems give rise to a plethora of collective structures. Predicting how the emergent structures depend on the microscopic interactions between the moving agents remains a challenge. By introducing a high-density actin gliding assay on a fluid membrane, we demonstrate the emergence of polar structures in a regime of nematic binary interactions dominated by steric repulsion. The transition from a microscopic nematic symmetry to a macroscopic polar structure is linked to microscopic polarity sorting mechanisms, including accumulation in wedge-like topological defects. Our results should be instrumental for a better understanding of pattern formation and polarity sorting processes in active matter. Collective motion of active matter is ubiquitously observed, ranging from propelled colloids to flocks of bird, and often features the formation of complex structures composed of agents moving coherently. However, it remains extremely challenging to predict emergent patterns from the binary interaction between agents, especially as only a limited number of interaction regimes have been experimentally observed so far. Here, we introduce an actin gliding assay coupled to a supported lipid bilayer, whose fluidity forces the interaction between self-propelled filaments to be dominated by steric repulsion. This results in filaments stopping upon binary collisions and eventually aligning nematically. Such a binary interaction rule results at high densities in the emergence of dynamic collectively moving structures including clusters, vortices, and streams of filaments. Despite the microscopic interaction having a nematic symmetry, the emergent structures are found to be polar, with filaments collectively moving in the same direction. This is due to polar biases introduced by the stopping upon collision, both on the individual filaments scale as well as on the scale of collective structures. In this context, positive half-charged topological defects turn out to be a most efficient trapping and polarity sorting conformation.
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28
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Moore JM, Glaser MA, Betterton MD. Chiral self-sorting of active semiflexible filaments with intrinsic curvature. SOFT MATTER 2021; 17:4559-4565. [PMID: 33949407 DOI: 10.1039/d0sm01163k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Many-body interactions in systems of active matter can cause particles to move collectively and self-organize into dynamic structures with long-range order. In cells, the self-assembly of cytoskeletal filaments is critical for cellular motility, structure, intracellular transport, and division. Semiflexible cytoskeletal filaments driven by polymerization or motor-protein interactions on a two-dimensional substrate, such as the cell cortex, can induce filament bending and curvature leading to interesting collective behavior. For example, the bacterial cell-division filament FtsZ is known to have intrinsic curvature that causes it to self-organize into rings and vortices, and recent experiments reconstituting the collective motion of microtubules driven by motor proteins on a surface have observed chiral symmetry breaking of the collective behavior due to motor-induced curvature of the filaments. Previous work on the self-organization of driven filament systems have not studied the effects of curvature and filament structure on collective behavior. In this work, we present Brownian dynamics simulation results of driven semiflexible filaments with intrinsic curvature and investigate how the interplay between filament rigidity and radius of curvature can tune the self-organization behavior in homochiral systems and heterochiral mixtures. We find a curvature-induced reorganization from polar flocks to self-sorted chiral clusters, which is modified by filament flexibility. This transition changes filament transport from ballistic to diffusive at long timescales.
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Affiliation(s)
- Jeffrey M Moore
- Department of Physics, University of Colorado, Boulder, CO 80309, USA.
| | - Matthew A Glaser
- Department of Physics, University of Colorado, Boulder, CO 80309, USA.
| | - Meredith D Betterton
- Department of Physics, University of Colorado, Boulder, CO 80309, USA. and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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29
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Shee A, Gupta N, Chaudhuri A, Chaudhuri D. A semiflexible polymer in a gliding assay: reentrant transition, role of turnover and activity. SOFT MATTER 2021; 17:2120-2131. [PMID: 33439187 DOI: 10.1039/d0sm01181a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We consider a model of an extensible semiflexible filament moving in two dimensions on a motility assay of motor proteins represented explicitly as active harmonic linkers. Their heads bind stochastically to polymer segments within a capture radius, and extend along the filament in a directed fashion before detaching. Both the extension and detachment rates are load-dependent and generate an active drive on the filament. The filament undergoes a first order phase transition from the open chain to spiral conformation and shows a reentrant behavior in both the active extension and the turnover, defined as the ratio of attachment-detachment rates. Associated with the phase transition, the size and shape of the polymer change non-monotonically, and the relevant autocorrelation functions display a double-exponential decay. The corresponding correlation times show a maximum signifying the dominance of spirals. The orientational dynamics captures the rotation of spirals, and its correlation time decays with activity as a power law.
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Affiliation(s)
- Amir Shee
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India. and Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Nisha Gupta
- Department of Physics, Indian Institute of Technology Palakkad, Palakkad 678557, India
| | - Abhishek Chaudhuri
- Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, SAS Nagar 140306, Punjab, India
| | - Debasish Chaudhuri
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India. and Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
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30
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Peled S, Ryan SD, Heidenreich S, Bär M, Ariel G, Be'er A. Heterogeneous bacterial swarms with mixed lengths. Phys Rev E 2021; 103:032413. [PMID: 33862716 DOI: 10.1103/physreve.103.032413] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/02/2021] [Indexed: 12/20/2022]
Abstract
Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly significant for understanding realistic bacterial swarms, which typically develop heterogeneities even when grown from a single cell. Here, mixed swarms of cells with different aspect ratios are studied both experimentally and in simulations. In contrast with previous theory, there is no macroscopic phase segregation. However, locally, long cells act as nucleation cites, around which aggregates of short, rapidly moving cells can form, resulting in enhanced swarming speeds. On the other hand, high fractions of long cells form a bottleneck for efficient swarming. Our results suggest a physical advantage for the spontaneous heterogeneity of bacterial swarm populations.
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Affiliation(s)
- Shlomit Peled
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 84990, Midreshet Ben-Gurion, Israel
| | - Shawn D Ryan
- Department of Mathematics and Statistics, Cleveland State University, Cleveland, Ohio 44115, USA
- Center for Applied Data Analysis and Modeling, Cleveland State University, Cleveland, Ohio 44115, USA
| | - Sebastian Heidenreich
- Department of Mathematical Modelling and Data Analysis, Physikalisch-Technische Bundesanstalt Braunschweig und Berlin, Abbestrasse 2-12, D-10587 Berlin, Germany
| | - Markus Bär
- Department of Mathematical Modelling and Data Analysis, Physikalisch-Technische Bundesanstalt Braunschweig und Berlin, Abbestrasse 2-12, D-10587 Berlin, Germany
| | - Gil Ariel
- Department of Mathematics, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Avraham Be'er
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 84990, Midreshet Ben-Gurion, Israel
- Department of Physics, Ben-Gurion University of the Negev 84105, Beer-Sheva, Israel
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31
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Chelakkot R, Hagan MF, Gopinath A. Synchronized oscillations, traveling waves, and jammed clusters induced by steric interactions in active filament arrays. SOFT MATTER 2021; 17:1091-1104. [PMID: 33289748 DOI: 10.1039/d0sm01162b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Autonomous active, elastic filaments that interact with each other to achieve cooperation and synchrony underlie many critical functions in biology. The mechanisms underlying this collective response and the essential ingredients for stable synchronization remain a mystery. Inspired by how these biological entities integrate elasticity with molecular motor activity to generate sustained oscillations, a number of synthetic active filament systems have been developed that mimic oscillations of these biological active filaments. Here, we describe the collective dynamics and stable spatiotemporal patterns that emerge in such biomimetic multi-filament arrays, under conditions where steric interactions may impact or dominate the collective dynamics. To focus on the role of steric interactions, we study the system using Brownian dynamics, without considering long-ranged hydrodynamic interactions. The simulations treat each filament as a connected chain of self-propelling colloids. We demonstrate that short-range steric inter-filament interactions and filament roughness are sufficient - even in the absence of inter-filament hydrodynamic interactions - to generate a rich variety of collective spatiotemporal oscillatory, traveling and static patterns. We first analyze the collective dynamics of two- and three-filament clusters and identify parameter ranges in which steric interactions lead to synchronized oscillations and strongly occluded states. Generalizing these results to large one-dimensional arrays, we find rich emergent behaviors, including traveling metachronal waves, and modulated wavetrains that are controlled by the interplay between the array geometry, filament activity, and filament elasticity. Interestingly, the existence of metachronal waves is non-monotonic with respect to the inter-filament spacing. We also find that the degree of filament roughness significantly affects the dynamics - specifically, filament roughness generates a locking-mechanism that transforms traveling wave patterns into statically stuck and jammed configurations. Taken together, simulations suggest that short-ranged steric inter-filament interactions could combine with complementary hydrodynamic interactions to control the development and regulation of oscillatory collective patterns. Furthermore, roughness and steric interactions may be critical to the development of jammed spatially periodic states; a spatiotemporal feature not observed in purely hydrodynamically interacting systems.
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Affiliation(s)
- Raghunath Chelakkot
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, India.
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32
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Moore JM, Thompson TN, Glaser MA, Betterton MD. Collective motion of driven semiflexible filaments tuned by soft repulsion and stiffness. SOFT MATTER 2020; 16:9436-9442. [PMID: 32959862 DOI: 10.1039/d0sm01036g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In active matter systems, self-propelled particles can self-organize to undergo collective motion, leading to persistent dynamical behavior out of equilibrium. In cells, cytoskeletal filaments and motor proteins form complex structures important for cell mechanics, motility, and division. Collective dynamics of cytoskeletal systems can be reconstituted using filament gliding experiments, in which cytoskeletal filaments are propelled by surface-bound motor proteins. These experiments have observed diverse dynamical states, including flocks, polar streams, swirling vortices, and single-filament spirals. Recent experiments with microtubules and kinesin motor proteins found that the collective behavior of gliding filaments can be tuned by altering the concentration of the crowding macromolecule methylcellulose in solution. Increasing the methylcellulose concentration reduced filament crossing, promoted alignment, and led to a transition from active, isotropically oriented filaments to locally aligned polar streams. This emergence of collective motion is typically explained as an increase in alignment interactions by Vicsek-type models of active polar particles. However, it is not yet understood how steric interactions and bending stiffness modify the collective behavior of active semiflexible filaments. Here we use simulations of driven filaments with tunable soft repulsion and rigidity in order to better understand how the interplay between filament flexibility and steric effects can lead to different active dynamic states. We find that increasing filament stiffness decreases the probability of filament alignment, yet increases collective motion and long-range order, in contrast to the assumptions of a Vicsek-type model. We identify swirling flocks, polar streams, buckling bands, and spirals, and describe the physics that govern transitions between these states. In addition to repulsion and driving, tuning filament stiffness can promote collective behavior, and controls the transition between active isotropic filaments, locally aligned flocks, and polar streams.
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Affiliation(s)
- Jeffrey M Moore
- Department of Physics, University of Colorado, Boulder, CO 80309, USA.
| | - Tyler N Thompson
- Department of Physics, University of Colorado, Boulder, CO 80309, USA.
| | - Matthew A Glaser
- Department of Physics, University of Colorado, Boulder, CO 80309, USA.
| | - Meredith D Betterton
- Department of Physics, University of Colorado, Boulder, CO 80309, USA. and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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33
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Affiliation(s)
- Roland G. Winkler
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
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34
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Zantop AW, Stark H. Squirmer rods as elongated microswimmers: flow fields and confinement. SOFT MATTER 2020; 16:6400-6412. [PMID: 32582901 DOI: 10.1039/d0sm00616e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microswimmers or active elements, such as bacteria and active filaments, have an elongated shape, which determines their individual and collective dynamics. There is still a need to identify what role long-range hydrodynamic interactions play in their fascinating dynamic structure formation. We construct rods of different aspect ratios using several spherical squirmer model swimmers. With the help of the mesoscale simulation method of multi-particle collision dynamics we analyze the flow fields of these squirmer rods both in a bulk fluid and in Hele-Shaw geometries of different slab widths. Based on the hydrodynamic multipole expansion either for bulk or confinement between two parallel plates, we categorize the different multipole contributions of neutral as well as pusher-type squirmer rods. We demonstrate how confinement alters the radial decay of the flow fields for a given force or source multipole moment compared to the bulk fluid.
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Affiliation(s)
- Arne W Zantop
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstraße 36, 10623 Berlin, Germany.
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35
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Deblais A, Woutersen S, Bonn D. Rheology of Entangled Active Polymer-Like T. Tubifex Worms. PHYSICAL REVIEW LETTERS 2020; 124:188002. [PMID: 32441969 DOI: 10.1103/physrevlett.124.188002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/18/2020] [Accepted: 04/13/2020] [Indexed: 06/11/2023]
Abstract
We experimentally study the rheology of long, slender, and entangled living worms (Tubifex Tubifex). Their level of activity can be controlled by changing the temperature or by adding small amounts of alcohol to make the worms temporarily inactive. Performing classical rheology experiments on this entangled polymer-like system, we find that the rheology is qualitatively similar to that of usual polymers, but, quantitatively, (i) shear thinning is reduced by activity, (ii) the characteristic shear rate for the onset of shear-thinning is given by the time scale of the activity, and (iii) the low shear viscosity as a function of concentration shows a very different scaling from that of regular polymers. Our study paves the way towards a new experimental research field of active "polymer-like worms."
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Affiliation(s)
- A Deblais
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - S Woutersen
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - D Bonn
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098XH Amsterdam, The Netherlands
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36
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Natali L, Caprini L, Cecconi F. How a local active force modifies the structural properties of polymers. SOFT MATTER 2020; 16:2594-2604. [PMID: 32091062 DOI: 10.1039/c9sm02258a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We study the dynamics of a polymer, described as a variant of a Rouse chain, driven by an active terminal monomer (head). The local active force induces a transition from a globule-like to an elongated state, as revealed by the study of the end-to-end distance, the variance of which is analytically predicted under suitable approximations. The change in the relaxation times of the Rouse-modes produced by the local self-propulsion is consistent with the transition from globule to elongated conformations. Moreover, also the bond-bond spatial correlation for the chain head are affected by the self-propulsion and a gradient of over-stretched bonds along the chain is observed. We compare our numerical results both with the phenomenological stiff-polymer theory and several analytical predictions in the Rouse-chain approximation.
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Affiliation(s)
- Laura Natali
- Dipartimento di Fisica, Università"Sapienza", Piazzale A. Moro 5, I00185 Rome, Italy
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37
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Anand SK, Singh SP. Conformation and dynamics of a self-avoiding active flexible polymer. Phys Rev E 2020; 101:030501. [PMID: 32289970 DOI: 10.1103/physreve.101.030501] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/14/2020] [Indexed: 06/11/2023]
Abstract
We investigate conformations and dynamics of a polymer considering its monomers to be active Brownian particles. This active polymer shows very intriguing physical behavior which is absent in an active Rouse chain. The chain initially shrinks with active force, which starts swelling on further increase in force. The shrinkage followed by swelling is attributed purely to excluded-volume interactions among the monomers. In the swelling regime, the chain shows a crossover from the self-avoiding behavior to the Rouse behavior with scaling exponent ν_{a}≈1/2 for end-to-end distance. The nonmonotonicity in the structure is analyzed through various physical quantities; specifically, radial distribution function of monomers, scattering time, as well as various energy calculations. The chain relaxes faster than the Rouse chain in the intermediate force regime, with a crossover in variation of relaxation time at large active force as given by a power law τ_{r}∼Pe^{-4/3} (Pe is Péclet number).
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Affiliation(s)
- Shalabh K Anand
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India
| | - Sunil P Singh
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India
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38
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Das S, Cacciuto A. Dynamics of an active semi-flexible filament in a spherical cavity. J Chem Phys 2019; 151:244904. [DOI: 10.1063/1.5132757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- S. Das
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
| | - A. Cacciuto
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
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39
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Mokhtari Z, Zippelius A. Dynamics of Active Filaments in Porous Media. PHYSICAL REVIEW LETTERS 2019; 123:028001. [PMID: 31386530 DOI: 10.1103/physrevlett.123.028001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Indexed: 06/10/2023]
Abstract
The motion of active polymers in a two-dimensional porous medium is shown to depend critically on flexibility, activity, and degree of polymerization. For a given Péclet number, we observe a transition from localization to diffusion as the stiffness of the chains is increased. Whereas stiff chains move almost unhindered through the porous medium, flexible ones spiral and get stuck. Their motion can be accounted for by the model of a continuous time random walk with a renewal process corresponding to unspiraling. The waiting time distribution is shown to develop heavy tails for decreasing stiffness, resulting in subdiffusive and ultimately caged behavior.
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Affiliation(s)
- Zahra Mokhtari
- Institute for Theoretical Physics, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Annette Zippelius
- Institute for Theoretical Physics, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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40
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Man Y, Kanso E. Morphological transitions of axially-driven microfilaments. SOFT MATTER 2019; 15:5163-5173. [PMID: 31215548 DOI: 10.1039/c8sm02397b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The interactions of microtubules with motor proteins are ubiquitous in cellular and sub-cellular processes that involve motility and cargo transport. In vitro motility assays have demonstrated that motor-driven microtubules exhibit rich dynamical behaviors from straight to curved configurations. Here, we theoretically investigate the dynamic instabilities of elastic filaments, with free-ends, driven by single follower forces that emulate the action of molecular motors. Using the resistive force theory at low Reynolds number, and a combination of numerical techniques with linear stability analysis, we show the existence of four distinct regimes of filament behavior, including a novel buckled state with locked curvature. These successive instabilities recapitulate the full range of experimentally-observed microtubule behavior, implying that neither structural nor actuation asymmetry are needed to elicit this rich repertoire of motion.
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Affiliation(s)
- Yi Man
- Department of Aerospace and Mechanical engineering, University of Southern California, CA 90007, USA.
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41
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Martín-Gómez A, Eisenstecken T, Gompper G, Winkler RG. Active Brownian filaments with hydrodynamic interactions: conformations and dynamics. SOFT MATTER 2019; 15:3957-3969. [PMID: 31012481 DOI: 10.1039/c9sm00391f] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The conformational and dynamical properties of active self-propelled filaments/polymers are investigated in the presence of hydrodynamic interactions by both, Brownian dynamics simulations and analytical theory. Numerically, a discrete linear chain composed of active Brownian particles is considered, analytically, a continuous linear semiflexible polymer with active velocities changing diffusively. The force-free nature of active monomers is accounted for-no Stokeslet fluid flow induced by active forces-and higher order hydrodynamic multipole moments are neglected. Hence, fluid-mediated interactions are assumed to arise solely due to intramolecular forces. The hydrodynamic interactions (HI) are taken into account analytically by the preaveraged Oseen tensor, and numerically by the Rotne-Prager-Yamakawa tensor. The nonequilibrium character of the active process implies a dependence of the stationary-state properties on HI via the polymer relaxation times. In particular, at moderate activities, HI lead to a substantial shrinkage of flexible and semiflexible polymers to an extent far beyond shrinkage of comparable free-draining polymers; even flexible HI-polymers shrink, while active free-draining polymers swell monotonically. Large activities imply a reswelling, however, to a less extent than for non-HI polymers, caused by the shorter polymer relaxation times due to hydrodynamic interactions. The polymer mean square displacement is enhanced, and an activity-determined ballistic regime appears. Over a wide range of time scales, flexible active polymers exhibit a hydrodynamically governed subdiffusive regime, with an exponent significantly smaller than that of the Rouse and Zimm models of passive polymers. Compared to simulations, the analytical approach predicts a weaker hydrodynamic effect. Overall, hydrodynamic interactions modify the conformational and dynamical properties of active polymers substantially.
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Affiliation(s)
- Aitor Martín-Gómez
- Theoretical Soft Matter and Biophysics, Institute for Advanced Simulation and Institute of Complex Systems, Forschungszentrum Jülich, D-52425 Jülich, Germany.
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42
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Gupta N, Chaudhuri A, Chaudhuri D. Morphological and dynamical properties of semiflexible filaments driven by molecular motors. Phys Rev E 2019; 99:042405. [PMID: 31108695 DOI: 10.1103/physreve.99.042405] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Indexed: 06/09/2023]
Abstract
We consider an explicit model of a semiflexible filament moving in two dimensions on a gliding assay of motor proteins, which attach to and detach from filament segments stochastically, with a detachment rate that depends on the local load experienced. Attached motor proteins move along the filament to one of its ends with a velocity that varies nonlinearly with the motor protein extension. The resultant force on the filament drives it out of equilibrium. The distance from equilibrium is reflected in the end-to-end distribution, modified bending stiffness, and a transition to spiral morphology of the polymer. The local stress dependence of activity results in correlated fluctuations in the speed and direction of the center of mass leading to a series of ballistic-diffusive crossovers in its dynamics.
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Affiliation(s)
- Nisha Gupta
- Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, SAS Nagar - 140306, Punjab, India
| | - Abhishek Chaudhuri
- Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, SAS Nagar - 140306, Punjab, India
| | - Debasish Chaudhuri
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India
- Homi Bhaba National Institute, Anushaktigar, Mumbai 400094, India
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43
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Daddi-Moussa-Ider A, Goh S, Liebchen B, Hoell C, Mathijssen AJTM, Guzmán-Lastra F, Scholz C, Menzel AM, Löwen H. Membrane penetration and trapping of an active particle. J Chem Phys 2019; 150:064906. [DOI: 10.1063/1.5080807] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Abdallah Daddi-Moussa-Ider
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Segun Goh
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Benno Liebchen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Christian Hoell
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | | | - Francisca Guzmán-Lastra
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
- Facultad de Ciencias, Universidad Mayor, Ave. Manuel Montt 367, Providencia, Santiago de Chile, Chile
| | - Christian Scholz
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Andreas M. Menzel
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
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44
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Manna RK, Kumar PBS. Emergent topological phenomena in active polymeric fluids. SOFT MATTER 2019; 15:477-486. [PMID: 30575844 DOI: 10.1039/c8sm01981a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Polymeric fluids show a wealth of topological phenomena, from entanglement and reptation at microscales to orientational ordering and defect production at macroscales, which can be explained by statistical-mechanical theories. In the presence of activity, the latter must be augmented by forces that cause spontaneous chain motion and fluid flow. Here, using such augmented Langevin equations, we study active polymeric solutions and melts composed of chains of hydrodynamically interacting stresslets. In a spherical volume, contractile chains are unstable and self-knot into entangled melts at both low and high densities. Extensile chains in the same geometry form an unentangled reptating state at low densities and an entangled, coherently moving, non-reptating state at high densities. On a spherical surface, contractile chains show transitions, with increasing areal density, between isotropic, orientationally ordered and micro-phase separated states. Extensile chains in the same geometry show a transition between isotropic and nematic states. In both cases, defects in orientationally ordered states are produced athermally and without conserving topological charge. Our work reproduces the phenomenology of several recent experiments, highlights the importance of hydrodynamic interactions in active polymer fluids, and suggests non-equilibrium kinetic routes to topological structures that are otherwise difficult to obtain in equilibrium.
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Affiliation(s)
- Raj Kumar Manna
- Department of Physics, Indian Institute of Technology Madras, Chennai, India.
| | - P B Sunil Kumar
- Department of Physics, Indian Institute of Technology Madras, Chennai, India. and Department of Physics, Indian Institute of Technology Palakkad, Palakkad 678557, India.
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45
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Ravichandran A, Duman Ö, Hoore M, Saggiorato G, Vliegenthart GA, Auth T, Gompper G. Chronology of motor-mediated microtubule streaming. eLife 2019; 8:e39694. [PMID: 30601119 PMCID: PMC6338466 DOI: 10.7554/elife.39694] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/28/2018] [Indexed: 12/19/2022] Open
Abstract
We introduce a filament-based simulation model for coarse-grained, effective motor-mediated interaction between microtubule pairs to study the time-scales that compose cytoplasmic streaming. We characterise microtubule dynamics in two-dimensional systems by chronologically arranging five distinct processes of varying duration that make up streaming, from microtubule pairs to collective dynamics. The structures found were polarity sorted due to the propulsion of antialigned microtubules. This also gave rise to the formation of large polar-aligned domains, and streaming at the domain boundaries. Correlation functions, mean squared displacements, and velocity distributions reveal a cascade of processes ultimately leading to microtubule streaming and advection, spanning multiple microtubule lengths. The characteristic times for the processes extend over three orders of magnitude from fast single-microtubule processes to slow collective processes. Our approach can be used to directly test the importance of molecular components, such as motors and crosslinking proteins between microtubules, on the collective dynamics at cellular scale.
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Affiliation(s)
- Arvind Ravichandran
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced SimulationForschungszentrum JülichJülichGermany
| | - Özer Duman
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced SimulationForschungszentrum JülichJülichGermany
| | - Masoud Hoore
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced SimulationForschungszentrum JülichJülichGermany
| | - Guglielmo Saggiorato
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced SimulationForschungszentrum JülichJülichGermany
| | - Gerard A Vliegenthart
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced SimulationForschungszentrum JülichJülichGermany
| | - Thorsten Auth
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced SimulationForschungszentrum JülichJülichGermany
| | - Gerhard Gompper
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced SimulationForschungszentrum JülichJülichGermany
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46
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Martín-Gómez A, Gompper G, Winkler RG. Active Brownian Filamentous Polymers under Shear Flow. Polymers (Basel) 2018; 10:E837. [PMID: 30960761 PMCID: PMC6403868 DOI: 10.3390/polym10080837] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 12/21/2022] Open
Abstract
The conformational and rheological properties of active filaments/polymers exposed to shear flow are studied analytically. Using the continuous Gaussian semiflexible polymer model extended by the activity, we derive analytical expressions for the dependence of the deformation, orientation, relaxation times, and viscosity on the persistence length, shear rate, and activity. The model yields a Weissenberg-number dependent shear-induced deformation, alignment, and shear thinning behavior, similarly to the passive counterpart. Thereby, the model shows an intimate coupling between activity and shear flow. As a consequence, activity enhances the shear-induced polymer deformation for flexible polymers. For semiflexible polymers/filaments, a nonmonotonic deformation is obtained because of the activity-induced shrinkage at moderate and swelling at large activities. Independent of stiffness, activity-induced swelling facilitates and enhances alignment and shear thinning compared to a passive polymer. In the asymptotic limit of large activities, a polymer length- and stiffness-independent behavior is obtained, with universal shear-rate dependencies for the conformations, dynamics, and rheology.
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Affiliation(s)
- Aitor Martín-Gómez
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany.
| | - Gerhard Gompper
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany.
| | - Roland G Winkler
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany.
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