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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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Sebtosheikh M, Naji A. Active osmoticlike pressure on permeable inclusions. Phys Rev E 2024; 109:034607. [PMID: 38632760 DOI: 10.1103/physreve.109.034607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/14/2024] [Indexed: 04/19/2024]
Abstract
We use a standard minimal active Brownian model to investigate the osmotic-like effective pressure generated by active fluids on fixed hollow inclusions. These inclusions are enclosed by a permeable (albeit nonflexible) membrane, and the interior and exterior regions of the inclusions have different particle motility strengths. We consider both rectangular and disklike inclusions and analyze the effects of various system parameters, such as excluded volume interaction between active particles, hardness of membrane, and active particle density, on the effective pressure produced on the enclosing membrane. We focus on the range of intermediate to high motility strengths and analyze the effective pressure in the steady state. Our findings for the active pressure produced in the interior and exterior regions of the inclusion indicate that the pressure is higher in the region with lower motility due to the relatively stronger accumulation of active particles.
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Affiliation(s)
- Mahmoud Sebtosheikh
- School of Nano Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19538-33511, Iran
- School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19538-33511, Iran
| | - Ali Naji
- School of Nano Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19538-33511, Iran
- Department of Physics, College of Science, Sultan Qaboos University, Muscat 123, Oman
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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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Hiraiwa T, Akiyama R, Inoue D, Kabir AMR, Kakugo A. Collision-induced torque mediates the transition of chiral dynamic patterns formed by active particles. Phys Chem Chem Phys 2022; 24:28782-28787. [PMID: 36382471 DOI: 10.1039/d2cp03879j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Controlling the patterns formed by self-propelled particles through dynamic self-organization is a challenging task. Although varieties of patterns associated with chiral self-propelled particles have been reported, essential factors that determine the morphology of the patterns have remained unclear. Here, we explore theoretically how torque formed upon collision of the particles affects the dynamic self-organization of the particles and determine the patterns. Based on a particle-based model with collision-induced torque and torque associated with self-propulsion, we find that introducing collision-induced torque turns the homogeneous bi-directionally aligned particles into rotating mono-polar flocks, which helps resolve a discrepancy in the earlier observations in microfilament gliding assays.
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Affiliation(s)
- Tetsuya Hiraiwa
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore. .,Universal Biology Institute, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Ryo Akiyama
- Department of Chemistry, Kyushu University, Fukuoka 819-0395, Japan
| | - Daisuke Inoue
- Faculty of Design, Kyushu University, Fukuoka 815-8540, Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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Shen C, Qin CR, Xu TL, Chen K, Tian WD. Structure and dynamics of an active polymer adsorbed on the surface of a cylinder. SOFT MATTER 2022; 18:1489-1497. [PMID: 35089305 DOI: 10.1039/d1sm01658j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The structure and dynamics of an active polymer on a smooth cylindrical surface are studied by Brownian dynamics simulations. The effect of an active force on the polymer adsorption behavior and the combined effect of chain mobility, length N, rigidity κ, and cylinder radius, R, on the phase diagrams are systemically investigated. We find that complete adsorption is replaced by the irregular alternative adsorption/desorption process at a large driving force. Three typical (spiral, helix-like, and rod-like) conformations of the active polymer are observed, dependent on N, κ, and R. Dynamically, the polymer shows rotational motion in the spiral state, snake-like motion in the intermediate state, and straight translational motion without turning back in the rod-like state. In the spiral state, we find that the rotation velocity ω and the chain length follow a power-law relation ω ∼ N-0.42, consistent with the torque-balance theory of general Archimedean spirals. And the polymer shows super-diffusive behavior along the cylinder for a long time in the helix-like and rod-like states. Our results highlight that the mobility, rigidity, and curvature of surface can be used to regulate the polymer behavior.
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Affiliation(s)
- Chen Shen
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
| | - Chao-Ran Qin
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
| | - Tian-Liang Xu
- 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.
| | - Wen-de Tian
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
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Ventejou B, Chaté H, Montagne R, Shi XQ. Susceptibility of Orientationally Ordered Active Matter to Chirality Disorder. PHYSICAL REVIEW LETTERS 2021; 127:238001. [PMID: 34936788 DOI: 10.1103/physrevlett.127.238001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
We investigate the susceptibility of long-range ordered phases of two-dimensional dry aligning active matter to population disorder, taken in the form of a distribution of intrinsic individual chiralities. Using a combination of particle-level models and hydrodynamic theories derived from them, we show that while in finite systems all ordered phases resist a finite amount of such chirality disorder, the homogeneous ones (polar flocks and active nematics) are unstable to any amount of disorder in the infinite-size limit. On the other hand, we find that the inhomogeneous solutions of the coexistence phase (bands) may resist a finite amount of chirality disorder even asymptotically.
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Affiliation(s)
- Bruno Ventejou
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
| | - Hugues Chaté
- Service de Physique de l'Etat Condensé, CEA, CNRS Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette, France
- Computational Science Research Center, Beijing 100193, China
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, 75005 Paris, France
| | - Raul Montagne
- Departamento de Fisica, Universidade Federal Rural de Pernambuco (UFRPE), 52171-900 Recife, Pernambuco, Brazil
| | - Xia-Qing Shi
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
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Sebtosheikh M, Naji A. Noncentral forces mediated between two inclusions in a bath of active Brownian rods. Sci Rep 2021; 11:23100. [PMID: 34845241 PMCID: PMC8630027 DOI: 10.1038/s41598-021-02295-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/12/2021] [Indexed: 11/09/2022] Open
Abstract
Using Brownian Dynamics simulations, we study effective interactions mediated between two identical and impermeable disks (inclusions) immersed in a bath of identical, active (self-propelled), Brownian rods in two spatial dimensions, by assuming that the self-propulsion axis of the rods may generally deviate from their longitudinal axis. When the self-propulsion is transverse (perpendicular to the rod axis), the accumulation of active rods around the inclusions is significantly enhanced, causing a more expansive steric layering (ring formation) of the rods around the inclusions, as compared with the reference case of longitudinally self-propelling rods. As a result, the transversally self-propelling rods also mediate a significantly longer ranged effective interaction between the inclusions. The bath-mediated interaction arises due to the overlaps between the active-rod rings formed around the inclusions, as they are brought into small separations. When the self-propulsion axis is tilted relative to the rod axis, we find an asymmetric imbalance of active-rod accumulation around the inclusion dimer. This leads to a noncentral interaction, featuring an anti-parallel pair of transverse force components and, hence, a bath-mediated torque on the dimer.
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Affiliation(s)
- Mahmoud Sebtosheikh
- School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran.
| | - Ali Naji
- School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran.
- School of Nano Science, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran.
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