1
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Yadav RS, Sharma S, Metzler R, Chakrabarti R. A passive star polymer in a dense active bath: insights from computer simulations. SOFT MATTER 2024; 20:3910-3922. [PMID: 38700098 DOI: 10.1039/d4sm00144c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Using computer simulations in two dimensions (2D), we explore the structure and dynamics of a star polymer with three arms made of passive monomers immersed in a bath of active Brownian particles (ABPs). We analyze the conformational and dynamical changes of the polymer as a function of activity and packing fraction. We also study the process of motility induced phase separation (MIPS) in the presence of a star polymer, which acts as a mobile nucleation center. The presence of the polymer increases the growth rate of the clusters in comparison to a bath without the polymer. In particular, for low packing fraction, both nucleation and cluster growth are affected by the inclusion of the star polymer. Clusters grow in the vicinity of the star polymer, resulting in the star polymer experiencing a caged motion similar to a tagged ABP in the dense phase. Due to the topological constraints of the star polymers and clustering nearby, the conformational changes of the star polymer lead to interesting observations. Inter alia, we observe the shrinking of the arm with increasing activity along with a short-lived hairpin structure of one arm formed. We also see the transient pairing of two arms of the star polymer, while the third is largely separated at high activity. We hope our findings will help in understanding the behavior of active-passive mixtures, including biopolymers of complex topology in dense active suspensions.
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Affiliation(s)
- Ramanand Singh Yadav
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Sanaa Sharma
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Ralf Metzler
- Institute of Physics and Astronomy, University of Potsdam, Germany.
- Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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2
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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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3
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Li C, Chen Q, Ding M. Escape dynamics of active ring polymers in a cylindrical nanochannel. SOFT MATTER 2024; 20:1719-1724. [PMID: 38284326 DOI: 10.1039/d3sm01524f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
We explore the escape dynamics of active ring polymers confined in a cylindrical nanochannel using Brownian dynamics. Our simulation results show that the escape time decreases with the increase of the Péclet number, which is not noticeable between the two stages of the escape process, based on whether the center of mass of the polymer is inside or outside the nanochannel. However, the monomer motion trajectory of the active polymer is very different from that of the passive polymer, similar to the snake-like motion with uniform velocity. The passive polymer, however, is in constant fugitive motion with increased velocity at the tail end of the escape. Our work is vital for understanding the escape dynamics of active ring polymers in the confined nanochannel, which provides new perspectives on their characterization and analysis.
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Affiliation(s)
- Chuqiao Li
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, China
| | - Qiaoyue Chen
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, China
| | - Mingming Ding
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, China
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, China.
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4
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Schiltz-Rouse E, Row H, Mallory SA. Kinetic temperature and pressure of an active Tonks gas. Phys Rev E 2023; 108:064601. [PMID: 38243499 DOI: 10.1103/physreve.108.064601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/06/2023] [Indexed: 01/21/2024]
Abstract
Using computer simulation and analytical theory, we study an active analog of the well-known Tonks gas, where active Brownian particles are confined to a periodic one-dimensional (1D) channel. By introducing the notion of a kinetic temperature, we derive an accurate analytical expression for the pressure and clarify the paradoxical behavior where active Brownian particles confined to 1D exhibit anomalous clustering but no motility-induced phase transition. More generally, this work provides a deeper understanding of pressure in active systems as we uncover a unique link between the kinetic temperature and swim pressure valid for active Brownian particles in higher dimensions.
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Affiliation(s)
- Elijah Schiltz-Rouse
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Hyeongjoo Row
- Department of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, California 94720, USA
| | - Stewart A Mallory
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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5
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Panda A, Winkler RG, Singh SP. Characteristic features of self-avoiding active Brownian polymers under linear shear flow. SOFT MATTER 2023; 19:8577-8586. [PMID: 37905462 DOI: 10.1039/d3sm01334k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
We present Brownian dynamics simulation results of a flexible linear polymer with excluded-volume interactions under shear flow in the presence of active noise. The active noise strongly affects the polymer's conformational and dynamical properties, such as the stretching in the flow direction and compression in the gradient direction, shear-induced alignment, and shear viscosity. In the asymptotic limit of large activities and shear rates, the power-law scaling exponents of these quantities differ significantly from those of passive polymers. The chain's shear-induced stretching at a given shear rate is reduced by active noise, and it displays a non-monotonic behavior, where an initial polymer compression is followed by its stretching with increasing active force. The compression of the polymer in the gradient direction follows the relation ∼WiPe-3/4 as a function of the activity-dependent Weissenberg number WiPe, which differs from the scaling observed in passive systems ∼WiPe-1/2. The flow-induced alignment at large Péclet numbers Pe ≫ 1, where Pe is the Péclet number, and large shear rates WiPe ≫ 1 displays the scaling behavior WiPe-1/2, with an exponent differing from the passive value -1/3. Furthermore, the polymer's zero-shear viscosity displays a non-monotonic behavior, decreasing in an intermediate activity regime due to excluded-volume interactions and increasing again for large Pe. Shear thinning appears with increasing Weissenberg number with the power-laws WiPe-1/2 and WiPe-3/4 for passive and active polymers, respectively. In addition, our simulation results are compared with the results of an analytical approach, which predicts quantitatively similar behaviors for the various aforementioned physical quantities.
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Affiliation(s)
- Arindam Panda
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India.
| | - Roland G Winkler
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52428 Jülich, Germany.
| | - Sunil P Singh
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India.
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6
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Fazli Z, Naji A. Rectification of polymer translocation through nanopores by nonchiral and chiral active particles. Phys Rev E 2023; 107:024602. [PMID: 36932605 DOI: 10.1103/physreve.107.024602] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
We study translocation of a flexible polymer chain through a membrane pore under the influence of active forces and steric exclusion using Langevin dynamics simulations within a minimal two-dimensional model. The active forces on the polymer are imparted by nonchiral and chiral active particles that are introduced on one side or both sides of a rigid membrane positioned across the midline of a confining box. We show that the polymer can translocate through the pore to either side of the dividing membrane in the absence of external forcing. Translocation of the polymer to a given side of the membrane is driven (hindered) by an effective pulling (pushing) exerted by the active particles that are present on that side. The effective pulling results from accumulation of active particles around the polymer. This crowding effect signifies persistent motion of active particles causing prolonged detention times for them close to the confining walls and the polymer. The effective pushing that hinders the translocation, on the other hand, results from steric collisions that occur between the polymer and active particles. As a result of the competition between these effective forces, we find a transition between two rectified cis-to-trans and trans-to-cis translocation regimes. This transition is identified by a sharp peak in the average translocation time. The effects of active particles on the transition is studied by analyzing how the translocation peak is regulated by the activity (self-propulsion) strength of these particles, their area fraction, and chirality strength.
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Affiliation(s)
- Zahra Fazli
- 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
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7
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Anderson CJ, Briand G, Dauchot O, Fernández-Nieves A. Polymer-chain configurations in active and passive baths. Phys Rev E 2022; 106:064606. [PMID: 36671158 DOI: 10.1103/physreve.106.064606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/15/2022] [Indexed: 12/23/2022]
Abstract
The configurations taken by polymers embedded in out-of-equilibrium baths may have broad implications in a variety of biological systems. As such, they have attracted considerable interest, particularly in simulation studies. Here we analyze the distribution of configurations taken by a passive flexible chain in a bath of hard, self-propelled, vibrated disks and systematically compare it to that of the same flexible chain in a bath of hard, thermal-like, vibrated disks. We demonstrate experimentally that the mean length and mean radius of gyration of both chains agree with Flory's law. However, the Kuhn length associated with the number of correlated monomers is smaller in the case of the active bath, corresponding to a higher effective temperature. Importantly, the active bath does not just simply map on a hot equilibrium bath. Close examination of the chains' configurations indicates a marked bias, with the chain in the active bath more likely assuming configurations with a single prominent bend.
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Affiliation(s)
- Caleb J Anderson
- Department of Condensed Matter Physics, University of Barcelona, 08028 Barcelona, Spain.,School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Guillaume Briand
- Laboratoire Gulliver, UMR CNRS 7083, ESPCI Paris, PSL University, 10, rue Vauquelin, 75231 Paris de cedex 05, France
| | - Olivier Dauchot
- Laboratoire Gulliver, UMR CNRS 7083, ESPCI Paris, PSL University, 10, rue Vauquelin, 75231 Paris de cedex 05, France
| | - Alberto Fernández-Nieves
- Department of Condensed Matter Physics, University of Barcelona, 08028 Barcelona, Spain.,School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain.,Institute for Complex Systems (UBICS), University of Barcelona, 08028 Barcelona, Spain
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8
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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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9
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Philipps CA, Gompper G, Winkler RG. Dynamics of active polar ring polymers. Phys Rev E 2022; 105:L062501. [PMID: 35854564 DOI: 10.1103/physreve.105.l062501] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The conformational and dynamical properties of isolated semiflexible active polar ring polymers are investigated analytically. A ring is modeled as a continuous Gaussian polymer exposed to tangential active forces. The analytical solution of the linear non-Hermitian equation of motion in terms of an eigenfunction expansion shows that ring conformations are independent of activity. In contrast, activity strongly affects the internal ring dynamics and yields characteristic time regimes, which are absent in passive rings. On intermediate timescales, flexible rings show an activity-enhanced diffusive regime, while semiflexible rings exhibit ballistic motion. Moreover, a second active time regime emerges on longer timescales, where rings display a snake-like motion, which is reminiscent to a tank-treading rotational dynamics in shear flow, dominated by the mode with the longest relaxation time.
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Affiliation(s)
- Christian A Philipps
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA, 52425 Jülich, Germany
- Department of Physics, RWTH Aachen University, 52056 Aachen, Germany
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA, 52425 Jülich, Germany
| | - Roland G Winkler
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich and JARA, 52425 Jülich, Germany
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10
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Chen Y, Yan R, Zhao N. Passive and active tracer dynamics in polymer solutions with isotropic-to-nematic phase transition. Phys Chem Chem Phys 2022; 24:7415-7429. [PMID: 35266498 DOI: 10.1039/d2cp00323f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Macromolecular crowding plays a crucial role in determining the dynamics in a living cell. We adopt Langevin dynamics simulations to investigate the anomalous diffusion dynamics of passive and active particles in a solution of polymer chains with tunable stiffness. The solution's anisotropic feature is modulated by changing both the polymer stiffness and volume fraction, where isotropic-to-nematic phase transition is involved. Our results demonstrate the significant impact of polymer flexibility on the dynamics of both passive and active probes. The distinct diffusion mechanism for an active particle is clarified by the interplay between polymer stiffness, crowdedness and activity. Polymer stiffness leads to a global inhibition effect on passive particle diffusion. The diffusion coefficient exhibits an intriguing non-monotonic variation at increasing polymer stiffness, which is due to the fact that the alignment of polymer chains is beneficial for diffusion along the nematic direction but unfavorable for that in the direction perpendicular to it. In sharp contrast, polymer stiffness plays a dominant role in facilitating active particle diffusion. Self-propulsion of the particle can utilize stiffness-induced elastic interactions more efficiently, which promotes its mobility in both directions. Meanwhile, an active particle might have a stronger ability to take advantage of the polymer alignment, contributing substantially enhanced diffusivity. In addition, the diffusion coefficient of an active particle is subject to a tendency of degeneration against varying volume fraction. This counter-intuitive behavior is due to the contrasting factors that increasing crowdedness induces a lower particle speed but a longer persistent motion time.
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Affiliation(s)
- Ying Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Ran Yan
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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11
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Gandikota MC, Cacciuto A. Effective forces between active polymers. Phys Rev E 2022; 105:034503. [PMID: 35428068 DOI: 10.1103/physreve.105.034503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
The characterization of the interactions between two fully flexible self-avoiding polymers is one of the classic and most important problems in polymer physics. In this paper we measure these interactions in the presence of active fluctuations. We introduce activity into the problem using two of the most popular models in this field, one where activity is effectively embedded into the monomers' dynamics, and the other where passive polymers fluctuate in an explicit bath of active particles. We establish the conditions under which the interaction between active polymers can be mapped into the classical passive problem. We observe that the active bath can drive the development of strong attractive interactions between the polymers and that, upon enforcing a significant degree of overlap, they come together to form a single double-stranded unit. A phase diagram tracing this change in conformational behavior is also reported.
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Affiliation(s)
- M C Gandikota
- 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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12
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Zhang B, Tan F, Zhao N. Polymer looping kinetics in active heterogeneous environments. SOFT MATTER 2021; 17:10334-10349. [PMID: 34734953 DOI: 10.1039/d1sm01259b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A typical biological environment is usually featured by crowding and heterogeneity, leading to complex reaction kinetics of the immersed macromolecules. In the present work, we adopt Langevin dynamics simulations to systematically investigate polymer looping kinetics in active heterogeneous media crowded with a mixture of mobile active particles and immobile obstacles. For comparison, a parallel study is also performed in the passive heterogeneous media. We explicitly analyze the change of looping time and looping probability with the variation of obstacle ratio, volume fraction and crowder size. We reveal the novel phenomena of inhibition-facilitation transition of the looping rate induced by heterogeneity, crowdedness and activity. In addition, our results demonstrate a very non-trivial crowder size effect on the looping kinetics. The underlying mechanism is rationalized by the interplay of polymer diffusion, conformational change and looping free-energy barrier. The competing effect arising from active particles and obstacles on structural and dynamical properties of the polymer yields a consistent scenario for our observations. Lastly, the non-exponential kinetics of the looping process is also analyzed. We find that both activity and crowding can strengthen the heterogeneity degree of the looping kinetics.
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Affiliation(s)
- Bingjie Zhang
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Fei Tan
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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13
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Mallory SA, Omar AK, Brady JF. Dynamic overlap concentration scale of active colloids. Phys Rev E 2021; 104:044612. [PMID: 34781543 DOI: 10.1103/physreve.104.044612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 10/06/2021] [Indexed: 11/07/2022]
Abstract
By introducing the notion of a dynamic overlap concentration scale, we identify additional universal features of the mechanical properties of active colloids. We codify these features by recognizing that the characteristic length scale of an active particle's trajectory, the run length, introduces a concentration scale ϕ^{*}. Large-scale simulations of repulsive active Brownian particles (ABPs) confirm that this run-length dependent concentration, the trajectory-space analog of the overlap concentration in polymer solutions, delineates distinct concentration regimes in which interparticle collisions alter particle trajectories. Using ϕ^{*} and concentration scales associated with colloidal jamming, the mechanical equation of state for ABPs collapses onto a set of principal curves that contain several overlooked features. The inclusion of these features qualitatively alters previous predictions of the behavior for active colloids, as we demonstrate by computing the spinodal for a suspension of purely repulsive ABPs. Our findings suggest that dynamic overlap concentration scales should help unravel the behavior of active and driven systems.
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Affiliation(s)
- Stewart A Mallory
- Department of Chemistry, The Pennsylvania State University, University Park, Pennyslvania 16802, USA
| | - Ahmad K Omar
- Department of Materials Science and Engineering, University of California, Berkeley, California 94720, USA
| | - John F Brady
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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14
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Papale A, Smrek J, Rosa A. Nanorheology of active-passive polymer mixtures differentiates between linear and ring polymer topology. SOFT MATTER 2021; 17:7111-7117. [PMID: 34254620 DOI: 10.1039/d1sm00665g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We study the motion of dispersed nanoprobes in entangled active-passive polymer mixtures. By comparing the two architectures of linear vs. unconcatenated and unknotted circular polymers, we demonstrate that novel, rich physics emerge. For both polymer architectures, nanoprobes of size smaller than the entanglement threshold of the solution move faster as activity is increased and more energy is pumped in the system. For larger nanoprobes, a surprising phenomenon occurs: while in linear solutions they move qualitatively as before, in active-passive ring solutions nanoprobes decelerate with respect to the purely passive conditions. We rationalize this effect in terms of the non-equilibrium, topology-dependent association (clustering) of nanoprobes to the cold component of the ring mixture reminiscent of the recently discovered [Weber et al., Phys. Rev. Lett., 2016, 116, 058301] phase separation in scalar active-passive mixtures. We conclude with a potential connection to the microrheology of the chromatin in the nuclei of the cells.
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Affiliation(s)
- Andrea Papale
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy.
| | - Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria.
| | - Angelo Rosa
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy.
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15
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Mousavi SM, Gompper G, Winkler RG. Active bath-induced localization and collapse of passive semiflexible polymers. J Chem Phys 2021; 155:044902. [PMID: 34340385 DOI: 10.1063/5.0058150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The conformational and dynamical properties of a passive polymer embedded in a bath of active Brownian particles (ABPs) are studied by Langevin dynamics simulations. Various activities and ABP concentrations below and above the critical values for motility-induced phase separation (MIPS) are considered. In a homogeneous ABP fluid, the embedded polymer swells with increasing bath activity, with stronger swelling for larger densities. The polymer dynamics is enhanced, with the diffusion coefficient increasing by a power-law with increasing activity, where the exponent depends on the ABP concentration. For ABP concentrations in the MIPS regime, we observe a localization of the polymer in the low-density ABP phase associated with polymer collapse for moderate activities and a reswelling for high activities accompanied by a preferred localization in the high-density ABP phase. Localization and reswelling are independent of the polymer stiffness, with stiff polymers behaving similarly to flexible polymers. The polymer collapse is associated with a slowdown of its dynamics and a significantly smaller center-of-mass diffusion coefficient. In general, the polymer dynamics can only partially be described by an effective (bath) temperature. Moreover, the properties of a polymer embedded in a homogeneous active bath deviate quantitatively from those of a polymer composed of active monomers, i.e., linear chains of ABPs; however, such a polymer exhibits qualitatively similar activity-dependent features.
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Affiliation(s)
- S Mahdiyeh Mousavi
- Theoretical Physics of Living Matter, Institute for Advanced Simulation and Institute of Biological Information Processing, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute for Advanced Simulation and Institute of Biological Information Processing, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Roland G Winkler
- Theoretical Physics of Living Matter, Institute for Advanced Simulation and Institute of Biological Information Processing, Forschungszentrum Jülich, D-52425 Jülich, Germany
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16
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Zhang B, Lei T, Zhao N. Comparative study of polymer looping kinetics in passive and active environments. Phys Chem Chem Phys 2021; 23:12171-12190. [PMID: 34008649 DOI: 10.1039/d1cp00591j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Intra-chain looping in complex environments is significant in advancing our understanding of biological processes in life. We adopt Langevin dynamics simulations to perform a comparative study of polymer looping kinetics in passive and active environments. From the analysis of looping quantities, including looping-unlooping times and looping probabilities, we unraveled the intriguing effects of active crowder size, activity and crowding. Firstly, we figured out the phase diagram involving a novel facilitation-inhibition transition in the parameter space of active crowder size and active force, and the two-fold roles of activity are clarified. In particular, we find that active particles of a size comparable to the polymer monomer are most favorable for facilitated looping, while those with a similar size to the polymer gyration radius impede the looping most seriously. Secondly, the underlying looping mechanisms in different active crowder size regimes are rationalized by the interplay among diffusion, polymer conformational change and the free-energy barrier. For small active crowders, activity significantly promotes end-to-end distance diffusion, which dominantly facilitates both looping and unlooping processes. In the case of moderate active crowders, the polymer chain suffers from prominent swelling, and thus inevitable inhibited looping will occur. For large active crowders, activity induces a counterintuitive non-cage effect on the looping kinetics, through yielding a higher effective temperature and larger unlooping free-energy barrier. This is in sharp contrast to the caging phenomena observed in passive media. Lastly, the volume-fraction dependence of the looping quantities in an active bath demonstrates dramatic discrepancies from that in a passive bath, which highlights the contrasting effects of activity and crowding.
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Affiliation(s)
- Bingjie Zhang
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Ting Lei
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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17
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Tan F, Chen Y, Zhao N. Effects of active crowder size and activity-crowding coupling on polymer translocation. SOFT MATTER 2021; 17:1940-1954. [PMID: 33427276 DOI: 10.1039/d0sm01906b] [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
Polymer translocation in complex environments is crucially important to many biological processes in life. In the present work, we adopted two-dimensional Langevin dynamics simulations to study the forced and unbiased polymer translocation dynamics in active and crowded media. The translocation time and probability are analyzed in terms of active force Fa, volume fraction φ and also the crowder size. The non-trivial active crowder size effect and activity-crowding coupling effect as well as the novel mechanism of unbiased translocation between two active environments with different active particle sizes are clarified. Firstly, for forced translocation, we reveal an intriguing non-monotonic dependence of the translocation time on the crowder size in the case of large activity. In particular, crowders of intermediate size similar to the polymer segment are proven to be the most favorable for translocation. Moreover, a facilitation-inhibition crossover of the translocation time with increasing volume fraction is observed, indicating a crucial activity-crowding coupling effect. Secondly, for unbiased translocation driven by different active crowder sizes, the translocation probability demonstrates a novel turnover phenomenon, implying the appearance of an opposite directional preference as the active force exceeds a critical value. The translocation time in both directions decreases monotonically with the active force. The asymmetric activity effect together with the entropic driving scenario provides a reasonable picture for the peculiar behavior observed in unbiased translocation.
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Affiliation(s)
- Fei Tan
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Ying Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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18
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Das S, Kennedy N, Cacciuto A. The coil-globule transition in self-avoiding active polymers. SOFT MATTER 2021; 17:160-164. [PMID: 33164018 DOI: 10.1039/d0sm01526a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We perform numerical simulations of an active fully flexible self-avoiding polymer as a function of the quality of the embedding solvent described in terms of an effective monomer-monomer interaction. Specifically, by extracting the Flory exponent of the active polymer under different conditions, we are able to pin down the location of the coil-globule transition for different strengths of the active forces. Remarkably, we find that a simple rescaling of the temperature is capable of qualitatively capturing the dependence of the Θ-point of the polymer on the amplitude of active fluctuations. We discuss the limits of this mapping and suggest that a negative active pressure between the monomers, not unlike the one that has already been found in suspensions of active hard spheres, may also be present in active polymers.
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Affiliation(s)
- S Das
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA.
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19
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Das S, Ghosh S, Chelakkot R. Aggregate morphology of active Brownian particles on porous, circular walls. Phys Rev E 2020; 102:032619. [PMID: 33075888 DOI: 10.1103/physreve.102.032619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 09/10/2020] [Indexed: 06/11/2023]
Abstract
We study the motility-induced aggregation of active Brownian particles (ABPs) on a porous, circular wall. We observe that the morphology of aggregated dense-phase on a static wall depends on the wall porosity, particle motility, and the radius of the circular wall. Our analysis reveals two morphologically distinct, dense aggregates; a connected dense cluster that spreads uniformly on the circular wall and a localized cluster that breaks the rotational symmetry of the system. These distinct morphological states are similar to the macroscopic structures observed in aggregates on planar, porous walls. We systematically analyze the parameter regimes where the different morphological states are observed. We further extend our analysis to motile circular rings. We show that the motile ring propels almost ballistically due to the force applied by the active particles when they form a localized cluster, whereas it moves diffusively when the active particles form a continuous cluster. This property demonstrates the possibility of extracting useful work from a system of ABPs, even without artificially breaking the rotational symmetry.
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Affiliation(s)
- Suchismita Das
- Department of Physics, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sounok Ghosh
- Department of Physics, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Raghunath Chelakkot
- Department of Physics, Indian Institute of Technology Bombay, Mumbai 400076, India
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20
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Du Y, Jiang H, Hou Z. Rod-assisted heterogeneous nucleation in active suspensions. SOFT MATTER 2020; 16:6434-6441. [PMID: 32588016 DOI: 10.1039/d0sm00672f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Motility induced phase separation as well as the nucleation process in active particle systems has gained extensive research attention very recently. Most studies so far have considered homogeneous cases without the influence of foreign seeds or impurities; however, the heterogeneous nucleation process, widely studied in passive systems, has not been systematically investigated yet. Here we study the heterogeneous nucleation process and phase behaviors of a suspension of active Brownian particles by introducing a rod-like passive seed. We found that such a seed can exponentially accelerate the nucleation rate and thus readily induce phase separation of a dilute active system, while a homogeneous one with the same volume fraction still maintains a single phase. It is observed that the seed would automatically detach from the dense phase after the completion of phase separation instead of staying inside as an impurity. Interestingly, we found that the phase behavior is re-entrant with the activity: single-phase states exist at both high and low activities, with phase separated states in between. Our results demonstrate that heterogeneous nucleation in an active system can show novel behaviors with respect to its passive counterpart, and pave the way for more future studies in relevant fields.
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Affiliation(s)
- Yunfei Du
- Hefei National Laboratory for Physical Sciences at Microscales and Department of Chemical Physics, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China.
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21
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Shafiei Aporvari M, Utkur M, Saritas EU, Volpe G, Stenhammar J. Anisotropic dynamics of a self-assembled colloidal chain in an active bath. SOFT MATTER 2020; 16:5609-5614. [PMID: 32519706 DOI: 10.1039/d0sm00318b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Anisotropic macromolecules exposed to non-equilibrium (active) noise are very common in biological systems, and an accurate understanding of their anisotropic dynamics is therefore crucial. Here, we experimentally investigate the dynamics of isolated chains assembled from magnetic microparticles at a liquid-air interface and moving in an active bath consisting of motile E. coli bacteria. We investigate both the internal chain dynamics and the anisotropic center-of-mass dynamics through particle tracking. We find that both the internal and center-of-mass dynamics are greatly enhanced compared to the passive case, i.e., a system without bacteria, and that the center-of-mass diffusion coefficient D features a non-monotonic dependence as a function of the chain length. Furthermore, our results show that the relationship between the components of D parallel and perpendicular with respect to the direction of the applied magnetic field is preserved in the active bath compared to the passive case, with a higher diffusion in the parallel direction, in contrast to previous findings in the literature. We argue that this qualitative difference is due to subtle differences in the experimental geometry and conditions and the relative roles played by long-range hydrodynamic interactions and short-range collisions.
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Affiliation(s)
- Mehdi Shafiei Aporvari
- UNAM - National Nanotechnology Research Center, Bilkent University, Ankara 06800, Turkey. and National Magnetic Resonance Research Center (UMRAM), Bilkent University, Ankara 06800, Turkey
| | - Mustafa Utkur
- National Magnetic Resonance Research Center (UMRAM), Bilkent University, Ankara 06800, Turkey and Department of Electrical and Electronics Engineering, Bilkent University, Ankara, Turkey
| | - Emine Ulku Saritas
- National Magnetic Resonance Research Center (UMRAM), Bilkent University, Ankara 06800, Turkey and Department of Electrical and Electronics Engineering, Bilkent University, Ankara, Turkey
| | - Giovanni Volpe
- Department of Physics, University of Gothenburg, SE-41296 Gothenburg, Sweden
| | - Joakim Stenhammar
- Division of Physical Chemistry, Lund University, Box 124, S-221 00 Lund, Sweden.
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22
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Liu X, Jiang H, Hou Z. Non-monotonic dependence of polymer chain dynamics on active crowder size. J Chem Phys 2020; 152:204906. [PMID: 32486672 DOI: 10.1063/5.0007570] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Configuration dynamics of flexible polymer chains is of ubiquitous importance in many biological processes. Here, we investigate a polymer chain immersed in a bath of size-changed active particles in two dimensional space using Langevin dynamics simulations. Particular attention is paid to how the radius of gyration Rg of the polymer chain depends on the size σc of active crowders. We find that Rg shows nontrivial non-monotonic dependence on σc: The chain first swells upon increasing σc, reaching a fully expanded state with maximum Rg, and then, Rg decreases until the chain collapses to a compact coil state if the crowder is large enough. Interestingly, the chain may oscillate between a collapse state and a stretched state at moderate crowder size. Analysis shows that it is the competition between two effects of active particles, one stretching the chain from inside due to persistence motion and the other compressing the chain from outside, that leads to the non-monotonic dependence. Besides, the diffusion of the polymer chain also shows nontrivial non-monotonic dependence on σc. Our results demonstrate the important interplay between particle activity and size associated with polymer configurations in active crowding environments.
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Affiliation(s)
- Xinshuang Liu
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at Microscales, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Huijun Jiang
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at Microscales, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhonghuai Hou
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at Microscales, University of Science and Technology of China, Hefei, Anhui 230026, China
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23
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Ye S, Liu P, Ye F, Chen K, Yang M. Active noise experienced by a passive particle trapped in an active bath. SOFT MATTER 2020; 16:4655-4660. [PMID: 32373861 DOI: 10.1039/d0sm00006j] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We study the properties of active noise experienced by a passive particle harmonically trapped in an active bath. The active bath is either explicitly simulated by an ensemble of active Brownian particles or abstractly represented by an active colored noise in theory. Assuming the equivalence of the two descriptions of the active bath, the active noise in the simulation system, which is directly extracted by fitting theoretical predictions to simulation measurements, is shown to depend on the constraint suffered by the passive tracer. This scenario is in significant contrast to the case of thermal noise that is independent of external trap potentials. The constraint dependence of active noise arises from the fact that the persistent force on the passive particle from the active bath can be influenced by the particle relaxation dynamics. Moreover, due to the interplay between the active collisions and particle relaxation dynamics, the effective temperature of the passive tracer quantified as the ratio of fluctuation to dissipation increases as the constraint strengthens, while the average potential and kinetic energies of the passive particle both decrease.
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Affiliation(s)
- Simin Ye
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. and School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Liu
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. and School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangfu Ye
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. and School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China and Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China and Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Ke Chen
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. and School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China and Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Mingcheng Yang
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. and School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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24
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Martin-Gomez A, Eisenstecken T, Gompper G, Winkler RG. Hydrodynamics of polymers in an active bath. Phys Rev E 2020; 101:052612. [PMID: 32575238 DOI: 10.1103/physreve.101.052612] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
The conformational and dynamical properties of active polymers in solution are determined by the nature of the activity. Here, the behavior of polymers with self-propelled, active Brownian particle-type monomers differs qualitatively from that of polymers with monomers driven externally by colored-noise forces. We present simulation and theoretical results for polymers in solution in the presence of external active noise. In simulations, a semiflexible bead-spring chain is considered, in analytical calculations, a continuous linear wormlike chain. Activity is taken into account by independent monomer or site velocities, with orientations changing in a diffusive manner. In simulations, hydrodynamic interactions (HIs) are taken into account by the Rotne-Prager-Yamakawa tensor or by an implementation of the active polymer in the multiparticle-collision-dynamics approach for fluids. To arrive at an analytical solution, the preaveraged Oseen tensor is employed. The active process implies a dependence of the stationary-state properties on HIs via the polymer relaxation times. With increasing activity, HIs lead to an enhanced swelling of flexible polymers, and the conformational properties differ substantially from those of polymers with self-propelled monomers in the presence of HIs, or free-draining polymers. The polymer mean-square displacement is enhanced by HIs. Over a wide range of timescales, hydrodynamics leads to a subdiffusive regime of the site mean-square displacement for flexible active polymers, with an exponent of 5/7, larger than that of the Rouse (1/2) and Zimm (2/3) models of passive polymers.
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Affiliation(s)
- Aitor Martin-Gomez
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Thomas Eisenstecken
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Gerhard Gompper
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Roland G Winkler
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany
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25
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Liu P, Ye S, Ye F, Chen K, Yang M. Constraint Dependence of Active Depletion Forces on Passive Particles. PHYSICAL REVIEW LETTERS 2020; 124:158001. [PMID: 32357018 DOI: 10.1103/physrevlett.124.158001] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/22/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Using simulations and experiments, we demonstrate that the effective interaction between passive particles in an active bath substantially depends on an external constraint suffered by the passive particles. Particularly, the effective interaction between two free passive particles, which is directly measured in simulation, is qualitatively different from the one between two fixed particles. Moreover, we find that the friction experienced by the passive particles-a kinematic constraint-similarly influences the effective interaction. These remarkable features are in significant contrast to the equilibrium cases, and mainly arise from the accumulation of the active particles near the concave gap formed by the passive spheres. This constraint dependence not only deepens our understanding of the "active depletion force," but also provides an additional tool to tune the effective interactions in an active bath.
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Affiliation(s)
- Peng Liu
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Simin Ye
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangfu Ye
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Ke Chen
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Mingcheng Yang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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26
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Cao X, Zhang B, Zhao N. Contrastive factors of activity and crowding on conformational properties of a flexible polymer. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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27
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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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28
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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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29
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Liu X, Jiang H, Hou Z. Configuration dynamics of a flexible polymer chain in a bath of chiral active particles. J Chem Phys 2019; 151:174904. [DOI: 10.1063/1.5125607] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xinshuang Liu
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at Microscales, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Huijun Jiang
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at Microscales, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhonghuai Hou
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at Microscales, University of Science and Technology of China, Hefei, Anhui 230026, China
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30
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Das S, Cacciuto A. Deviations from Blob Scaling Theory for Active Brownian Filaments Confined Within Cavities. PHYSICAL REVIEW LETTERS 2019; 123:087802. [PMID: 31491198 DOI: 10.1103/physrevlett.123.087802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Indexed: 06/10/2023]
Abstract
Scaling arguments used to predict the radius of gyration of passive self-avoiding flexible polymers have been shown to hold for polymers under the influence of active fluctuations. In this Letter, we establish how the standard blob scaling theory representation of a polymer, capable of capturing the essential physics of passive polymers under a variety of settings, breaks down when dealing with active polymers under confinement. Using numerical simulations, we show how the predicted exponents associated to the forces applied by a polymer when restricted within cavities of different geometries hold only whenever the persistence length generated on the polymer by the active forces is much smaller than the size of the characteristic blob in the scaling theory.
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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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31
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Shan WJ, Zhang F, Tian WD, Chen K. Assembly structures and dynamics of active colloidal cells. SOFT MATTER 2019; 15:4761-4770. [PMID: 31150037 DOI: 10.1039/c9sm00619b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Many types of active matter are deformable, such as epithelial cells and bacteria. To mimic the feature of deformability, we built a model called an active colloidal cell (ACC), i.e. a vesicle enclosed with self-propelled particles (SPPs), which as a whole can move actively. Based on the model, we then study the role of deformability in the assembly structures and dynamics of ACCs by Langevin dynamics simulation. We find that deformability weakens the self-trapping effect and hence suppresses the clustering and phase separation of the deformable soft ACCs (sACCs). Instead of forming a large compact cluster like ordinary SPPs, sACCs pack into a loose network or porous structure in the phase-separation region. The condensed phase is liquid-like, in which sACCs are strongly compressed and deformed but still keep high motility. The interface between the gas and the condensed phases is blurry and unstable, and the effective interfacial energy is very low. Our work gives new insights into the role of deformability in the assembly of active matter and also provides a reference for further studies on different types of deformable active matter.
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Affiliation(s)
- Wen-Jie Shan
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
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32
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Crowding-Activity Coupling Effect on Conformational Change of a Semi-Flexible Polymer. Polymers (Basel) 2019; 11:polym11061021. [PMID: 31185626 PMCID: PMC6631676 DOI: 10.3390/polym11061021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 11/17/2022] Open
Abstract
The behavior of a polymer in a passive crowded medium or in a very dilute active bath has been well studied, while a polymer immersed in an environment featured by both crowding and activity remains an open problem. In this paper, a systematic Langevin simulation is performed to investigate the conformational change of a semi-flexible chain in a concentrated solution packed with spherical active crowders. A very novel shrinkage-to-swelling transition is observed for a polymer with small rigidity. The underlying phase diagram is constructed in the parameter space of active force and crowder size. Moreover, the variation of the polymer gyration radius demonstrates a non-monotonic dependence on the dynamical persistence length of the active particle. Lastly, the activity-crowding coupling effect in different crowder size baths is clarified. In the case of small crowders, activity strengthens the crowding-induced shrinkage to the chain. As crowder size increases, activity turns out to be a contrasting factor to crowding, resulting in a competitive shrinkage and swelling. In the large size situation, the swelling effect arising from activity eventually becomes dominant. The present study provides a deeper understanding of the unusual behavior of a semi-flexible polymer in an active and crowded medium, associated with the nontrivial activity-crowding coupling and the cooperative crowder size effect.
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33
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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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34
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Xia YQ, Shen ZL, Tian WD, Chen K. Unfolding of a diblock chain and its anomalous diffusion induced by active particles. J Chem Phys 2019; 150:154903. [PMID: 31005072 DOI: 10.1063/1.5095850] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We study the structural and dynamical behavior of an A-B diblock chain in the bath of active Brownian particles (ABPs) by Brownian dynamics simulations in two dimensions. We are interested in the situation that the effective interaction between the A segments is attractive, while that between the B segments is repulsive. Therefore, in thermal (nonactive) equilibrium, the A block "folds" into a compact globule, while the B block is in the expanded coil state. Interestingly, we find that the A block could "unfold" sequentially like unknitting a sweater, driven by the surrounding ABPs when the propelling strength on them is beyond a certain value. This threshold value decreases and then levels off as the length of the B block increases. We also find a simple power-law relation between the unfolding time of the A block and the self-propelling strength and an exponential relation between the unfolding time and the length of the B block. Finally, we probe the translational and rotational diffusion of the chain and find that both of them show "super-diffusivity" in a large time window, especially when the self-propelling strength is small and the A block is in the folded state. Such super-diffusivity is due to the strong asymmetric distribution of ABPs around the chain. Our work provides new insights into the behavior of a polymer chain in the environment of active objects.
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Affiliation(s)
- Yi-Qi Xia
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Zhuang-Lin Shen
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Wen-de Tian
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Kang Chen
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
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35
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Chaki S, Chakrabarti R. Enhanced diffusion, swelling, and slow reconfiguration of a single chain in non-Gaussian active bath. J Chem Phys 2019; 150:094902. [DOI: 10.1063/1.5086152] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Subhasish Chaki
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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36
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Angelani L. Spontaneous assembly of colloidal vesicles driven by active swimmers. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:075101. [PMID: 30523954 DOI: 10.1088/1361-648x/aaf516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We explore the self-assembly process of colloidal structures immersed in active baths. By considering low-valence particles we numerically investigate the irreversible aggregation dynamics originated by the presence of run-and-tumble swimmers. We observe the formation of long closed chains-vesicles-densely filled by active swimmers. On the one hand the active bath drives the self-assembly of closed colloidal structures, and on the other hand the vesicles formation fosters the self-trapping of swimmers, suggesting new ways both to build structured nanomaterials and to trap microorganisms.
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Affiliation(s)
- Luca Angelani
- ISC-CNR, Institute for Complex Systems, and Dipartimento di Fisica, Università Sapienza, Piazzale Aldo Moro 2, I-00185 Rome, Italy
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37
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Xia YQ, Tian WD, Chen K, Ma YQ. Globule-stretch transition of a self-attracting chain in the repulsive active particle bath. Phys Chem Chem Phys 2019; 21:4487-4493. [PMID: 30734786 DOI: 10.1039/c8cp05976d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Folding and unfolding of a chain structure are often manipulated in experiments by tuning the pH, temperature, single-molecule forces or shear fields. Here, we carry out Brownian dynamics simulations to explore the behavior of a single self-attracting chain in a suspension of self-propelling particles (SPPs). As the propelling force increases, the globule-stretch (G-S) transition of the chain occurs due to the enhanced disturbance from the SPPs. Two distinct mechanisms of the transition in the limits of low and high rotational diffusion rates of SPPs have been observed: shear-induced stretching at a low rate and collision-induced melting at a high rate. The G-S and S-G (stretch-globule) curves form a hysteresis loop at the low rate, while they merge at the high rate. Besides, we find that two competing effects result in a non-monotonic dependence of the G-S transition on SPP density at the low rate. Our results suggest an alternative approach to manipulating the folding and unfolding of (bio)polymers by utilizing active agents.
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Affiliation(s)
- Yi-Qi Xia
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China.
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38
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Affiliation(s)
- S. Mahdiyeh Mousavi
- 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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39
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Yuan C, Chen A, Zhang B, Zhao N. Activity–crowding coupling effect on the diffusion dynamics of a self-propelled particle in polymer solutions. Phys Chem Chem Phys 2019; 21:24112-24125. [DOI: 10.1039/c9cp04498a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The anomalous diffusion dynamics of an active particle in polymer solutions is studied based on a Langevin Brownian dynamics simulation.
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Affiliation(s)
- Chengli Yuan
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
| | - Anpu Chen
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
| | - Bingjie Zhang
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
| | - Nanrong Zhao
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
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40
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Kurzthaler C. Elastic behavior of a semiflexible polymer in 3D subject to compression and stretching forces. SOFT MATTER 2018; 14:7634-7644. [PMID: 30168558 DOI: 10.1039/c8sm01403e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We elucidate the elastic behavior of a wormlike chain in 3D under compression and provide exact solutions for the experimentally accessible force-extension relation in terms of generalized spheroidal wave functions. In striking contrast to the classical Euler buckling instability, the force-extension relation of a clamped semiflexible polymer exhibits a smooth crossover from an almost stretched to a buckled configuration. In particular, the associated susceptibility, which measures the strength of the response of the polymer to the applied force, displays a prominent peak in the vicinity of the critical Euler buckling force. For increasing persistence length, the force-extension relation and the susceptibility of semiflexible polymers approach the behavior of a classical rod, whereas thermal fluctuations permit more flexible polymers to resist the applied force. Furthermore, we find that semiflexible polymers confined to 2D can oppose the applied force more strongly than in 3D.
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Affiliation(s)
- Christina Kurzthaler
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria.
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41
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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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42
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Yang W, Misko VR, Marchesoni F, Nori F. Colloidal transport through trap arrays controlled by active microswimmers. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:264004. [PMID: 29775184 DOI: 10.1088/1361-648x/aac61b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We investigate the dynamics of a binary mixture consisting of active and passive colloidal particles diffusing in a 2D array of truncated harmonic wells, or traps. We explore the possibility of using a small fraction of active particles to manipulate a much larger fraction of passive particles, for instance, to confine them in or extract them from the traps. The results of our study have potential application in biology and medical sciences, for example, to remove dead cells or undesired contaminants from biological systems by means of self-propelled nano-robots.
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Affiliation(s)
- Wen Yang
- College of Materials Science and Engineering, Taiyuan University of Science and Technology, Taiyuan 030024, People's Republic of China
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43
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Eisenstecken T, Gompper G, Winkler RG. Internal dynamics of semiflexible polymers with active noise. J Chem Phys 2018; 146:154903. [PMID: 28433012 DOI: 10.1063/1.4981012] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The intramolecular dynamics of flexible and semiflexible polymers in response to active noise is studied theoretically. The active noise may either originate from interactions of a passive polymer with a bath of active Brownian particles or the polymer itself is comprised of active Brownian particles. We describe the polymer by the continuous Gaussian semiflexible-polymer model, taking into account the finite polymer extensibility. Our analytical calculations predict a strong dependence of the polymer dynamics on the activity. In particular, active semiflexible polymers exhibit a crossover from a bending elasticity-dominated dynamics at weak activity to that of flexible polymers at strong activity. The end-to-end vector correlation function decays exponentially for times longer than the longest polymer relaxation time. Thereby, the polymer relaxation determines the decay of the correlation function for long and flexible polymers. For shorter and stiffer polymers, the relaxation behavior of individual active Brownian particles dominates the decay above a certain activity. The diffusive dynamics of a polymer is substantially enhanced by the activity. Three regimes can be identified in the mean square displacement for sufficiently strong activities: an activity-induced ballistic regime at short times, followed by a Rouse-type polymer-specific regime for any polymer stiffness, and free diffusion at long times, again determined by the activity.
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Affiliation(s)
- Thomas Eisenstecken
- 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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44
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Affiliation(s)
| | - Chantal Valeriani
- Departamento de Física Aplicada I, Facultad de Ciencias Físicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Angelo Cacciuto
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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45
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Klymko K, Mandal D, Mandadapu KK. Statistical mechanics of transport processes in active fluids: Equations of hydrodynamics. J Chem Phys 2017; 147:194109. [PMID: 29166113 DOI: 10.1063/1.4997091] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The equations of hydrodynamics including mass, linear momentum, angular momentum, and energy are derived by coarse-graining the microscopic equations of motion for systems consisting of rotary dumbbells driven by internal torques. In deriving the balance of linear momentum, we find that the symmetry of the stress tensor is broken due to the presence of non-zero torques on individual particles. The broken symmetry of the stress tensor induces internal spin in the fluid and leads us to consider the balance of internal angular momentum in addition to the usual moment of momentum. In the absence of spin, the moment of momentum is the same as the total angular momentum. In deriving the form of the balance of total angular momentum, we find the microscopic expressions for the couple stress tensor that drives the spin field. We show that the couple stress contains contributions from both intermolecular interactions and the active forces. The presence of spin leads to the idea of balance of moment of inertia due to the constant exchange of particles in a small neighborhood around a macroscopic point. We derive the associated balance of moment of inertia at the macroscale and identify the moment of inertia flux that induces its transport. Finally, we obtain the balances of total and internal energy of the active fluid and identify the sources of heat and heat fluxes in the system.
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Affiliation(s)
- Katherine Klymko
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA
| | - Dibyendu Mandal
- Department of Physics, University of California at Berkeley, Berkeley, California 94720, USA
| | - Kranthi K Mandadapu
- Department of Chemical and Biomolecular Engineering, University of California at Berkeley, Berkeley, California 94720, USA
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46
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Li HS, Wang C, Tian WD, Ma YQ, Xu C, Zheng N, Chen K. Spontaneous symmetry breaking induced unidirectional rotation of a chain-grafted colloidal particle in the active bath. SOFT MATTER 2017; 13:8031-8038. [PMID: 29034931 DOI: 10.1039/c7sm01772c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Exploiting the energy of randomly moving active agents such as bacteria is a fascinating way to power a microdevice. Here we show, by simulations, that a chain-grafted disk-like colloidal particle can rotate unidirectionally and hence output work when immersed in a thin film of active particle suspension. The collective spontaneous symmetry breaking of chain configurations is the origin of the unidirectional rotation. Long persistence time, large propelling force and/or small rotating friction are keys to sustaining the collective broken symmetry and realizing the rotation. In the rotating state, we find very simple linear relations, e.g. between the mean angular speed and the propelling force. The time-evolving asymmetry of chain configurations reveals that there are two types of non-rotating state. The basic phenomena are also observed in the macroscopic granular experiments, implying the generic nature of these phenomena. Our findings provide new insights into the collective spontaneous symmetry breaking in active systems with flexible objects and also open the way to conceive new soft/deformable microdevices.
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Affiliation(s)
- Hui-Shu Li
- Center for Soft Condensed Matter Physics & Interdisciplinary Research, College of Physics, Optoelectronics and Energy, Soochow University, Suzhou 215006, China.
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47
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Shin J, Cherstvy AG, Kim WK, Zaburdaev V. Elasticity-based polymer sorting in active fluids: a Brownian dynamics study. Phys Chem Chem Phys 2017; 19:18338-18347. [DOI: 10.1039/c7cp02947k] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
While the dynamics of polymer chains in equilibrium media is well understood by now, the polymer dynamics in active non-equilibrium environments can be very different.
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Affiliation(s)
- Jaeoh Shin
- Max Planck Institute for the Physics of Complex Systems
- 01187 Dresden
- Germany
| | - Andrey G. Cherstvy
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
| | - Won Kyu Kim
- Institut für Weiche Materie and Funktionale Materialen
- Helmholtz-Zentrum Berlin
- 14109 Berlin
- Germany
| | - Vasily Zaburdaev
- Max Planck Institute for the Physics of Complex Systems
- 01187 Dresden
- Germany
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48
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Sakaue T, Saito T. Active diffusion of model chromosomal loci driven by athermal noise. SOFT MATTER 2016; 13:81-87. [PMID: 27296909 DOI: 10.1039/c6sm00775a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Active diffusion, i.e., fluctuating dynamics driven by athermal noise, is found in various out-of-equilibrium systems. Here we discuss the nature of the active diffusion of tagged monomers in a flexible polymer. A scaling argument based on the notion of tension propagation clarifies how the polymeric effect is reflected in the anomalous diffusion exponent, which may be of relevance to the dynamics of chromosomal loci in living cells.
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Affiliation(s)
- Takahiro Sakaue
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan.
| | - Takuya Saito
- Fukui Institute for Fundamental Chemistry, Kyoto 606-8103, Japan
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49
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Pu M, Jiang H, Hou Z. Polymer translocation through nanopore into active bath. J Chem Phys 2016; 145:174902. [PMID: 27825228 DOI: 10.1063/1.4966591] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Polymer translocation through nanopores into a crowded environment is of ubiquitous importance in many biological processes. Here we investigate polymer translocation through a nanopore into an active bath of self-propelled particles in two-dimensional space using Langevin dynamics simulations. Interestingly, we find that the mean translocation time τ can show a bell-shape dependence on the particle activity Fa at a fixed volume fraction ϕ, indicating that the translocation process may become slower for small activity compared to the case of the passive media, and only when the particle activity becomes large enough can the translocation process be accelerated. In addition, we also find that τ can show a minimum as a function of ϕ if the particle activity is large enough, implying that an intermediate volume fraction of active particles is most favorable for the polymer translocation. Detailed analysis reveals that such nontrivial behaviors result from the two-fold effect of active bath: one that active particles tend to accumulate near the pore, providing an extra pressure hindering the translocation, and the other that they also aggregate along the polymer chain, generating an effective pulling force accelerating the translocation. Such results demonstrate that active bath plays rather subtle roles on the polymer translocation process.
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Affiliation(s)
- Mingfeng Pu
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at Microscales, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Huijun Jiang
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at Microscales, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhonghuai Hou
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at Microscales, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China
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50
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Paoluzzi M, Di Leonardo R, Marchetti MC, Angelani L. Shape and Displacement Fluctuations in Soft Vesicles Filled by Active Particles. Sci Rep 2016; 6:34146. [PMID: 27678166 PMCID: PMC5039690 DOI: 10.1038/srep34146] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/07/2016] [Indexed: 11/09/2022] Open
Abstract
We investigate numerically the dynamics of shape and displacement fluctuations of two-dimensional flexible vesicles filled with active particles. At low concentration most of the active particles accumulate at the boundary of the vesicle where positive particle number fluctuations are amplified by trapping, leading to the formation of pinched spots of high density, curvature and pressure. At high concentration the active particles cover the vesicle boundary almost uniformly, resulting in fairly homogeneous pressure and curvature, and nearly circular vesicle shape. The change between polarized and spherical shapes is driven by the number of active particles. The center-of-mass of the vesicle performs a persistent random walk with a long time diffusivity that is strongly enhanced for elongated active particles due to orientational correlations in their direction of propulsive motion. In our model shape-shifting induces directional sensing and the cell spontaneously migrate along the polarization direction.
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Affiliation(s)
- Matteo Paoluzzi
- Department of Physics and Syracuse Soft Matter Program, Syracuse University, Syracuse NY 13244, USA
- Dipartimento di Fisica Università Sapienza, P.le A Moro 2, 00185 Rome, Italy
| | - Roberto Di Leonardo
- Dipartimento di Fisica Università Sapienza, P.le A Moro 2, 00185 Rome, Italy
- NANOTEC-CNR, Institute of Nanotechnology, Soft and Living Matter Laboratory, Piazzale A. Moro 2, I-00185, Roma, Italy
| | - M. Cristina Marchetti
- Department of Physics and Syracuse Soft Matter Program, Syracuse University, Syracuse NY 13244, USA
| | - Luca Angelani
- Dipartimento di Fisica Università Sapienza, P.le A Moro 2, 00185 Rome, Italy
- ISC-CNR, Institute for Complex Systems, Piazzale A. Moro 2, I-00185 Roma, Italy
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