1
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Shi A, Schwartz DK. Bridging Macroscopic Diffusion and Microscopic Cavity Escape of Brownian and Active Particles in Irregular Porous Networks. ACS NANO 2024. [PMID: 39146529 DOI: 10.1021/acsnano.4c02873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
While irregular and geometrically complex pore networks are ubiquitous in nature and industrial processes, there is no universal model describing nanoparticle transport in these environments. 3D super-resolution nanoparticle tracking was employed to study the motion of passive (Brownian) and active (self-propelled) species within complex networks, and universally identified a mechanism involving successive cavity exploration and escape. In all cases, the long-time ensemble-averaged diffusion coefficient was proportional to a quantity involving the characteristic length scale and time scale associated with microscopic cavity exploration and escape (D ∼ r2/ttrap), where the proportionality coefficient reflected the apparent porous network connectivity. For passive nanoparticles, this coefficient was always lower than expected theoretically for a random walk, indicating reduced network accessibility. In contrast, the coefficient for active nanomotors, in the same pore spaces, aligned with the theoretical value, suggesting that active particles navigate "intelligently" in porous environments, consistent with kinetic Monte Carlo simulations in networks with variable pore sizes. These findings elucidate a model of successive cavity exploration and escape for nanoparticle transport in porous networks, where pore accessibility is a function of motive force, providing insights relevant to applications in filtration, controlled release, and beyond.
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Affiliation(s)
- Anni Shi
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
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2
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Karan C, Chaudhuri A, Chaudhuri D. Inertia and activity: spiral transitions in semi-flexible, self-avoiding polymers. SOFT MATTER 2024; 20:6221-6230. [PMID: 39049672 DOI: 10.1039/d4sm00511b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
We consider a two-dimensional, tangentially active, semi-flexible, self-avoiding polymer to find a dynamical re-entrant transition between motile open chains and spinning achiral spirals with increasing activity. Utilizing probability distributions of the turning number, we ascertain the comparative stability of the spiral structure and present a detailed phase diagram within the activity inertia plane. The onset of spiral formation at low activity levels is governed by a torque balance and is independent of inertia. At higher activities, however, inertial effects lead to spiral destabilization, an effect absent in the overdamped limit. We further delineate alterations in size and shape by analyzing the end-to-end distance distribution and the radius of gyration tensor. The Kullback-Leibler divergence from equilibrium distributions exhibits a non-monotonic relationship with activity, reaching a peak at the most compact spirals characterized by the most persistent spinning. As inertia increases, this divergence from equilibrium diminishes.
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Affiliation(s)
- Chitrak Karan
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Abhishek Chaudhuri
- Department of Physical Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, Knowledge City, S. A. S. Nagar, Manauli, PO 140306, India.
| | - Debasish Chaudhuri
- Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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3
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Voigtländer A, Houssais M, Bacik KA, Bourg IC, Burton JC, Daniels KE, Datta SS, Del Gado E, Deshpande NS, Devauchelle O, Ferdowsi B, Glade R, Goehring L, Hewitt IJ, Jerolmack D, Juanes R, Kudrolli A, Lai CY, Li W, Masteller C, Nissanka K, Rubin AM, Stone HA, Suckale J, Vriend NM, Wettlaufer JS, Yang JQ. Soft matter physics of the ground beneath our feet. SOFT MATTER 2024. [PMID: 39012310 DOI: 10.1039/d4sm00391h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The soft part of the Earth's surface - the ground beneath our feet - constitutes the basis for life and natural resources, yet a general physical understanding of the ground is still lacking. In this critical time of climate change, cross-pollination of scientific approaches is urgently needed to better understand the behavior of our planet's surface. The major topics in current research in this area cross different disciplines, spanning geosciences, and various aspects of engineering, material sciences, physics, chemistry, and biology. Among these, soft matter physics has emerged as a fundamental nexus connecting and underpinning many research questions. This perspective article is a multi-voice effort to bring together different views and approaches, questions and insights, from researchers that work in this emerging area, the soft matter physics of the ground beneath our feet. In particular, we identify four major challenges concerned with the dynamics in and of the ground: (I) modeling from the grain scale, (II) near-criticality, (III) bridging scales, and (IV) life. For each challenge, we present a selection of topics by individual authors, providing specific context, recent advances, and open questions. Through this, we seek to provide an overview of the opportunities for the broad Soft Matter community to contribute to the fundamental understanding of the physics of the ground, strive towards a common language, and encourage new collaborations across the broad spectrum of scientists interested in the matter of the Earth's surface.
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Affiliation(s)
- Anne Voigtländer
- German Research Centre for Geosciences (GFZ), Geomorphology, Telegrafenberg, 14473 Potsdam, Germany.
- Lawrence Berkeley National Laboratory (LBNL), Energy Geosciences Division, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Morgane Houssais
- Department of Physics, Clark University, 950 Main St, Worcester, MA 01610, USA
| | - Karol A Bacik
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Ian C Bourg
- Civil and Environmental Engineering (CEE) and High Meadows Environmental Institute (HMEI), Princeton University, E208 EQuad, Princeton, NJ 08540, USA
| | - Justin C Burton
- Department of Physics, Emory University, 400 Dowman Dr, Atlanta, GA 30033, USA
| | - Karen E Daniels
- North Carolina State University, 2401 Stinson Dr, Raleigh, NC 27607, USA
| | - Sujit S Datta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Emanuela Del Gado
- Department of Physics, Institute for Soft Matter Synthesis and Metrology, Georgetown University, Washington, DC, USA
| | - Nakul S Deshpande
- North Carolina State University, 2401 Stinson Dr, Raleigh, NC 27607, USA
| | - Olivier Devauchelle
- Institut de Physique du Globe de Paris, Université Paris Cité, 1 rue Jussieu, CNRS, F-75005 Paris, France
| | - Behrooz Ferdowsi
- Department of Civil and Environmental Engineering, jUniversity of Houston, Houston, TX 77204, USA
| | - Rachel Glade
- Earth & Environmental Sciences Department and Mechanical Engineering Department, University of Rochester, 227 Hutchison Hall, P.O. Box 270221, Rochester, NY 14627, USA
| | - Lucas Goehring
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK
| | - Ian J Hewitt
- Mathematical Institute, University of Oxford, Woodstock Road, Oxford OX2 6GG, UK
| | - Douglas Jerolmack
- Department of Earth & Environmental Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ruben Juanes
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Arshad Kudrolli
- Department of Physics, Clark University, 950 Main St, Worcester, MA 01610, USA
| | - Ching-Yao Lai
- Department of Geophysics, Stanford University, Stanford, CA 94305, USA
| | - Wei Li
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Stony Brook University, Department of Civil Engineering, Stony Brook, NY 11794, USA
| | - Claire Masteller
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - Kavinda Nissanka
- Department of Physics, Emory University, 400 Dowman Dr, Atlanta, GA 30033, USA
| | - Allan M Rubin
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Jenny Suckale
- Computational and Mathematical Engineering, and Environmental Engineering, Stanford University, Stanford, CA 94305, USA
| | - Nathalie M Vriend
- Department of Mechanical Engineering, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - John S Wettlaufer
- Departments of Earth & Planetary Sciences, Mathematics and Physics, Yale University, New Haven, CT 06520, USA
- Nordic Institute for Theoretical Physics, 106 91, Stockholm, Sweden
| | - Judy Q Yang
- Saint Anthony Falls Laboratory and Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, MN, USA
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4
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Keogh RR, Kozhukhov T, Thijssen K, Shendruk TN. Active Darcy's Law. PHYSICAL REVIEW LETTERS 2024; 132:188301. [PMID: 38759204 DOI: 10.1103/physrevlett.132.188301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 03/11/2024] [Indexed: 05/19/2024]
Abstract
While bacterial swarms can exhibit active turbulence in vacant spaces, they naturally inhabit crowded environments. We numerically show that driving disorderly active fluids through porous media enhances Darcy's law. While purely active flows average to zero flux, hybrid active/driven flows display greater drift than purely pressure-driven flows. This enhancement is nonmonotonic with activity, leading to an optimal activity to maximize flow rate. We incorporate the active contribution into an active Darcy's law, which may serve to help understand anomalous transport of swarming in porous media.
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Affiliation(s)
- Ryan R Keogh
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, United Kingdom
| | - Timofey Kozhukhov
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, United Kingdom
| | - Kristian Thijssen
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen, Denmark
| | - Tyler N Shendruk
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, United Kingdom
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5
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Zhu G, Gao L, Sun Y, Wei W, Yan LT. Non-equilibrium structural and dynamic behaviors of active polymers in complex and crowded environments. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 87:054601. [PMID: 38608453 DOI: 10.1088/1361-6633/ad3e11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/12/2024] [Indexed: 04/14/2024]
Abstract
Active matter systems, which convert internal chemical energy or energy from the environment into directed motion, are ubiquitous in nature and exhibit a range of emerging non-equilibrium behaviors. However, most of the current works on active matter have been devoted to particles, and the study of active polymers has only recently come into the spotlight due to their prevalence within living organisms. The intricate interplay between activity and conformational degrees of freedom gives rise to novel structural and dynamical behaviors of active polymers. Research in active polymers remarkably broadens diverse concepts of polymer physics, such as molecular architecture, dynamics, scaling and so on, which is of significant importance for the development of new polymer materials with unique performance. Furthermore, active polymers are often found in strongly interacting and crowded systems and in complex environments, so that the understanding of this behavior is essential for future developments of novel polymer-based biomaterials. This review thereby focuses on the study of active polymers in complex and crowded environments, and aims to provide insights into the fundamental physics underlying the adaptive and collective behaviors far from equilibrium, as well as the open challenges that the field is currently facing.
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Affiliation(s)
- Guolong Zhu
- School of Physics and Electronics, Hunan University, Changsha 410082, People's Republic of China
| | - Lijuan Gao
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yihang Sun
- School of Physics and Electronics, Hunan University, Changsha 410082, People's Republic of China
| | - Wenjie Wei
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
| | - Li-Tang Yan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
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6
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Jin C, Sengupta A. Microbes in porous environments: from active interactions to emergent feedback. Biophys Rev 2024; 16:173-188. [PMID: 38737203 PMCID: PMC11078916 DOI: 10.1007/s12551-024-01185-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024] Open
Abstract
Microbes thrive in diverse porous environments-from soil and riverbeds to human lungs and cancer tissues-spanning multiple scales and conditions. Short- to long-term fluctuations in local factors induce spatio-temporal heterogeneities, often leading to physiologically stressful settings. How microbes respond and adapt to such biophysical constraints is an active field of research where considerable insight has been gained over the last decades. With a focus on bacteria, here we review recent advances in self-organization and dispersal in inorganic and organic porous settings, highlighting the role of active interactions and feedback that mediates microbial survival and fitness. We discuss open questions and opportunities for using integrative approaches to advance our understanding of the biophysical strategies which microbes employ at various scales to make porous settings habitable.
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Affiliation(s)
- Chenyu Jin
- Physics of Living Matter Group, Department of Physics and Materials Science, University of Luxembourg, 162 A, Avenue de la Faïencerie, Luxembourg City, L-1511 Luxembourg
| | - Anupam Sengupta
- Physics of Living Matter Group, Department of Physics and Materials Science, University of Luxembourg, 162 A, Avenue de la Faïencerie, Luxembourg City, L-1511 Luxembourg
- Institute for Advanced Studies, University of Luxembourg, 2 Avenue de l’Université, Esch-sur-Alzette, L-4365 Luxembourg
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7
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Miranda JP, Locatelli E, Valeriani C. Self-Organized States from Solutions of Active Ring Polymers in Bulk and under Confinement. J Chem Theory Comput 2024; 20:1636-1645. [PMID: 38153343 DOI: 10.1021/acs.jctc.3c00818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
In the present work, we study, by means of numerical simulations, the structural and dynamical behavior of a suspension of active ring polymers in bulk and under lateral confinement. At high activity, when changing the distance between the confining planes and the polymers' density, we identify the emergence of a self-organized dynamical state, characterized by the coexistence of slowly diffusing clusters of rotating disks and faster rings moving in between them. We further assess that self-organization is robust in a range of polymer sizes, and we identify a critical value of the activity, necessary to trigger cluster formation. This system has distinctive features resembling at the same time polymers, liquid crystals, and active systems, where the interplay between activity, topology, and confinement leads to a spontaneous segregation in an initially one-component solution.
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Affiliation(s)
- Juan Pablo Miranda
- Dep. Est. de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, 28040 Madrid, Spain
- GISC - Grupo Interdisciplinar de Sistemas Complejos, 28040 Madrid, Spain
| | - Emanuele Locatelli
- Department of Physics and Astronomy, University of Padova, 35131 Padova, Italy
- INFN, Sezione di Padova, via Marzolo 8, I-35131 Padova, Italy
| | - Chantal Valeriani
- Dep. Est. de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, 28040 Madrid, Spain
- GISC - Grupo Interdisciplinar de Sistemas Complejos, 28040 Madrid, Spain
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8
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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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9
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Chan CW, Wu D, Qiao K, Fong KL, Yang Z, Han Y, Zhang R. Chiral active particles are sensitive reporters to environmental geometry. Nat Commun 2024; 15:1406. [PMID: 38365770 PMCID: PMC10873462 DOI: 10.1038/s41467-024-45531-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/24/2024] [Indexed: 02/18/2024] Open
Abstract
Chiral active particles (CAPs) are self-propelling particles that break time-reversal symmetry by orbiting or spinning, leading to intriguing behaviors. Here, we examined the dynamics of CAPs moving in 2D lattices of disk obstacles through active Brownian dynamics simulations and granular experiments with grass seeds. We find that the effective diffusivity of the CAPs is sensitive to the structure of the obstacle lattice, a feature absent in achiral active particles. We further studied the transport of CAPs in obstacle arrays under an external field and found a reentrant directional locking effect, which can be used to sort CAPs with different activities. Finally, we demonstrated that parallelogram lattices of obstacles without mirror symmetry can separate clockwise and counter-clockwise CAPs. The mechanisms of the above three novel phenomena are qualitatively explained. As such, our work provides a basis for designing chirality-based tools for single-cell diagnosis and separation, and active particle-based environmental sensors.
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Affiliation(s)
- Chung Wing Chan
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
| | - Daihui Wu
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
| | - Kaiyao Qiao
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
| | - Kin Long Fong
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748, Garching, Germany
| | - Zhiyu Yang
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
| | - Yilong Han
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
| | - Rui Zhang
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR.
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10
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Tan F, Wang J, Yan R, Zhao N. Forced and spontaneous translocation dynamics of a semiflexible active polymer in two dimensions. SOFT MATTER 2024; 20:1120-1132. [PMID: 38224190 DOI: 10.1039/d3sm01409f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Polymer translocation is a fundamental topic in non-equilibrium physics and is crucially important to many biological processes in life. In the present work, we adopt two-dimensional Langevin dynamics simulations to study the forced and spontaneous translocation dynamics of an active filament. The influence of polymer stiffness on the underlying dynamics is explicitly analyzed. For the forced translocation, the results show a robust stiffness-induced inhibition, and the translocation time exhibits a dual-exponent scaling relationship with the bending modulus. Tension propagation (TP) is also examined, where we find prominent modifications in terms of both activity and stiffness. For spontaneous translocation into a pure solvent, the translocation time is almost independent of the polymer stiffness. However, when the polymer is translocated into a porous medium, an intriguing non-monotonic alteration of translocation time with increasing chain stiffness is demonstrated. The semiflexible chain is beneficial for translocation while the rigid chain is not conducive. Stiffness regulation on the diffusion dynamics of the polymer in porous media shows a consistent scenario. The interplay of activity, stiffness, and porous crowding provides a new mechanism for understanding the non-trivial translocation dynamics of an active filament in complex environments.
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Affiliation(s)
- Fei Tan
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Jingli Wang
- 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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Saintillan D. Dispersion of run-and-tumble microswimmers through disordered media. Phys Rev E 2023; 108:064608. [PMID: 38243487 DOI: 10.1103/physreve.108.064608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/20/2023] [Indexed: 01/21/2024]
Abstract
Understanding the transport properties of microorganisms and self-propelled particles in porous media has important implications for human health as well as microbial ecology. In free space, most microswimmers perform diffusive random walks as a result of the interplay of self-propulsion and orientation decorrelation mechanisms such as run-and-tumble dynamics or rotational diffusion. In an unstructured porous medium, collisions with the microstructure result in a decrease in the effective spatial diffusivity of the particles from its free-space value. Here, we analyze this problem for a simple model system consisting of noninteracting point particles performing run-and-tumble dynamics through a two-dimensional disordered medium composed of a random distribution of circular obstacles, in the absence of Brownian diffusion or hydrodynamic interactions. The particles are assumed to collide with the obstacles as hard spheres and subsequently slide on the obstacle surface with no frictional resistance while maintaining their orientation, until they either escape or tumble. We show that the variations in the long-time diffusivity can be described by a universal dimensionless hindrance function f(ϕ,Pe) of the obstacle area fraction ϕ and Péclet number Pe, or ratio of the swimmer run length to the obstacle size. We analytically derive an asymptotic expression for the hindrance function valid for dilute media (Peϕ≪1), and its extension to denser media is obtained using stochastic simulations. As we explain, the model is also easily generalized to describe dispersion in three dimensions.
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Affiliation(s)
- David Saintillan
- Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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12
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Lohrmann C, Holm C. Optimal motility strategies for self-propelled agents to explore porous media. Phys Rev E 2023; 108:054401. [PMID: 38115480 DOI: 10.1103/physreve.108.054401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 10/12/2023] [Indexed: 12/21/2023]
Abstract
Microrobots for, e.g., biomedical applications, need to be equipped with motility strategies that enable them to navigate through complex environments. Inspired by biological microorganisms we re-create motility patterns such as run-and-reverse, run-and-tumble, or run-reverse-flick applied to active rodlike particles in silico. We investigate their capability to efficiently explore disordered porous environments with various porosities and mean pore sizes ranging down to the scale of the active particle. By calculating the effective diffusivity for the different patterns, we can predict the optimal one for each porous sample geometry. We find that providing the agent with very basic sensing and decision-making capabilities yields a motility pattern outperforming the biologically inspired patterns for all investigated porous samples.
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Affiliation(s)
- Christoph Lohrmann
- Institute for Computational Physics, University of Stuttgart, 70569 Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, 70569 Stuttgart, Germany
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13
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Yan R, Tan F, Wang J, Zhao N. Conformation and dynamics of an active filament in crowded media. J Chem Phys 2023; 158:114905. [PMID: 36948796 DOI: 10.1063/5.0142559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
Abstract
The structural and dynamical properties of active filamentous objects under macromolecular crowding have a great relevance in biology. By means of Brownian dynamics simulations, we perform a comparative study for the conformational change and diffusion dynamics of an active chain in pure solvents and in crowded media. Our result shows a robust compaction-to-swelling conformational change with the augment of the Péclet number. The presence of crowding facilitates self-trapping of monomers and, thus, reinforces the activity mediated compaction. In addition, the efficient collisions between the self-propelled monomers and crowders induce a coil-to-globulelike transition, indicated by a marked change of the Flory scaling exponent of the gyration radius. Moreover, the diffusion dynamics of the active chain in crowded solutions demonstrates activity-enhanced subdiffusion. The center of mass diffusion manifests rather new scaling relations with respect to both the chain length and Péclet number. The interplay of chain activity and medium crowding provides a new mechanism to understand the non-trivial properties of active filaments in complex environments.
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Affiliation(s)
- Ran Yan
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Fei Tan
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Jingli Wang
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China
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14
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Modica KJ, Omar AK, Takatori SC. Boundary design regulates the diffusion of active matter in heterogeneous environments. SOFT MATTER 2023; 19:1890-1899. [PMID: 36790413 DOI: 10.1039/d2sm01421a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Physical boundaries play a key role in governing the overall transport properties of nearby self-propelled particles. In this work, we develop dispersion theories and conduct Brownian dynamics simulations to predict the coupling between surface accumulation and effective diffusivity of active particles in boundary-rich media. We focus on three models that are well-understood for passive systems: particle transport in (i) an array of fixed volume-excluding obstacles; (ii) a pore with spatially heterogeneous width; and (iii) a tortuous path with kinks and corners. While the impact of these entropic barriers on passive particle transport is well established, we find that these classical models of porous media flows break down due to the unique interplay between activity and the microstructure of the internal geometry. We study the activity-induced slowdown of effective diffusivity by formulating a Smoluchowski description of long-time self diffusivity which contains contributions from the density and fluctuation fields of the active particles. Particle-based and finite element simulations corroborate this perspective and reveal important nonequilibrium considerations of active transport.
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Affiliation(s)
- Kevin J Modica
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
| | - Ahmad K Omar
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sho C Takatori
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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15
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Debets VE, Löwen H, Janssen LMC. Glassy Dynamics in Chiral Fluids. PHYSICAL REVIEW LETTERS 2023; 130:058201. [PMID: 36800471 DOI: 10.1103/physrevlett.130.058201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
Chiral active matter is enjoying a rapid increase of interest, spurred by the rich variety of asymmetries that can be attained in, e.g., the shape or self-propulsion mechanism of active particles. Though this has already led to the observance of so-called chiral crystals, active chiral glasses remain largely unexplored. A possible reason for this could be the naive expectation that interactions dominate the glassy dynamics and the details of the active motion become increasingly less relevant. Here, we show that quite the opposite is true by studying the glassy dynamics of interacting chiral active Brownian particles. We demonstrate that when our chiral fluid is pushed to glassy conditions, it exhibits highly nontrivial dynamics, especially compared to a standard linear active fluid such as common active Brownian particles. Despite the added complexity, we are still able to present a full rationalization for all identified dynamical regimes. Most notably, we introduce a new "hammering" mechanism, unique to rapidly spinning particles in high-density conditions, that can fluidize a chiral active solid.
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Affiliation(s)
- Vincent E Debets
- Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, Netherlands
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany
| | - Liesbeth M C Janssen
- Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, Netherlands
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16
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Qin B, Arratia PE. Confinement, chaotic transport, and trapping of active swimmers in time-periodic flows. SCIENCE ADVANCES 2022; 8:eadd6196. [PMID: 36475804 PMCID: PMC9728977 DOI: 10.1126/sciadv.add6196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
Microorganisms encounter complex unsteady flows, including algal blooms in marine settings, microbial infections in airways, and bioreactors for vaccine and biofuel production. Here, we study the transport of active swimmers in two-dimensional time-periodic flows using Langevin simulations and experiments with swimming bacteria. We find that long-term swimmer transport is controlled by two parameters, the pathlength of the unsteady flow and the normalized swimmer speed. The pathlength nonmonotonically controls swimmer dispersion dynamics, giving rise to three distinct dispersion regimes. Weak flows hinder swimmer transport by confining cells toward flow manifolds. As pathlength increases, chaotic transport along flow manifolds initiates, maximizing the number of unique flow cells traveled. Last, strong flows trap swimmers at the vortex core, suppressing dispersal. Experiments with Vibrio cholerae showed qualitative agreement with model dispersion patterns. Our results reveal that nontrivial chaotic transport can arise in simple unsteady flows and suggest a potentially optimal dispersal strategy for microswimmers in nature.
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Affiliation(s)
- Boyang Qin
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Paulo E. Arratia
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
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17
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Liu J, Jin Y, Bao JD, Chen X. Coexistence of ergodicity and nonergodicity in the aging two-state random walks. SOFT MATTER 2022; 18:8687-8699. [PMID: 36349834 DOI: 10.1039/d2sm01093c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The two-state stochastic phenomenon is observed in various systems and is attracting more interest, and it can be described by the two-state random walk (TSRW) model. The TSRW model is a typical two-state renewal process alternating between the continuous-time random walk state and the Lévy walk state, in both of which the sojourn time distributions follow a power law. In this paper, by discussing the statistical properties and calculating the ensemble averaged and time averaged mean squared displacement, the ergodic property and the ultimate diffusive behavior of the aging TSRW is studied. Results reveal that because of the two-state intermittent feature, ergodicity and nonergodicity can coexist in the aging TSRW, which behave as the time scalings of the time averages and ensemble averages not being identically equal. In addition, we find that the unique state occupation mechanism caused by the diverging mean of the sojourn times of one state, determines the aging TSRW's ultimate diffusive behavior at extremely large timescales, i.e., instead of the term with the larger diffusion exponent, the diffusion is surprisingly characterized by the term with the smaller one, which is distinctly different from previous conclusions and known results. At last, we note that the Lévy walk with rests model which also displays aging and ergodicity breaking, can be generalized by the TSRW model.
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Affiliation(s)
- Jian Liu
- Department of Physics, Beijing Technology and Business University, Beijing, 100048, China.
- Institute of Systems Science, Beijing Technology and Business University, Beijing, 100048, China
- Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Yuliang Jin
- Institute of Theoretical 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 325000, China
| | - Jing-Dong Bao
- Department of Physics, Beijing Normal University, Beijing, 100875, China
| | - Xiaosong Chen
- School of Systems Science, Beijing Normal University, Beijing, 100875, China
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18
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Theeyancheri L, Sahoo R, Kumar P, Chakrabarti R. In Silico Studies of Active Probe Dynamics in Crowded Media. ACS OMEGA 2022; 7:33637-33650. [PMID: 36188301 PMCID: PMC9520552 DOI: 10.1021/acsomega.2c04709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Active systems are made of agents, each of which takes energy from the environment and converts it to directed motion. Therefore, by construction, these systems function out of equilibrium and cannot be described using equilibrium statistical mechanics. Though the most studied aspect has been the collective motion of active particles, the motion at the individual particle level in crowded media is also of prime importance. Examples include the motion of bacteria in hydrogels, single cell migration as a way to search for food or escape from toxic agents, and synthetic active agents transporting through soft crowded media. This review presents an overview of our understanding of single active probe dynamics in crowded media from computer simulations. The active probe is a Janus or a dumbbell-shaped particle, and the medium is made of crowders that are either sticky or repulsive to the probe and could be frozen or mobile. The density and the topology of the crowders also play an important role. We hope our in silico studies will help to elucidate the mechanism of activity-driven transport in crowded media in general and design nanomachines for targeted delivery.
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19
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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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20
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van Roon DM, Volpe G, Telo da Gama MM, Araújo NAM. The role of disorder in the motion of chiral active particles in the presence of obstacles. SOFT MATTER 2022; 18:6899-6906. [PMID: 36043894 DOI: 10.1039/d2sm00694d] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The presence of obstacles is intuitively expected to hinder the diffusive transport of active particles. However, for chiral active particles, a low density of obstacles near a surface can enhance their diffusive behavior. Here, we study numerically the role that disorder plays in determining the transport dynamics of chiral active particles on surfaces with obstacles. We consider different densities of regularly spaced obstacles and distinct types of disorder: noise in the dynamics of the particle, quenched noise in the positions of the obstacles as well as obstacle size polydispersity. We show that, depending on the type and strength of the disorder, the presence of obstacles can either enhance or hinder transport, and discuss implications for the control of active transport in disordered media.
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Affiliation(s)
- Danne M van Roon
- Centro de Física Teórica e Computacional, Faculdade de Ciências, Universidade de Lisboa, P1-1749-016, Lisboa, Portugal.
| | - Giorgio Volpe
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Margarida M Telo da Gama
- Centro de Física Teórica e Computacional, Faculdade de Ciências, Universidade de Lisboa, P1-1749-016, Lisboa, Portugal.
| | - Nuno A M Araújo
- Centro de Física Teórica e Computacional, Faculdade de Ciências, Universidade de Lisboa, P1-1749-016, Lisboa, Portugal.
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21
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Zhang S, Wang J, Ge T. Force-driven active dynamics of thin nanorods in unentangled polymer melts. SOFT MATTER 2022; 18:6582-6591. [PMID: 35968884 DOI: 10.1039/d2sm00731b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent advances in the functional material and biomedical applications of nanorods call for a fundamental understanding of the active motion of nanorods in a viscoelastic medium. Molecular dynamics simulations are performed to investigate a model system consisting of force-driven active thin nanorods in a melt of unentangled polymers. The activeness of a thin nanorod arises from a constant external force applied uniformly along the rod. The simulations demonstrate that the active force overcomes the randomness of the diffusive motion and results in a ballistic motion along the direction of the applied force at long timescales. The constant speed of the force-driven ballistic motion is determined by the balance of the active force and the friction from the coupling of the nanorod with the polymer viscosity. The friction coefficient, which is computed as the ratio of the active force and the speed, decreases as the active force increases. The origin of the reduction in the friction coefficient is the high speed that allows the nanorod to renew its local environment faster than the relaxation time of melt chains. A scaling theory is developed to quantify the dependence of the friction coefficient on the strength of the active force. The simulations also demonstrate that the force-driven ballistic motion suppresses the rotational diffusion of the rod and cuts off the de-correlation of the rod axis with time. On the scaling level, the long-time trajectory of a force-driven active nanorod piercing through unentangled polymers may be described as a stretched array of "active blobs", where the short-time random-walk trajectory within an active blob is unperturbed by the active force.
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Affiliation(s)
- Siteng Zhang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA.
| | - Jiuling Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA.
| | - Ting Ge
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA.
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22
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Kim Y, Joo S, Kim WK, Jeon JH. Active Diffusion of Self-Propelled Particles in Flexible Polymer Networks. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Yeongjin Kim
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang37673, Republic of Korea
| | - Sungmin Joo
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang37673, Republic of Korea
| | - Won Kyu Kim
- School of Computational Sciences, Korea Institute for Advanced Study (KIAS), Seoul02455, Republic of Korea
| | - Jae-Hyung Jeon
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang37673, Republic of Korea
- Asia Pacific Center for Theoretical Physics (APCTP), Pohang37673, Republic of Korea
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23
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Theeyancheri L, Chaki S, Bhattacharjee T, Chakrabarti R. Migration of active rings in porous media. Phys Rev E 2022; 106:014504. [PMID: 35974648 DOI: 10.1103/physreve.106.014504] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Inspired by how the shape deformations in active organisms help them to migrate through disordered porous environments, we simulate active ring polymers in two-dimensional random porous media. Flexible and inextensible active ring polymers navigate smoothly through the disordered media. In contrast, semiflexible rings undergo transient trapping inside the pore space; the degree of trapping is inversely correlated with the increase in activity. We discover that flexible rings swell while inextensible and semiflexible rings monotonically shrink upon increasing the activity. Together, our findings identify the optimal migration of active ring polymers through porous media.
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Affiliation(s)
- Ligesh Theeyancheri
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Subhasish Chaki
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Tapomoy Bhattacharjee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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24
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Collective behavior and nongenetic inheritance allow bacterial populations to adapt to changing environments. Proc Natl Acad Sci U S A 2022; 119:e2117377119. [PMID: 35727978 DOI: 10.1073/pnas.2117377119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Collective behaviors require coordination among a group of individuals. As a result, individuals that are too phenotypically different from the rest of the group can be left out, reducing heterogeneity, but increasing coordination. If individuals also reproduce, the offspring can have different phenotypes from their parent(s). This raises the question of how these two opposing processes-loss of diversity by collective behaviors and generation of it through growth and inheritance-dynamically shape the phenotypic composition of an isogenic population. We examine this question theoretically using collective migration of chemotactic bacteria as a model system, where cells of different swimming phenotypes are better suited to navigate in different environments. We find that the differential loss of phenotypes caused by collective migration is environment-dependent. With cell growth, this differential loss enables migrating populations to dynamically adapt their phenotype compositions to the environment, enhancing migration through multiple environments. Which phenotypes are produced upon cell division depends on the level of nongenetic inheritance, and higher inheritance leads to larger composition adaptation and faster migration at steady state. However, this comes at the cost of slower responses to new environments. Due to this trade-off, there is an optimal level of inheritance that maximizes migration speed through changing environments, which enables a diverse population to outperform a nondiverse one. Growing populations might generally leverage the selection-like effects provided by collective behaviors to dynamically shape their own phenotype compositions, without mutations.
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25
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Irani E, Mokhtari Z, Zippelius A. Dynamics of Bacteria Scanning a Porous Environment. PHYSICAL REVIEW LETTERS 2022; 128:144501. [PMID: 35476466 DOI: 10.1103/physrevlett.128.144501] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
It has recently been reported that bacteria, such as Escherichia coli Bhattacharjee and Datta, Nat. Commun. 10, 2075 (2019).NCAOBW2041-172310.1038/s41467-019-10115-1 and Pseudomonas putida Alirezaeizanjani et al., Sci. Adv. 6, eaaz6153 (2020).SACDAF2375-254810.1126/sciadv.aaz6153, perform distinct modes of motion when placed in porous media as compared to dilute regions or free space. This has led us to suggest an efficient strategy for active particles in a disordered environment: reorientations are suppressed in locally dilute regions and intensified in locally dense ones. Thereby the local geometry determines the optimal path of the active agent and substantially accelerates the dynamics for up to 2 orders of magnitude. We observe a nonmonotonic behavior of the diffusion coefficient in dependence on the tumbling rate and identify a localization transition, either by increasing the density of obstacles or by decreasing the reorientation rate.
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Affiliation(s)
- Ehsan Irani
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), The Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany
| | - Zahra Mokhtari
- Freie Universität Berlin, Department of Mathematics and Computer Science, Institute of Mathematics, Arnimallee 9, 14195 Berlin, Germany
| | - Annette Zippelius
- Georg-August-Universität Göttingen, Institut für Theoretische Physik, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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26
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Mattingly HH, Kamino K, Machta BB, Emonet T. Escherichia coli chemotaxis is information limited. NATURE PHYSICS 2021; 17:1426-1431. [PMID: 35035514 PMCID: PMC8758097 DOI: 10.1038/s41567-021-01380-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 09/10/2021] [Indexed: 05/08/2023]
Abstract
Organisms acquire and use information from their environment to guide their behaviour. However, it is unclear whether this information quantitatively limits their behavioural performance. Here, we relate information to the ability of Escherichia coli to navigate up chemical gradients, the behaviour known as chemotaxis. First, we derive a theoretical limit on the speed with which cells climb gradients, given the rate at which they acquire information. Next, we measure cells' gradient-climbing speeds and the rate of information acquisition by their chemotaxis signaling pathway. We find that E. coli make behavioural decisions with much less than the one bit required to determine whether they are swimming up-gradient. Some of this information is irrelevant to gradient climbing, and some is lost in communication to behaviour. Despite these limitations, E. coli climb gradients at speeds within a factor of two of the theoretical bound. Thus, information can limit the performance of an organism, and sensory-motor pathways may have evolved to efficiently use information acquired from the environment.
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Affiliation(s)
- H H Mattingly
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- Quantitative Biology Institute, Yale University
| | - K Kamino
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- Quantitative Biology Institute, Yale University
| | - B B Machta
- Department of Physics, Yale University
- Systems Biology Institute, West Campus, Yale University
| | - T Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- Quantitative Biology Institute, Yale University
- Department of Physics, Yale University
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