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Jonas HJ, Schall P, Bolhuis PG. Activity affects the stability, deformation and breakage dynamics of colloidal architectures. SOFT MATTER 2024; 20:2162-2177. [PMID: 38351836 DOI: 10.1039/d3sm01255g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Living network architectures, such as the cytoskeleton, are characterized by continuous energy injection, leading to rich but poorly understood non-equilibrium physics. There is a need for a well-controlled (experimental) model system that allows basic insight into such non-equilibrium processes. Activated self-assembled colloidal architectures can fulfill this role, as colloidal patchy particles can self-assemble into colloidal architectures such as chains, rings and networks, while self-propelled colloidal particles can simultaneously inject energy into the architecture, alter the dynamical behavior of the system, and cause the self-assembled structures to deform and break. To gain insight, we conduct a numerical investigation into the effect of introducing self-propelled colloids modeled as active Brownian particles, into self-assembling colloidal dispersions of dipatch and tripatch particles. For the interaction potential, we use a previously designed model that accurately can reproduce experimental colloidal self-assembly via the critical Casimir force [Jonas et al., J. Chem. Phys., 2021, 135, 034902]. Here, we focus primarily on the breakage dynamics of three archetypal substructures, namely, dimers, chains, and rings. We find a rich response behavior to the introduction of self-propelled particles, in which the activity can enhance as well as reduce the stability of the architecture, deform the intact structures and alter the mechanisms of fragmentation. We rationalize these findings in terms of the rate and mechanisms of breakage as a function of the direction and magnitude of the active force by separating the bond breakage process into two stages: escaping the potential well and separation of the particles. The results set the stage for investigating more complex architectures.
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Affiliation(s)
- H J Jonas
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, PO Box 94157, 1090 GD Amsterdam, The Netherlands.
| | - P Schall
- van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, PO Box 94485, 1090 GL Amsterdam, The Netherlands
| | - P G Bolhuis
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, PO Box 94157, 1090 GD Amsterdam, The Netherlands.
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2
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Rudyak VY, Lopushenko A, Palyulin VV, Chertovich AV. Long-range ordering of velocity-aligned active polymers. J Chem Phys 2024; 160:044905. [PMID: 38275191 DOI: 10.1063/5.0181252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
In this work, we study the effect of covalent bonding on the behavior of non-equilibrium systems with the active force acting on particles along their velocity. Self-ordering of single particles does not occur in this model. However, starting from some critical polymerization degree, the ordered state is observed. It is homogeneous and exhibits no phase separation. In the ordered state, the chains prefer a near-two-dimensional configuration and all move in one direction. Importantly, the self-ordering is obtained only at intermediate active force magnitudes. At high magnitudes, the transition from the disordered to ordered state is suppressed by the swelling of the chains during the transition, as we show by the transition kinetics analysis. We demonstrate the bistable behavior of the system in a particular range of polymerization degrees, amplitudes of active force, densities, and thermostat temperatures. Overall, we show that covalent bonding greatly aids the self-ordering in this active particle model, in contrast to active Brownian particles.
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Affiliation(s)
- Vladimir Yu Rudyak
- Semenov Federal Research Center for Chemical Physics, Kosygina, 4, 119991 Moscow, Russia
| | - Alexander Lopushenko
- Semenov Federal Research Center for Chemical Physics, Kosygina, 4, 119991 Moscow, Russia
| | - Vladimir V Palyulin
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia
| | - Alexander V Chertovich
- Semenov Federal Research Center for Chemical Physics, Kosygina, 4, 119991 Moscow, Russia
- Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
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3
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Goswami K, Metzler R. Trapped tracer in a non-equilibrium bath: dynamics and energetics. SOFT MATTER 2023; 19:8802-8819. [PMID: 37946588 DOI: 10.1039/d3sm01177a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
We study the dynamics of a tracer that is elastically coupled to active particles being kept at two different temperatures, as a prototype of tracer dynamics in a non-equilibrium bath. Employing analytical techniques, we find the exact solution of the probability density function for the effective motion of the tracer. The analytical results are supported by numerical simulations. By combining the experimentally accessible quantities such as the response function and the power spectrum, we measure the non-equilibrium fluctuations in terms of the effective temperature. In addition, we compute the energy dissipation rate to find the precise effects of activity. Our study is relevant in understanding athermal fluctuations arising in cytoskeletal networks or inside a chromosome.
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Affiliation(s)
- Koushik Goswami
- Institute of Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany.
| | - Ralf Metzler
- Institute of Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany.
- Asia Pacific Centre for Theoretical Physics, Pohang 37673, Republic of Korea.
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Karsai A, Cassidy GJ, Rajanala AP, Yang L, Kerimoglu D, Gumbart JC, Kim HD, Goldman DI. Toward a 3D physical model of diffusive polymer chains. FRONTIERS IN PHYSICS 2023; 11:1142004. [PMID: 37538992 PMCID: PMC10399318 DOI: 10.3389/fphy.2023.1142004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Recent studies in polymer physics have created macro-scale analogs to solute microscopic polymer chains like DNA by inducing diffusive motion on a chain of beads. These bead chains have persistence lengths of O(10) links and undergo diffusive motion under random fluctuations like vibration. We present a bead chain model within a new stochastic forcing system: an air fluidizing bed of granular media. A chain of spherical 6 mm resin beads crimped onto silk thread are buffeted randomly by the multiphase flow of grains and low density rising air "bubbles". We "thermalize" bead chains of various lengths at different fluidizing airflow rates, while X-ray imaging captures a projection of the chains' dynamics within the media. With modern 3D printing techniques, we can better represent complex polymers by geometrically varying bead connections and their relative strength, e.g., mimicking the variable stiffness between adjacent nucleotide pairs of DNA. We also develop Discrete Element Method (DEM) simulations to study the 3D motion of the bead chain, where the bead chain is represented by simulated spherical particles connected by linear and angular spring-like bonds. In experiment, we find that the velocity distributions of the beads follow exponential distributions rather than the Gaussian distributions expected from polymers in solution. Through use of the DEM simulation, we find that this difference can likely be attributed to the distributions of the forces imparted onto the chain from the fluidized bed environment. We anticipate expanding this study in the future to explore a wide range of chain composition and confinement geometry, which will provide insights into the physics of large biopolymers.
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Affiliation(s)
- Andras Karsai
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Grace J Cassidy
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Aradhya P Rajanala
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Lixinhao Yang
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, United States
| | - Deniz Kerimoglu
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, United States
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Daniel I Goldman
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
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Abstract
The human genome is arranged in the cell nucleus nonrandomly, and phase separation has been proposed as an important driving force for genome organization. However, the cell nucleus is an active system, and the contribution of nonequilibrium activities to phase separation and genome structure and dynamics remains to be explored. We simulated the genome using an energy function parametrized with chromosome conformation capture (Hi-C) data with the presence of active, nondirectional forces that break the detailed balance. We found that active forces that may arise from transcription and chromatin remodeling can dramatically impact the spatial localization of heterochromatin. When applied to euchromatin, active forces can drive heterochromatin to the nuclear envelope and compete with passive interactions among heterochromatin that tend to pull them in opposite directions. Furthermore, active forces induce long-range spatial correlations among genomic loci beyond single chromosome territories. We further showed that the impact of active forces could be understood from the effective temperature defined as the fluctuation-dissipation ratio. Our study suggests that nonequilibrium activities can significantly impact genome structure and dynamics, producing unexpected collective phenomena.
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Affiliation(s)
- Zhongling Jiang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Yifeng Qi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Kartik Kamat
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
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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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Kim WK, Milster S, Roa R, Kanduč M, Dzubiella J. Permeability of Polymer Membranes beyond Linear Response. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00605] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Won Kyu Kim
- Korea Institute for Advanced Study, 85 Hoegiro, Seoul 02455, Republic of Korea
| | - Sebastian Milster
- Applied Theoretical Physics−Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
| | - Rafael Roa
- Departamento de Física Aplicada I, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071 Málaga, Spain
| | - Matej Kanduč
- Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Joachim Dzubiella
- Applied Theoretical Physics−Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universität Freiburg, D-79110 Freiburg, Germany
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Lisin EA, Vaulina OS, Lisina II, Petrov OF. Motion of a self-propelled particle with rotational inertia. Phys Chem Chem Phys 2022; 24:14150-14158. [PMID: 35648110 DOI: 10.1039/d2cp01313d] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Overdamped active Brownian motion of self-propelled particles in a liquid has been fairly well studied. However, there are a variety of situations in which the overdamped approximation is not justified, for instance, when self-propelled particles move in a low-viscosity medium or when their rotational diffusivity is enhanced by internal active processes or external control. Examples of various origins include biofilaments driven by molecular motors, living and artificial microflyers and interfacial surfers, field-controlled and superfluid microswimmers, vibration-driven granular particles and autonomous mini-robots with sensorial delays, etc. All of them extend active Brownian motion to the underdamped case, i.e., to active Langevin motion, which takes into account inertia. Despite a rich experimental background, there is a gap in the theory in the field where rotational inertia significantly affects the random walk of active particles on all time scales. In particular, although the well-known models of active Brownian and Ornstein-Uhlenbeck particles include a memory effect of the direction of motion, they are not applicable in the underdamped case, because the rotational inertia, which they do not account for, can partially prevent "memory loss" with increasing rotational diffusion. We describe the two-dimensional motion of a self-propelled particle with both translational and rotational inertia and velocity fluctuations. The proposed generalized analytical equations for the mean kinetic energy, mean-square displacement and noise-averaged trajectory of the self-propelled particle are confirmed by numerical simulations in a wide range of self-propulsion velocities, moments of inertia, rotational diffusivities, medium viscosities and observation times.
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Affiliation(s)
- E A Lisin
- Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow, 125412, Russia.
| | - O S Vaulina
- Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow, 125412, Russia.
| | - I I Lisina
- Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow, 125412, Russia.
| | - O F Petrov
- Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow, 125412, Russia.
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Kumar P, Theeyancheri L, Chakrabarti R. Chemically symmetric and asymmetric self-driven rigid dumbbells in a 2D polymer gel. SOFT MATTER 2022; 18:2663-2671. [PMID: 35311848 DOI: 10.1039/d1sm01820e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We employ computer simulations to unveil the translational and rotational dynamics of self-driven chemically symmetric and asymmetric rigid dumbbells in a two-dimensional polymer gel. Our results show that the activity or the self-propulsion always enhances the dynamics of the dumbbells. Making the self-propelled dumbbell chemically asymmetric leads to further enhancement in dynamics. Additionally, the direction of self-propulsion is a key factor for chemically asymmetric dumbbells, where self-propulsion towards the non-sticky half of the dumbbell results in faster translational and rotational dynamics compared to the case with the self-propulsion towards the sticky half of the dumbbell. Our analyses show that both the symmetric and asymmetric passive rigid dumbbells get trapped inside the mesh of the polymer gel, but the chemical asymmetry always facilitates the mesh to mesh motion of the dumbbell and it is even more pronounced when the dumbbell is self-propelled. This results in multiple peaks in the van Hove function with increasing self-propulsion. In a nutshell, we believe that our in silico study can guide researchers to design efficient artificial microswimmers possessing potential applications in site-specific delivery.
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Affiliation(s)
- Praveen Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Ligesh Theeyancheri
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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Goswami K, Chakrabarti R. Motion of an active particle with dynamical disorder. SOFT MATTER 2022; 18:2332-2345. [PMID: 35244134 DOI: 10.1039/d1sm01816g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We propose a model for investigating the motion of a single active particle in a heterogeneous environment where the heterogeneity may arise due to crowding, conformational fluctuations and/or slow rearrangement of the surroundings. Describing the active particle in terms of the Ornstein-Uhlenbeck process (OUP) and incorporating heterogeneity in a thermal bath using two separate models, namely "diffusing diffusivity" and "switching diffusion", we explore the essential dynamical properties of the particle for its one-dimensional motion. In addition, we show how the dynamical behavior is controlled by dynamical variables associated with active noise such as strength and persistence time. Our model is relevant in the context of single particle dynamics in a crowded environment, driven by activity.
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Affiliation(s)
- Koushik Goswami
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Powai 400076, India.
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Powai 400076, India.
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Intertwined and Finely Balanced: Endoplasmic Reticulum Morphology, Dynamics, Function, and Diseases. Cells 2021; 10:cells10092341. [PMID: 34571990 PMCID: PMC8472773 DOI: 10.3390/cells10092341] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/02/2021] [Accepted: 09/04/2021] [Indexed: 02/07/2023] Open
Abstract
The endoplasmic reticulum (ER) is an organelle that is responsible for many essential subcellular processes. Interconnected narrow tubules at the periphery and thicker sheet-like regions in the perinuclear region are linked to the nuclear envelope. It is becoming apparent that the complex morphology and dynamics of the ER are linked to its function. Mutations in the proteins involved in regulating ER structure and movement are implicated in many diseases including neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and amyotrophic lateral sclerosis (ALS). The ER is also hijacked by pathogens to promote their replication. Bacteria such as Legionella pneumophila and Chlamydia trachomatis, as well as the Zika virus, bind to ER morphology and dynamics-regulating proteins to exploit the functions of the ER to their advantage. This review covers our understanding of ER morphology, including the functional subdomains and membrane contact sites that the organelle forms. We also focus on ER dynamics and the current efforts to quantify ER motion and discuss the diseases related to ER morphology and dynamics.
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Lin X, Qi Y, Latham AP, Zhang B. Multiscale modeling of genome organization with maximum entropy optimization. J Chem Phys 2021; 155:010901. [PMID: 34241389 PMCID: PMC8253599 DOI: 10.1063/5.0044150] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022] Open
Abstract
Three-dimensional (3D) organization of the human genome plays an essential role in all DNA-templated processes, including gene transcription, gene regulation, and DNA replication. Computational modeling can be an effective way of building high-resolution genome structures and improving our understanding of these molecular processes. However, it faces significant challenges as the human genome consists of over 6 × 109 base pairs, a system size that exceeds the capacity of traditional modeling approaches. In this perspective, we review the progress that has been made in modeling the human genome. Coarse-grained models parameterized to reproduce experimental data via the maximum entropy optimization algorithm serve as effective means to study genome organization at various length scales. They have provided insight into the principles of whole-genome organization and enabled de novo predictions of chromosome structures from epigenetic modifications. Applications of these models at a near-atomistic resolution further revealed physicochemical interactions that drive the phase separation of disordered proteins and dictate chromatin stability in situ. We conclude with an outlook on the opportunities and challenges in studying chromosome dynamics.
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Affiliation(s)
- Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Yifeng Qi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Andrew P. Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Levin M, Bel G, Roichman Y. Measurements and characterization of the dynamics of tracer particles in an actin network. J Chem Phys 2021; 154:144901. [PMID: 33858166 DOI: 10.1063/5.0045278] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The underlying physics governing the diffusion of a tracer particle in a viscoelastic material is a topic of some dispute. The long-term memory in the mechanical response of such materials should induce diffusive motion with a memory kernel, such as fractional Brownian motion (fBM). This is the reason that microrheology is able to provide the shear modulus of polymer networks. Surprisingly, the diffusion of a tracer particle in a network of a purified protein, actin, was found to conform to the continuous time random walk type (CTRW). We set out to resolve this discrepancy by studying the tracer particle diffusion using two different tracer particle sizes, in actin networks of different mesh sizes. We find that the ratio of tracer particle size to the characteristic length scale of a bio-polymer network plays a crucial role in determining the type of diffusion it performs. We find that the diffusion of the tracer particles has features of fBm when the particle is large compared to the mesh size, of normal diffusion when the particle is much smaller than the mesh size, and of the CTRW in between these two limits. Based on our findings, we propose and verify numerically a new model for the motion of the tracer in all regimes. Our model suggests that diffusion in actin networks consists of fBm of the tracer particle coupled with caging events with power-law distributed escape times.
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Affiliation(s)
- Maayan Levin
- Raymond and Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Golan Bel
- Department of Solar Energy and Environmental Physics, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 8499000, Israel
| | - Yael Roichman
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
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