It was previously believed that diffusion of a tracer particle in a viscoelastic material should be of the fractional Brownian motion (fBm) type. This is due to the long-term memory in the response of such materials to mechanical perturbations. 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 (CTRW) type in one study that focused on the ensemble average characteristics. Here, we analyze the dynamics of two differently sized tracer particles 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 the particle performs. We find that the tracer particle diffusion 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 CTRW in between these two limits. Based on our findings, we propose and verify numerically a new model for the tracer particle's motion in all regimes. Our model suggests that diffusion in actin networks consists of fBm of the tracer particle coupled with occasional caging events with power-law-distributed escape times.
We derive the long-time dynamics of a tracer immersed in a one-dimensional active bath. In contrast to previous studies, we find that the damping and noise correlations possess long-time tails with exponents that depend on the tracer symmetry. For generic tracers, shape asymmetry induces ratchet effects that alter fluctuations and lead to superdiffusion and friction that grows with time when the tracer is dragged at a constant speed. In the singular limit of a completely symmetric tracer, we recover normal diffusion and finite friction. Furthermore, for small symmetric tracers, the active cont…
We study the nonlinear response to an external force of an inertial tracer advected by a two-dimensional incompressible laminar flow and subject to thermal noise. In addition to the driving external field $F$, the main parameters in the system are the noise amplitude $D_0$ and the characteristic Stokes time $τ$ of the tracer. The relation velocity vs force shows interesting effects, such as negative differential mobility (NDM), namely a non-monotonic behavior of the tracer velocity as a function of the applied force, and absolute negative mobility (ANM), i.e. a net motion against the bias. By …
Measurements of local stresses on the cancer cells (CCs), inferred by embedding inert compressible tracer particles (TPs) in a growing multicellular spheroid (MCS), show that pressure decreases monotonically as the distance from the core of the MCS increases. How faithfully do the TPs report the local stresses in the CCs is an important question because pressure buildup in the MCS is dynamically generated due to CC division, which implies that the CC dynamics should be minimally altered by the TPs. Here using theory and simulations, we show that although the TP dynamics is unusual, exhibiting …
We consider the diffusion-advection problem in two simple cellular flow models (often invoked as examples for subdiffusive tracer's motion) and concentrate on the intermediate time range, in which the tracer's motion indeed may show subdiffusion. We have performed extensive numerical simulations of the systems under different initial conditions, and show that the pure intermediate-time subdiffusion regime is only evident when the particles start at the border between different cells, i.e. at the separatrix, and is less pronounced or absent for other initial conditions. The motion moreover show…
Optical tracking in vivo experiments reveal that diffusion of particles in biological cells is strongly enhanced in the presence of ATP and the experimental data for animal cells could previously be reproduced within a phenomenological model of a gel with myosin motors acting within it [EPL 110, 48005 (2015)]. Here, the two-fluid model of a gel is considered where active macromolecules, described as force dipoles, cyclically operate both in the elastic and the fluid components. Through coarse-graining, effective equations of motions for tracer particles displaying local deformations and local …
Actin cross-linking organizes basal body patterning through anomalous diffusion transitions
Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Department of Biomedical Sciences, University of Copenhagen（哥本哈根大学生物医学科学系，诺和诺德基金会干细胞医学中心(reNEW)）；Biocomplexity, Niels Bohr Institute, Faculty of Science, University of Copenhagen（哥本哈根大学理学院尼尔斯·玻尔研究所生物复杂性研究中心）；Department of Civil Engineering, Indian Institute of Technology Bombay（印度孟买理工学院土木工程系）
Anomalous Diffusion in Driven Electrolytes due to Hydrodynamic Fluctuations
Max Planck Institute for Dynamics and Self-Organization（马克斯·普朗克动力学与自组织研究所）；Rudolf Peierls Centre for Theoretical Physics, University of Oxford（牛津大学鲁道夫·皮尔斯理论物理中心）
A particle-resolved rheological study of chirality transfer and odd transport
Raymond & Beverly Sackler School of Chemistry, Tel Aviv University（特拉维夫大学雷蒙德和贝弗利·萨克勒化学学院）；Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf（杜塞尔多夫海因里希·海涅大学理论物理第二研究所：软物质）；Physics department, University of Rome La Sapienza（罗马第一大学物理系）；Raymond & Beverly Sackler School of Physics and astronomy, Tel Aviv University（特拉维夫大学雷蒙德和贝弗利·萨克勒物理与天文学学院）
Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection, and gene therapy. Here we elucidate the transport properties and conformational dynamics of linear and ring DNA molecules diffusing through entangled and crosslinked composite networks of actin and microtubules. We couple single-molecule conformational tracking with differential dynamic microscopy to reveal that ring and linear DNA exhibit surprisingly distin…
The actin cytoskeleton in living cells generates forces in conjunction with myosin motor proteins to directly and indirectly drive essential cellular processes. The semiflexible filaments of the cytoskeleton can respond nonlinearly to the collective action of motors. We here investigate mechanics and force generation in a model actin cytoskeleton, reconstituted in vitro, by observing the response and fluctuations of embedded micron-scale probe particles. Myosin mini-filaments can be modelled as force dipoles and give rise to deformations in the surrounding network of cross-linked actin. Anomal…
Using extensive numerical studies we demonstrate that absolute negative mobility of a Brownian particle (i.e. the net motion into the direction opposite to a constant biasing force acting around zero bias) does coexist with anomalous diffusion. The latter is characterized in terms of a nonlinear scaling with time of the mean-square deviation of the particle position. Such anomalous diffusion covers "coherent" motion (i.e. the position dynamics x(t) approaches in evolving time a constant dispersion), ballistic diffusion, subdiffusion, superdiffusion and hyperdiffusion. In providing evidence for…
Tracer particles immersed in suspensions of biological microswimmers such as E. coli or C. reinhardtii display phenomena unseen in conventional equilibrium systems, including strongly enhanced diffusivity relative to the Brownian value and non-Gaussian displacement statistics. In dilute, 3-dimensional suspensions, these phenomena have typically been explained by the hydrodynamic advection of point tracers by isolated microswimmers, while, at higher concentrations, correlations between pusher microswimmers such as E. coli can increase the effective diffusivity even further. Anisotropic tracers …
Crowded environments modify the diffusion of macromolecules, generally slowing their movement and inducing transient anomalous subdiffusion. The presence of obstacles also modifies the kinetics and equilibrium behavior of tracers. While previous theoretical studies of particle diffusion have typically assumed either impenetrable obstacles or binding interactions that immobilize the particle, in many cellular contexts bound particles remain mobile. Examples include membrane proteins or lipids with some entry and diffusion within lipid domains and proteins that can enter into membraneless organe…
By developing a molecular dynamics model of bacterial chemotaxis, we present the first investigation of tracer statistics in bacterial suspensions where chemotactic effects are considered. We demonstrate that the non-Gaussian statistics of full-coated tracer arises from the athermal bacterial noise. Moreover, Janus (half-coated) tracer performs a composite random walk combining power-law-tail distributed Lévy flights with Brownian jiggling at low coating concentration, but turns to an enhanced directional transport (EDT) when coating concentration is high. Unlike conventional self-propelled pa…
Active matter such as swarming bacteria and motile colloids exhibits exotic properties different from conventional equilibrium materials. Among these properties, the enhanced diffusion of tracer particles is generally deemed as a hallmark of active matter. Here, rather than spherical tracers, we investigate the diffusion of isolated ellipsoids in quasi-two-dimensional bacterial bath. Our study reveals a nonlinear enhancement of both translational and rotational diffusions. More importantly, we uncover an anomalous coupling between translation and rotation that is strictly prohibited in the cla…
Strong positional correlations between particles render the diffusion of a tracer particle in a single file anomalous and non-Markovian. While ensemble average observables of tracer particles are nowadays well understood, little is known about the statistics of the corresponding functionals, i.e. the time-average observables. It even remains unclear how the non-Markovian nature emerges from correlations between particle trajectories at different times. Here, we first present rigorous results for fluctuations and two-tag correlations of general bounded functionals of ergodic Markov processes wi…
