Fractional Brownian motion in crowded fluids

Ernst, Dominique; Hellmann, Marcel; Köhler, Jürgen; Weiß, Matthias

doi:10.1039/c2sm25220a

Cited by 151 publications

(129 citation statements)

References 30 publications

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“…Other than the mechanisms in confined geometries that lead to subdiffusive behaviors (corralled, hop, and cage diffusion, as discussed in Fig. S8), mechanisms in ''unconfined'' geometries, such as continuous time random walk (93)(94)(95), fractional Brownian motion (96,97), and random walk on a fractal structure (98), can also give subdiffusive MSD curves (11,41,99). A sophisticated differentiation decision tree, such as the one proposed by Meroz's group (41), should be established and rigorously tested.…”

Section: Challenges In Molecular Trajectory Analysismentioning

confidence: 99%

Segmentation of 3D Trajectories Acquired by TSUNAMI Microscope: An Application to EGFR Trafficking

Liu

Perillo

Liu

et al. 2016

Biophysical Journal

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Whereas important discoveries made by single-particle tracking have changed our view of the plasma membrane organization and motor protein dynamics in the past three decades, experimental studies of intracellular processes using singleparticle tracking are rather scarce because of the lack of three-dimensional (3D) tracking capacity. In this study we use a newly developed 3D single-particle tracking method termed TSUNAMI (Tracking of Single particles Using Nonlinear And Multiplexed Illumination) to investigate epidermal growth factor receptor (EGFR) trafficking dynamics in live cells at 16/43 nm (xy/z) spatial resolution, with track duration ranging from 2 to 10 min and vertical tracking depth up to tens of microns. To analyze the long 3D trajectories generated by the TSUNAMI microscope, we developed a trajectory analysis algorithm, which reaches 81% segment classification accuracy in control experiments (termed simulated movement experiments). When analyzing 95 EGF-stimulated EGFR trajectories acquired in live skin cancer cells, we find that these trajectories can be separated into three groups-immobilization (24.2%), membrane diffusion only (51.6%), and transport from membrane to cytoplasm (24.2%). When EGFRs are membrane-bound, they show an interchange of Brownian diffusion and confined diffusion. When EGFRs are internalized, transitions from confined diffusion to directed diffusion and from directed diffusion back to confined diffusion are clearly seen. This observation agrees well with the model of clathrin-mediated endocytosis.

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Section: Challenges In Molecular Trajectory Analysismentioning

confidence: 99%

Segmentation of 3D Trajectories Acquired by TSUNAMI Microscope: An Application to EGFR Trafficking

Liu

Perillo

Liu

et al. 2016

Biophysical Journal

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“…Yet explanations as to why differ widely. Using a range of different techniques, Weiss et al 24,53 have established that the anomalous diffusion observed in crowded dextran solutions is an ergodic process (ruling out CTRW), and have proposed that it was consistent with FBM. In another series of FCS studies, Waxham et al 50,51 have argued that the anomalous behaviour observed arose from heterogeneities in the micro-environment experienced by the tracer particles, leading to a discrete distributions of diffusion coefficients.…”

Section: The Anomalous Yet Brownian Motion Of Proteins In Crowded Dementioning

confidence: 99%

“…Other studies in similar systems have also suggested that protein diffusion in crowded marginally entangled polymer solutions deviates from simple Fickian diffusion 15,24,[50][51][52][53] . This, however, remains somewhat controversial, as mobile obstacles are not expected to produce anomalous diffusion 23 .…”

Section: Introductionmentioning

confidence: 99%

“…In these conditions, the polymer chains are entangled, yet fully mobile, as was shown using different techniques 16,56 . This system (tracer proteins in marginally entangled dextran solutions) has been repeatedly studied by us and others and shown to support anomalous diffusion 16,24,50,51,53 . Yet explanations as to why differ widely.…”

Section: The Anomalous Yet Brownian Motion Of Proteins In Crowded Dementioning

confidence: 99%

“…Gaussian models of anomalous diffusion, such as the FBM model, have a Gaussian propagator combined with an MSD that is sublinear in time 53,86 . Others, like the continuous time random walk (CTRW) model 69,87 or the obstructed diffusion model 23,[88][89][90][91] have neither a Gaussian propagator nor a linear MSD.…”

Section: On the Importance Of Characterizing Complex Diffusion Procesmentioning

confidence: 99%

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Characterizing anomalous diffusion in crowded polymer solutions and gels over five decades in time with variable-lengthscale fluorescence correlation spectroscopy

et al. 2016

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The diffusion of macromolecules in cells and in complex fluids is often found to deviate from simple Fickian diffusion. One explanation offered for this behavior is that molecular crowding renders diffusion anomalous, where the mean-squared displacement of the particles scales as r 2 ∝ t α with α < 1. Unfortunately, methods such as fluorescence correlation spectroscopy (FCS) or fluorescence recovery after photobleaching (FRAP) probe diffusion only over a narrow range of lengthscales and cannot directly test the dependence of the mean-squared displacement (MSD) on time. Here we show that variable-lengthscale FCS (VLS-FCS), where the volume of observation is varied over several orders of magnitude, combined with a numerical inversion procedure of the correlation data, allows retrieving the MSD for up to five decades in time, bridging the gap between diffusion experiments performed at different lengthscales. In addition, we show that VLS-FCS provides a way to assess whether the propagator associated with the diffusion is Gaussian or non-Gaussian. We used VLS-FCS to investigate two systems where anomalous diffusion had been previously reported. In the case of dense cross-linked agarose gels, the measured MSD confirmed that the diffusion of small beads was anomalous at short lengthscales, with a cross-over to simple diffusion around ≈ 1 µm, consistent with a caged diffusion process. On the other hand, for solutions crowded with marginally entangled dextran molecules, we uncovered an apparent discrepancy between the MSD, found to be linear, and the propagators at short lengthscales, found to be non-Gaussian. These contradicting features call to mind the "anomalous, yet Brownian" diffusion observed in several biological systems, and the recently proposed "diffusing diffusivity" model.

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