Coarse-graining intermittent intracellular transport: Two- and three-dimensional models

Lawley, Sean D.; Tuft, Marie; Brooks, Heather A.

doi:10.1103/physreve.92.042709

Cited by 6 publications

(16 citation statements)

References 35 publications

(54 reference statements)

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“…In specific biological studies (e.g. virus trafficking [59]), the drift term can be calibrated from local interactions with environment, including cytoplasmic intermediate filaments, actin filaments [60] and microtubule network [59,61], which compose the cytoskeleton.…”

Section: Brownian With Driftmentioning

confidence: 99%

An overview of diffusion models for intracellular dynamics analysis

Briane

Vimond

Kervrann

2019

Briefings in Bioinformatics

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We present an overview of diffusion models commonly used for quantifying the dynamics of intracellular particles (e.g. biomolecules) inside eukaryotic living cells. It is established that inference on the modes of mobility of molecules is central in cell biology since it reflects interactions between structures and determines functions of biomolecules in the cell. In that context, Brownian motion is a key component in short distance transportation (e.g. connectivity for signal transduction). Another dynamical process that has been heavily studied in the past decade is the motor-mediated transport (e.g. dynein, kinesin and myosin) of molecules. Primarily supported by actin filament and microtubule network, it ensures spatial organization and temporal synchronization in the intracellular mechanisms and structures. Nevertheless, the complexity of internal structures and molecular processes in the living cell influence the molecular dynamics and prevent the systematic application of pure Brownian or directed motion modeling. On the one hand, cytoskeleton density will hinder the free displacement of the particle, a phenomenon called subdiffusion. On the other hand, the cytoskeleton elasticity combined with thermal bending can contribute a phenomenon called superdiffusion. This paper discusses the basics of diffusion modes observed in eukariotic cells, by introducing the essential properties of these processes. Applications of diffusion models include protein trafficking and transport and membrane diffusion.

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Section: Brownian With Driftmentioning

confidence: 99%

An overview of diffusion models for intracellular dynamics analysis

Briane

Vimond

Kervrann

2019

Briefings in Bioinformatics

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“…Consider a finite set of N identical, evenly spaced microtubules radiating from the center of the disk [10,16]. That is, Ω 2 is partitioned into N equal slices, each of angular width / π ϒ ≡ N 2 (see figure 9), whose boundaries correspond to microtubules.…”

Section: The Diskmentioning

confidence: 99%

“…That is, Ω 2 is partitioned into N equal slices, each of angular width / π ϒ ≡ N 2 (see figure 9), whose boundaries correspond to microtubules. Following Lawley et al [16], we will derive an effective advection-diffusion equation for motor transport by considering the dynamics of a single molecular motor moving within a single slice…”

Section: The Diskmentioning

confidence: 99%

“…At this point the motor-cargo complex is reinserted into the slice at the current radius for some randomly selected angle between 0 and ϒ. If X(t) represents the motor's radial distance from the origin and ( ) θ t represents some angle between [ ] ϒ 0, , the motor's motion is described by the following system of SDEs [10,16]:…”

Section: The Diskmentioning

confidence: 99%

“…We find that for irreversible delivery the steady-state vesicle density decays according to a modified Bessel function, whereas a uniform density can be obtained when delivery is reversible. In case (ii) we derive PDEs for the motor density based on stochastic differential equations (SDEs) for individual motor dynamics in the 2D and 3D domains following along the lines of Lawley et al [16]. Throughout the paper we ignore boundary effects away from the source of motorcargo complexes.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Effects of cell geometry on reversible vesicular transport

Karamched

Bressloff²

2017

J. Phys. A: Math. Theor.

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A major question in cell biology concerns the biophysical mechanism underlying delivery of newly synthesized macromolecules to specific targets within a cell. A recent modeling paper investigated this phenomenon in the context of vesicular delivery to en passant synapses in neurons (Bressloff and Levien 2015 Phys. Rev. Lett.). It was shown how reversibility in vesicular delivery to synapses could play a crucial role in achieving uniformity in the distribution of resources throughout an axon, which is consistent with experimental observations in C. elegans and Drosophila. In this work we generalize the previous model by investigating steady-state vesicular distributions on a Cayley tree, a disk, and a sphere. We show that for irreversible transport on a tree, branching increases the rate of decay of the steady-state distribution of vesicles. On the other hand, the steady-state profiles for reversible transport are similar to the 1D case. In the case of higher-dimensional geometries, we consider two distinct types of radially-symmetric microtubular network: (i) a continuum and (ii) a discrete set. In the continuum case, we model the motorcargo dynamics using a phenomenologically-based advection-diffusion equation in polar (2D) and spherical (3D) coordinates. On the other-hand, in the discrete case, we derive the population model from a stochastic model of a single motor switching between ballistic motion and diffusion. For all of the geometries we find that reversibility in vesicular delivery to target sites allows for a more uniform distribution of vesicles, provided that cargocarrying motors are not significantly slowed by their cargo. In each case we characterize the loss of uniformity as a function of the dispersion in velocities.

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Simulating rolling paths and reorientation behavior of ball-rolling dung beetles

Yin

Zinn-Björkman

2020

Journal of Theoretical Biology

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Coarse-graining intermittent intracellular transport: Two- and three-dimensional models

Cited by 6 publications

References 35 publications

An overview of diffusion models for intracellular dynamics analysis

An overview of diffusion models for intracellular dynamics analysis

Effects of cell geometry on reversible vesicular transport

Simulating rolling paths and reorientation behavior of ball-rolling dung beetles

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