TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data

Reina, Francesco; Wigg, John M.A.; Dmitrieva, Mariia; Lefebvre, Joël; Rittscher, Jens; Eggeling, Christian

doi:10.12688/f1000research.54788.1

Cited by 6 publications

(2 citation statements)

References 34 publications

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“…Recent Bayesian model-assessment analysis [189][190][191] as well as modern machine-learning approaches [192][193][194][195][196][197][198] could then determine relative probabilities of possible diffusion models involved. In the end, certain predictions regarding the diffusion characteristics based on physical properties of the environment of crowders might be possible.…”

Section: B Physical Rationales and Further Discussionmentioning

confidence: 99%

Non-Gaussian, transiently anomalous, and ergodic self-diffusion of flexible dumbbells in crowded two-dimensional environments: Coupled translational and rotational motions

et al. 2021

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We employ Langevin-dynamics simulations to unveil non-Brownian and non-Gaussian center-ofmass self-diffusion of massive flexible dumbbell-shaped particles in crowded two-dimensional solutions. We also study the intra-dumbbell dynamics due to the relative motion of the two constituent elastically-coupled disks. Our main focus is on effects of the crowding fraction φ and the particle structure on the diffusion characteristics. We evaluate the time-averaged mean-squared displacement (TAMSD), the displacement probability-density function (PDF) and the displacement autocorrelation function (ACF) of the dimers. For the TAMSD at highly crowded conditions of dumbbells, e.g., we observe a transition from the short-time ballistic behavior, via an intermediate subdiffusive regime, to long-time Brownian-like spreading dynamics. The crowded system of dimers exhibits two distinct diffusion regimes distinguished by the scaling exponent of the TAMSD, the dependence of the diffusivity on φ, and the features of the displacement-ACF. We attribute these regimes to a crowding-induced transition from a viscous to a viscoelastic diffusion medium upon growing φ. We also analyze the relative motion in the dimers, finding that larger φ suppress their vibrations and yield strongly non-Gaussian PDFs of rotational displacements. For the diffusion coefficients D(φ) of translational and rotational motion of the dumbbells an exponential decay with φ for weak and a power-law D(φ) ∝ (φ − φ ) 2.4 for strong crowding is found. A comparison of simulation results with theoretical predictions for D(φ) is discussed and some relevant experimental systems are overviewed.

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Section: B Physical Rationales and Further Discussionmentioning

confidence: 99%

Non-Gaussian, transiently anomalous, and ergodic self-diffusion of flexible dumbbells in crowded two-dimensional environments: Coupled translational and rotational motions

et al. 2021

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show abstract

Section: B Physical Rationales and Further Discussionmentioning

confidence: 99%

Non-Gaussian, transiently anomalous and ergodic self-diffusion of flexible dumbbells in crowded two-dimensional environments: coupled translational and rotational motions

Klett

Cherstvy

Shin

et al. 2021

Preprint

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We employ Langevin-dynamics simulations to unveil non-Brownian and non-Gaussian center-of-mass self-diffusion of massive flexible dumbbell-shaped particles in crowded two-dimensional solutions. We also study the intra-dumbbell dynamics due to the relative motion of the two constituent elastically-coupled disks. Our main focus is on effects of the crowding fraction φ and the particle structure on the diffusion characteristics. We evaluate the time-averaged mean-squared displacement (TAMSD), the displacement probability-density function (PDF) and the displacement autocorrelation function (ACF) of the dimers. For the TAMSD at highly crowded conditions of dumbbells, e.g., we observe a transition from the short-time ballistic behavior, via an intermediate subdiffusive regime, to long-time Brownian-like spreading dynamics. The crowded system of dimers exhibits two distinct diffusion regimes distinguished by the scaling exponent of the TAMSD, the dependence of the diffusivity on φ, and the features of the displacement-ACF. We attribute these regimes to a crowding-induced transition from a viscous to a viscoelastic diffusion medium upon growing φ. We also analyze the relative motion in the dimers, finding that larger φ suppress their vibrations and yield strongly non-Gaussian PDFs of rotational displacements. For the diffusion coefficients D(φ) of translational and rotational motion of the dumbbells an exponential decay with φ for weak and a power-law D(φ) ∝ (φ - φ*)2.4 for strong crowding is found. A comparison of simulation results with theoretical predictions for D(φ) is discussed and some relevant experimental systems are overviewed.

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Slitflow: A Python framework for single-molecule dynamics and localization analysis

Ito¹,

Hirose²,

Tokunaga³

2023

SoftwareX

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TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data

Cited by 6 publications

References 34 publications

Non-Gaussian, transiently anomalous, and ergodic self-diffusion of flexible dumbbells in crowded two-dimensional environments: Coupled translational and rotational motions

Non-Gaussian, transiently anomalous, and ergodic self-diffusion of flexible dumbbells in crowded two-dimensional environments: Coupled translational and rotational motions

Non-Gaussian, transiently anomalous and ergodic self-diffusion of flexible dumbbells in crowded two-dimensional environments: coupled translational and rotational motions

Slitflow: A Python framework for single-molecule dynamics and localization analysis

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