Particle tracking in living cells: a review of the mean square displacement method and beyond

2013 ◽  
Vol 52 (5) ◽  
pp. 425-443 ◽  
Author(s):  
Naama Gal ◽  
Diana Lechtman-Goldstein ◽  
Daphne Weihs
Keyword(s):  
Particle Tracking ◽  
Mean Square Displacement ◽  
Living Cells ◽  
Mean Square ◽  
Displacement Method ◽  
The Mean

scholarly journals A simple and powerful analysis of lateral subdiffusion using single particle tracking

2017 ◽  
Author(s):  
Marianne Renner ◽  
Lili Wang ◽  
Sabine Levi ◽  
Laetitia Hennekinne ◽  
Antoine Triller
Keyword(s):  
Particle Tracking ◽  
Lipid Composition ◽  
Mean Square Displacement ◽  
Complex Mixture ◽  
Lateral Diffusion ◽  
Single Particle Tracking ◽  
Mean Square ◽  
The Mean ◽  
Very High ◽  
Lipid Probe

AbstractIn biological membranes many factors such as cytoskeleton, lipid composition, crowding and molecular interactions deviate lateral diffusion from the expected random walks. These factors have different effects on diffusion but act simultaneously so the observed diffusion is a complex mixture of diffusive behaviors (directed, >Brownian, anomalous or confined). Therefore commonly used approaches to quantify diffusion based on averaging of the displacements, such as the mean square displacement, are not adapted to the analysis of this heterogeneity. We introduce a new parameter, the packing coefficient Pc, which gives an estimate of the degree of free movement that a molecule displays in a period of time independently of its global diffusivity. Applying this approach to two different situations (diffusion of a lipid probe and trapping of receptors at synapses), we show that Pc detected and localized temporary changes of diffusive behavior both in time and in space. More importantly, it allowed the detection of periods with very high confinement (~immobility), their frequency and duration, and thus it can be used to calculate the effective kon and koff of scaffolding interactions such those that immobilize receptors at synapses.

scholarly journals Reconstruction of Diffusion Coefficients and Power Exponents from Single Lagrangian Trajectories

Fluids ◽  
2021 ◽  
Vol 6 (3) ◽  
pp. 111
Author(s):  
Leonid M. Ivanov ◽  
Collins A. Collins ◽  
Tetyana Margolina
Keyword(s):  
Black Sea ◽  
Diffusion Coefficients ◽  
Current System ◽  
Mean Square Displacement ◽  
California Current ◽  
The Black Sea ◽  
Mean Square ◽  
California Current System ◽  
The Mean ◽  
Non Gaussian

Using discrete wavelets, a novel technique is developed to estimate turbulent diffusion coefficients and power exponents from single Lagrangian particle trajectories. The technique differs from the classical approach (Davis (1991)’s technique) because averaging over a statistical ensemble of the mean square displacement (<X2>) is replaced by averaging along a single Lagrangian trajectory X(t) = {X(t), Y(t)}. Metzler et al. (2014) have demonstrated that for an ergodic (for example, normal diffusion) flow, the mean square displacement is <X2> = limT→∞τX2(T,s), where τX2 (T, s) = 1/(T − s) ∫0T−s(X(t+Δt) − X(t))2 dt, T and s are observational and lag times but for weak non-ergodic (such as super-diffusion and sub-diffusion) flows <X2> = limT→∞≪τX2(T,s)≫, where ≪…≫ is some additional averaging. Numerical calculations for surface drifters in the Black Sea and isobaric RAFOS floats deployed at mid depths in the California Current system demonstrated that the reconstructed diffusion coefficients were smaller than those calculated by Davis (1991)’s technique. This difference is caused by the choice of the Lagrangian mean. The technique proposed here is applied to the analysis of Lagrangian motions in the Black Sea (horizontal diffusion coefficients varied from 105 to 106 cm2/s) and for the sub-diffusion of two RAFOS floats in the California Current system where power exponents varied from 0.65 to 0.72. RAFOS float motions were found to be strongly non-ergodic and non-Gaussian.

Molecular Dynamics Study of Microscopic Mechanism of Diffusion in Li2SiO3 System

1991 ◽  
Vol 46 (7) ◽  
pp. 616-620 ◽  
Author(s):  
Junko Habasaki
Keyword(s):  
Molecular Dynamics ◽  
Coordination Number ◽  
Md Simulation ◽  
Mean Square Displacement ◽  
Mean Square ◽  
Lithium Ions ◽  
Microscopic Mechanism ◽  
Trapping Model ◽  
The Mean

MD simulation has been performed to learn the microscopic mechanism of diffusion of ions in the Li2SiO3 system. The motion of lithium ions can be explained by the trapping model, where lithium is trapped in the polyhedron and moves with fluctuation of the coordination number. The mean square displacement of lithium was found to correlate well with the net changes in coordination number.

THE EFFECT OF PREMELTING: STUDY FOR SEMI-INFINITE CRYSTALS AND NANO-SYSTEMS

1994 ◽  
Vol 08 (24) ◽  
pp. 3411-3422 ◽  
Author(s):  
W. SCHOMMERS
Keyword(s):  
Pair Correlation ◽  
Mean Square Displacement ◽  
Phonon Density ◽  
Mean Square ◽  
Phonon Density Of States ◽  
Molecular Dynamics Calculations ◽  
Theory Of Melting ◽  
The Mean ◽  
Dynamical Properties ◽  
Reliable Interaction

The effect of premelting is of particular interest in connection with the theory of melting. In this paper, we discuss the structural and dynamical properties of the surfaces of semi-infinite crystals as well as of nano-clusters, which show the effect of premelting. The investigations are based on molecular-dynamics calculations: different models are used for the systematic study of the effect of premelting. In particular, the behaviour of the following functions have been studied: pair correlation function, generalized phonon density of states, and the mean-square displacement as a function of time. The calculations have been done for krypton since for this substance a reliable interaction potential is available.

Non-Markovian effect of the fractional damping environment and Newton’s second law of motion

2018 ◽  
Vol 32 (19) ◽  
pp. 1850210
Author(s):  
Chun-Yang Wang ◽  
Zhao-Peng Sun ◽  
Ming Qin ◽  
Yu-Qing Xu ◽  
Shu-Qin Lv ◽  
...  
Keyword(s):  
Diffusion Process ◽  
Mean Square Displacement ◽  
Dynamical Analysis ◽  
Second Law ◽  
Mean Square ◽  
Fractional Damping ◽  
Dynamical Mechanism ◽  
Brownian Particles ◽  
The Mean ◽  
Dissipative Environments

We report, in this paper, a recent study on the dynamical mechanism of Brownian particles diffusing in the fractional damping environment, where several important quantities such as the mean square displacement (MSD) and mean square velocity are calculated for dynamical analysis. A particular type of backward motion is found in the diffusion process. The reason of it is analyzed intrinsically by comparing with the diffusion in various dissipative environments. Results show that the diffusion in the fractional damping environment obeys the Langevin dynamics which is quite different form what is expected.

Transient Response of a Shear Beam to Correlated Random Boundary Excitation

1977 ◽  
Vol 44 (3) ◽  
pp. 487-491 ◽  
Author(s):  
S. F. Masri ◽  
F. Udwadia
Keyword(s):  
Time Delays ◽  
Spectral Characteristics ◽  
Mean Square Displacement ◽  
Dimensionless Time ◽  
Mean Square ◽  
Random Boundary ◽  
Mean Square Response ◽  
Shear Beam ◽  
The Mean ◽  
Support Motion

The transient mean-square displacement, slope, and relative motion of a viscously damped shear beam subjected to correlated random boundary excitation is presented. The effects of various system parameters including the spectral characteristics of the excitation, the delay time between the beam support motion, and the beam damping have been investigated. Marked amplifications in the mean-square response are shown to occur for certain dimensionless time delays.

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