, quantifying the dynamics of intracellular particles (e.g. biomolecules) inside living cells
, This paper summarizes the mathematical definitions of superdiffusion, free diffusion and subdiffusion, wellgrounded in Einstein's and Langevin's theories
, ? Applications of diffusion models include protein trafficking and transport, and membrane diffusion
Single particle tracking. Analysis of diffusion and flow in two-dimensional systems, Biophys J, vol.60, p.910, 1991. ,
Single-particle tracking: applications to membrane dynamics, Annu Rev Biophys Biomol Struct, vol.26, pp.373-99, 1997. ,
Statistical analysis of particle trajectories in living cells, Phys Rev E, vol.97, p.62121, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01961971
Molecular motors pulling cargos in the viscoelastic cytosol: power strokes beat subdiffusion, Phys Chem Chem Phys, vol.16, pp.16524-16559, 2014. ,
The random walk's guide to anomalous diffusion: a fractional dynamics approach, Phys Rep, vol.339, pp.1-77, 2000. ,
Statistical methods for large ensembles of super-resolution stochastic single particle trajectories in cell biology, Annu Rev Stat Appl, vol.4, pp.189-223, 2017. ,
Anomalous diffusion due to obstacles: a Monte Carlo study, Biophys J, vol.66, p.394, 1994. ,
Anomalous diffusion due to hindering by mobile obstacles undergoing brownian motion or Ornstein-Ulhenbeck processes, Phys Rev E, vol.89, p.22708, 2014. ,
Viscoelastic subdiffusion: from anomalous to normal, Phys Rev E, vol.80, p.46125, 2009. ,
Constrained diffusion or immobile fraction on cell surfaces: a new interpretation, Biophys J, vol.70, p.2767, 1996. ,
Quantitative analysis of single particle trajectories: mean maximal excursion method, Biophys J, vol.98, pp.1364-72, 2010. ,
Particle tracking in living cells: a review of the mean square displacement method and beyond, Rheologica Acta, vol.52, pp.425-468, 2013. ,
Spattrack: an imaging toolbox for analysis of vesicle motility and distribution in living cells, Traffic, vol.15, pp.1406-1435, 2014. ,
Model comparison and assessment for single particle tracking in biological fluids, J Am Stat Assoc, vol.111, pp.1413-1439, 2016. ,
Mean square displacement analysis of singleparticle trajectories with localization error: Brownian motion in an isotropic medium, Phys Rev E, vol.82, p.41914, 2010. ,
Numerical analysis of particle trajectories in living cells under uncertainty conditions, Biophysics, vol.60, pp.810-817, 2015. ,
Bayesian approach to msdbased analysis of particle motion in live cells, Biophys J, vol.103, pp.616-642, 2012. ,
A toolbox for determining subdiffusive mechanisms, Phys Rep, vol.573, pp.1-29, 2015. ,
Course in Stochasic Processes, 1981. ,
Introduction to Stochastic Calculus with Applications, 2012. ,
Fractional brownian motions, fractional noises and applications, SIAM Rev, vol.10, pp.422-459, 1968. ,
Mouvement brownien et calcul d'Itô: Cours et Exercices corrigés, 2008. ,
The local structure of turbulence in incompressible viscous fluid for very large Reynolds numbers, Dokl Akad Nauk SSSR, vol.30, pp.299-303, 1941. ,
Long-term storage capacity of reservoirs, Trans Amer Soc Civil Eng, vol.116, pp.770-808, 1951. ,
Stochastic analysis of the fractional brownian motion, Potential Anal, vol.10, pp.177-214, 1999. ,
Stochastic analysis, rough path analysis and fractional brownian motions, Probab Theory Relat Fields, vol.122, pp.108-148, 2002. ,
URL : https://hal.archives-ouvertes.fr/hal-00266874
On the motion of small particles suspended in liquids at rest required by the molecular-kinetic theory of heat, Ann Phys, vol.17, pp.549-60, 1905. ,
Anomalous transport in the crowded world of biological cells, Rep Prog Phys, vol.76, p.46602, 2013. ,
on liquid diffusion, Philos Mag Ser, vol.4, pp.30-39 ,
Sur la théorie du mouvement brownien, C R Acad Sci, vol.146, p.530, 1908. ,
Stochastic modeling in nanoscale biophysics: subdiffusion within proteins, Ann Appl Stat, vol.2, pp.501-536, 2008. ,
, Theory and Applications of Stochastic Processes: An Analytical Approach, vol.170, 2009.
On the theory of the brownian motion, Phys Rev, vol.36, p.823, 1930. ,
, Stochastic Processes in Physics and Chemistry, vol.1, 1992.
On the physics of media that are composed of free and perfectly elastic molecules in a state of motion, Philos Trans R Soc Lond A, vol.183, pp.1-79, 1892. ,
, Stochastic Processes in Cell Biology, vol.41, 2014.
Models and anomalous diffusion in crowded environments, Soft Matter, vol.8, pp.9043-52, 2012. ,
In vivo anomalous diffusion and weak ergodicity breaking of lipid granules, Phys Rev Lett, vol.106, p.48103, 2011. ,
Bacterial chromosomal loci move subdiffusively through a viscoelastic cytoplasm, Phys Rev Lett, vol.104, p.238102, 2010. ,
Nonequilibrium statistical mechanics, 2001. ,
Introduction to modern statistical mechanics, 1987. ,
Anomalous transit-time dispersion in amorphous solids, Phys Rev B, vol.12, p.2455, 1975. ,
Modelling axon growing using CTRW, 2015. ,
Diffusion in disordered media, Adv Phys, vol.36, pp.695-798, 1987. ,
Crowding effects on diffusion in solutions and cells, Annu Rev Biophys, vol.37, pp.247-63, 2008. ,
Narrow escape through a funnel and effective diffusion on a crowded membrane, Phys Rev E, vol.84, p.21906, 2011. ,
Conductivity exponent and backbone dimension in 2-D percolation, Physica A, vol.262, pp.251-63, 1999. ,
Paradigm shift of the plasma membrane concept from the two-dimensional continuum fluid to the partitioned fluid: high-speed singlemolecule tracking of membrane molecules, Annu Rev Biophys Biomol Struct, vol.34, pp.351-78, 2005. ,
Confined lateral diffusion of membrane receptors as studied by single particle tracking (nanovid microscopy). Effects of calcium-induced differentiation in cultured epithelial cells, Biophys J, vol.65, p.2021, 1993. ,
Lateral diffusion in an archipelago. Singleparticle diffusion, Biophys J, vol.64, pp.1766-80, 1993. ,
A note on confined diffusion, Physica A, vol.377, pp.24-32, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-01553040
Brownian motion in a field of force and the diffusion model of chemical reactions, Phys Ther, vol.7, pp.284-304, 1940. ,
Modélisation et méthodes d'analyse de la diffusion et agrégation au niveau moléculaire pour l'organisation sous-cellulaire, 2013. ,
Routes, destinations and delays: recent advances in ampa receptor trafficking, Trends Neurosci, vol.34, pp.258-68, 2011. ,
Brownian motors: noisy transport far from equilibrium, Phys Rep, vol.361, pp.57-265, 2002. ,
How molecular motors work in the crowded environment of living cells: coexistence and efficiency of normal and anomalous transport, PLoS One, vol.9, p.91700, 2014. ,
Coordinated hydrolysis explains the mechanical behavior of kinesin, Biophys J, vol.68, p.202, 1995. ,
A macroscopic description of biomolecular transport, J Math Biol, vol.41, pp.189-206, 2000. ,
Effective motion of a virus trafficking inside a biological cell, SIAM J Appl Math, vol.68, pp.1146-67, 2008. ,
Transport by active filaments, Europhys Lett, vol.31, pp.69-74, 1995. ,
Coarse-graining intermittent intracellular transport: two-and three-dimensional models, Phys Rev E, vol.92, p.42709, 2015. ,
, Rev Mod Phys, vol.87, pp.483-530, 2015.
First steps in random walks: from tools to applications, 2011. ,
Scale-invariant motion in intermittent chaotic systems, Phys Rev E, vol.47, p.851, 1993. ,
Random walks with random velocities, Phys Rev E, vol.78, p.11119, 2008. ,
Memoryless self-reinforcing directionality in endosomal active transport within living cells, Nat Mater, vol.14, p.589, 2015. ,
Memory effects and Lévy walk dynamics in intracellular transport of cargoes, Phys Rev E, vol.98, p.42136, 2018. ,
Non-Markovian intracellular transport with sub-diffusion and runlength dependent detachment rate, PLoS One, vol.13, p.207436, 2018. ,
Objective comparison of particle tracking methods, Nat Methods, vol.11, p.281, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-00932869
Stochastic models of intracellular transport, Rev Mod Phys, vol.85, p.135, 2013. ,
Non-specific interactions govern cytosolic diffusion of nanosized objects in mammalian cells, Nat Mater, vol.17, pp.740-746, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01871099
Accounting for diffusion in agent based models of reaction-diffusion systems with application to cytoskeletal diffusion, PLoS One, vol.6, p.25306, 2011. ,
Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid marcromolecular crowdoing effect, PLoS Comput Biol, vol.9, p.1003038, 2013. ,
Single molecule simulation of diffusion and enzyme kinetics, J Phys Chem B, vol.120, pp.3809-3829, 2016. ,