Abstract
Many reactions in complex fluids, e.g. signaling cascades in the cytoplasm of living cells, are governed by a diffusion-driven encounter of reactants. Yet, diffusion in complex fluids often exhibits an anomalous characteristic ('subdiffusion'). Since different types of subdiffusion have distinct effects on timing and equilibria of chemical reactions, a thorough determination of the reactants' type of random walk is key to a quantitative understanding of reactions in complex fluids. Here we introduce a straightforward and simple approach for determining the type of subdiffusion from single-particle tracking data. Unlike previous approaches, our method also is sensitive to transient subdiffusion phenomena, e.g. obstructed diffusion below the percolation threshold. We validate our strategy with data from experiment and simulation.
Highlights
A wide class of reactions in complex fluids, e.g. signaling cascades and protein complex formation in the cytoplasm of living cells, are governed by a diffusion-mediated encounter
Diffusion anomalies have been observed in many complex fluids with a high concentration of macromolecules (‘crowders’), e.g. in living cells[5,6,7,8,9,10,11,12] or in artificial fluids.[13,14,15,16,17]
Validating our approach with experimental trajectories obtained for nanobeads diffusing in complex fluids and simulations on transient subdiffusion of the OD type, we find that our approach is more sensitive in reporting on transient subdiffusion phenomena than previously considered methods
Summary
A wide class of reactions in complex fluids, e.g. signaling cascades and protein complex formation in the cytoplasm of living cells, are governed by a diffusion-mediated encounter. Diffusion in viscoelastic fluids or in porous media may be governed by compact random walks and, as a consequence, the reaction coefficient k may become time-dependent.[3,4]. Diffusion anomalies have been observed in many complex fluids with a high concentration of macromolecules (‘crowders’), e.g. in living cells[5,6,7,8,9,10,11,12] or in artificial fluids.[13,14,15,16,17] Defining subdiffusion via the MSD’s scaling, does not reveal the molecules’ type of random walk that may feature distinct consequences on chemical reactions. Three general types of subdiffusive random walks have been invoked to explain experimental observations of subdiffusion in complex/crowded fluids. Validating our approach with experimental trajectories obtained for nanobeads diffusing in complex fluids and simulations on transient subdiffusion of the OD type, we find that our approach is more sensitive in reporting on transient subdiffusion phenomena than previously considered methods
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