Tracer diffusion inside fibrinogen layers

Cieśla, Michał; Gudowska–Nowak, Ewa; Sagués, Francesc; Sokolov, Igor M.

doi:10.1063/1.4862170

Cited by 10 publications

(10 citation statements)

References 33 publications

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“…A number of experimental [58,49], theoretical [59,60], and simulation [46,[61][62][63][64][65][66][67][68][69][70][71] studies in recent years were devoted to tackling various aspects of particle diffusion in crowded environments. From the simulation perspective, for instance, studies of tracer diffusion in non-inert [72], heterogeneously distributed and polydisperse [73], restrictively mobile [61] squishy [59], and anisotropic [74,75] obstacles were performed. The list of crowded three-and two-dimensional systems includes dense glassy systems of colloidal particles and hard spheres [76][77][78].…”

Section: Introductionmentioning

confidence: 99%

Self-subdiffusion in solutions of star-shaped crowders: non-monotonic effects of inter-particle interactions

2015

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We examine by extensive computer simulations the self-diffusion of anisotropic star-like particles in crowded two-dimensional solutions. We investigate the implications of the area coverage fraction f of the crowders and the crowder-crowder adhesion properties on the regime of transient anomalous diffusion. We systematically compute the mean squared displacement (MSD) of the particles, their time averaged MSD, and the effective diffusion coefficient. The diffusion is ergodic in the limit of long traces, such that the mean time averaged MSD converges towards the ensemble averaged MSD, and features a small residual amplitude spread of the time averaged MSD from individual trajectories. At intermediate time scales, we quantify the anomalous diffusion in the system. Also, we show that the translational-but not rotational-diffusivity of the particles D is a nonmonotonic function of the attraction strength between them. Both diffusion coefficients decrease as the power law D 1with the area fraction f occupied by the crowders and the critical value . f Our results might be applicable to rationalising the experimental observations of non-Brownian diffusion for a number of standard macromolecular crowders used in vitro to mimic the cytoplasmic conditions of living cells.

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Section: Introductionmentioning

confidence: 99%

Self-subdiffusion in solutions of star-shaped crowders: non-monotonic effects of inter-particle interactions

2015

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“…Considering the generalised Einstein relation, where the MSD can have a nonlinear dependence on time, i.e. ∆r 2 λ = 2dD λ t β λ , we can define the apparent exponent β λ as follows [43]:…”

Section: Model and Simulation Methodologymentioning

confidence: 99%

Diffusion of Globular Macromolecules in Liquid Crystals of Colloidal Cuboids

Tonti¹,

Daza²,

Patti³

2021

Preprint

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Macromolecular diffusion in dense colloidal suspensions is an intriguing topic of interdisciplinary relevance in Science and Engineering. While significant efforts have been undertaken to establish the impact of crowding on the dynamics of macromolecules, less clear is the role played by long-range ordering. In this work, we perform Dynamic Monte Carlo simulations to assess the importance of ordered crowding on the diffusion of globular macromolecules, here modelled as spherical tracers, in suspensions of colloidal cuboids. We first investigate the diffusion of such guest tracers in very weakly ordered host phases of cuboids and, by increasing density above the isotropic-to-nematic phase boundary, study the influence of long-range orientational ordering imposed by the occurrence of liquid-crystalline phases. To this end, we analyse a spectrum of dynamical properties that clarify the existence of slow and fast tracers and the extent of deviations from Gaussian behaviour. Our results unveil the existence of randomly oriented clusters of cuboids that display a relatively large size in dense isotropic phases, but are basically absent in the nematic phase. We believe that these clusters are responsible for a pronounced non-Gaussian dynamics that is much weaker in the nematic phase, where orientational ordering smooths out such structural heterogeneities.

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“…For example, recent theoretical advancements have extended Saxton's lattice-based results to lattice-free frameworks [30,35,36], including studying the role of obstacle orientation [37]. Progress has also been made by combining experimental and theoretical approaches, for example, studying overlapping circular and elliptical obstacles [38] and studying more complicated environments containing up to 15 different types of obstacles [31].…”

Section: Introductionmentioning

confidence: 98%

“…Such FDE models have been analyzed in various biological settings including chemical reactions [23], reaction fronts [22,24] and reaction-diffusion mechanisms [25]. We would like to emphasize that the group of studies described here, focusing explicitly on motion through crowded environments using experimental and simulation data [30][31][32][33][35][36][37][38][39], have not attempted to interpret their results using any kind of FDE framework. Conversely, the group of studies described here focusing on FDE models [21][22][23][24][25] have not attempted to connect the solution of any FDE model to measurements from any simulation or experiment which explicitly represents transport through a crowded environment.…”

Section: Introductionmentioning

confidence: 98%

Modeling transport through an environment crowded by a mixture of obstacles of different shapes and sizes

Ellery

Baker

McCue

et al. 2016

Physica A: Statistical Mechanics and its Applications

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h i g h l i g h t s• Stochastic simulations of individual and collective motion through a crowded environment. • Crowded environments populated by mixtures of obstacles of different shapes and sizes.• Transport properties depend on the obstacle volume fraction and details of the obstacle shape and size distribution. • Standard fractional diffusion equation descriptions ought to be used with care. a b s t r a c tMany biological environments are crowded by macromolecules, organelles and cells which can impede the transport of other cells and molecules. Previous studies have sought to describe these effects using either random walk models or fractional order diffusion equations. Here we examine the transport of both a single agent and a population of agents through an environment containing obstacles of varying size and shape, whose relative densities are drawn from a specified distribution. Our simulation results for a single agent indicate that smaller obstacles are more effective at retarding transport than larger obstacles; these findings are consistent with our simulations of the collective motion of populations of agents. In an attempt to explore whether these kinds of stochastic random walk simulations can be described using a fractional order diffusion equation framework, we calibrate the solution of such a differential equation to our averaged agent density information. Our approach suggests that these kinds of commonly used differential equation models ought to be used with care since we are unable to match the solution of a fractional order diffusion equation to our data in a consistent fashion over a finite time period.

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Tracer diffusion inside fibrinogen layers

Cited by 10 publications

References 33 publications

Self-subdiffusion in solutions of star-shaped crowders: non-monotonic effects of inter-particle interactions

Self-subdiffusion in solutions of star-shaped crowders: non-monotonic effects of inter-particle interactions

Diffusion of Globular Macromolecules in Liquid Crystals of Colloidal Cuboids

Modeling transport through an environment crowded by a mixture of obstacles of different shapes and sizes

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