Diffusion of tracer particles in early growing biofilms a computer simulation study.

Optical tracking in vivo experiments reveal that diffusion of particles in biological cells is strongly enhanced in the presence of ATP and the experimental data for animal cells could previously be reproduced within a phenomenological model of a gel with myosin motors acting within it (Fodor É. et al., EPL, 110 (2015) 48005). Here, the two-fluid model of a gel is considered where active macromolecules, described as force dipoles, cyclically operate both in the elastic and the fluid components. Through coarse-graining, effective equations of motions for idealized tracer particles displaying local deformations and local fluid flows are derived. The equation for deformation tracers coincides with the earlier phenomenological model and thus confirms it. For flow tracers, diffusion enhancement caused by active force dipoles in the fluid component, and thus due to metabolic activity, is found. The latter effect may explain why ATP-dependent diffusion enhancement could also be observed in bacteria that lack molecular motors in their skeleton or when the activity of myosin motors was chemically inhibited in eukaryotic cells.

We have investigated an alternative to the standard periodic boundary conditions for simulating the diffusion of tracer particles in a polymer gel by performing Brownian dynamics simulations using spherical boundary conditions. The gel network is constructed by randomly distributing tetravalent cross-linking nodes and connecting nearest pairs. The final gel structure is characterised by the radial distribution functions, chain lengths and end-to-end distances, and the pore size distribution. We have looked at the diffusion of tracer particles with a wide range of sizes, diffusing in both static and dynamic networks of two different volume fractions. It is quantitatively shown that the dynamical effect of the network becomes more important in facilitating the diffusional transport for larger particle sizes, and that one obtains a finite diffusion also for particle sizes well above the maximum in the pore size distribution.

Diffusion of tracer particles in active bath has attracted extensive attention in recent years. So far, most studies have considered isotropic spherical tracer particles, while the diffusion of anisotropic particles has rarely been involved. Here we investigate the diffusion dynamics of a rigid rod tracer in a bath of active particles by using Langevin dynamics simulations in a two-dimensional space. Particular attention is paid to how the translation (rotation) diffusion coefficient DT (DR) change with the length of rod L and active strength Fa. In all cases, we find that rod exhibits superdiffusion behavior in a short time scale and returns to normal diffusion in the long time limit. Both DT and DR increase with Fa, but interestingly, a nonmonotonic dependence of DT (DR) on the rod length has been observed. We have also studied the translation-rotation coupling of rod, and interestingly, a negative translation-rotation coupling is observed, indicating that rod diffuses more slowly in the parallel direction compared to that in the perpendicular direction, a counterintuitive phenomenon that would not exist in an equilibrium counterpart system. Moreover, this anomalous (diffusion) behavior is reentrant with the increase of Fa, suggesting two competitive roles played by the active feature of bath particles.

Mucus plays an important role in the protection of the epithelial cells from various pathogens and low pH environments besides helping in the absorption of nutrients. Alteration of the rheology of the mucus layer leads to various disease conditions such as cystic fibrosis, Crohn's disease, and gastric ulcers, among others. Importantly, mucus consists of various mucins along with proteins such as immunoglobulin, lysozyme, and albumin. In the present study, we explore the effect of pH on the interactions between bovine serum albumin (BSA) and porcine gastric mucins using diffusing wave spectroscopy (DWS). The study unveils that BSA actively binds with mucin to form mucin-BSA complexes, which is largely driven by electrostatic interactions. Interestingly, such physical interactions significantly alter the microrheology of these biomaterials, which is indicated by a reduction in the diffusivity of tracer particles in DWS. An array of DWS experiments suggests that the interaction between mucin and BSA is the highest at pH 7.4 and the least at pH 3. Further analyses using atomic force microscopy showed the formation of a compact cross-linked colloidal network of mucin-BSA complexes at pH 7.4, which is the main reason for the reduction in the diffusivity of the tracer particles in DWS. Furthermore, the circular dichroism analysis revealed that the secondary structures of mucin-BSA complexes are markedly different from those of only mucin at pH 7.4. Importantly, such a difference has not been observed at pH 3, which confirms that largely electrostatic interactions drive the formation of mucin-BSA complexes at neutral pH. In such a scenario, the presence of Ca2+ ions is also found to facilitate bridging between BSA molecules, which is also reflected in the microrheology of the suspension of BSA-mucin complexes.

A phenomenological theory of diffusion and cross-diffusion of tracer particles in concentrated hard-sphere suspensions is developed. Expressions for the diffusion coefficients as functions of the host particle volume fraction are obtained up to the close-packing limit. In concentrated systems the tracer diffusivity decreases because of the reduced pore space available for diffusion. The tracer diffusivity can be modelled by a Stokes–Einstein equation with an effective viscosity that depends on the pore size. Tracer diffusion and segregation during sedimentation cease at a critical trapping volume fraction corresponding to a tracer glass transition. The tracer cross-diffusion coefficient, however, increases near the glass transition and diverges in the close-packed limit.

Introduction Previous studies, e.g., by NMR,1,2 fluorescence pho­ tobleaching,3 and dynamic light scattering (DLS),4,5 have shown that the diffusion of noninteracting probe particles in polymer solutions and gels primarily de­ pends on the polymer concentration and the size of the probe. In interpreting these results, it is widely assumed that polymer gels behave like semidilute polymer solu­ tions, while the structural differences due to the pres­ ence of permanent cross-links are ignored. These dif­ ferences have been revealed and characterized by scat­ tering experiments, such as small-angle neutron scat­ tering (SANS) and light scattering, which show signifi­ cant structural rearrangement of the polymer chains upon gelation.6 This observation is corroborated by results from elasticity measurements, indicating that gelation is accompanied by an increase in the elastic modulus of the samples.7 However, the effect of crosslinking on the diffusion of small particles in a gel has yet to be fully elucidated and understood.4,7 In this paper, we demonstrate how fluorescence correlation spectroscopy (FCS) can provide quantitative measurements on the diffusion of particles in polymer systems. We apply FCS to measure the diffusion time of fluorescent TAMRA molecules in poly(vinyl alcohol) (PVA) solutions and gels prepared at various polymer concentrations and cross-link densities. The measure­ ments indicate that the diffusion of probe particles is affected not only by the polymer concentration but also by the cross-link density of the gel. Remarkably, we find a simple linear relation between the diffusion times and the elastic moduli of the same gels.

The diffusion of tracer particles in 3D macromolecular crowded media has been studied using two methodologies, simulation and experimental, with the aim of comparing their results. First, the diffusion of a tracer in an obstructed 3D lattice with mobile and big size obstacles has been analyzed through a Monte Carlo (MC) simulation procedure. Secondly, fluorescence recovery after photobleaching (FRAP) experiments have been carried out to study the diffusion of a model protein (alpha-chymotrypsin) in in vitro crowded solution where two type of Dextran molecules are used as crowder agents. To facilitate the comparison, the relative size between the tracer and the crowder is the same in both studies. The results indicate a qualitative agreement between the diffusional behaviors observed in the two studies. The dependence of the anomalous diffusion exponent and the limiting diffusion coefficient on the obstacle size and excluded volume shows, in both cases, a similar tendency. The introduction of a reduced mobility parameter in the simulation model accounting for the short-range tracer–obstacle interactions allows obtaining a quantitative agreement between the limiting diffusion coefficient values yielded by both procedures. The simulation–experiment quantitative agreement for the anomalous diffusion exponent requires further improvements. As far as we know, this is the first reported work where both techniques are used in parallel to study the diffusion in macromolecular crowded media.

The ideas of advection and diffusion of sediment particles are probabilistic constructs that emerge when the Master equation, a precise, probabilistic description of particle conservation, is approximated as a Fokker–Planck equation. The diffusive term approximates nonlocal transport. It ‘looks’ upstream and downstream for variations in particle activity and velocities, whose effects modify the advective term. High‐resolution measurements of bedload particle motions indicate that the mean squared displacement of tracer particles, when treated as a virtual plume, primarily reflects a nonlinear increase in the variance in hop distances with increasing travel time, manifest as apparent anomalous diffusion. In contrast, an ensemble calculation of the mean squared displacement involving paired coordinate positions independent of starting time indicates a transition from correlated random walks to normal (Fickian) diffusion. This normal behavior also is reflected in the particle velocity autocorrelation function. Spatial variations in particle entrainment produce a flux from sites of high entrainment toward sites of low entrainment. In the case of rain splash transport, this leads to topographic roughening, where differential rain splash beneath the canopy of a desert shrub contributes to the growth of a soil mound beneath the shrub. With uniform entrainment, rain splash transport, often described as a diffusive process, actually represents an advective particle flux that is proportional to the land surface slope. Particle diffusion during both bedload and rain splash transport involves motions that mostly are patchy, intermittent and rarefied. The probabilistic framework of the Master equation reveals that continuous formulations of the flux and its divergence (the Exner equation) represent statistically expected behavior, analogous to Reynolds‐averaged conditions. Key topics meriting clarification include the mechanical basis of particle diffusion, effects of rarefied conditions involving patchy, intermittent motions, and effects of rest times on diffusion of tracer particles and particle‐borne substances. Copyright © 2016 John Wiley & Sons, Ltd.

The connection between the diffusion of passive tracer particles and the anomalous turbulent flux in electrostatic drift-wave turbulence is investigated by direct numerical solutions of the 2D Hasegawa–Wakatani equations. The probability density functions for the point-wise and flux surface averaged turbulent particle flux are measured and compare well to a folded Gaussian, respectively a log-normal distribution. By following a large number of passive tracer particles we evaluate the diffusion coefficient based on the particle dispersion. It is found that the particle diffusion coefficient is in good agreement with the one derived from the turbulent E×B-flux by using Fick’s law. Employing the Lagrangian conservation of the “Potential Vorticity” in the Hasegawa–Wakatani equations, the analytical support for this result is obtained. The transport estimated by passive tracer dispersion and turbulent plasma flux are found to coincide.

Evanescent wave microscopy is used to study the dynamics of probe particles inside a laponite suspension, when the size of the latex probes is of the order of the diameter of the laponite disks. A correlation procedure is introduced that allows us to study quantitatively the diffusion of small probes. For all studied sizes, the motion exhibits two modes: a fast relaxation mode and a slow relaxation mode. In the fast relaxation mode, the probes diffuse in a viscous medium, whose viscosity does not depend on the diameter of the probes and is slightly larger than the viscosity of water. Then, the diffusion of the particles is restricted over distances larger than their diameters, which increase when the particle diameter decreases. In this regime, the probe particles experience the elasticity of the solution and the apparent elastic modulus increases when the diameter of the probe particle increases, whereas for large enough particles, the macroscopic behavior is recovered, in which the diffusing particles experience a homogeneous medium, and the macroscopic elastic modulus is recovered.

The structure of cellulose nanofibril networks at low concentrations and their stabilizing action on colloidal particles

The diffusion of fluorescent tracers can be studied using fluorescence correlation spectroscopy (FCS). This powerful method offers the possibility to monitor very small tracers at low concentrations, down to single molecules. Furthermore it possesses a sub-femtoliter detection volume that can be precisely positioned in a heterogeneous environment to probe the local dynamics. Despite its great potential and high versatility in addressing the diffusion and transport properties in complex systems, FCS has been predominantly applied in molecular and cell biology. Here we present some applications that are more relevant for material and soft matter science. First, we study the diffusion of single tracers with molecular sizes in undiluted polymer systems. Next, the diffusion of small molecules and semiconductor nanoparticles (quantum dots) in silica inverse opals is studied and correlated to the size and morphology of the inverse opals. Finally, we show how FCS can be used to measure the diffusion coefficient of nanoparticles at water-oil interfaces.

An investigation of the behavior of self-propelled particles in complex media finds a transition from thermal diffusion to collision-driven diffusion as the particle area fraction is increased. Collisions with passive particles increases the rotational diffusion of the self-propelled particles, leading to their ``self-trapping.''

30% of the DNA in E. coli bacteria is covered by proteins. Such a high degree of crowding affects the dynamics of generic biological processes (e.g. gene regulation, DNA repair, protein diffusion etc) in ways that are not yet fully understood. In this paper, we theoretically address the diffusion constant of a tracer particle in a one-dimensional system surrounded by impenetrable crowder particles. While the tracer particle always stays on the lattice, crowder particles may unbind to a surrounding bulk and rebind at another, or the same, location. In this scenario we determine how the long time diffusion constant (after many unbinding events) depends on (i) the unbinding rate of crowder particles , and (ii) crowder particle line density ρ, from simulations (using the Gillespie algorithm) and analytical calculations. For small , we find when crowder particles do not diffuse on the line, and when they are diffusing; D is the free particle diffusion constant. For large , we find agreement with mean-field results which do not depend on . From literature values of and D, we show that the small -limit is relevant for in vivo protein diffusion on crowded DNA. Our results apply to single-molecule tracking experiments.

Using fluorescence recovery after photobleaching, we have studied the diffusion of fluorescein-labeled, size-fractionated Ficoll in the cytoplasmic space of living Swiss 3T3 cells as a probe of the physical chemical properties of cytoplasm. The results reported here corroborate and extend the results of earlier experiments with fluorescein-labeled, size-fractionated dextran: diffusion of nonbinding particles in cytoplasm is hindered in a size-dependent manner. Extrapolation of the data suggests that particles larger than 260 A in radius may be completely nondiffusible in the cytoplasmic space. In contrast, diffusion of Ficoll in protein solutions of concentration comparable to the range reported for cytoplasm is not hindered in a size-dependent manner. Although we cannot at present distinguish among several physical chemical models for the organization of cytoplasm, these results make it clear that cytoplasm possesses some sort of higher-order intermolecular interactions (structure) not found in simple aqueous protein solutions, even at high concentration. These results also suggest that, for native cytoplasmic particles whose smallest radial dimension approaches 260 A, size may be as important a determinant of cytoplasmic diffusibility as binding specificity. This would include most endosomes, polyribosomes, and the larger multienzyme complexes.