### Refine

#### Year of publication

- 2014 (43) (remove)

#### Keywords

- anomalous diffusion (14)
- living cells (8)
- dynamics (4)
- infection pathway (4)
- nonergodicity (4)
- physiological consequences (4)
- random-walks (4)
- single-particle tracking (4)
- transport (4)
- weak ergodicity breaking (3)
- Fokker-Planck equations (2)
- adenoassociated virus (2)
- ageing (2)
- behavior (2)
- brownian-motion (2)
- cambridge cb4 0wf (2)
- cambs (2)
- coefficient (2)
- coefficients (2)
- cytoplasm (2)
- dna coiling (2)
- dynamics simulation (2)
- endosomal escape (2)
- england (2)
- equation approach (2)
- escherichia-coli (2)
- excluded volume (2)
- flight search patterns (2)
- fluctuation-dissipation theorem (2)
- fluorescence photobleaching recovery (2)
- folding kinetics (2)
- fractional dynamics (2)
- fractional dynamics approach (2)
- gene-regulation kinetics (2)
- in-vitro (2)
- intermittent chaotic systems (2)
- intracellular-transport (2)
- langevin equation (2)
- levy flights (2)
- membrane (2)
- membrane channel (2)
- milton rd (2)
- mixtures (2)
- models (2)
- monte-carlo (2)
- osmotic-pressure (2)
- photon-counting statistics (2)
- posttranslational protein translocation (2)
- royal soc chemistry (2)
- science park (2)
- single-stranded-dna (2)
- solid-state nanopores (2)
- spatial-organization (2)
- stochastic processes (2)
- structured polynucleotides (2)
- subdiffusion (2)
- thomas graham house (2)
- time random-walks (2)
- trafficking (2)
- Levy foraging hypothesis (1)
- Sinai diffusion (1)
- confinement (1)
- continuous time random walks (1)
- crowding (1)
- diffusion (1)
- driven diffusive systems (theory) (1)
- escence correlation spectroscopy (1)
- first passage (1)
- fluctuations (theory) (1)
- fluorescence correlation spectroscopy (1)
- gel network (1)
- polymer translocation (1)
- polymers (1)
- potential landscape (1)
- quenched energy landscape (1)
- search optimization (1)
- single-file diffusion (1)
- stochastic processes (theory) (1)
- van Hove correlation (1)

#### Institute

Diffusion of finite-size particles in two-dimensional channels with random wall configurations
(2014)

Diffusion of chemicals or tracer molecules through complex systems containing irregularly shaped channels is important in many applications. Most theoretical studies based on the famed Fick-Jacobs equation focus on the idealised case of infinitely small particles and reflecting boundaries. In this study we use numerical simulations to consider the transport of finite-size particles through asymmetrical two-dimensional channels. Additionally, we examine transient binding of the molecules to the channel walls by applying sticky boundary conditions. We consider an ensemble of particles diffusing in independent channels, which are characterised by common structural parameters. We compare our results for the long-time effective diffusion coefficient with a recent theoretical formula obtained by Dagdug and Pineda

Diffusion of finite-size particles in two-dimensional channels with random wall configurations
(2014)

Diffusion of chemicals or tracer molecules through complex systems containing irregularly shaped channels is important in many applications. Most theoretical studies based on the famed Fick–Jacobs equation focus on the idealised case of infinitely small particles and reflecting boundaries. In this study we use numerical simulations to consider the transport of finite-size particles through asymmetrical two-dimensional channels. Additionally, we examine transient binding of the molecules to the channel walls by applying sticky boundary conditions. We consider an ensemble of particles diffusing in independent channels, which are characterised by common structural parameters. We compare our results for the long-time effective diffusion coefficient with a recent theoretical formula obtained by Dagdug and Pineda [J. Chem. Phys., 2012, 137, 024107].

Diffusion of finite-size particles in two-dimensional channels with random wall configurations
(2014)

We study the stochastic behavior of heterogeneous diffusion processes with the power-law dependence D(x) similar to vertical bar x vertical bar(alpha) of the generalized diffusion coefficient encompassing sub- and superdiffusive anomalous diffusion. Based on statistical measures such as the amplitude scatter of the time-averaged mean-squared displacement of individual realizations, the ergodicity breaking and non-Gaussianity parameters, as well as the probability density function P(x, t), we analyze the weakly nonergodic character of the heterogeneous diffusion process and, particularly, the degree of irreproducibility of individual realizations. As we show, the fluctuations between individual realizations increase with growing modulus vertical bar alpha vertical bar of the scaling exponent. The fluctuations appear to diverge when the critical value alpha = 2 is approached, while for even larger alpha the fluctuations decrease, again. At criticality, the power-law behavior of the mean-squared displacement changes to an exponentially fast growth, and the fluctuations of the time-averaged mean-squared displacement do not converge for increasing number of realizations. From a systematic comparison we observe some striking similarities of the heterogeneous diffusion process with the familiar subdiffusive continuous time random walk process with power-law waiting time distribution and diverging characteristic waiting time.

We study the thermal Markovian diffusion of tracer particles in a 2D medium with spatially varying diffusivity D(r), mimicking recently measured, heterogeneous maps of the apparent diffusion coefficient in biological cells. For this heterogeneous diffusion process (HDP) we analyse the mean squared displacement (MSD) of the tracer particles, the time averaged MSD, the spatial probability density function, and the first passage time dynamics from the cell boundary to the nucleus. Moreover we examine the non-ergodic properties of this process which are important for the correct physical interpretation of time averages of observables obtained from single particle tracking experiments. From extensive computer simulations of the 2D stochastic Langevin equation we present an in-depth study of this HDP. In particular, we find that the MSDs along the radial and azimuthal directions in a circular domain obey anomalous and Brownian scaling, respectively. We demonstrate that the time averaged MSD stays linear as a function of the lag time and the system thus reveals a weak ergodicity breaking. Our results will enable one to rationalise the diffusive motion of larger tracer particles such as viruses or submicron beads in biological cells.

We study the effects of ageing-the time delay between initiation of the physical process at t = 0 and start of observation at some time t(a) > 0-and spatial confinement on the properties of heterogeneous diffusion processes (HDPs) with deterministic power-law space-dependent diffusivities, D(x) = D-0 vertical bar x vertical bar(alpha). From analysis of the ensemble and time averaged mean squared displacements and the ergodicity breaking parameter quantifying the inherent degree of irreproducibility of individual realizations of the HDP we obtain striking similarities to ageing subdiffusive continuous time random walks with scale-free waiting time distributions. We also explore how both processes can be distinguished. For confined HDPs we study the long-time saturation of the ensemble and time averaged particle displacements as well as the magnitude of the inherent scatter of time averaged displacements and contrast the outcomes to the results known for other anomalous diffusion processes under confinement.

Based on extensive Monte Carlo simulations and analytical considerations we study the electrostatically driven adsorption of flexible polyelectrolyte chains onto charged Janus nanospheres. These net-neutral colloids are composed of two equally but oppositely charged hemispheres. The critical binding conditions for polyelectrolyte chains are analysed as function of the radius of the Janus particle and its surface charge density, as well as the salt concentration in the ambient solution. Specifically for the adsorption of finite-length polyelectrolyte chains onto Janus nanoparticles, we demonstrate that the critical adsorption conditions drastically differ when the size of the Janus particle or the screening length of the electrolyte are varied. We compare the scaling laws obtained for the adsorption–desorption threshold to the known results for uniformly charged spherical particles, observing significant disparities. We also contrast the changes to the polyelectrolyte chain conformations close to the surface of the Janus nanoparticles as compared to those for simple spherical particles. Finally, we discuss experimentally relevant physico-chemical systems for which our simulations results may become important. In particular, we observe similar trends with polyelectrolyte complexation with oppositely but heterogeneously charged proteins.

Based on extensive Monte Carlo simulations and analytical considerations we study the electrostatically driven adsorption of flexible polyelectrolyte chains onto charged Janus nanospheres. These net-neutral colloids are composed of two equally but oppositely charged hemispheres. The critical binding conditions for polyelectrolyte chains are analysed as function of the radius of the Janus particle and its surface charge density, as well as the salt concentration in the ambient solution. Specifically for the adsorption of finite-length polyelectrolyte chains onto Janus nanoparticles, we demonstrate that the critical adsorption conditions drastically differ when the size of the Janus particle or the screening length of the electrolyte are varied. We compare the scaling laws obtained for the adsorption-desorption threshold to the known results for uniformly charged spherical particles, observing significant disparities. We also contrast the changes to the polyelectrolyte chain conformations close to the surface of the Janus nanoparticles as compared to those for simple spherical particles. Finally, we discuss experimentally relevant physicochemical systems for which our simulations results may become important. In particular, we observe similar trends with polyelectrolyte complexation with oppositely but heterogeneously charged proteins.