Entropic transport - A test bed for the Fick-Jacobs approximation

Biased diffusive transport of Brownian particles through irregularly shaped, narrow confining quasi-one-dimensional structures is investigated. The complexity of the higher dimensional diffusive dynamics is reduced by means of the so-called Fick-Jacobs approximation, yielding an effective one-dimensional stochastic dynamics. Accordingly, the elimination of transverse, equilibrated degrees of freedom stemming from geometrical confinements and/or bottlenecks cause entropic potential barriers which the particles have to overcome when moving forward noisily. The applicability and the validity of the reduced kinetic description is tested by comparing the approximation with Brownian dynamics simulations in full configuration space. This non-equilibrium transport in such quasi-one-dimensional irregular structures implies for moderate-to-strong bias a characteristic violation of the Sutherland-Einstein fluctuation-dissipation relation.Comment: 15 pages, 6 figures ; Phil. Trans. R. Soc. A (2009), in pres

Intrinsically localized chaos in discrete nonlinear extended systems

The phenomenon of intrinsic localization in discrete nonlinear extended systems, i.e. the (generic) existence of discrete breathers, is shown to be not restricted to periodic solutions but it also extends to more complex (chaotic) dynamical behaviour. We illustrate this with two different forced and damped systems exhibiting this type of solutions: In an anisotropic Josephson junction ladder, we obtain intrinsically localized chaotic solutions by following periodic rotobreather solutions through a cascade of period-doubling bifurcations. In an array of forced and damped van der Pol oscillators, they are obtained by numerical continuation (path-following) methods from the uncoupled limit, where its existence is trivially ascertained, following the ideas of the anticontinuum limit.Comment: 6 pages, 6 figures, to appear in Europhysics Letter

New data concerning Neanderthal occupation in the Iberian System: First results from the late Pleistocene (MIS 3) Aguilón P5 cave site (NE Iberia)

This work presents the first results from the Aguilón P5 (Zaragoza) cave site on the northern slope of the Iberian System (NE Iberia). The fieldwork carried out since 2010 on several archaeological layers containing remnants of human occupations has revealed lithic remains, processed faunal bones and charred plant remains from combustion events. Due to the lithic tool assemblage and radiocarbon dating (>50.0–41.9 kyr BP), the attribution of this human occupation to the Mousterian techno-complex is clear, contemporary with other important Late Mousterian sites in the Ebro Basin (NE Iberia) and Mediterranean region. Preliminary results concerning stratigraphic, chronometric, techno-tipological and palaeoenvironmental data from the last human occupations of the cave (archaeological layers “cnc”, “mcp” and “e”) are provided in this paper. To contextualize the Neanderthal occupation of the Aguilón P5 cave, a timeline of Middle Paleolithic in the Iberian System is proposed. A total of 45 dates from 19 stratigraphic units (including speleothems) are available from 10 sites. Chronometric dating series allow us to establish the temporary framework of Mousterian industries in the Iberian System coinciding with the abrupt climate changes related to Heinrich Events which characterize MIS 3. In summary, this paper provides new chronometric and archaeological information about Neanderthal settlement and subsistence in an under-investigated region

Diffusion of multiple species with excluded-volume effects

Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial differential equations. In this paper we consider multiple interacting subpopulations/species and study how the inter-species competition emerges at the population level. Each individual is described as a finite-size hard core interacting particle undergoing Brownian motion. The link between the discrete stochastic equations of motion and the continuum model is considered systematically using the method of matched asymptotic expansions. The system for two species leads to a nonlinear cross-diffusion system for each subpopulation, which captures the enhancement of the effective diffusion rate due to excluded-volume interactions between particles of the same species, and the diminishment due to particles of the other species. This model can explain two alternative notions of the diffusion coefficient that are often confounded, namely collective diffusion and self-diffusion. Simulations of the discrete system show good agreement with the analytic results

Biased random walks on complex networks: the role of local navigation rules

We study the biased random walk process in random uncorrelated networks with arbitrary degree distributions. In our model, the bias is defined by the preferential transition probability, which, in recent years, has been commonly used to study efficiency of different routing protocols in communication networks. We derive exact expressions for the stationary occupation probability, and for the mean transit time between two nodes. The effect of the cyclic search on transit times is also explored. Results presented in this paper give the basis for theoretical treatment of the transport-related problems on complex networks, including quantitative estimation of the critical value of the packet generation rate.Comment: 5 pages (Phys. Rev style), 3 Figure

Deterministic Brownian motion generated from differential delay equations

This paper addresses the question of how Brownian-like motion can arise from the solution of a deterministic differential delay equation. To study this we analytically study the bifurcation properties of an apparently simple differential delay equation and then numerically investigate the probabilistic properties of chaotic solutions of the same equation. Our results show that solutions of the deterministic equation with randomly selected initial conditions display a Gaussian-like density for long time, but the densities are supported on an interval of finite measure. Using these chaotic solutions as velocities, we are able to produce Brownian-like motions, which show statistical properties akin to those of a classical Brownian motion over both short and long time scales. Several conjectures are formulated for the probabilistic properties of the solution of the differential delay equation. Numerical studies suggest that these conjectures could be "universal" for similar types of "chaotic" dynamics, but we have been unable to prove this.Comment: 15 pages, 13 figure

Measuring fast gene dynamics in single cells with time-lapse luminescence microscopy.

Time-lapse fluorescence microscopy is an important tool for measuring in vivo gene dynamics in single cells. However, fluorescent proteins are limited by slow chromophore maturation times and the cellular autofluorescence or phototoxicity that arises from light excitation. An alternative is luciferase, an enzyme that emits photons and is active upon folding. The photon flux per luciferase is significantly lower than that for fluorescent proteins. Thus time-lapse luminescence microscopy has been successfully used to track gene dynamics only in larger organisms and for slower processes, for which more total photons can be collected in one exposure. Here we tested green, yellow, and red beetle luciferases and optimized substrate conditions for in vivo luminescence. By combining time-lapse luminescence microscopy with a microfluidic device, we tracked the dynamics of cell cycle genes in single yeast with subminute exposure times over many generations. Our method was faster and in cells with much smaller volumes than previous work. Fluorescence of an optimized reporter (Venus) lagged luminescence by 15-20 min, which is consistent with its known rate of chromophore maturation in yeast. Our work demonstrates that luciferases are better than fluorescent proteins at faithfully tracking the underlying gene expression