Power spectrum of mass and activity fluctuations in a sandpile

We consider a directed abelian sandpile on a strip of size $2\times n$, driven by adding a grain randomly at the left boundary after every $T$ time-steps. We establish the exact equivalence of the problem of mass fluctuations in the steady state and the number of zeroes in the ternary-base representation of the position of a random walker on a ring of size $3^n$. We find that while the fluctuations of mass have a power spectrum that varies as $1/f$ for frequencies in the range $3^{-2n} \ll f \ll 1/T$, the activity fluctuations in the same frequency range have a power spectrum that is linear in $f$.Comment: 8 pages, 10 figure

Shear flow induced isotropic to nematic transition in a suspension of active filaments

We study the effects of externally applied shear flow on a model of suspensions of motors and filaments, via the equations of active hydrodynamics [PRL {\bf 89} (2002) 058101; {\bf 92} (2004) 118101]. In the absence of shear, the orientationally ordered phase of {\it both} polar and apolar active particles is always unstable at zero-wavenumber. An imposed steady shear large enough to overcome the active stresses stabilises both apolar and moving polar phases. Our work is relevant to {\it in vitro} studies of active filaments, the reorientation of endothelial cells subject to shear flow and shear-induced motility of attached cells.Comment: 8 pages, 4 figures submitted to Europhysics Letter

Nonequilibrium Phase Transitions in a Driven Sandpile Model

We construct a driven sandpile slope model and study it by numerical simulations in one dimension. The model is specified by a threshold slope \sigma_c\/, a parameter \alpha\/, governing the local current-slope relation (beyond threshold), and $j_{\rm in}$, the mean input current of sand. A nonequilibrium phase diagram is obtained in the \alpha\, -\, j_{\rm in}\/ plane. We find an infinity of phases, characterized by different mean slopes and separated by continuous or first-order boundaries, some of which we obtain analytically. Extensions to two dimensions are discussed.Comment: 11 pages, RevTeX (preprint format), 4 figures available upon requs

Do current-density nonlinearities cut off the glass transition?

Extended mode coupling theories for dense fluids predict that nonlinear current-density couplings cut off the singular `ideal glass transition', present in the standard mode coupling theory where such couplings are ignored. We suggest here that, rather than allowing for activated processes as sometimes supposed, contributions from current-density couplings are always negligible close to a glass transition. We discuss in schematic terms how activated processes can nonetheless cut off the transition, by causing the memory function to become linear in correlators at late times.Comment: 4 page

Molecular aggregation structures into ternary system deca glycerol dioleate/ heptane/water

The phase diagram for the ternary system deca glycerol dioleate(DGD)/heptane/water was established at 25°C. In this phase diagram it was seen that the reverse micellar solution phase extends in its area until the water content reaches 35-45 wt%, at which a liquid crystalline phase begins to appear. On the basis of the experimental results of specific conductivity, viscosity, etc. for the samples containing a definite amount of DGD (0,1 M), and varying relative amounts of heptane and water, the mechanism of the transition of reverse micellar structures to liquid crystalline phase is discussed

Sensitivity Analysis for Shortest Path Problems and Maximum Capacity Path Problems in Undirected Graphs

This paper addresses sensitivity analysis questions concerning the shortest path problem and the maximum capacity path problem in an undirected network. For both problems, we determine the maximum and minimum weights that each edge can have so that a given path remains optimal. For both problems, we show how to determine these maximum and minimum values for all edges in O(m + K log K) time, where m is the number of edges in the network, and K is the number of edges on the given optimal path

Spontaneous flow states in active nematics: a unified picture

Continuum hydrodynamic models of active liquid crystals have been used to describe dynamic self-organising systems such as bacterial swarms and cytoskeletal gels. A key prediction of such models is the existence of self-stabilising kink states that spontaneously generate fluid flow in quasi-one dimensional channels. Using simple stability arguments and numerical calculations we extend previous studies to give a complete characterisation of the phase space for both contractile and extensile particles (ie pullers and pushers) moving in a narrow channel as a function of their flow alignment properties and initial orientation. This gives a framework for unifying many of the results in the literature. We describe the response of the kink states to an imposed shear, and investigate how allowing the system to be polar modifies its dynamical behaviour.Comment: 6 pages, 6 figures; submitted to Europhysics Letter

Global parameter identification of stochastic reaction networks from single trajectories

We consider the problem of inferring the unknown parameters of a stochastic biochemical network model from a single measured time-course of the concentration of some of the involved species. Such measurements are available, e.g., from live-cell fluorescence microscopy in image-based systems biology. In addition, fluctuation time-courses from, e.g., fluorescence correlation spectroscopy provide additional information about the system dynamics that can be used to more robustly infer parameters than when considering only mean concentrations. Estimating model parameters from a single experimental trajectory enables single-cell measurements and quantification of cell--cell variability. We propose a novel combination of an adaptive Monte Carlo sampler, called Gaussian Adaptation, and efficient exact stochastic simulation algorithms that allows parameter identification from single stochastic trajectories. We benchmark the proposed method on a linear and a non-linear reaction network at steady state and during transient phases. In addition, we demonstrate that the present method also provides an ellipsoidal volume estimate of the viable part of parameter space and is able to estimate the physical volume of the compartment in which the observed reactions take place.Comment: Article in print as a book chapter in Springer's "Advances in Systems Biology

Two-Component Fluid Membranes Near Repulsive Walls: Linearized Hydrodynamics of Equilibrium and Non-equilibrium States

We study the linearized hydrodynamics of a two-component fluid membrane near a repulsive wall, via a model which incorporates curvature- concentration coupling as well as hydrodynamic interactions. This model is a simplified version of a recently proposed one [J.-B. Manneville et al. Phys. Rev. E, 64, 021908 (2001)] for non-equilibrium force-centres embedded in fluid membranes, such as light-activated bacteriorhodopsin pumps incorporated in phospholipid (EPC) bilayers. The pump/membrane system is modeled as an impermeable, two-component bilayer fluid membrane in the presence of an ambient solvent, in which one component, representing active pumps, is described in terms of force dipoles displaced with respect to the bilayer midpoint. We first discuss the case in which such pumps are rendered inactive, computing the mode structure in the bulk as well as the modification of hydrodynamic properties by the presence of a nearby wall. We then discuss the fluctuations and mode structure in steady state of active two-component membranes near a repulsive wall. We find that proximity to the wall smoothens membrane height fluctuations in the stable regime, resulting in a logarithmic scaling of the roughness even for initially tensionless membranes. This explicitly non-equilibrium result, a consequence of the incorporation of curvature-concentration coupling in our treatment, also indicates that earlier scaling arguments which obtained an increase in the roughness of active membranes near repulsive walls may need to be reevaluated.Comment: 39 page Latex file, 3 encapsulated Postscript figure