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

A Dynamic Renormalization Group Study of Active Nematics

We carry out a systematic construction of the coarse-grained dynamical equation of motion for the orientational order parameter for a two-dimensional active nematic, that is a nonequilibrium steady state with uniaxial, apolar orientational order. Using the dynamical renormalization group, we show that the leading nonlinearities in this equation are marginally \textit{irrelevant}. We discover a special limit of parameters in which the equation of motion for the angle field of bears a close relation to the 2d stochastic Burgers equation. We find nevertheless that, unlike for the Burgers problem, the nonlinearity is marginally irrelevant even in this special limit, as a result of of a hidden fluctuation-dissipation relation. 2d active nematics therefore have quasi-long-range order, just like their equilibrium counterpartsComment: 31 pages 6 figure

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

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

Live Soap: Order, Fluctuations and Instabilities in Active Smectics

We construct a hydrodynamic theory of noisy, apolar active smectics, in bulk suspension or on a substrate. Our predictions include: quasi-long-ranged smectic order in dimension d = 2, and long- ranged in d = 3, extending previously published results to all dynamical regimes; Kosterlitz-Thouless melting to an active nematic at high and low concentrations in d = 2; nonzero second-sound speed parallel to the layers; the suppression of giant number fluctuations by smectic elasticity; instability to spontaneous undulation and flow in bulk contractile smectics; a layer spacing instability, possibly oscillatory, for large enough extensile active stresses.Comment: 5 pages, 1 figure, submitted to Phys Rev Let

Design and performance of subirrigation system in maize (Zea mays) in Kumulur farm, Trichy district, Tamil Nadu, India

Subirrigation system can furnish water to plants. The upward flux and the discharge rate must satisfy the plant’s lifesaving irrigation needs during summer. The experiment was laid out in  A-block of Eastern farm, Agricultural Engineering College and Research Institute, Kumulur, Trichy, Tamil Nadu. Subirrigation system spacing was arrived using Moody's equation calculated as 10 m. The experiment was laid out in spilt plot design with three replications. Four drain spacing levels (7.5, 10, 12.5 and 15 m) were the main plot treatments and two levels of depth and diameter of drain pipes (75 cm, 60 cm & 75 mm, 63 mm) were the sub plot treatments. The highest volumetric water content was recorded in 7.5 m spacing + 45 cm soil depth + lower reach (S1T3T1). Capillary rise on water table management system under subirrigation mode was fixed as 33.5 cm and the average deep percolation loss was obtained in 0.3 cm/d at development stage of crop period. The highest maize yield (4.30 t/ha) was obtained in 7.5 m spacing + 60 cm drain depth + 75 mm diameter (S1D3). The highest water use efficiency of (0.86 kg/m3) was recorded in 7.5 m spacing + 60 cm drain depth + 75 mm drain diameter (S1D3). This subirrigation system could furnish water to plants due to upward flux and the same system also functioned efficiently under drainage modes and removed the waterlogging during wet periods.       

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

Drift and trapping in biased diffusion on disordered lattices

We reexamine the theory of transition from drift to no-drift in biased diffusion on percolation networks. We argue that for the bias field B equal to the critical value B_c, the average velocity at large times t decreases to zero as 1/log(t). For B < B_c, the time required to reach the steady-state velocity diverges as exp(const/|B_c-B|). We propose an extrapolation form that describes the behavior of average velocity as a function of time at intermediate time scales. This form is found to have a very good agreement with the results of extensive Monte Carlo simulations on a 3-dimensional site-percolation network and moderate bias.Comment: 4 pages, RevTex, 3 figures, To appear in International Journal of Modern Physics C, vol.

Melting-freezing cycles in a relatively sheared pair of crystalline monolayers

The nonequilibrium dynamical behaviour that arises when two ordered two-dimensional monolayers of particles are sheared over each other is studied in Brownian dynamics simulations. A curious sequence of nonequilibrium states is observed as the driving rate is increased, the most striking of which is a sliding state with irregular alternation between disordered and ordered states. We comment on possible mechanisms underlying these cycles, and experiments that could observe them.Comment: 7 pages, 8 figures, minor changes in text and figures, references adde