Microrheological Characterisation of Anisotropic Materials

We describe the measurement of anisotropic viscoelastic moduli in complex soft materials, such as biopolymer gels, via video particle tracking microrheology of colloid tracer particles. The use of a correlation tensor to find the axes of maximum anisotropy, and hence the mechanical director, is described. The moduli of an aligned DNA gel are reported, as a test of the technique; this may have implications for high DNA concentrations in vivo. We also discuss the errors in microrheological measurement, and describe the use of frequency space filtering to improve displacement resolution, and hence probe these typically high modulus materials.Comment: 5 pages, 5 figures. Replaced after refereeing/ improvement. Main results are the same. The final, published version of the paper is here http://link.aps.org/abstract/PRE/v73/e03190

Gaussian approximation for finitely extensible bead-spring chains with hydrodynamic interaction

The Gaussian Approximation, proposed originally by Ottinger [J. Chem. Phys., 90 (1) : 463-473, 1989] to account for the influence of fluctuations in hydrodynamic interactions in Rouse chains, is adapted here to derive a new mean-field approximation for the FENE spring force. This "FENE-PG" force law approximately accounts for spring-force fluctuations, which are neglected in the widely used FENE-P approximation. The Gaussian Approximation for hydrodynamic interactions is combined with the FENE-P and FENE-PG spring force approximations to obtain approximate models for finitely-extensible bead-spring chains with hydrodynamic interactions. The closed set of ODE's governing the evolution of the second-moments of the configurational probability distribution in the approximate models are used to generate predictions of rheological properties in steady and unsteady shear and uniaxial extensional flows, which are found to be in good agreement with the exact results obtained with Brownian dynamics simulations. In particular, predictions of coil-stretch hysteresis are in quantitative agreement with simulations' results. Additional simplifying diagonalization-of-normal-modes assumptions are found to lead to considerable savings in computation time, without significant loss in accuracy.Comment: 26 pages, 17 figures, 2 tables, 75 numbered equations, 1 appendix with 10 numbered equations Submitted to J. Chem. Phys. on 6 February 200

Two-dimensional turbulence of dilute polymer solutions

We investigate theoretically and numerically the effect of polymer additives on two-dimensional turbulence by means of a viscoelastic model. We provide compelling evidence that at vanishingly small concentrations, such that the polymers are passively transported, the probability distribution of polymer elongation has a power law tail: its slope is related to the statistics of finite-time Lyapunov exponents of the flow, in quantitative agreement with theoretical predictions. We show that at finite concentrations and sufficiently large elasticity the polymers react on the flow with manifold consequences: velocity fluctuations are drastically depleted, as observed in soap film experiments; the velocity statistics becomes strongly intermittent; the distribution of finite-time Lyapunov exponents shifts to lower values, signalling the reduction of Lagrangian chaos.Comment: 4 pages, 5 figure

Supersymmetry solution for finitely extensible dumbbell model

Exact relaxation times and eigenfunctions for a simple mechanical model of polymer dynamics are obtained using supersymmetry methods of quantum mechanics. The model includes the finite extensibility of the molecule and does not make use of the self-consistently averaging approximation. The finite extensibility reduces the relaxation times when compared to a linear force. The linear viscoelastic behaviour is obtained in the form of the ``generalized Maxwell model''. Using these results, a numerical integration scheme is proposed in the presence of a given flow kinematics.Comment: 5 pages, 2 figure

Evaluating the Applicability of the Fokker-Planck Equation in Polymer Translocation: A Brownian Dynamics Study

Brownian dynamics (BD) simulations are used to study the translocation dynamics of a coarse-grained polymer through a cylindrical nanopore. We consider the case of short polymers, with a polymer length, N, in the range N=21-61. The rate of translocation is controlled by a tunable friction coefficient, gamma_{0p}, for monomers inside the nanopore. In the case of unforced translocation, the mean translocation time scales with polymer length N as ~ (N-N_p)^alpha, where N_p is the average number of monomers in the nanopore. The exponent approaches the value alpha=2 when the pore friction is sufficiently high, in accord with the prediction for the case of the quasi-static regime where pore friction dominates. In the case of forced translocation, the polymer chain is stretched and compressed on the cis and trans sides, respectively, for low gamma_{0p}. However, the chain approaches conformational quasi-equilibrium for sufficiently large gamma_{0p}. In this limit the observed scaling of with driving force and chain length supports the FP prediction that is proportional to N/f_d for sufficiently strong driving force. Monte Carlo simulations are used to calculate translocation free energy functions for the system. The free energies are used with the Fokker-Planck equation to calculate translocation time distributions. At sufficiently high gamma_{0p}, the predicted distributions are in excellent agreement with those calculated from the BD simulations. Thus, the FP equation provides a valid description of translocation dynamics for sufficiently high pore friction for the range of polymer lengths considered here. Increasing N will require a corresponding increase in pore friction to maintain the validity of the FP approach. Outside the regime of low N and high pore friction, the polymer is out of equilibrium, and the FP approach is not valid.Comment: 13 pages, 11 figure

Lattice-Boltzmann Method for Non-Newtonian Fluid Flows

We study an ad hoc extension of the Lattice-Boltzmann method that allows the simulation of non-Newtonian fluids described by generalized Newtonian models. We extensively test the accuracy of the method for the case of shear-thinning and shear-thickening truncated power-law fluids in the parallel plate geometry, and show that the relative error compared to analytical solutions decays approximately linear with the lattice resolution. Finally, we also tested the method in the reentrant-flow geometry, in which the shear-rate is no-longer a scalar and the presence of two singular points requires high accuracy in order to obtain satisfactory resolution in the local stress near these points. In this geometry, we also found excellent agreement with the solutions obtained by standard finite-element methods, and the agreement improves with higher lattice resolution

Anomalous lateral diffusion in a viscous membrane surrounded by viscoelastic media

We investigate the lateral dynamics in a purely viscous lipid membrane surrounded by viscoelastic media such as polymeric solutions. We first obtain the generalized frequency-dependent mobility tensor and focus on the case when the solvent is sandwiched by hard walls. Due to the viscoelasticity of the solvent, the mean square displacement of a disk embedded in the membrane exhibits an anomalous diffusion. An useful relation which connects the mean square displacement and the solvent modulus is provided. We also calculate the cross-correlation of the particle displacements which can be applied for two-particle tracking experiments.Comment: 6 pages, 2 figure

Models of granular ratchets

We study a general model of granular Brownian ratchet consisting of an asymmetric object moving on a line and surrounded by a two-dimensional granular gas, which in turn is coupled to an external random driving force. We discuss the two resulting Boltzmann equations describing the gas and the object in the dilute limit and obtain a closed system for the first few moments of the system velocity distributions. Predictions for the net ratchet drift, the variance of its velocity fluctuations and the transition rates in the Markovian limit, are compared to numerical simulations and a fair agreement is observed.Comment: 15 pages, 4 figures, to be published on Journal of Statistical Mechanics: Theory and Experiment

Microcanonical entropy inflection points: Key to systematic understanding of transitions in finite systems

We introduce a systematic classification method for the analogs of phase transitions in finite systems. This completely general analysis, which is applicable to any physical system and extends towards the thermodynamic limit, is based on the microcanonical entropy and its energetic derivative, the inverse caloric temperature. Inflection points of this quantity signal cooperative activity and thus serve as distinct indicators of transitions. We demonstrate the power of this method through application to the long-standing problem of liquid-solid transitions in elastic, flexible homopolymers.Comment: 4 pages, 3 figure

Non-linear rheology of active particle suspensions: Insights from an analytical approach

We consider active suspensions in the isotropic phase subjected to a shear flow. Using a set of extended hydrodynamic equations we derive a variety of {\em analytical} expressions for rheological quantities such as shear viscosity and normal stress differences. In agreement to full-blown numerical calculations and experiments we find a shear thickening or -thinning behaviour depending on whether the particles are contractile or extensile. Moreover, our analytical approach predicts that the normal stress differences can change their sign in contrast to passive suspensions.Comment: 11 pages, 10 figures, appear in PR