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Disclination configurations of a nematic liquid crystal are studied within a self-consistent molecular field theory. The theory is based on a tensor order parameter, and can accommodate anisotropic elastic energies without the known divergences in the Landau-de Gennes formulation. Our results agree with the asymptotic results of Dzyaloshinskii for the Frank-Oseen energy far from the defect core, but reveal biaxial order at intermediate distances from the core, crossing over to uniaxial but axisymmetric configurations as the core is approached. The elastic terms considered in our energy allow for the separate control of surface tension, anchoring, and elasticity contrast, and are used to analyze recent results for lyotropic chromonic liquid crystals. The latter display unusually large defect cores (on the order of tens of microns) which can be used for a quantitative comparison with the theory. Both ±1/2 disclination configurations are well reproduced by our calculations. Elastic anisotropy is also shown to lead to qualitative changes in the disclination polarization, a quantity that is proportional to the active stress in models of active matter.

Nematic liquid crystals exhibit configurations in which the underlying ordering changes markedly on macroscopic length scales. Such structures include topological defects in the nematic phase and tactoids within nematic-isotropic coexistence. We discuss a computational study of inhomogeneous configurations that is based on a field theory extension of the Maier-Saupe molecular model of a uniaxial, nematic liquid crystal. A tensor order parameter is defined as the second moment of an orientational probability distribution, leading to a free energy that is not convex within the isotropic-nematic coexistence region, and that goes to infinity if the eigenvalues of the order parameter become nonphysical. Computations of the spatial profile of the order parameter are presented for an isotropic-nematic interface in one dimension, a tactoid in two dimensions, and a nematic disclination in two dimensions. We compare our results to those given by the Landau-de Gennes free energy for the same configurations and discuss the advantages of such a model over the latter.

Recent research on interfacial instabilities of smectic films has shown unexpected morphologies that are not fully explained by classical local equilibrium thermodynamics. Annealing focal conic domains can lead to conical pyramids, changing the sign of the Gaussian curvature and exposing smectic layers at the interface. In order to explore the role of the Gaussian curvature on the stability and evolution of the film-vapor interface, we introduce a phase-field model of a smectic-isotropic system as a first step in the study. Through asymptotic analysis of the model, we generalize the classical condition of local equilibrium, the Gibbs-Thomson equation, to include contributions from surface bending and torsion and a dependence on the layer orientation at the interface. A full numerical solution of the phase-field model is then used to study the evolution of focal conic structures in smectic domains in contact with the isotropic phase via local evaporation and condensation of smectic layers. As in experiments, numerical solutions show that pyramidal structures emerge near the center of the focal conic owing to evaporation of adjacent smectic planes and to their orientation relative to the interface. Near the center of the focal conic domain, a correct description of the motion of the interface requires the additional curvature terms obtained in the asymptotic analysis, thus clarifying the limitations in modeling motion of hyperbolic surfaces solely driven by mean curvature.

A consistent small-scale description of plasticity and dislocation motion in a crystalline solid is presented based on the phase field crystal description. By allowing for independent mass motion and lattice distortion, the crystal can maintain elastic equilibrium on the timescale of plastic motion. We show that the singular (incompatible) strains are determined by the phase field crystal density, while the smooth distortions are constrained to satisfy elastic equilibrium. A numerical implementation of the model is presented and used to study a benchmark problem: the motion of an edge dislocation dipole in a triangular lattice. The time dependence of the dipole separation agrees with continuum elasticity with no adjustable parameters.

Electrokinetic phenomena in a nematic suspension are considered when one or more dielectric particles are suspended in a liquid crystal matrix in its nematic phase. The long-range orientational order of the nematic constitutes a fluid with anisotropic properties. This anisotropy enables charge separation in the bulk under an applied electric field, and leads to streaming flows even when the applied field is oscillatory. In the cases considered, charge separation is seen to result from director field distortions in the matrix that are created by the suspended particles. We use a recently introduced electrokinetic model to study the motion of a single-particle hyperbolic hedgehog pair. We find this motion to be parallel to the defect-particle center axis, independent of field orientation. For a two-particle configuration, we find that the relative force of electrokinetic origin is attractive in the case of particles with perpendicular director anchoring, and repulsive for particles with tangential director anchoring. The study reveals large scale flow properties that are respectively derived from the topology of the configuration alone and from short scale hydrodynamics phenomena in the vicinity of the particle and defect.

Transport of fluids and particles at the microscale is an important theme in both fundamental and applied science. One of the most successful approaches is to use an electric field, which requires the system to carry or induce electric charges. We describe a versatile approach to generate electrokinetic flows by using a liquid crystal (LC) with surface-patterned molecular orientation as an electrolyte. The surface patterning is produced by photoalignment. In the presence of an electric field, the spatially varying orientation induces space charges that trigger flows of the LC. The active patterned LC electrolyte converts the electric energy into the LC flows and transport of embedded particles of any type (fluid, solid, gaseous) along a predesigned trajectory, posing no limitation on the electric nature (charge, polarizability) of these particles and interfaces. The patterned LC electrolyte exhibits a quadratic field dependence of the flow velocities; it induces persistent vortices of controllable rotation speed and direction that are quintessential for micro- and nanoscale mixing applications.

We obtain the location of the Hopf bifurcation threshold for a modified van der Pol oscillator, parametrically driven by a stochastic source and including delayed feedback in both position and velocity. We introduce a multiple scale expansion near threshold, and we solve the resulting Fokker-Planck equation associated with the evolution at the slowest time scale. The analytical results are compared with a direct numerical integration of the model equation. Delay modifies the Hopf frequency at threshold and leads to a stochastic bifurcation that is shifted relative to the deterministic limit by an amount that depends on the delay time, the amplitude of the feedback terms, and the intensity of the noise. Interestingly, stochasticity generally increases the region of stability of the limit cycle.

We obtain the characteristic correlation time associated with a model stochastic differential equation that includes the normal form of a pitchfork bifurcation and delayed feedback. In particular, the validity of the common assumption of statistical independence between the state at time t and that at t-τ, where τ is the delay time, is examined. We find that the correlation time diverges at the model's bifurcation line, thus signaling a sharp bifurcation threshold, and the failure of statistical independence near threshold. We determine the correlation time both by numerical integration of the governing equation, and analytically in the limit of small τ. The correlation time T diverges as T~a(-1), where a is the control parameter so that a=0 is the bifurcation threshold. The small-τ expansion correctly predicts the location of the bifurcation threshold, but there are systematic deviations in the magnitude of the correlation time.

Analytical expressions for pitchfork and Hopf bifurcation thresholds are given for a nonlinear stochastic differential delay equation with feedback. Our results assume that the delay time τ is small compared to other characteristic time scales, not a significant limitation close to the bifurcation line. A pitchfork bifurcation line is found, the location of which depends on the conditional average , where x(t) is the dynamical variable. This conditional probability incorporates the combined effect of fluctuation correlations and delayed feedback. We also find a Hopf bifurcation line which is obtained by a multiple scale expansion around the oscillatory solution near threshold. We solve the Fokker-Planck equation associated with the slowly varying amplitudes and use it to determine the threshold location. In both cases, the predicted bifurcation lines are in excellent agreement with a direct numerical integration of the governing equations. Contrary to the known case involving no delayed feedback, we show that the stochastic bifurcation lines are shifted relative to the deterministic limit and hence that the interaction between fluctuation correlations and delay affect the stability of the solutions of the model equation studied.

The bifurcation diagram of a model stochastic differential equation with delayed feedback is presented. We are motivated by recent research on stochastic effects in models of transcriptional gene regulation. We start from the normal form for a pitchfork bifurcation, and add multiplicative or parametric noise and linear delayed feedback. The latter is sufficient to originate a Hopf bifurcation in that region of parameters in which there is a sufficiently strong negative feedback. We find a sharp bifurcation in parameter space, and define the threshold as the point in which the stationary distribution function p(x) changes from a delta function at the trivial state x=0 to p(x) approximately x(alpha) at small x (with alpha=-1 exactly at threshold). We find that the bifurcation threshold is shifted by fluctuations relative to the deterministic limit by an amount that scales linearly with the noise intensity. Analytic calculations of the bifurcation threshold are also presented in the limit of small delay tau-->0 that compare quite favorably with the numerical solutions even for moderate values of tau .

In order to study solvation effects on protein folding, we analyze the collapse transition of a self-avoiding random walk composed of hydrophobic segments that is embedded in a lattice model of a solvent. As expected, hydrophobic interactions lead to an attractive potential of mean force among chain segments. As a consequence, the random walk in solvent undergoes a collapse transition at a higher temperature than in its absence. Chain collapse is accompanied by the formation of a region depleted of solvent around the chain. In our simulation, the depleted region at collapse is as large as our computational domain.

We study the formation of columnar structures of uniaxial dipoles in an external magnetic field both experimentally and theoretically. By applying an external magnetic field parallel to a thin layer of a magnetorheological fluid, we manipulate a single initial cluster of suspended colloidal particles. We find that the cluster breaks up into columns that have approximately uniform widths and intercolumnar spacings. Both the average column width and inter column spacing are observed to vary linearly with column length. The observed linear relationships between column width and spacing versus the column length are interpreted theoretically by computing the potential energy of an ensemble of closed-packed columns of spherical dipolar particles.

We describe numerical solutions of two nonpotential models of pattern formation in nonequilibrium systems to address the motion and decay of grain boundaries separating domains of stripe configurations of different orientations. We first address wave-number selection because of the boundary, and possible decay modes when the periodicity of the stripe phases is different from the selected wave number for a stationary boundary. We discuss several decay modes including long wavelength undulations of the moving boundary, as well as the formation of localized defects and their subsequent motion. We find three different regimes as a function of the distance to the stripe phase threshold and initial wave number, and then correlate these findings with domain morphology during domain coarsening in a large aspect ratio configuration.

In order to address the selection mechanism that is responsible for the unique lamellar orientation observed in block copolymers under oscillatory shears, we use a constitutive law for the dissipative part of the stress tensor that respects the uniaxial symmetry of a lamellar phase. An interface separating two domains oriented parallel and perpendicular to the shear is shown to be hydrodynamically unstable, a situation analogous to the thin layer instability of stratified fluids under shears. The resulting secondary flows break the degeneracy between the parallel and perpendicular lamellar orientation, leading to a preferred perpendicular orientation in certain ranges of parameters of the polymer and of the shear.

We identify a finite wave-number instability of a 90 degrees tilt grain boundary in three-dimensional lamellar phases which is absent in two-dimensional configurations. Both a stability analysis of the slowly varying amplitude or envelope equation for the boundary, and a direct numerical solution of an order parameter model equation are presented. The instability mode involves two-dimensional perturbations of the planar base boundary, and is suppressed for purely one-dimensional perturbations. We find that both the most unstable wave numbers and their growth rate increase with epsilon , the dimensionless distance away from threshold of the lamellar phase.

A phenomenological model of parametric surface waves (Faraday waves) is introduced in the limit of small viscous dissipation that accounts for the coupling between surface motion and slowly varying streaming and large-scale flows (mean flow). The primary bifurcation of the model is to a set of standing waves (stripes, given the functional form of the model nonlinearities chosen here). Our results for the secondary instabilities of the primary wave show that the mean flow leads to a weak destabilization of the base state against Eckhaus and transverse amplitude modulation instabilities, and introduces a longitudinal oscillatory instability which is absent without the coupling. We compare our results with recent one-dimensional amplitude equations for this system systematically derived from the governing hydrodynamic equations.

We study the effect of an externally imposed oscillatory shear on the motion of a grain boundary that separates differently oriented domains of the lamellar phase of a diblock copolymer. A direct numerical solution of the Swift-Hohenberg equation in shear flow is used for the case of a transverse/parallel grain boundary in the limits of weak nonlinearity and low shear frequency. We focus on the region of parameters in which both transverse and parallel lamellae are linearly stable. Shearing leads to excess free energy in the transverse region relative to the parallel region, which is in turn dissipated by net motion of the boundary toward the transverse region. The observed boundary motion is a combination of rigid advection by the flow and order parameter diffusion. The latter includes break up and reconnection of lamellae, as well as a weak Eckhaus instability in the boundary region for sufficiently large strain amplitude that leads to slow wave number readjustment. The net average velocity is seen to increase with frequency and strain amplitude, and can be obtained by a multiple scale expansion of the governing equations.

We study the motion of a grain boundary separating two otherwise stationary domains of hexagonal symmetry. Starting from an order parameter equation, a multiple scale analysis leads to an analytical equation of motion for the boundary that shares many properties with that of a crystalline solid. We find that defect motion is generically opposed by a pinning force that arises from nonadiabatic corrections to the standard amplitude equations. The magnitude of this force depends sharply on the misorientation angle between adjacent domains: the most easily pinned grain boundaries are those with a low angle (typically 4 degrees < or =theta;< or =8 degrees ). Although pinning effects may be small, they can be orders of magnitude larger than those present in smectic phases.

We study numerically and analytically the coarsening of stripe phases in two spatial dimensions, and show that transient configurations do not achieve long ranged orientational order but rather evolve into glassy configurations with very slow dynamics. In the absence of thermal fluctuations, defects such as grain boundaries become pinned in an effective periodic potential that is induced by the underlying periodicity of the stripe pattern itself. Pinning arises without quenched disorder from the nonadiabatic coupling between the slowly varying envelope of the order parameter around a defect, and its fast variation over the stripe wavelength. The characteristic size of ordered domains asymptotes to a finite value R(g) approximately lambda(0)epsilon(-1/2)exp(absolute value of a/square root of epsilon), where epsilon<<1 is the dimensionless distance away from threshold, lambda(0) the stripe wavelength, and a a constant of order unity. Random fluctuations allow defect motion to resume until a new characteristic scale is reached, function of the intensity of the fluctuations. We finally discuss the relationship between defect pinning and the coarsening laws obtained in the intermediate time regime.

We study domain coarsening of two-dimensional stripe patterns by numerically solving the Swift-Hohenberg model of Rayleigh-Bénard convection. Near the bifurcation threshold, the evolution of disordered configurations is dominated by grain-boundary motion through a background of largely immobile curved stripes. A numerical study of the distribution of local stripe curvatures, of the structure factor of the order parameter, and a finite size scaling analysis of the grain-boundary perimeter, suggest that the linear scale of the structure grows as a power law of time t(1/z), with z=3. We interpret theoretically the exponent z=3 from the law of grain-boundary motion.

We obtain the stationary probability distribution functions of the order parameter near onset for the one-dimensional real Ginzburg-Landau and Swift-Hohenberg equations with a fluctuating control parameter. A perturbative expansion in the intensity of the fluctuations leads to a hierarchy of Fokker-Planck equations for conditional probability distribution functions that relate components of the order parameter that evolve in different time scales. Successive integration leads to a Fokker-Planck equation for the slowest mode, which we solve analytically for the models studied. In all cases, the probability distribution function above onset is of the form P(A0) approximately A(delta)(0)e(-gammaA20), where A0 is the slow component of the order parameter and the values of delta and gamma depend explicitly on the intensity of the fluctuations. Knowledge of P(A0) allows the calculation of an effective bifurcation threshold and of the moments of A0 above threshold.

We study the motion of a grain boundary that separates two sets of mutually perpendicular rolls in Rayleigh-Bénard convection above onset. The problem is treated either analytically from the corresponding amplitude equations, or numerically by solving the Swift-Hohenberg equation. We find that if the rolls are curved by a slow transversal modulation, a net translation of the boundary follows. We show analytically that although this motion is a nonlinear effect, it occurs in a time scale much shorter than that of the linear relaxation of the curved rolls. The total distance traveled by the boundary scales as epsilon(-1/2), where epsilon is the reduced Rayleigh number. We obtain analytical expressions for the relaxation rate of the modulation and for the time-dependent traveling velocity of the boundary, and especially their dependence on wave number. The results agree well with direct numerical solutions of the Swift-Hohenberg equation. We finally discuss the implications of our results on the coarsening rate of an ensemble of differently oriented domains in which grain-boundary motion through curved rolls is the dominant coarsening mechanism.