Grain boundary dynamics in stripe phases of non potential systems

We describe numerical solutions of two non potential 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 wavenumber selection because of the boundary, and possible decay modes when the periodicity of the stripe phases is different from the selected wavenumber 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 wavenumber, and then correlate these findings with domain morphology during domain coarsening in a large aspect ratio configuration.Comment: 8 pages, 8 figure

Tilt grain boundary instabilities in three dimensional lamellar patterns

We identify a finite wavenumber instability of a 90$^{\circ}$ 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 wavenumbers and their growth rate increase with $\epsilon$, the dimensionless distance away from threshold of the lamellar phase.Comment: 11 pages, 7 figures, to be published in Phys. Rev.

Stability of parallel/perpendicular domain boundaries in lamellar block copolymers under oscillatory shear

We introduce a model constitutive law for the dissipative stress tensor of lamellar phases to account for low frequency and long wavelength flows. Given the uniaxial symmetry of these phases, we argue that the stress tensor must be the same as that of a nematic but with the local order parameter being the slowly varying lamellar wavevector. This assumption leads to a dependence of the effective dynamic viscosity on orientation of the lamellar phase. We then consider a model configuration comprising a domain boundary separating laterally unbounded domains of so called parallel and perpendicularly oriented lamellae in a uniform, oscillatory, shear flow, and show that the configuration can be hydrodynamically unstable for the constitutive law chosen. It is argued that this instability and the secondary flows it creates can be used to infer a possible mechanism for orientation selection in shear experiments.Comment: 26 pages, 10 figure

Orientation selection in lamellar phases by oscillatory shears

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 shear. The resulting secondary flows break the degeneracy between parallel and perpendicular lamellar orientation, leading to a preferred perpendicular orientation in certain ranges of parameters of the polymer and of the shear.Comment: 4 pages, 3 figure

Weakly nonlinear theory of grain boundary motion in patterns with crystalline symmetry

We study the motion of a grain boundary separating two otherwise stationary domains of hexagonal symmetry. Starting from an order parameter equation appropriate for hexagonal patterns, 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 non-adiabatic corrections to the standard amplitude equation. The magnitude of this force depends sharply on the mis-orientation angle between adjacent domains so that the most easily pinned grain boundaries are those with an angle between four and eight degrees. Although pinning effects may be small, they do not vanish asymptotically near the onset of this subcritical bifurcation, and can be orders of magnitude larger than those present in smectic phases that bifurcate supercritically

Ordering kinetics of stripe patterns

We study domain coarsening of two dimensional stripe patterns by numerically solving the Swift-Hohenberg model of Rayleigh-Benard 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 with a craracteristic exponent z=3. We interpret theoretically the exponent z=3 from the law of grain boundary motion.Comment: 4 pages, 4 figure

Post-encoding reactivation is related to learning of episodes in humans

Prior animal and human studies have shown that post-encoding reinstatement plays an important role in organizing the temporal sequence of unfolding episodes in memory. Here, we investigated whether post-encoding reinstatement serves to promote the encoding of "one-shot" episodic learning beyond the temporal structure in humans. In Experiment 1, participants encoded sequences of pictures depicting unique and meaningful episodic-like events. We used representational similarity analysis on scalp EEG recordings during encoding and found evidence of rapid picture-elicited EEG pattern reinstatement at episodic offset (around 500 msec post-episode). Memory reinstatement was not observed between successive elements within an episode, and the degree of memory reinstatement at episodic offset predicted later recall for that episode. In Experiment 2, participants encoded a shuffled version of the picture sequences from Experiment 1, rendering each episode meaningless to the participant but temporally structured as in Experiment 1, and we found no evidence of memory reinstatement at episodic offset. These results suggest that post-encoding memory reinstatement is akin to the rapid formation of unique and meaningful episodes that unfold over time

A phenomenological model of weakly damped Faraday waves and the associated mean flow

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 new 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.Comment: Complete paper with embedded figures (PostScript, 3 Mb) http://www.csit.fsu.edu/~vinals/mss/jmv1.p

Accelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processor

FM-index is a compact data structure suitable for fast matches of short reads to large reference genomes. The matching algorithm using this index exhibits irregular memory access patterns that cause frequent cache misses, resulting in a memory bound problem. This paper analyzes different FM-index versions presented in the literature, focusing on those computing aspects related to the data access. As a result of the analysis, we propose a new organization of FM-index that minimizes the demand for memory bandwidth, allowing a great improvement of performance on processors with high-bandwidth memory, such as the second-generation Intel Xeon Phi (Knights Landing, or KNL), integrating ultra high-bandwidth stacked memory technology. As the roofline model shows, our implementation reaches 95% of the peak random access bandwidth limit when executed on the KNL and almost all the available bandwidth when executed on other Intel Xeon architectures with conventional DDR memory. In addition, the obtained throughput in KNL is much higher than the results reported for GPUs in the literature. IEE

Shear induced grain boundary motion for lamellar phases in the weakly nonlinear regime

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 wavenumber 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