Chromonic liquid crystals and packing configurations of bacteriophage viruses.

We study equilibrium configurations of hexagonal columnar liquid crystals in the context of characterizing packing structures of bacteriophage viruses in a protein capsid. These are viruses that infect bacteria and are currently the focus of intense research efforts, with the goal of finding new therapies for bacteria-resistant antibiotics. The energy that we propose consists of the Oseen-Frank free energy of nematic liquid crystals that penalizes bending of the columnar directions, in addition to the cross-sectional elastic energy accounting for distortions of the transverse hexagonal structure; we also consider the isotropic contribution of the core and the energy of the unknown interface between the outer ordered region of the capsid and the inner disordered core. The problem becomes of free boundary type, with constraints. We show that the concentric, azimuthal, spool-like configuration is the absolute minimizer. Moreover, we present examples of toroidal structures formed by DNA in free solution and compare them with the analogous ones occurring in experiments with other types of lyotropic liquid crystals, such as food dyes and additives. This article is part of the theme issue 'Topics in mathematical design of complex materials'.

Stability analysis of flow of active extensile fibers in confined domains.

In this article, we study shear flow of active extensile filaments confined in a narrow channel. They behave as nematic liquid crystals that we assumed are governed by the Ericksen-Leslie equations of balance of linear and angular momentum. The addition of an activity source term in the Leslie stress captures the role of the biofuel prompting the dynamics. The dimensionless form of the governing system includes the Ericksen, activity, and Reynolds numbers together with the aspect ratio of the channel as the main driving parameters affecting the stability of the system. The active system that guides our analysis is composed of microtubules concentrated in bundles, hundreds of microns long, placed in a narrow channel domain, of aspect ratios in the range between 10-2 and 10-3 dimensionless units, which are able to align due to the combination of adenosine triphosphate-supplied energy and confinement effects. Specifically, this work aims at studying the role of confinement on the behavior of active matter. It is experimentally observed that, at an appropriately low activity and channel width, the active flow is laminar, with the linear velocity profile and the angle of alignment analogous to those in passive shear, developing defects and becoming chaotic, at a large activity and a channel aspect ratio. The present work addresses the laminar regime, where defect formation does not play a role. We perform a normal mode stability analysis of the base shear flow. A comprehensive description of the stability properties is obtained in terms of the driving parameters of the system. Our main finding, in addition to the geometry and magnitude of the flow profiles, and also consistent with the experimental observations, is that the transition to instability of the uniformly aligned shear flow occurs at a threshold value of the activity parameter, with the transition also being affected by the channel aspect ratio. The role of the parameters on the vorticity and angular profiles of the perturbing flow is also analyzed and found to agree with the experimentally observed transition to turbulent regimes. A spectral method based on Chebyshev polynomials is used to solve the generalized eigenvalue problems arising in the stability analysis.

Debonding waves in gel thin films.

We develop a mathematical model for the sliding of a gel sheet adhered to a moving substrate. The sliding takes place by the motion of detached region between the gel sheet and the substrates, i.e. the propagation of a Schallamach wave. Efficient numerical methods are developed to solve the problem. Numerical examples illustrate that the model can describe the Schallamach wave and are consistent with the existing experiments qualitatively.