Modelling the effects of charge on antibiotic diffusion and adsorption in liquid crystalline virus suspensions.

We develop a microscopic model of antibiotic diffusion in virus suspensions in a liquid crystalline state. We then approximate this with an effective homogenised model that is more amenable to analytical investigation, to understand the effect of charge on the antibiotic tolerance. We show that liquid crystalline virus suspensions slow down antibiotics significantly, and that electric charge strongly contributes to this by influencing the effective diameter and adsorptive capacity of the liquid crystalline viruses so that charged antibiotics diffuse much slower than neutral ones; this can be directly and efficiently derived from the homogenised model and is in good agreement with experiments in microbiology. Charge is also found to affect the relationship between antibiotic diffusion and viral packing density in a nontrivial way. The results elucidate the effect of charge on antibiotic tolerance in liquid crystalline biofilms in a manner that is straightforwardly extendable to other soft matter systems.

Spectral properties of intermediate to high refractive index nanocubes.

Plasmonic resonances in sub-wavelength cavities, created by metallic nanocubes separated from a metallic surface by a dielectric gap, lead to strong light confinement and strong Purcell effect, with many applications in spectroscopy, enhanced light emission and optomechanics. However, the limited choice of metals, and the constraints on the sizes of the nanocubes, restrict the optical wavelength range of applications. We show that dielectric nanocubes made of intermediate to high refractive index materials exhibit similar but significantly blue shifted and enriched optical responses due to the interaction between gap plasmonic modes and internal modes. This result is explained, and the efficiency of dielectric nanocubes for light absorption and spontaneous emission is quantified by comparing the optical response and induced fluorescence enhancement of nanocubes made of barium titanate, tungsten trioxide, gallium phosphide, silicon, silver and rhodium.

Analysis of light diffraction by azobenzene-based photoalignment layers.

Photoalignment materials, such as the azobenzene-based PAAD series studied here, are becoming increasingly important in liquid crystal-based optical devices and displays. Yet their properties and, in particular, their response to light, are still not fully understood. We investigate, experimentally and theoretically, the photoinduced birefringence, the order parameter and the formation of surface relief gratings, as well as the diffraction caused by them. We show that some of the azobenzene PAAD materials are suitable for the formation of surface relief gratings with high modulation depth, while others exhibit strong photoinduced birefringence. The two effects are inversely correlated: the stronger the surface relief grating is, the weaker is photoinduced birefringence. Analytical formulas based on the Raman-Nath approximation and numerical simulations of Maxwell's equations are used to quantify the diffraction caused by the induced diffraction gratings, showing excellent agreement between theory and experiment.

Characterization of optically thin cells and experimental liquid crystals.

The current development of new liquid crystal devices often requires the use of thin cells and new experimental materials. Characterizing these devices and materials with optical methods can be challenging if (1) the total phase lag is small ("thin cells") or (2) the liquid crystal optical and dielectric properties are only partially known. We explore the limitations of these two challenges for efficient characterization and assessment of new, to the best of our knowledge, liquid crystal devices. We show that it is possible to extract a wealth of liquid crystal parameters even for cells with a phase lag of ΔΦ≈π, such as E7 liquid crystal in a 1.5 µm cell, using cross-polarized intensity measurements. The reliability of the optical method is also demonstrated for liquid crystals without precise values of dielectric or refractive index coefficients.

Thermal, Quantum Antibunching and Lasing Thresholds from Single Emitters to Macroscopic Devices.

Starting from a fully quantized Hamiltonian for an ensemble of identical emitters coupled to the modes of an optical cavity, we determine analytically regimes of thermal, collective anti-bunching and laser emission that depend explicitly on the number of emitters. The lasing regime is reached for a number of emitters above a critical number-which depends on the light-matter coupling, detuning, and the dissipation rates-via a universal transition from thermal emission to collective anti-bunching to lasing as the pump increases. Cases where the second order intensity correlation fails to predict laser action are also presented.

Efficient scattering model of multilayer systems with anisotropic films.

We present an intuitive and efficient method for modeling light propagation in layered isotropic and anisotropic media, which we call the Iterated Ray Method. Considering a single layer sandwiched between semi-infinite layers, the infinite reflected and transmitted rays are summed to obtain effective Fresnel coefficients for the center layer. Thus, the system can be represented as two semi-infinite layers with an effective boundary. The model is coupled to a recursive algorithm to describe an arbitrarily large layered system in the same way. It is numerically stable in the presence of evanescent waves and computationally efficient, both in terms of operation counts and vectorization. We demonstrate its importance for the optical analysis and optimization of layered media, such as those used in photo-addressable liquid crystal cells, thin-film coatings, and Bragg gratings, by measuring the refractive index and thickness of a thin azobenzene dye photo-alignment layer, PAAD-22E, on an indium tin oxide coated glass slide.

Wide area mapping of liquid crystal devices with passive and active command layers.

We track the non-uniformity of a wide area liquid crystal device using multiple cross-polarized intensity measurements. They give us not only accurate estimates of the core physical liquid crystal parameters, such as elastic constants, but also spatial maps of the device properties, including the liquid crystal thickness and pretilt angle. A bootstrapping statistical analysis, coupled with the multiple measurements, gives us reliable error bars on all the measured parameters.

Optical measurements of the twist constant and angle in nematic liquid crystal cells.

We present a reliable optical method for measuring the twist elastic constant K 2 and for assessing the total twist angle in a standard nematic twist cell. The method relies on the use of a non-standard configuration of crossed polarisers and a twist cell, which allows us to measure accurately the twist-cell parameters by reducing the degeneracy between them. Grid patching and an efficient beam propagation method are utilised in the numerical models used for fitting the experimental data. The modelling shows that the polarisation dynamics in a twist cell is non-trivial and much more complex than in a planar cell. The twist elastic constant of three commonly used liquid crystals (5CB, 6CHBT and E7) was successfully extracted from cross-polarised intensity measurements.

Thermoplasmonic Controlled Optical Absorber Based on a Liquid Crystal Metasurface.

Metasurfaces can be realized by organizing subwavelength elements (e.g., plasmonic nanoparticles) on a reflective surface covered with a dielectric layer. Such an array of resonators, acting collectively, can completely absorb the resulting resonant wavelength. Unfortunately, despite the excellent optical properties of metasurfaces, they lack the tunability to perform as adaptive optical components. To boost the utilization of metasurfaces and realize a new generation of dynamically controlled optical components, we report our recent finding based on the powerful combination of an innovative metasurface-optical absorber and nematic liquid crystals (NLCs). The metasurface consists of self-assembled silver nanocubes (AgNCs) immobilized on a 50 nm thick gold layer by using a polyelectrolyte multilayer as a dielectric spacer. The resulting optical absorbers show a well-defined reflection band centered in the near-infrared of the electromagnetic spectrum (750-770 nm), a very high absorption efficiency (∼60%) at the resonant wavelength, and an elevated photothermal efficiency estimated from the time constant value (34 s). Such a metasurface-based optical absorber, combined with an NLC layer, planarly aligned via a photoaligned top cover glass substrate, shows homogeneous NLC alignment and an absorption band photothermally tunable over approximately 46 nm. Detailed thermographic studies and spectroscopic investigations highlight the extraordinary capability of the active metasurface to be used as a light-controllable optical absorber.

Topological Learning for the Classification of Disorder: An Application to the Design of Metasurfaces.

Structural disorder can improve the optical properties of metasurfaces, whether it is emerging from some large-scale fabrication methods or explicitly designed and built lithographically. For example, correlated disorder, induced by a minimum inter-nanostructure distance or by hyperuniformity properties, is particularly beneficial for light extraction. Inspired by topology, we introduce numerical descriptors to provide quantitative measures of disorder with universal properties, suitable to treat both uncorrelated and correlated disorder at all length scales. The accuracy of these topological descriptors is illustrated both theoretically and experimentally by using them to design plasmonic metasurfaces with controlled disorder that we then correlate to the strength of their surface lattice resonances. These descriptors are an example of topological tools that can be used for the fast and accurate design of disordered structures or as aid in improving their fabrication methods.

Photorefractive control of surface plasmon polaritons in a hybrid liquid crystal cell.

We present a photorefractive hybrid liquid crystal system that allows strong photorefractive effects on surface plasmon polaritons. We demonstrate its capability to couple energy between two 1.03 eV surface plasmon polariton modes with an efficiency of 25.3±2.3%. We present the energy and grating pitch dependence of the diffraction and a model that can qualitatively explain them.

Modelling of filamentous phage-induced antibiotic tolerance of P. aeruginosa.

Filamentous molecules tend to spontaneously assemble into liquid crystalline droplets with a tactoid morphology in environments with high concentration on non-adsorbing molecules. Tactoids of filamentous Pf bacteriophage, such as those produced by Pseudomonas aeruginosa, have been linked to increased antibiotic tolerance. We modelled this system and show that tactoids composed of filamentous Pf virions can lead to antibiotic tolerance by acting as an adsorptive diffusion barrier. The continuum model, reminiscent of descriptions of reactive diffusion in porous media, has been solved numerically and good agreement was found with the analytical results, obtained using a homogenisation approach. We find that the formation of tactoids significantly increases antibiotic diffusion times which may lead to stronger antibiotic resistance.

Nanoparticle-Induced Property Changes in Nematic Liquid Crystals.

Doping liquid crystals with nanoparticles is a widely accepted method to enhance liquid crystal's intrinsic properties. In this study, a quick and reliable method to characterise such colloidal suspensions using an optical multi-parameter analyser, a cross-polarised intensity measurement-based device, is presented. Suspensions characterised in this work are either plasmonic (azo-thiol gold AzoGNPs) or ferroelectric Sn2P2S6 (SPS) nanoparticles in nematic liquid crystals. The elastic constants and rotational viscosity showed nonlinear dependence on the concentration of AzoGNPs, initially increasing at lower concentrations and then decreasing at higher concentrations, indicating some degree of particle aggregation. For the SPS suspension, the elastic constant decreased with doping, while the rotational viscosity increased, in agreement with previous findings. Through viscosity measurements, the stability of SPS suspension over ten years is also highlighted.

High-frequency stimulation in Parkinson's disease: more or less?

Deep-brain stimulation at high frequency is now considered the most effective neurosurgical therapy for movement disorders. An electrode is chronically implanted in a particular area of the brain and, when continuously stimulated, it significantly alleviates motor symptoms. In Parkinson's disease, common target nuclei of high-frequency stimulation (HFS) are ventral thalamic nuclei and basal ganglia nuclei, such as the internal segment of the pallidum and the subthalamic nucleus (STN), with a preference for the STN in recent years. Two fundamental mechanisms have been proposed to underlie the beneficial effects of HFS: silencing or excitation of STN neurons. Relying on recent experimental data, we suggest that both are instrumental: HFS switches off a pathological disrupted activity in the STN (a 'less' mechanism) and imposes a new type of discharge in the upper gamma-band frequency that is endowed with beneficial effects (a 'more' mechanism). The intrinsic capacity of basal ganglia and particular STN neurons to generate oscillations and shift rapidly from a physiological to a pathogenic pattern is pivotal in the operation of these circuits in health and disease.

The ion channel inverse problem: neuroinformatics meets biophysics.

Ion channels are the building blocks of the information processing capability of neurons: any realistic computational model of a neuron must include reliable and effective ion channel components. Sophisticated statistical and computational tools have been developed to study the ion channel structure-function relationship, but this work is rarely incorporated into the models used for single neurons or small networks. The disjunction is partly a matter of convention. Structure-function studies typically use a single Markov model for the whole channel whereas until recently whole-cell modeling software has focused on serial, independent, two-state subunits that can be represented by the Hodgkin-Huxley equations. More fundamentally, there is a difference in purpose that prevents models being easily reused. Biophysical models are typically developed to study one particular aspect of channel gating in detail, whereas neural modelers require broad coverage of the entire range of channel behavior that is often best achieved with approximate representations that omit structural features that cannot be adequately constrained. To bridge the gap so that more recent channel data can be used in neural models requires new computational infrastructure for bringing together diverse sources of data to arrive at best-fit models for whole-cell modeling. We review the current state of channel modeling and explore the developments needed for its conclusions to be integrated into whole-cell modeling.

Dual effect of high-frequency stimulation on subthalamic neuron activity.

Although it is well known that high-frequency stimulation (HFS) of the subthalamic nucleus (STN) alleviates the cardinal symptoms of Parkinson's disease, the underlying mechanisms are not fully understood. We investigated the effect of stimulation from low to high frequencies on rat STN neurons in naive and dopamine-depleted slices using whole-cell, current-clamp techniques and on-line artifact suppression. Stimulation at 10 Hz evoked 10 Hz single spikes but did not significantly modify ongoing STN activity. In contrast, at therapeutically relevant frequencies (80-185 Hz), stimulation had a dual effect: it fully suppressed STN spontaneous activity and generated a robust pattern of recurrent bursts of spikes, with each spike being time-locked to a stimulus pulse. Neither the suppression of spontaneous activity nor the generation of spikes was prevented by the antagonists of the metabotropic and ionotropic receptors of glutamate and gamma-aminobutyric acid. Tetrodotoxin, the Na+ channel blocker, suppressed all HFS-evoked spikes, whereas nifedipin, an L-type Ca2+-channel blocker, abolished the membrane oscillations underlying bursts. Therefore, we conclude that HFS drives the STN neuronal activity by directly activating the neuronal membrane. We suggest that this pattern may remove the deleterious activity of the basal ganglia network in the parkinsonian state and drive target neurons to a high-frequency state of activity, dependent on the characteristics of STN efferent synapses and resonant properties of target membranes.

A cross-platform freeware tool for digital reconstruction of neuronal arborizations from image stacks.

Digital reconstruction of neuronal arborizations is an important step in the quantitative investigation of cellular neuroanatomy. In this process, neurites imaged by microscopy are semi-manually traced through the use of specialized computer software and represented as binary trees of branching cylinders (or truncated cones). Such form of the reconstruction files is efficient and parsimonious, and allows extensive morphometric analysis as well as the implementation of biophysical models of electrophysiology. Here, we describe Neuron_ Morpho, a plugin for the popular Java application ImageJ that mediates the digital reconstruction of neurons from image stacks. Both the executable and code of Neuron_ Morpho are freely distributed (www.maths. soton.ac.uk/staff/D'Alessandro/morpho or www.krasnow.gmu.edu/L-Neuron), and are compatible with all major computer platforms (including Windows, Mac, and Linux). We tested Neuron_Morpho by reconstructing two neurons from each of the two preparations representing different brain areas (hippocampus and cerebellum), neuritic type (pyramidal cell dendrites and olivar axonal projection terminals), and labeling method (rapid Golgi impregnation and anterograde dextran amine), and quantitatively comparing the resulting morphologies to those of the same cells reconstructed with the standard commercial system, Neurolucida. None of the numerous morphometric measures that were analyzed displayed any significant or systematic difference between the two reconstructing systems.

Large effect of a small bias field in liquid-crystal magnetic transitions.

Most liquid crystals show low sensitivity to magnetic field. However, in this paper we show that a small bias magnetic field not only breaks the symmetry of the ground state, but also plays a crucial role in facilitating the reorientation induced by a large test magnetic field. In particular, a small bias field may alter significantly the strength of the test field needed to observe a given reorientation of the liquid crystal. Moreover, the bias field interacts with other symmetry breaking features of the cell, e.g., pretilt, to change also the qualitative features of the equilibrium state.