Brilliant whiteness in shrimp from ultra-thin layers of birefringent nanospheres

Organic Crystals and Optical Functions in Biology: Knowns and Unknowns

Organic crystals are widely used by animals to manipulate light for producing structural colors and for improving vision. To date only seven crystal types are known to be used, and among them β-guanine crystals are by far the most widespread. The fact that almost all these crystals have unusually high refractive indices (RIs) is consistent with their light manipulation function. Here, the physical, structural, and optical principles of how light interacts with the polarizable free-electron-rich environment of these quasiaromatic molecules are addressed. How the organization of these molecules into crystalline arrays introduces optical anisotropy and finally how organisms control crystal morphology and superstructural organization to optimize functions in light reflection and scattering are also discussed. Many open questions remain in this fascinating field, some of which arise out of this in-depth analysis of the interaction of light with crystal arrays. More types of organic crystals will probably be discovered, as well as other organisms that use these crystals to manipulate light. The insights gained from biological systems can also be harnessed for improving synthetic light-manipulating materials.

Nanoscale ultrastructures increase the visual conspicuousness of signalling traits in obligate cleaner shrimps

Signal theory predicts organisms should evolve signals that are conspicuous to intended receivers in natural signalling environments. Cleaner shrimps remove ectoparasites from reef fish clients and many signal their intent to clean by whipping long, white antennae. As white is a reliably conspicuous colour in aquatic environments, we hypothesized that selection has acted to increase broad-spectrum antennal reflectance in cleaners. Using scanning electron microscopy, optical models and reflectance measurements, we found that the antennae in three obligate cleaner species from two families (Palaemonidae and Lysmatidae) had thick (∼6 µm) chitinous layers or densely packed high refractive index spheres (300-400 nm diameter), which models show increase reflectance (400-700 nm). Two facultative and non-cleaning species had no visible antennae ultrastructure beyond the chitinous exoskeleton. Antennae reflectance was significantly higher in obligate cleaners than in facultative and non-cleaning species. Our results suggest that some obligate cleaners may have evolved ultrastructures that increase the conspicuousness of their antennae as signals.

Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype

Structural color is an optical phenomenon resulting from light interacting with nanostructured materials. Although structural color (SC) is widespread in the tree of life, the underlying genetics and genomics are not well understood. Here, we collected and sequenced a set of 87 structurally colored bacterial isolates and 30 related strains lacking SC. Optical analysis of colonies indicated that diverse bacteria from at least two different phyla (Bacteroidetes and Proteobacteria) can create two-dimensional packing of cells capable of producing SC. A pan-genome-wide association approach was used to identify genes associated with SC. The biosynthesis of uroporphyrin and pterins, as well as carbohydrate utilization and metabolism, was found to be involved. Using this information, we constructed a classifier to predict SC directly from bacterial genome sequences and validated it by cultivating and scoring 100 strains that were not part of the training set. We predicted that SCr is widely distributed within gram-negative bacteria. Analysis of over 13,000 assembled metagenomes suggested that SC is nearly absent from most habitats associated with multicellular organisms except macroalgae and is abundant in marine waters and surface/air interfaces. This work provides a large-scale ecogenomics view of SC in bacteria and identifies microbial pathways and evolutionary relationships that underlie this optical phenomenon.

Bio-Inspired Crystalline Core-Shell Guanine Spherulites

Spherical particles with diameters within the wavelength of visible light, known as spherulites, manipulate light uniquely due to their spatial organization and their structural birefringence. Most of the known crystalline spherulites are branched, and composed of metals, alloys, and semi-crystalline polymers. Recently, a different spherulite architecture is discovered in the vision systems of decapod crustaceans - core-shell spherulites composed of highly birefringent (Δ n ≈ 30 % $\Delta n \approx \ 30\%$ ) organic single-crystal platelets, with exceptional optical properties. These metastructures, which efficiently scatter light even in dense aqueous environments, have no synthetic equivalence and serve as a natural proof-of-concept as well as synthetic inspiration for thin scattering media. Here, the synthesis of core-shell spherulites composed of guanine crystal platelets ((Δ n ≈ 25 % $\Delta n \approx 25\%$ ) is presented in a two-step emulsification process in which a water/oil/water emulsion and induced pH changes are used to promote interfacial crystallization. Carboxylic acids neutralize the dissolved guanine salts to form spherulites composed of single, radially stacked, β-guanine platelets, which are oriented tangentially to the spherulite surface. Using Mie theory calculations and forward scattering measurements from single spherulites, it is found that due to the single-crystal properties and orientation, the synthetic spherulites possess a high tangential refractive index, similarly to biogenic particles.

Biomimetic synthesis of single-crystalline anhydrous xanthine nanoplates in an aqueous solution with high reflectivity

Biogenic purine crystals can function in vision as light scatters, mirrors, and multilayer reflectors and produce structural colors or depolarization for camouflage. Xanthine crystals form irregular multifocal mirrors in the median ocellus of Archaeognatha. It is important to broaden the study of crystallization strategies to obtain organic crystals with purine rings in the laboratory. In this work, a facile one-step synthesis route to fabricate bio-inspired xanthine crystals is reported for the first time. The obtained rhomboidal xanthine nanoplates have similar morphology and size to biogenic xanthine crystals. Their length and thickness are about 2-4 μm and 50 nm, respectively. Lattice parameters, crystal structure, formation mechanism and optical properties of synthetic single-crystalline xanthine nanoplates were investigated in detail in this work. The obtained xanthine nanoplate crystals are proposed to be anhydrous xanthine with monoclinic symmetry, and the xanthine nanoplates mainly expose the (100) plane. It is proposed that the anhydrous xanthine nanoplates are formed via an amorphous xanthine intermediate precursor. The synthetic anhydrous xanthine nanoplates exhibit excellent optical properties, including high diffuse reflectivity, strong depolarization and pearlescent luster. This work provides a new design to synthesize bio-inspired organic molecular crystals with excellent optical properties.

Using high-resolution microscopy data to generate realistic structures for electromagnetic FDTD simulations from complex biological models

Finite-difference time-domain (FDTD) electromagnetic simulations are a computational method that has seen much success in the study of biological optics; however, such simulations are often hindered by the difficulty of faithfully replicating complex biological microstructures in the simulation space. Recently, we designed simulations to calculate the trajectory of electromagnetic light waves through realistically reconstructed retinal photoreceptors and found that cone photoreceptor mitochondria play a substantial role in shaping incoming light. In addition to vision research and ophthalmology, such simulations are broadly applicable to studies of the interaction of electromagnetic radiation with biological tissue. Here, we present our method for discretizing complex 3D models of cellular structures for use in FDTD simulations using MEEP, the MIT Electromagnetic Equation Propagation software, including subpixel smoothing at mesh boundaries. Such models can originate from experimental imaging or be constructed by hand. We also include sample code for use in MEEP. Implementation of this algorithm in new code requires understanding of 3D mathematics and may require several weeks of effort, whereas use of our sample code requires knowledge of MEEP and C++ and may take up to a few hours to prepare a model of interest for 3D FDTD simulation. In all cases, access to a facility supercomputer with parallel processing capabilities is recommended. This protocol offers a practical solution to a significant challenge in the field of computational electrodynamics and paves the way for future advancements in the study of light interaction with biological structures.

Surface-Guided Crystallization of Xanthine Derivatives for Optical Metamaterial Applications

Numerous bio-organisms employ template-assisted crystallization of molecular solids to yield crystal morphologies with unique optical properties that are difficult to reproduce synthetically. Here, a facile procedure is presented to deposit bio-inspired birefringent crystals of xanthine derivatives on a template of single-crystal quartz. Crystalline sheets that are several millimeters in length, several hundred micrometers in width, and 300-600 nm thick, are obtained. The crystal sheets are characterized with a well-defined orientation both in and out of the substrate plane, giving rise to high optical anisotropy in the plane parallel to the quartz surface, with a refractive index difference Δn ≈ 0.25 and a refractive index along the slow axis of n ≈ 1.7. It is further shown that patterning of the crystalline stripes with a tailored periodic grating leads to a thin organic polarization-dependent diffractive meta-surface, opening the door to the fabrication of various optical devices from a platform of small-molecule based organic dielectric crystals.

Backgrounds and the evolution of visual signals

Color signals which mediate behavioral interactions across taxa and contexts are often thought of as color 'patches' - parts of an animal that appear colorful compared to other parts of that animal. Color patches, however, cannot be considered in isolation because how a color is perceived depends on its visual background. This is of special relevance to the function and evolution of signals because backgrounds give rise to a fundamental tradeoff between color signal detectability and discriminability: as its contrast with the background increases, a color patch becomes more detectable, but discriminating variation in that color becomes more difficult. Thus, the signal function of color patches can only be fully understood by considering patch and background together as an integrated whole.

Prediction of Optical Properties in Particulate Media Using Double Optimization of Dependent Scattering and Particle Distribution

The prediction of optical properties dominated by light scattering in particulate media composed of high-concentration and polydisperse particles is greatly important in various optical applications. However, the accuracy and efficiency of light propagation simulations are still limited by the huge computational burden and complex interactions between dense and polydisperse particles. Here, we proposed a new optimization strategy that can effectively and accurately predict optical properties based on Monte Carlo simulation with particle size and dependent scattering corrections. Both the scattering parameters of particles and the experimental reflectance spectrum are fully examined for verification. Furthermore, using the weighted solar reflectance of particulate media as a representative optical property, both numerical simulations and experiments confirm the superiority and universality of the proposed optimization approach in a variety of materials systems. Moreover, our work can guide the design of particulate media with specific optical features insightfully and will be applicable in many fields involving multiparticle scattering.