Highly Reproducible, Bio-Based Slab Photonic Crystals Grown by Diatoms

Shaping in the Third Direction: Colloidal Photonic Crystals with Quadratic Surfaces Self-Assembled by Hanging-Drop Method

High-quality, 3D-shaped, SiO2 colloidal photonic crystals (ellipsoids, hyperboloids, and others) were fabricated by self-assembly. They possess a quadratic surface and are wide-angle-independent, direction-dependent, diffractive reflection crystals. Their size varies between 1 and 5 mm and can be achieved as mechanical-resistant, free-standing, thick (hundreds of ordered layers) objects. High-quality, 3D-shaped, polystyrene inverse-opal photonic superstructures (highly similar to diatom frustules) were synthesized by using an inside infiltration method as wide-angle-independent, reflective diffraction objects. They possess multiple reflection bands given by their special architecture (a torus on the top of an ellipsoid) and by their different sized holes (384 nm and 264 nm). Our hanging-drop self-assembly approach uses setups which deform the shape of an ordinary spherical drop; thus, the colloidal self-assembly takes place on a non-axisymmetric liquid/air interface. The deformed drop surface is a kind of topological interface which changes its shape in time, remaining as a quality template for the self-assembly process. Three-dimensional-shaped colloidal photonic crystals might be used as devices for future spectrophotometers, aspheric or freeform diffracting mirrors, or metasurfaces for experiments regarding space-time curvature analogy.

Multiple-pathways light modulation in Pleurosigma strigosum bi-raphid diatom

Ordered, quasi-ordered, and even disordered nanostructures can be identified as constituent components of several protists, plants and animals, making possible an efficient manipulation of light for intra- and inter- species communication, camouflage, or for the enhancement of primary production. Diatoms are ubiquitous unicellular microalgae inhabiting all the aquatic environments on Earth. They developed, through tens of millions of years of evolution, ultrastructured silica cell walls, the frustules, able to handle optical radiation through multiple diffractive, refractive, and wave-guiding processes, possibly at the basis of their high photosynthetic efficiency. In this study, we employed a range of imaging, spectroscopic and numerical techniques (including transmission imaging, digital holography, photoluminescence spectroscopy, and numerical simulations based on wide-angle beam propagation method) to identify and describe different mechanisms by which Pleurosigma strigosum frustules can modulate optical radiation of different spectral content. Finally, we correlated the optical response of the frustule to the interaction with light in living, individual cells within their aquatic environment following various irradiation treatments. The obtained results demonstrate the favorable transmission of photosynthetic active radiation inside the cell compared to potentially detrimental ultraviolet radiation.

Extending the diatom's color palette: non-iridescent, disorder-mediated coloration in marine diatom-inspired nanomembranes

The intricate, siliceous exoskeleton of many marine diatoms (single-celled phytoplankton) is decorated with an array of sub-micron, quasi-ordered pores that are known to provide protective and multiple life-sustaining functions. However, the optical functionality of any given diatom valve is limited because valve geometry, composition, and ordering are genetically programmed. Nonetheless, the near- and sub-wavelength features of diatom valves provide inspiration for novel photonic surfaces and devices. Herein, we explore the optical design space for optical transmission, reflection, and scattering in diatom-like structures by computationally deconstructing the diatom frustule, assigning and nondimensionalizing Fano-resonant behavior with configurations of increasing refractive index contrast (Δn), and gauging the effects of structural disorder on the resulting optical response. Translational pore disorder, especially in higher-index materials, was found to evolve Fano resonances from near-unity reflection and transmission to modally confined, angle-independent scattering, which is key to non-iridescent coloration in the visible wavelength range. High-index, frustule-like TiO₂ nanomembranes were then designed to maximize backscattering intensity and fabricated using colloidal lithography. These synthetic diatom surfaces showed saturated, non-iridescent coloration across the visible spectrum. Overall, this diatom-inspired platform could be useful in designing tailored, functional, and nanostructured surfaces for applications in optics, heterogeneous catalysis, sensing, and optoelectronics.

Numerical Analysis of the Light Modulation by the Frustule of Gomphonema parvulum: The Role of Integrated Optical Components

Siliceous diatom frustules present a huge variety of shapes and nanometric pore patterns. A better understanding of the light modulation by these frustules is required to determine whether or not they might have photobiological roles besides their possible utilization as building blocks in photonic applications. In this study, we propose a novel approach for analyzing the near-field light modulation by small pennate diatom frustules, utilizing the frustule of Gomphonema parvulum as a model. Numerical analysis was carried out for the wave propagation across selected 2D cross-sections in a statistically representative 3D model for the valve based on the finite element frequency domain method. The influences of light wavelength (vacuum wavelengths from 300 to 800 nm) and refractive index changes, as well as structural parameters, on the light modulation were investigated and compared to theoretical predictions when possible. The results showed complex interference patterns resulting from the overlay of different optical phenomena, which can be explained by the presence of a few integrated optical components in the valve. Moreover, studies on the complete frustule in an aqueous medium allow the discussion of its possible photobiological relevance. Furthermore, our results may enable the simple screening of unstudied pennate frustules for photonic applications.

Measuring Photonics in Photosynthesis: Combined Micro-Fourier Image Spectroscopy and Pulse Amplitude Modulated Chlorophyll Fluorimetry at the Micrometre-Scale

Natural photonic structures are common across the biological kingdoms, serving a diversity of functionalities. The study of implications of photonic structures in plants and other phototrophic organisms is still hampered by missing methodologies for determining in situ photonic properties, particularly in the context of constantly adapting photosynthetic systems controlled by acclimation mechanisms on the cellular scale. We describe an innovative approach to determining spatial and spectral photonic properties and photosynthesis activity, employing micro-Fourier Image Spectroscopy and Pulse Amplitude Modulated Chlorophyll Fluorimetry in a combined microscope setup. Using two examples from the photosynthetic realm, the dynamic Bragg-stack-like thylakoid structures of Begonia sp. and complex 2.5 D photonic crystal slabs from the diatom Coscinodiscus granii, we demonstrate how the setup can be used for measuring self-adapting photonic-photosynthetic systems and photonic properties on single-cell scales. We suggest that the setup is well-suited for the determination of photonic–photosynthetic systems in a diversity of organisms, facilitating the cellular, temporal, spectral and angular resolution of both light distribution and combined chlorophyll fluorescence determination. As the catalogue of photonic structure from photosynthetic organisms is rich and diverse in examples, a deepened study could inspire the design of novel optical- and light-harvesting technologies.

Diatom biosilica in plasmonics: applications in sensing, diagnostics and therapeutics [Invited]

Several living organisms are able to synthesize complex nanostructures provided with peculiar physical and chemical properties by means of finely-tuned, genetically controlled biomineralization processes. Frustules, in particular, are micro- and nano-structured silica shells produced by ubiquitous diatom microalgae, whose optical properties have been recently exploited in photonics, solar energy harvesting, and biosensing. Metallization of diatom biosilica, both in the shape of intact frustules or diatomite particles, can trigger plasmonic effects that in turn can find application in high-sensitive detection platforms, allowing to obtain effective nanosensors at low cost and on a large scale. The aim of the present review article is to provide a wide, complete overview on the main metallization techniques applied to diatom biosilica and on the principal applications of diatom-based plasmonic devices mainly but not exclusively in the fields of biochemical sensing, diagnostics and therapeutics.

Underwater Light Manipulation by the Benthic Diatom Ctenophora pulchella: From PAR Efficient Collection to UVR Screening

Several species of diatoms, unicellular microalgae which constitute the main component of phytoplankton, are characterized by an impressive photosynthetic efficiency while presenting a noticeable tolerance versus exposure to detrimental UV radiation (UVR). In particular, the growth rate of the araphid diatom Ctenophora pulchella is not significantly affected by harsh treatments with UVR, even in absence of detectable, specific UV-absorbing pigments and even if it is not able to avoid high UV exposure by motility. In this work we applied a multi-disciplinary approach involving numerical computation, photonics, and biological parameters in order to investigate the possible role of the frustule, micro- and nano-patterned silica shell which encloses the cell, in the ability of C. pulchella to efficiently collect photosynthetic active radiation (PAR) and to simultaneously screen the protoplasm from UVR. The characterization of the photonic properties of the frustule has been accompanied by in vivo experiments conducted in water in order to investigate its function as optical coupler between light and plastids.

Finite-difference Time-domain (FDTD) Optical Simulations: A Primer for the Life Sciences and Bio-Inspired Engineering

Light influences most ecosystems on earth, from sun-dappled forests to bioluminescent creatures in the ocean deep. Biologists have long studied nano- and micro-scale organismal adaptations to manipulate light using ever-more sophisticated microscopy, spectroscopy, and other analytical equipment. In combination with experimental tools, simulations of light interacting with objects can help researchers determine the impact of observed structures and explore how variations affect optical function. In particular, the finite-difference time-domain (FDTD) method is widely used throughout the nanophotonics community to efficiently simulate light interacting with a variety of materials and optical devices. More recently, FDTD has been used to characterize optical adaptations in nature, such as camouflage in fish and other organisms, colors in sexually-selected birds and spiders, and photosynthetic efficiency in plants. FDTD is also common in bioengineering, as the design of biologically-inspired engineered structures can be guided and optimized through FDTD simulations. Parameter sweeps are a particularly useful application of FDTD, which allows researchers to explore a range of variables and modifications in natural and synthetic systems (e.g., to investigate the optical effects of changing the sizes, shape, or refractive indices of a structure). Here, we review the use of FDTD simulations in biology and present a brief methods primer tailored for life scientists, with a focus on the commercially available software Lumerical FDTD. We give special attention to whether FDTD is the right tool to use, how experimental techniques are used to acquire and import the structures of interest, and how their optical properties such as refractive index and absorption are obtained. This primer is intended to help researchers understand FDTD, implement the method to model optical effects, and learn about the benefits and limitations of this tool. Altogether, FDTD is well-suited to (i) characterize optical adaptations and (ii) provide mechanistic explanations; by doing so, it helps (iii) make conclusions about evolutionary theory and (iv) inspire new technologies based on natural structures.

Physical, Chemical, and Genetic Techniques for Diatom Frustule Modification: Applications in Nanotechnology

Diatom frustules represent one of the most complex examples of micro- and nano-structured materials found in nature, being the result of a biomineralization process refined through tens of milions of years of evolution. They are constituted by an intricate, ordered porous silica matrix which recently found several applications in optoelectronics, sensing, solar light harvesting, filtering, and drug delivery, to name a few. The possibility to modify the composition and the structure of frustules can further broaden the range of potential applications, adding new functions and active features to the material. In the present work the most remarkable physical and chemical techniques aimed at frustule modification are reviewed, also examining the most recent genetic techniques developed for its controlled morphological mutation.

Biosilica slab photonic crystals as an alternative to cleanroom nanofabrication?

Photonics, the manipulation of light at nanoscale, is a key enabling technology with impact in health and energy applications, among others. In most cases photonics still relies on materials and fabrication methods inherited from other disciplines, usually requiring expensive, time-consuming and environmentally-unfriendly processes. Recent experiments demonstrated that advanced photonic materials, as complex as those known as 2.5 dimensional slab photonic crystals, also occur naturally in diatoms. These microscopic algae precipitate silicic acid from water to produce silicon dioxide membranes, relying on intracellular biomineralization mechanisms. Addressing some important aspects for the potential industrial utilization of these structures, we here propose that optical materials produced by the diatoms could serve as cost-effective and environmentally friendly alternatives to cleanroom nanofabrication. We demonstrate that photonic materials grown by the diatom species Coscinodiscus granii can be separated based on its hydrokinetic characteristics. We further show that the photonic membranes present low defect rates of ca. 1/100 unit cells and that variation in pore diameter, as observed between individual membranes, can affect the photonic properties at large, but only marginally at low refractive index contrast. Finally, we list algal culture collections operating worldwide, thus providing a global network for live diatoms and diatom materials. We discuss the feasibility and bottlenecks related to scaled-up growth for direct utilization of photonic materials from diatoms.