SPIRE-a software tool for bicontinuous phase recognition: application for plastid cubic membranes.

Bicontinuous membranes in cell organelles epitomize nature's ability to create complex functional nanostructures. Like their synthetic counterparts, these membranes are characterized by continuous membrane sheets draped onto topologically complex saddle-shaped surfaces with a periodic network-like structure. Their structure sizes, (around 50-500 nm), and fluid nature make transmission electron microscopy (TEM) the analysis method of choice to decipher their nanostructural features. Here we present a tool, Surface Projection Image Recognition Environment (SPIRE), to identify bicontinuous structures from TEM sections through interactive identification by comparison to mathematical "nodal surface" models. The prolamellar body (PLB) of plant etioplasts is a bicontinuous membrane structure with a key physiological role in chloroplast biogenesis. However, the determination of its spatial structural features has been held back by the lack of tools enabling the identification and quantitative analysis of symmetric membrane conformations. Using our SPIRE tool, we achieved a robust identification of the bicontinuous diamond surface as the dominant PLB geometry in angiosperm etioplasts in contrast to earlier long-standing assertions in the literature. Our data also provide insights into membrane storage capacities of PLBs with different volume proportions and hint at the limited role of a plastid ribosome localization directly inside the PLB grid for its proper functioning. This represents an important step in understanding their as yet elusive structure-function relationship.

Quo vadis biophotonics? Wearing serendipity and slow science as a badge of pride, and embracing biology.

This article is a reflection on the themes of the Faraday Discussion meeting on 'Biological and bio-inspired optics' held from 20 to 22 July 2020. It is a personal perspective on the nature of this field as a broad and interdisciplinary field that has led to a sound understanding of the material properties of biological nanostructured and optical materials. The article describes how the nature of the field and the themes of the conference are reflected in particular in work on the 3D bicontinuous biophotonic nanostructures known as single gyroids and in bicontinuous structures more broadly. Such single gyroid materials are found for example in the butterfly Thecla opisena, where the questions of biophotonic response, of bio-inspired optics, of the relationship between structure and function, and of the relationship between natural and synthetic realisations are closely interlinked. This multitude of facets of research on single gyroid structures reflects the beauty of the broader field of biophotonics, namely as a field that lives through embracing the serendipitous discovery of the biophotonic marvels that nature offers to us as seeds for in-depth analysis and understanding. The meandering nature of its discoveries, and the need to accept the slowness that comes from exploration of intellectually new or foreign territory, mean that the field shares some traits with biological evolution itself. Looking into the future, I consider that a closer engagement with living tissue and with the biological questions of function and formation, rather than with the materials science of biological materials, will help ensure the continuing great success of this field.

Low-temperature statistical mechanics of the Quantizer problem: Fast quenching and equilibrium cooling of the three-dimensional Voronoi liquid.

The quantizer problem is a tessellation optimization problem where point configurations are identified such that the Voronoi cells minimize the second moment of the volume distribution. While the ground state (optimal state) in 3D is almost certainly the body-centered cubic lattice, disordered and effectively hyperuniform states with energies very close to the ground state exist that result as stable states in an evolution through the geometric Lloyd's algorithm [M. A. Klatt et al. Nat. Commun. 10, 811 (2019)]. When considered as a statistical mechanics problem at finite temperature, the same system has been termed the "Voronoi liquid" by Ruscher, Baschnagel, and Farago [Europhys. Lett. 112, 66003 (2015)]. Here, we investigate the cooling behavior of the Voronoi liquid with a particular view to the stability of the effectively hyperuniform disordered state. As a confirmation of the results by Ruscher et al., we observe, by both molecular dynamics and Monte Carlo simulations, that upon slow quasi-static equilibrium cooling, the Voronoi liquid crystallizes from a disordered configuration into the body-centered cubic configuration. By contrast, upon sufficiently fast non-equilibrium cooling (and not just in the limit of a maximally fast quench), the Voronoi liquid adopts similar states as the effectively hyperuniform inherent structures identified by Klatt et al. and prevents the ordering transition into a body-centered cubic ordered structure. This result is in line with the geometric intuition that the geometric Lloyd's algorithm corresponds to a type of fast quench.

Self-assembly and entropic effects in pear-shaped colloid systems. I. Shape sensitivity of bilayer phases in colloidal pear-shaped particle systems.

The role of particle shape in self-assembly processes is a double-edged sword. On the one hand, particle shape and particle elongation are often considered the most fundamental determinants of soft matter structure formation. On the other hand, structure formation is often highly sensitive to details of shape. Here, we address the question of particle shape sensitivity for the self-assembly of hard pear-shaped particles by studying two models for this system: (a) the pear hard Gaussian overlap (PHGO) and (b) the hard pears of revolution (HPR) model. Hard pear-shaped particles, given by the PHGO model, are known to form a bicontinuous gyroid phase spontaneously. However, this model does not replicate an additive object perfectly and, hence, varies slightly in shape from a "true" pear-shape. Therefore, we investigate in the first part of this series the stability of the gyroid phase in pear-shaped particle systems. We show, based on the HPR phase diagram, that the gyroid phase does not form in pears with such a "true" hard pear-shaped potential. Moreover, we acquire first indications from the HPR and PHGO pair-correlation functions that the formation of the gyroid is probably attributed to the small non-additive properties of the PHGO potential.

Self-assembly and entropic effects in pear-shaped colloid systems. II. Depletion attraction of pear-shaped particles in a hard-sphere solvent.

We consider depletion effects of a pear-shaped colloidal particle in a hard-sphere solvent for two different model realizations of the pear-shaped colloidal particle. The two models are the pear hard Gaussian overlap (PHGO) particles and the hard pears of revolution (HPR). The motivation for this study is to provide a microscopic understanding for the substantially different mesoscopic self-assembly properties of these pear-shaped colloids, in dense suspensions, that have been reported in the previous studies. This is done by determining their differing depletion attractions via Monte Carlo simulations of PHGO and HPR particles in a pool of hard spheres and comparing them with excluded volume calculations of numerically obtained ideal configurations on the microscopic level. While the HPR model behaves as predicted by the analysis of excluded volumes, the PHGO model showcases a preference for splay between neighboring particles, which can be attributed to the special non-additive characteristics of the PHGO contact function. Lastly, we propose a potentially experimentally realizable pear-shaped particle model, the non-additive hard pear of revolution model, which is based on the HPR model but also features non-additive traits similar to those of PHGO particles to mimic their depletion behavior.

Patchy particles by self-assembly of star copolymers on a spherical substrate: Thomson solutions in a geometric problem with a color constraint.

Confinement or geometric frustration is known to alter the structure of soft matter, including copolymeric melts, and can consequently be used to tune structure and properties. Here we investigate the self-assembly of ABC and ABB 3-miktoarm star copolymers confined to a spherical shell using coarse-grained dissipative particle dynamics simulations. In bulk and flat geometries the ABC stars form hexagonal tilings, but this is topologically prohibited in a spherical geometry which normally is alleviated by forming pentagonal tiles. However, the molecular architecture of the ABC stars implies an additional 'color constraint' which only allows even tilings (where all polygons have an even number of edges) and we study the effect of these simultaneous constraints. We find that both ABC and ABB systems form spherical tiling patterns, the type of which depends on the radius of the spherical substrate. For small spherical substrates, all solutions correspond to patterns solving the Thomson problem of placing mobile repulsive electric charges on a sphere. In ABC systems we find three coexisting, possibly different tilings, one in each color, each of them solving the Thomson problem simultaneously. For all except the smallest substrates, we find competing solutions with seemingly degenerate free energies that occur with different probabilities. Statistically, an observer who is blind to the differences between B and C can tell from the structure of the A domains if the system is an ABC or an ABB star copolymer system.

Geometric effects in random assemblies of ellipses.

Assemblies of anisotropic particles commonly appear in studies of active many-body systems. However, in two dimensions, the geometric ramifications of the finite density of such objects are not entirely understood. To fully characterize these effects, we perform an in-depth study of random assemblies generated by a slow compression of frictionless elliptical particles. The obtained configurations are then analysed using the Set Voronoi tessellation, which takes the particle shape into account. Not only do we analyse most scalar and vectorial morphological measures, which are commonly discussed in the literature or which have recently been addressed in experiments, but we also systematically explore the correlations between them. While in a limited range of parameters similarities with findings in 3D assemblies could be identified, important differences are found when a broad range of aspect ratios and packing fractions are considered. The data discussed in this study should thus provide a unique reference set such that geometric effects and differences from random assemblies could be clearly identified in more complex systems, including ones with soft and active particles that are typically found in biological systems.

Metallic gyroids with broadband circular dichroism.

Circular dichroism is a useful property for filtering or separating beams containing opposite spin angular momentum. Of the many geometries exhibiting circular dichroism, the gyroid has proven to be an excellent template for exploring circular dichroism in three dimensions. However, the bandwidth of the circular dichroism from dielectric gyroids is limited by its narrow circularly polarized stop band. Here we investigate conductive silver gyroid micro-structures using direct laser writing of polymeric templates followed by the electroless deposition of a uniform silver coating. We show that the transformation from dielectric to silver gyroid micro-structure can increase the circular dichroism bandwidth by close to a factor of 3.

Density functional theory for hard uniaxial particles: Complex ordering of pear-shaped and spheroidal particles near a substrate.

We develop a density functional for hard particles with a smooth uniaxial shape (including non-inversion-symmetric particles) within the framework of fundamental measure theory. By applying it to a system of tapered, aspherical liquid-crystal formers, reminiscent of pears, we analyse their behaviour near a hard substrate. The theory predicts a complex orientational ordering close to the substrate, which can be directly related to the particle shape, in good agreement with our simulation results. Furthermore, the lack of particle inversion-symmetry implies the possibility of alternating orientations in subsequent layers as found in a smectic/lamellar phase of such particles. Both theory and Monte Carlo simulations confirm that such ordering occurs in our system. Our results are relevant for adsorption processes of asymmetric colloidal particles and molecules at hard interfaces and show once again that tapering strongly affects the properties of orientationally ordered phases.

Coexistence of both gyroid chiralities in individual butterfly wing scales of Callophrys rubi.

The wing scales of the Green Hairstreak butterfly Callophrys rubi consist of crystalline domains with sizes of a few micrometers, which exhibit a congenitally handed porous chitin microstructure identified as the chiral triply periodic single-gyroid structure. Here, the chirality and crystallographic texture of these domains are investigated by means of electron tomography. The tomograms unambiguously reveal the coexistence of the two enantiomeric forms of opposite handedness: the left- and right-handed gyroids. These two enantiomers appear with nonequal probabilities, implying that molecularly chiral constituents of the biological formation process presumably invoke a chiral symmetry break, resulting in a preferred enantiomeric form of the gyroid structure. Assuming validity of the formation model proposed by Ghiradella H (1989) J Morphol 202(1):69-88 and Saranathan V, et al. (2010) Proc Natl Acad Sci USA 107(26):11676-11681, where the two enantiomeric labyrinthine domains of the gyroid are connected to the extracellular and intra-SER spaces, our findings imply that the structural chirality of the single gyroid is, however, not caused by the molecular chirality of chitin. Furthermore, the wing scales are found to be highly textured, with a substantial fraction of domains exhibiting the <001> directions of the gyroid crystal aligned parallel to the scale surface normal. Both findings are needed to completely understand the photonic purpose of the single gyroid in gyroid-forming butterflies. More importantly, they show the level of control that morphogenesis exerts over secondary features of biological nanostructures, such as chirality or crystallographic texture, providing inspiration for biomimetic replication strategies for synthetic self-assembly mechanisms.

Harmonic distortions enhance circular dichroism of dielectric single gyroids.

The departure from strict periodic order in two-phase dielectric materials can offer properties that are otherwise inaccessible to perfectly ordered photonic crystals. Herewith, we investigate the circular dichroism of the single gyroid photonic crystal in the presence of spatial distortions. FDTD simulations and microwave transmission measurements on 3D-printed replicas show that certain harmonic long-wavelength spatial distortions ("sinusoidal chirp") nearly doubles the imbalance of the circular polarisation reflectances, as well as significantly strengthens polarisation-incoherent reflectance. The observed changes are partially rationalised by comparison with simpler distortion models (linear chirp and tetragonal deformation) of the Gyroid.

Splitting of the Universality Class of Anomalous Transport in Crowded Media.

We investigate the emergence of subdiffusive transport by obstruction in continuum models for molecular crowding. While the underlying percolation transition for the accessible space displays universal behavior, the dynamic properties depend in a subtle nonuniversal way on the transport through narrow channels. At the same time, the different universality classes are robust with respect to introducing correlations in the obstacle matrix as we demonstrate for quenched hard-sphere liquids as underlying structures. Our results confirm that the microscopic dynamics can dominate the relaxational behavior even at long times, in striking contrast to glassy dynamics.

The microscopic structure of mono-disperse granular heaps and sediments of particles on inclined surfaces.

Granular heaps of particles created by deposition of mono-disperse particles raining from an extended source of finite size are characterized by a non-homogeneous field of density. It was speculated that this inhomogeneity is due to the transient shape of the sediment during the process of construction of the heap, thus reflecting the history of the creation of the heap. By comparison of structural characteristics of the heap with sediments created on top of inclined planes exploiting the method of Minkowski tensors, we provide further evidence to support this hypothesis. Moreover, for the case of sediments generated by homogeneous rain on surfaces, we provide relationships between the inclination of the surface and the Minkowski measures characterizing the isotropy of local particle environments.

Observation of optical activity in dielectric biomimetic 8-srs networks.

We demonstrate the first experimental realization of the 8-srs network by direct laser writing in a dielectric medium. The optical properties of this photonic crystal are both numerically simulated and experimentally measured. The numerical simulations indicate a strong optical activity (OA) for regions of the spectrum close to the unit cell size (3 µm) and a high sensitivity to angular resolution. Experimentally, we observe 40° of OA for a region of the spectrum between 3 and 3.5 µm, confirming both simulation predictions.

Local origin of global contact numbers in frictional ellipsoid packings.

In particulate soft matter systems the average number of contacts Z of a particle is an important predictor of the mechanical properties of the system. Using x-ray tomography, we analyze packings of frictional, oblate ellipsoids of various aspect ratios α, prepared at different global volume fractions ϕg. We find that Z is a monotonically increasing function of ϕg for all α. We demonstrate that this functional dependence can be explained by a local analysis where each particle is described by its local volume fraction ϕl computed from a Voronoi tessellation. Z can be expressed as an integral over all values of ϕl: Z(ϕg,α,X)=∫Zl(ϕl,α,X)P(ϕl|ϕg)dϕl. The local contact number function Zl(ϕl,α,X) describes the relevant physics in term of locally defined variables only, including possible higher order terms X. The conditional probability P(ϕl|ϕg) to find a specific value of ϕl given a global packing fraction ϕg is found to be independent of α and X. Our results demonstrate that for frictional particles a local approach is not only a theoretical requirement but also feasible.

Comment on "Discovery of a tetracontinuous, aqueous lyotropic network phase with unusual 3D-hexagonal symmetry" by M. Mahanthappa, G. Sorenson and A. Schmitt.

The article by Sorenson et al. (Soft Matter10, 8229, 2014) reports a novel phase formed by gemini surfactants in water, of symmetry P63/mcm and based on a triple intergrowth of three identical degree-three networks, known as 3etc(193). This phase is the first lyotropic liquid crystalline phase based on the intergrowth of a triplet of network- or labyrinth-like hydrophobic domains. We provide here results from self-consistent field theory that demonstrate that the same morphology is almost stable in standard AB diblock copolymer melts; at the phase transition between the double gyroid phase and the hexagonal columnar phase, the 3etc(193) morphology only incurs a marginal free energy penalty compared to the equilibrium phases. Interestingly, the ratio of lattice parameters c/a = 0.955 of the 3etc(193) as a diblock morphology is very close to that of the gemini surfactant phase and of the related IBN-9 mesoporous silicate phase (Han et al., Nat. Chem.1, 123, 2009). Based on the combination of these results, we hypothesise that the 3etc(193) morphology is likely a generic phase in soft materials, rather than an oddity.

Adaptive optics enhanced direct laser writing of high refractive index gyroid photonic crystals in chalcogenide glass.

Chiral gyroid photonic crystals are fabricated in the high refractive index chalcogenide glass arsenic trisulfide with an adaptive optics enhanced direct laser writing system. The severe spherical aberration imparted when focusing into the arsenic trisulfide is mitigated with a defocus decoupled aberration compensation technique that reduces the level of aberration that must be compensated by over an order of magnitude. The fabricated gyroids are shown to have excellent uniformity after our adaptive optics method is employed, and the transmission spectra of the gyroids are shown to have good agreement with numerical simulations that are based on a uniform and diffraction limited fabrication resolution.

Composite material in the sea urchin Cidaris rugosa: ordered and disordered micrometre-scale bicontinuous geometries.

The sponge-like biomineralized calcite materials found in echinoderm skeletons are of interest in terms of both structure formation and biological function. Despite their crystalline atomic structure, they exhibit curved interfaces that have been related to known triply periodic minimal surfaces. Here, we investigate the endoskeleton of the sea urchin Cidaris rugosa that has long been known to form a microstructure related to the Primitive surface. Using X-ray tomography, we find that the endoskeleton is organized as a composite material consisting of domains of bicontinuous microstructures with different structural properties. We describe, for the first time, the co-occurrence of ordered single Primitive and single Diamond structures and of a disordered structure within a single skeletal plate. We show that these structures can be distinguished by structural properties including solid volume fraction, trabeculae width and, to a lesser extent, interface area and mean curvature. In doing so, we present a robust method that extracts interface areas and curvature integrals from voxelized datasets using the Steiner polynomial for parallel body volumes. We discuss these very large-scale bicontinuous structures in the context of their function, formation and evolution.

Networklike propagation of cell-level stress in sheared random foams.

Quasistatic simple shearing flow of random monodisperse soap froth is investigated by analyzing surface evolver simulations of spatially periodic foams. Elastic-plastic behavior is caused by irreversible topological rearrangements (T1s) that occur when Plateau's laws are violated; the first T1 determines the elastic limit and frequent T1 avalanches sustain the yield-stress plateau at large strains. The stress and shape anisotropy of individual cells is quantified by Q, a scalar derived from an interface tensor that gauges the cell's contribution to the global stress. During each T1 avalanche, the connected set of cells with decreasing Q, called the stress release domain, is networklike and nonlocal. Geometrically, the networklike nature of the stress release domains is corroborated through morphological analysis using the Euler characteristic. The stress release domain is distinctly different from the set of cells that change topology during a T1 avalanche. Our results highlight the connection between the unique rheological behavior of foams and the complex large-scale cooperative rearrangements of foam cells that accompany distinctly local topological transitions.

Shortcomings of the bond orientational order parameters for the analysis of disordered particulate matter.

Local structure characterization with the bond-orientational order parameters q(4), q(6), ... introduced by Steinhardt et al. [Phys. Rev. B 28, 784 (1983)] has become a standard tool in condensed matter physics, with applications including glass, jamming, melting or crystallization transitions, and cluster formation. Here, we discuss two fundamental flaws in the definition of these parameters that significantly affect their interpretation for studies of disordered systems, and offer a remedy. First, the definition of the bond-orientational order parameters considers the geometrical arrangement of a set of nearest neighboring (NN) spheres, NN(p), around a given central particle p; we show that the choice of neighborhood definition can have a bigger influence on both the numerical values and qualitative trend of q(l) than a change of the physical parameters, such as packing fraction. Second, the discrete nature of neighborhood implies that NN(p) is not a continuous function of the particle coordinates; this discontinuity, inherited by q(l), leads to a lack of robustness of the q(l) as structure metrics. Both issues can be avoided by a morphometric approach leading to the robust Minkowski structure metrics q(l)'. These q(l)' are of a similar mathematical form as the conventional bond-orientational order parameters and are mathematically equivalent to the recently introduced Minkowski tensors [G. E. Schröder-Turk et al., Europhys. Lett. 90, 34001 (2010); S. Kapfer et al., Phys. Rev. E 85, 030301(R) (2012)].