The bee Tetragonula builds its comb like a crystal.

Stingless bees of the genus Tetragonula construct a brood comb with a spiral or a target pattern architecture in three dimensions. Crystals possess these same patterns on the molecular scale. Here, we show that the same excitable-medium dynamics governs both crystal nucleation and growth and comb construction in Tetragonula, so that a minimal coupled-map lattice model based on crystal growth explains how these bees produce the structures seen in their bee combs.

Assessment of van der Waals inclusive density functional theory methods for layered electroactive materials.

The discovery of computationally driven materials requires efficient and accurate methods. Density functional theory (DFT) meets these two requirements for many classes of materials. However, DFT-based methods have limitations. One significant shortcoming is the inadequate treatment of weak van der Waals (vdW) interactions, which are crucial for layered materials. Here we assess the performance of various vdW-inclusive DFT approaches for predicting the structure and voltage of layered electroactive materials for Li-ion batteries, considering a set of 20 different compounds. We find that the so-called optB86b-vdW density functional improves the agreement with the experimental data, closely followed by the latest generation of dispersion correction methods. These approaches yield average relative errors for the structural parameters smaller than 3%. The average deviations for redox potentials are below 0.15 V. Looking ahead, this study identifies accurate methods for Li-ion vdW bound systems, providing enhanced predictive power to DFT-assisted design for developing new types of electroactive materials in general.

Constant pressure hybrid Monte Carlo simulations in GROMACS.

Adaptation and implementation of the Generalized Shadow Hybrid Monte Carlo (GSHMC) method for molecular simulation at constant pressure in the NPT ensemble are discussed. The resulting method, termed NPT-GSHMC, combines Andersen barostat with GSHMC to enable molecular simulations in the environment natural for biological applications, namely, at constant pressure and constant temperature. Generalized Hybrid Monte Carlo methods are designed to maintain constant temperature and volume and extending their functionality to preserving pressure is not trivial. The theoretical formulation of NPT-GSHMC was previously introduced. Our main contribution is the implementation of this methodology in the GROMACS molecular simulation package and the evaluation of properties of NPT-GSHMC, such as accuracy, performance, effectiveness for real physical systems in comparison with well-established molecular simulation techniques. Benchmarking tests are presented and the obtained preliminary results are promising. For the first time, the generalized hybrid Monte Carlo simulations at constant pressure are available within the popular open source molecular dynamics software package.

Runaway electrification of friable self-replicating granular matter.

We establish that the nonlinear dynamics of collisions between particles favors the charging of an insulating, friable, self-replicating granular material that undergoes nucleation, growth, and fission processes; we demonstrate with a minimal dynamical model that secondary nucleation produces a positive feedback in an electrification mechanism that leads to runaway charging. We discuss ice as an example of such a self-replicating granular material: We confirm with laboratory experiments in which we grow ice from the vapor phase in situ within an environmental scanning electron microscope that charging causes fast-growing and easily breakable palmlike structures to form, which when broken off may form secondary nuclei. We propose that thunderstorms, both terrestrial and on other planets, and lightning in the solar nebula are instances of such runaway charging arising from this nonlinear dynamics in self-replicating granular matter.

Brinicles as a case of inverse chemical gardens.

Brinicles are hollow tubes of ice from centimeters to meters in length that form under floating sea ice in the polar oceans when dense, cold brine drains downward from sea ice to seawater close to its freezing point. When this extremely cold brine leaves the ice, it freezes the water it comes into contact with: a hollow tube of ice-a brinicle-growing downward around the plume of descending brine. We show that brinicles can be understood as a form of the self-assembled tubular precipitation structures termed chemical gardens, which are plantlike structures formed on placing together a soluble metal salt, often in the form of a seed crystal, and an aqueous solution of one of many anions, often silicate. On one hand, in the case of classical chemical gardens, an osmotic pressure difference across a semipermeable precipitation membrane that filters solutions by rejecting the solute leads to an inflow of water and to its rupture. The internal solution, generally being lighter than the external solution, flows up through the break, and as it does so, a tube grows upward by precipitation around the jet of internal solution. Such chemical-garden tubes can grow to many centimeters in length. In the case of brinicles, on the other hand, in floating sea ice we have porous ice in a mushy layer that filters out water, by freezing it, and allows concentrated brine through. Again there is an osmotic pressure difference leading to a continuing ingress of seawater in a siphon pump mechanism that is sustained as long as the ice continues to freeze. Because the brine that is pumped out is denser than the seawater and descends rather than rises, a brinicle is a downward-growing tube of ice, an inverse chemical garden.

Crystal growth as an excitable medium.

Crystal growth has been widely studied for many years, and, since the pioneering work of Burton, Cabrera and Frank, spirals and target patterns on the crystal surface have been understood as forms of tangential crystal growth mediated by defects and by two-dimensional nucleation. Similar spirals and target patterns are ubiquitous in physical systems describable as excitable media. Here, we demonstrate that this is not merely a superficial resemblance, that the physics of crystal growth can be set within the framework of an excitable medium, and that appreciating this correspondence may prove useful to both fields. Apart from solid crystals, we discuss how our model applies to the biomaterial nacre, formed by layer growth of a biological liquid crystal.

Chemical-garden formation, morphology, and composition. I. Effect of the nature of the cations.

We have grown chemical gardens in different sodium silicate solutions from several metal-ion salts--calcium chloride, manganese chloride, cobalt chloride, and nickel sulfate--with cations from period 4 of the periodic table. We have studied their formation process using photography, examined the morphologies produced using scanning electron microscopy (SEM), and analyzed chemical compositions using X-ray powder diffraction (XRD) and energy dispersive X-ray analysis (EDX) to understand better the physical and chemical processes involved in the chemical-garden reaction. We have identified different growth regimes in these salts that are dependent on the concentration of silicate solution and the nature of the cations involved.

Chemical-garden formation, morphology, and composition. II. Chemical gardens in microgravity.

We studied the growth of metal-ion silicate chemical gardens under Earth gravity (1 g) and microgravity (µg) conditions. Identical sets of reaction chambers from an automated system (the Silicate Garden Habitat or SGHab) were used in both cases. The µg experiment was performed on board the International Space Station (ISS) within a temperature-controlled setup that provided still and video images of the experiment downlinked to the ground. Calcium chloride, manganese chloride, cobalt chloride, and nickel sulfate were used as seed salts in sodium silicate solutions of several concentrations. The formation and growth of osmotic envelopes and microtubes was much slower under µg conditions. In 1 g, buoyancy forces caused tubes to grow upward, whereas a random orientation for tube growth was found under µg conditions.

Chemical gardens from silicates and cations of group 2: a comparative study of composition, morphology and microstructure.

We have compared the behaviour of the chloride salts of the cations Ca(2+), Sr(2+) and Ba(2+) of Group 2 of the Periodic Table in the formation of chemical gardens in silicate solutions. We performed analyses of morphology, composition and microstructure using environmental scanning electron microscopy (ESEM), X-ray diffraction (XRD) and energy dispersive X-ray analysis (EDX). We have identified different growth regimes in these salts (jetting and budding), which are dependent on the concentration of the silicate solution. The behaviour is similar for all the cations but reactivity decreases down the group and is directly proportional to the solubility of the salts: Ca(2+) > Sr(2+) > Ba(2+).

Spiral and target patterns in bivalve nacre manifest a natural excitable medium from layer growth of a biological liquid crystal.

Nacre is an exquisitely structured biocomposite of the calcium carbonate mineral aragonite with small amounts of proteins and the polysaccharide chitin. For many years, it has been the subject of research, not just because of its beauty, but also to discover how nature can produce such a superior product with excellent mechanical properties from such relatively weak raw materials. Four decades ago, Wada [Wada K (1966) Spiral growth of nacre. Nature 211:1427] proposed that the spiral patterns in nacre could be explained by using the theory Frank [Frank F (1949) The influence of dislocations on crystal growth. Discuss Faraday Soc 5:48-54] had put forward of the growth of crystals by means of screw dislocations. Frank's mechanism of crystal growth has been amply confirmed by experimental observations of screw dislocations in crystals, but it is a growth mechanism for a single crystal, with growth fronts of molecules. However, the growth fronts composed of many tablets of crystalline aragonite visible in micrographs of nacre are not a molecular-scale but a mesoscale phenomenon, so it has not been evident how the Frank mechanism might be of relevance. Here, we demonstrate that nacre growth is organized around a liquid-crystal core of chitin crystallites, a skeleton that the other components of nacre subsequently flesh out in a process of hierarchical self-assembly. We establish that spiral and target patterns can arise in a liquid crystal formed layer by layer through the Burton-Cabrera-Frank [Burton W, Cabrera N, Frank F (1951) The growth of crystals and the equilibrium structure of their surfaces. Philos Trans R Soc London Ser A 243:299-358] dynamics, and furthermore that this layer growth mechanism is an instance of an important class of physical systems termed excitable media. Artificial liquid crystals grown in this way may have many technological applications.

Dynamics of tidal synchronization and orbit circularization of celestial bodies.

We take a dynamical-systems approach to study the qualitative dynamical aspects of the tidal locking of the rotation of secondary celestial bodies with their orbital motion around the primary. We introduce a minimal model including the essential features of gravitationally induced elastic deformation and tidal dissipation that demonstrates the details of the energy transfer between the orbital and rotovibrational degrees of freedom. Despite its simplicity, our model can account for both synchronization into the 1:1 spin-orbit resonance and the circularization of the orbit as the only true asymptotic attractors, together with the existence of relatively long-lived metastable orbits with the secondary in p:q synchronous rotation.