Evolution of the dense packings of spherotetrahedral particles: from ideal tetrahedra to spheres.
ABSTRACT: Particle shape plays a crucial role in determining packing characteristics. Real particles in nature usually have rounded corners. In this work, we systematically investigate the rounded corner effect on the dense packings of spherotetrahedral particles. The evolution of dense packing structure as the particle shape continuously deforms from a regular tetrahedron to a sphere is investigated, starting both from the regular tetrahedron and the sphere packings. The dimer crystal and the quasicrystal approximant are used as initial configurations, as well as the two densest sphere packing structures. We characterize the evolution of spherotetrahedron packings from the ideal tetrahedron (s?=?0) to the sphere (s?=?1) via a single roundness parameter s. The evolution can be partitioned into seven regions according to the shape variation of the packing unit cell. Interestingly, a peak of the packing density ? is first observed at s???0.16 in the ?-s curves where the tetrahedra have small rounded corners. The maximum density of the deformed quasicrystal approximant family (????0.8763) is slightly larger than that of the deformed dimer crystal family (????0.8704), and both of them exceed the densest known packing of ideal tetrahedra (????0.8563).
Project description:We report the discovery of Al34Ni9Fe2, the first natural known periodic crystalline approximant to decagonite (Al71Ni24Fe5), a natural quasicrystal composed of a periodic stack of planes with quasiperiodic atomic order and ten-fold symmetry. The new mineral has been approved by the International Mineralogical Association (IMA 2018-038) and officially named proxidecagonite, which derives from its identity to periodic approximant of decagonite. Both decagonite and proxidecagonite were found in fragments from the Khatyrka meteorite. Proxidecagonite is the first natural quasicrystal approximant to be found in the Al-Ni-Fe system. Within this system, the decagonal quasicrystal phase has been reported to transform at ~940?°C to Al13(Fe,Ni)4, Al3(Fe,Ni)2 and the liquid phase, and between 800 and 850?°C to Al13(Fe,Ni)4, Al3(Fe,Ni) and Al3(Fe,Ni)2. The fact that proxidecagonite has not been observed in the laboratory before and formed in a meteorite exposed to high pressures and temperatures during impact-induced shocks suggests that it might be a thermodynamically stable compound at high pressure. The most prominent structural motifs are pseudo-pentagonal symmetry subunits, such as pentagonal bipyramids, that share edges and corners with trigonal bipyramids and which maximize shortest Ni-Al over Ni-Ni contacts.
Project description:It is well known that two regular tetrahedra can be combined with a single regular octahedron to tile (complete fill) three-dimensional Euclidean space . This structure was called the "octet truss" by Buckminster Fuller. It was believed that such a tiling, which is the Delaunay tessellation of the face-centered cubic (fcc) lattice, and its closely related stacking variants, are the only tessellations of that involve two different regular polyhedra. Here we identify and analyze a unique family comprised of a noncountably infinite number of periodic tilings of whose smallest repeat tiling unit consists of one regular octahedron and six smaller regular tetrahedra. We first derive an extreme member of this unique tiling family by showing that the "holes" in the optimal lattice packing of octahedra, obtained by Minkowski over a century ago, are congruent tetrahedra. This tiling has 694 distinct concave (i.e., nonconvex) repeat units, 24 of which possess central symmetry, and hence is distinctly different and combinatorically richer than the fcc tetrahedra-octahedra tiling, which only has two distinct tiling units. Then we construct a one-parameter family of octahedron packings that continuously spans from the fcc to the optimal lattice packing of octahedra. We show that the "holes" in these packings, except for the two extreme cases, are tetrahedra of two sizes, leading to a family of periodic tilings with units composed four small tetrahedra and two large tetrahedra that contact an octahedron. These tilings generally possess 2,068 distinct concave tiling units, 62 of which are centrally symmetric.
Project description:The structure of a complicated quasicrystal approximant epsilon(16) was predicted from a known and related quasicrystal approximant epsilon(6) by the strong-reflections approach. Electron-diffraction studies show that in reciprocal space, the positions of the strongest reflections and their intensity distributions are similar for both approximants. By applying the strong-reflections approach, the structure factors of epsilon(16) were deduced from those of the known epsilon(6) structure. Owing to the different space groups of the two structures, a shift of the phase origin had to be applied in order to obtain the phases of epsilon(16). An electron-density map of epsilon(16) was calculated by inverse Fourier transformation of the structure factors of the 256 strongest reflections. Similar to that of epsilon(6), the predicted structure of epsilon(16) contains eight layers in each unit cell, stacked along the b axis. Along the b axis, epsilon(16) is built by banana-shaped tiles and pentagonal tiles; this structure is confirmed by high-resolution transmission electron microscopy (HRTEM). The simulated precession electron-diffraction (PED) patterns from the structure model are in good agreement with the experimental ones. Epsilon(16) with 153 unique atoms in the unit cell is the most complicated approximant structure ever solved or predicted.
Project description:Restriction enzymes recognize and bind to specific sequences on invading bacteriophage DNA. Like a key in a lock, these proteins require many contacts to specify the correct DNA sequence. Using information theory we develop an equation that defines the number of independent contacts, which is the dimensionality of the binding. We show that EcoRI, which binds to the sequence GAATTC, functions in 24 dimensions. Information theory represents messages as spheres in high dimensional spaces. Better sphere packing leads to better communications systems. The densest known packing of hyperspheres occurs on the Leech lattice in 24 dimensions. We suggest that the single protein EcoRI molecule employs a Leech lattice in its operation. Optimizing density of sphere packing explains why 6 base restriction enzymes are so common.
Project description:Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction ??0.56, which is the same as dense, random packing of amino-acid-shaped particles. In this article, we compare the structural properties of protein cores and jammed packings of amino-acid-shaped particles in much greater depth by measuring their local and connected void regions. We find that the distributions of surface Voronoi cell volumes and local porosities obey similar statistics in both systems. We also measure the probability that accessible, connected void regions percolate as a function of the size of a spherical probe particle and show that both systems possess the same critical probe size. We measure the critical exponent ? that characterizes the size distribution of connected void clusters at the onset of percolation. We find that the cluster size statistics are similar for void percolation in packings of amino-acid-shaped particles and randomly placed spheres, but different from that for void percolation in jammed sphere packings. We propose that the connected void regions are a defining structural feature of proteins and can be used to differentiate experimentally observed proteins from decoy structures that are generated using computational protein design software. This work emphasizes that jammed packings of amino-acid-shaped particles can serve as structural and mechanical analogs of protein cores, and could therefore be useful in modeling the response of protein cores to cavity-expanding and -reducing mutations.
Project description:Dynamics of drainage is analyzed for packings of spheres, using numerical experiments. For this purpose, a dynamic pore-scale model was developed to simulate water flow during drainage. The pore space inside a packing of spheres was extracted using regular triangulation, resulting in an assembly of grain-based tetrahedra. Then, pore units were constructed by identifying and merging tetrahedra that belong to the same pore, resulting in an assembly of pore units. Each pore unit was approximated by a volume-equivalent regular shape (e.g., cube and octahedron), for which a local capillary pressure-saturation relationship was obtained. To simulate unsaturated flow, a pore-scale version of IMPES (implicit pressure solver and explicit saturation update) was employed in order to calculate pressure and saturation distributions as a function of time for the assembly of pore units. To test the dynamic model, it was used on a packing of spheres to reproduce the corresponding measured quasi-static capillary pressure-saturation curve for a sand packing. Calculations were done for a packing of spheres with the same grain size distribution and porosity as the sand. We obtained good agreement, which confirmed the ability of the dynamic code to accurately describe drainage under low flow rates. Simulations of dynamic drainage revealed that drainage occurred in the form of finger-like infiltration of air into the pore space, caused by heterogeneities in the pore structure. During the finger-like infiltration, the pressure difference between air and water was found to be significantly higher than the capillary pressure. Furthermore, we tested the effects of the averaging, boundary conditions, domain size, and viscosity on the dynamic flow behavior. Finally, the dynamic coefficient was determined and compared to experimental data.
Project description:The refined x-ray crystal structure of the phase Mg(27)Al(10.7(2))Zn(47.3(2)) (Pa3) establishes it as the new 2/1 Bergman-type approximant of the icosahedral quasicrystal. The primitive cubic lattice consists of condensed triacontahedral and novel prolate rhombohedral (PR) clusters. Each triacontahedron encapsulates the traditional, multiply endohedral Bergman-type clusters, and each PR encapsulates an Al(2) dimer. This phase exhibits the same long-range order as recently established for the Tsai-type Sc-Mg-Zn 2/1 approximant crystal, with substantial geometric and atomic distribution differences between the two only in the short range orders. This common feature suggests that Bergman- and Tsai-type quasicrystals may be more similar than earlier conceived. Factors germane to the formation of, and the differences between, Bergman- vs. Tsai-type 1/1 and 2/1 approximate structures are considered, including notably different distributions of the more electropositive elements.
Project description:Superconductivity is ubiquitous as evidenced by the observation in many crystals including carrier-doped oxides and diamond. Amorphous solids are no exception. However, it remains to be discovered in quasicrystals, in which atoms are ordered over long distances but not in a periodically repeating arrangement. Here we report electrical resistivity, magnetization, and specific-heat measurements of Al-Zn-Mg quasicrystal, presenting convincing evidence for the emergence of bulk superconductivity at a very low transition temperature of [Formula: see text] K. We also find superconductivity in its approximant crystals, structures that are periodic, but that are very similar to quasicrystals. These observations demonstrate that the effective interaction between electrons remains attractive under variation of the atomic arrangement from periodic to quasiperiodic one. The discovery of the superconducting quasicrystal, in which the fractal geometry interplays with superconductivity, opens the door to a new type of superconductivity, fractal superconductivity.
Project description:Dense particle packing in a confining volume remains a rich, largely unexplored problem, despite applications in blood clotting, plasmonics, industrial packaging and transport, colloidal molecule design, and information storage. Here, we report densest found clusters of the Platonic solids in spherical confinement, for up to [Formula: see text] constituent polyhedral particles. We examine the interplay between anisotropic particle shape and isotropic 3D confinement. Densest clusters exhibit a wide variety of symmetry point groups and form in up to three layers at higher N. For many N values, icosahedra and dodecahedra form clusters that resemble sphere clusters. These common structures are layers of optimal spherical codes in most cases, a surprising fact given the significant faceting of the icosahedron and dodecahedron. We also investigate cluster density as a function of N for each particle shape. We find that, in contrast to what happens in bulk, polyhedra often pack less densely than spheres. We also find especially dense clusters at so-called magic numbers of constituent particles. Our results showcase the structural diversity and experimental utility of families of solutions to the packing in confinement problem.
Project description:Diamond lattices formed by atomic or colloidal elements exhibit remarkable functional properties. However, building such structures via self-assembly has proven to be challenging because of the low packing fraction, sensitivity to bond orientation, and local heterogeneity. We report a strategy for creating a diamond superlattice of nano-objects via self-assembly and demonstrate its experimental realization by assembling two variant diamond lattices, one with and one without atomic analogs. Our approach relies on the association between anisotropic particles with well-defined tetravalent binding topology and isotropic particles. The constrained packing of triangular binding footprints of truncated tetrahedra on a sphere defines a unique three-dimensional lattice. Hence, the diamond self-assembly problem is solved via its mapping onto two-dimensional triangular packing on the surface of isotropic spherical particles.