Concept: Point groups in three dimensions
Symmetry is a biologically relevant, mathematically involving, and aesthetically compelling visual phenomenon. Mirror symmetry detection is considered particularly rapid and efficient, based on experiments with random noise. Symmetry detection in natural settings, however, is often accomplished against structured backgrounds. To measure salience of symmetry in diverse contexts, we assembled mirror symmetric patterns from 101 natural textures. Temporal thresholds for detecting the symmetry axis ranged from 28 to 568 ms indicating a wide range of salience (1/Threshold). We built a model for estimating symmetry-energy by connecting pairs of mirror-symmetric filters that simulated cortical receptive fields. The model easily identified the axis of symmetry for all patterns. However, symmetry-energy quantified at this axis correlated weakly with salience. To examine context effects on symmetry detection, we used the same model to estimate approximate symmetry resulting from the underlying texture throughout the image. Magnitudes of approximate symmetry at flanking and orthogonal axes showed strong negative correlations with salience, revealing context interference with symmetry detection. A regression model that included the context-based measures explained the salience results, and revealed why perceptual symmetry can differ from mathematical characterizations. Using natural patterns thus produces new insights into symmetry perception and its possible neural circuits.
We report the first occurrence of an icosahedral quasicrystal with composition Al62.0(8)Cu31.2(8)Fe6.8(4), outside the measured equilibrium stability field at standard pressure of the previously reported Al-Cu-Fe quasicrystal (AlxCuyFez, with x between 61 and 64, y between 24 and 26, z between 12 and 13%). The new icosahedral mineral formed naturally and was discovered in the Khatyrka meteorite, a recently described CV3 carbonaceous chondrite that experienced shock metamorphism, local melting (with conditions exceeding 5 GPa and 1,200 °C in some locations), and rapid cooling, all of which likely resulted from impact-induced shock in space. This is the first example of a quasicrystal composition discovered in nature prior to being synthesized in the laboratory. The new composition was found in a grain that has a separate metal assemblage containing icosahedrite (Al63Cu24Fe13), currently the only other known naturally occurring mineral with icosahedral symmetry (though the latter composition had already been observed in the laboratory prior to its discovery in nature). The chemistry of both the icosahedral phases was characterized by electron microprobe, and the rotational symmetry was confirmed by means of electron backscatter diffraction.
Restricting our scope to the dynamical motion of the leaflets, we present a computational model for a symmetric, tri-leaflet, bioprosthetic heart valve (BHV) at the end of five complete cardiac pressure cycles, reaching the steady state of deformation during both closing and opening phases. To this end, we utilized a highly anisotropic material model for the large deformation behavior of the tissue material, for which an experimental validation was provided. The important findings are: (1) material anisotropy has significant effect on the valve opening/closing; (2) the asymmetric deformations, especially in the fully closed configuration, justify the use of cyclic symmetry; (3) adopting the fully-open position as an initial/reference configuration has the advantage of completely bypassing any complications arising from the need to assume the size and shape of the contact area in the coaptation regions of the leaflets that is necessary when the alternative, commonly-used, approach of selecting the fully-closed position is used as a reference; and (4) with proper treatments for both material anisotropy and tissue-to-tissue contact, the overall BHV model provide realistic results in conformity with the ex vivo/in vitro experiments.
We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.
- Proceedings of the National Academy of Sciences of the United States of America
- Published 3 months ago
The formation of quasi-spherical cages from protein building blocks is a remarkable self-assembly process in many natural systems, where a small number of elementary building blocks are assembled to build a highly symmetric icosahedral cage. In turn, this has inspired synthetic biologists to design de novo protein cages. We use simple models, on multiple scales, to investigate the self-assembly of a spherical cage, focusing on the regularity of the packing of protein-like objects on the surface. Using building blocks, which are able to pack with icosahedral symmetry, we examine how stable these highly symmetric structures are to perturbations that may arise from the interplay between flexibility of the interacting blocks and entropic effects. We find that, in the presence of those perturbations, icosahedral packing is not the most stable arrangement for a wide range of parameters; rather disordered structures are found to be the most stable. Our results suggest that (i) many designed, or even natural, protein cages may not be regular in the presence of those perturbations and (ii) optimizing those flexibilities can be a possible design strategy to obtain regular synthetic cages with full control over their surface properties.
Self-assembly of rigid building blocks with explicit shape and symmetry is substantially influenced by the geometric factors and remains largely unexplored. We report the selective assembly behaviors of a class of precisely defined, nanosized giant tetrahedra constructed by placing different polyhedral oligomeric silsesquioxane (POSS) molecular nanoparticles at the vertices of a rigid tetrahedral framework. Designed symmetry breaking of these giant tetrahedra introduces precise positional interactions and results in diverse selectively assembled, highly ordered supramolecular lattices including a Frank-Kasper A15 phase, which resembles the essential structural features of certain metal alloys but at a larger length scale. These results demonstrate the power of persistent molecular geometry with balanced enthalpy and entropy in creating thermodynamically stable supramolecular lattices with properties distinct from those of other self-assembling soft materials.
The isomerizations of 3-aza-3-ium-dihydrobenzvalene, 3,4-diaza-3-ium-dihydrobenzvalene, and 3,4-diaza-diium-dihydrobenzvalene to their respective cyclic-diene products have been studied using electronic structure methods with a multiconfigurational wavefunction and several single reference methods. Transition states for both the allowed (conrotatory) and forbidden (disrotatory) pathways were located. The conrotatory pathways of each structure all proceed through a cyclic intermediate with a trans double bond in the ring: this trans double bond destroys the aromatic stabilization of the π electrons due to poor orbital overlap between the cis and trans π bonds. The 3, 4-diaza-3-ium-dihydrobenzvalene structure has C1 symmetry, and there are four separate allowed and forbidden pathways for this structure. The 3-aza-3-ium-dihydrobenzvalene structure is Cs symmetric, and there are two separate allowed and forbidden pathways for this structure. For 3, 4-diaza-3, 4-diium-benzvalene, there was a single allowed and single forbidden pathway due to the C2v symmetry. The separation of the barrier heights for all three molecules was studied, and we found the difference in activation barriers for the lowest allowed and lowest forbidden pathways in 3, 4-diaza-3-ium-dihydrobenzvalene, 3-aza-3-ium-dihydrobenzvalene, and 3, 4-diaza-diium-benzvalene to be 9.1, 7.4, and 3.7 kcal/mol, respectively. The allowed and forbidden barriers of 3, 4-diaza-diium-dihydrobenzvalene were separated by 3.7 kcal/mol, which is considerably less than the 12-15 kcal/mol expected based on the orbital symmetry rules. The addition of the secondary ammonium group tends to shift the conrotatory and disrotatory barriers up in energy (approximately 12-14 kcal/mol (conrotatory) and 5-10 kcal/mol (disrotatory) per secondary NH2 group) relative to the barriers of dihydrobenzvalene, but there is negligible effect on E, Z to Z, Z isomerization barriers, which remain in the expected range of > 4 kcal/mol.
In this work, we look at the symmetry of normal modes in symmetric structures, particularly structures with cyclic symmetry. We show that normal modes of symmetric structures have different levels of symmetry, or symmetricity. One novel theoretical result of this work is that, for a ring structure with m subunits, the symmetricity of the normal modes falls into m groups of equal size, with normal modes in each group having the same symmetricity. The normal modes in each group can be computed separately, using a much smaller amount of memory and time (up to m(3) less). Lastly, we show that symmetry in normal modes depends strongly on symmetry in structure. This work suggests a deeper reason for the existence of symmetric complexes: that they may be formed not only for structural purpose, but likely also for a dynamical reason, that certain structural symmetry is needed to obtain certain symmetric motions that are functionally critical.
Optics-based sensing platform working under unpolarized light illumination is of practical importance in the sensing applications. For this reason, sensing platforms based on localized surface plasmons are preferred to their integrated optics counterparts for their simple mode excitation and inexpensive implementation. However, their optical response under unpolarized light excitation is typically weak due to their strong polarization dependence. Herein, the role of rotational symmetry for realizing robust sensing platform exhibiting strong optical contrast and high sensitivity is explored. Specifically, gammadion and star-shaped gold nanostructures with different internal and external rotational symmetries are fabricated and studied in detail, from which their mode characteristics are demonstrated as superposition of their constituent longitudinal plasmons that are in conductive coupling with each other. We demonstrate that introducing and increasing internal rotational symmetry would lead to the enhancement in optical contrast up to ~3x under unpolarized light illumination. Finally, we compare the sensing performances of rotationally symmetric gold nanostructures with a more rigorous figure-of-merit based on sensitivity, Q-factor, and spectral contrast.
Spanning the scales of mechanical metamaterials using time domain simulations in transformed crystals, graphene flakes and structured soils
- Journal of physics. Condensed matter : an Institute of Physics journal
- Published 4 months ago
We begin with a brief historical survey of discoveries of quasi-crystals and graphene, and then introduce the concept of transformation crystallography, which consists of the application of geometric transforms to periodic structures. We consider motifs with three-fold, four-fold and six-fold symmetries according to the crystallographic restriction theorem. Furthermore, we define motifs with five-fold symmetry such as quasi-crystals generated by a cut-and-projection method from periodic structures in higher-dimensional space. We analyze elastic wave propagation in the transformed crystals and (Penrose-type) quasi-crystals with the finite difference time domain freeware SimSonic. We consider geometric transforms underpinning the design of seismic cloaks with square, circular, elliptical and peanut shapes in the context of honeycomb crystals that can be viewed as scaled-up versions of graphene. Interestingly, the use of morphing techniques leads to the design of cloaks with interpolated geometries reminiscent of Victor Vasarely’s artwork. Employing the case of transformed graphene-like (honeycomb) structures allows one to draw useful analogies between large-scale seismic metamaterials such as soils structured with columns of concrete or grout with soil and nanoscale biochemical metamaterials. We further identify similarities in designs of cloaks for elastodynamic and hydrodynamic waves and cloaks for diffusion (heat or mass) processes, as these are underpinned by geometric transforms. Experimental data extracted from field test analysis of soil structured with boreholes demonstrates the application of crystallography to large scale phononic crystals, coined as seismic metamaterials, as they might exhibit low frequency stop bands. This brings us to future outlook of mechanical metamaterials, with control of phonon emission in graphene through extreme anisotropy, attenuation of vibrations of suspension bridges via low frequency stop bands and the concept of transformed meta-cities. We conclude that these novel materials hold strong applications spanning different disciplines or across different scales including from biophysics to geophysics.