Fivefold Symmetry Research Articles

Structural Characterization of Canine Minute Virus, Rat and Porcine Bocavirus.

Bocaparvovirus is an expansive genus of the Parvovirinae, with a wide range of vertebrate hosts. This study investigates Canine minute virus (CnMV), Rat bocavirus (RBoV), and Porcine bocavirus 1 (PBoV1). Both CnMV and PBoV1 have been found in gastrointestinal infections in their respective hosts, with CnMV responsible for spontaneous abortions in dogs, while PBoV has been associated with encephalomyelitis in piglets. The pathogenicity of the recently identified RBoV is currently unknown. To initiate the characterization of these viruses, their capsids structures were determined by cryo-electron microscopy at resolutions ranging from 2.3 to 2.7 Å. Compared to other parvoviruses, the CnMV, PBoV1, and RBoV capsids showed conserved features, such as the channel at the fivefold symmetry axis. However, major differences were observed at the two- and threefold axes. While CnMV displays prominent threefold protrusions, the same region is more recessed in PBoV1 and RBoV. Furthermore, the typical twofold axis depression of parvoviral capsids is absent in CnMV or very small in PBoV and RBoV. These capsid structures extend the structural portfolio for the Bocaparvovirus genus and will allow future characterization of these pathogens on a molecular level. This is important, as no antivirals or vaccines exist for these viruses.

Co-evolution of the atomic/nano scale structural heterogeneities and magnetic properties of Fe-Si-B-Cu metallic glass during relaxation with composition fluctuations

The metallic glass (MG) exhibits composition fluctuation or chemical heterogeneity during relaxation. However, the influence of this factor on the evolution of the intrinsic structural heterogeneity of MGs remains unclear. In this study, we systematically examined the co-evolution between atomic and nano-scale structural heterogeneities of Fe-Si-B-Cu MGs during relaxation. We discovered that, despite some degree of fluctuation in composition during the relaxation of Fe-Si-B-Cu MGs, it does not prevent the reduction of structural heterogeneities at the atomic/nano scale. The results demonstrate an overall increase in the number density and number of types of densely packed clusters with a high degree of local five-fold symmetry and a decrease in the number density and number of types of loosely packed clusters with a low degree of local five-fold symmetry. Furthermore, a certain degree of compositional fluctuation during relaxation of Fe-Si-B-Cu MGs facilitates the formation of uniformly distributed Fe-rich regions and Cu-rich regions.

Five-fold symmetry structure inhibiting the growth of an otherwise perfect η2 phase in Al-Zn-Mg-Cu alloys

Using high angle annular dark-field scanning transmission electron microscopy, we report the formation of a five-fold symmetry structure at the (1¯100)η//(110)Al edge interface of otherwise defect-free η2 precipitates in Al-Zn-Mg-Cu alloys. This quasicrystal entity has a demonstrated ability to hinder growth at the interface where it resides. Assisted by calculations based on density functional theory, the five-fold symmetry structure is shown to form easily at Zn-rich conditions due to favorable interfacial energies at all stages of evolution. These findings offer an enhanced perspective of precipitate stabilization in an alloy of widespread industrial interest, presenting a potential alternative path to alloy design.

AB5-Type Toxin as a Pentameric Scaffold in Recombinant Vaccines against the Japanese Encephalitis Virus.

Japanese encephalitis virus (JEV) is an enveloped icosahedral capsid virus with a prime neutralizing epitope present in E protein domain III (EDIII). E dimers are rearranged into a five-fold symmetry of icosahedrons. Cholera toxin B (CTB) and heat-labile enterotoxin B (LTB) of AB5-type toxin was used as the structural scaffold for emulating the pentameric axis of EDIII. We produced homo-pentameric EDIII through the genetic fusion of LTB or CTB in E. coli without recourse to additional refolding steps. Harnessing an RNA-mediated chaperone further enhanced the soluble expression and pentameric assembly of the chimeric antigen. The pentameric assembly was validated by size exclusion chromatography (SEC), non-reduced gel analysis, and a GM1 binding assay. CTB/LTB-EDIII chimeric antigen triggered high neutralizing antibodies against the JEV Nakayama strain after immunization in mice. Altogether, our proof-of-principle study creating a JEV-protective antigen via fusion with an AB5-type toxin as both a pentameric scaffold and a built-in adjuvant posits the bacterially produced recombinant chimeric antigen as a cost-effective alternative to conventional inactivated vaccines against JEV.

Electron Paramagnetic Resonance Spectra of Pentagonal Bipyramidal Gadolinium Complexes

Gadolinium is a special case in spectroscopy because of the near isotropic nature of the 4f7 configuration of the +3 oxidation state. Gd3+ complexes have been studied in several symmetries to understand the underlying mechanisms of the ground state splitting. The abundance of information in Gd3+ spectra can be used as a probe for properties of the other rare earth ions in the same complexes. In this work, the zero-field splitting (ZFS) of a series of Gd3+ pentagonal bipyramidal complexes of the form [GdX1X2(Leq)5]n+ [n = 1, X = axial ligands: Cl-, -OtBu, -OArF5 or n = 3, X = tBuPO(NHiPr)2, Leq = equatorial ligand: Py, THF or H2O] with near fivefold symmetry axes along X1-Gd-X2 was investigated. The ZFS parameters were determined by fitting of room-temperature continuous wave electron paramagnetic resonance (EPR) spectra (at X-, K-, and Q-band) to a spin Hamiltonian incorporating extended Stevens operators compatible with C5 symmetry. Examination of the acquired parameters led to the conclusion that the ZFS is dominated by the B20 term and that the magnitude of B20 is almost entirely dependent on, and inversely proportional to, the donor strength of the axial ligands. Surveying the continuous shape measure and the X1-Gd-X2 angle of the complexes showed that there is some correlation between the proximity of each complex to D5h symmetry and the magnitude of the B65 parameter, but that the deformation of the X1-Gd-X2 angle is more significant than other distortions. Finally, the magnitude of B20 was found to be inversely proportional to the thermal barrier for the reversal of the magnetic moment (Ueff) of the corresponding isostructural Dy3+ complexes.

Ab initio study of chemical effect on structural properties of Ti–Al melts

We study chemical effect on the structural properties of Ti–Al melts, with the Al concentration systematically changed, via ab initio molecular dynamics simulations. By calculating the partial coordination numbers, we find a preferred connection between the nearest neighbors for Al–Ti pairs. This induces an excess Ti coordination in the cluster characterized by local five-fold symmetry in Voronoi tessellation. Structural entropy measured from the diversity of Voronoi polyhedrons shows an intriguing non-monotonic tendency with concentration: it first decreases to a minimum value at Ti40Al60, and then increases beyond this concentration. This implies a more ordered local structure induced by the chemical interaction at the intermediate compositions. The spatial correlation among the crystalline-like or the icosahedral-like clusters also exhibits the highest intensity for Al–Ti pairs, verifying the important role played by the chemical interaction in the local structure connectivity.

Quasicrystalline clusters transformed from C14-MgZn2 nanoprecipitates in Al alloys

Ultrafine faulty C14-MgZn2 Laves phase precipitates containing quasicrystalline clusters and demonstrating the formation of binary quasicrystalline precipitates with Penrose-like random-tiling were observed in the over-aged FCC matrix of a commercial 7N01 Al-Zn-Mg alloy, using high angle annular dark field scanning transmission electron microscopy. The evolution from C14-Laves phase to quasicrystalline clusters is illustrated, and five-fold symmetry can be found in both real and reciprocal spaces. Our findings reveal the possibility of quasicrystalline formation from Laves phase in a highly plastic metal matrix like Al and demonstrate the structural relationship between Laves phase and quasicrystals.

Torsion Geometry 5-Fold Symmetry, Anholonomic Phases, Klein Bottle Logophysics, Chaos, Resonance: Applications Towards a Novel Paradigm for the Neurosciences and Consciousness

Torsion Geometry 5-Fold Symmetry, Anholonomic Phases, Klein Bottle Logophysics, Chaos, Resonance: Applications Towards a Novel Paradigm for the Neurosciences and Consciousness

Non-equilibrium virus particle dynamics: Microsecond MD simulations of the complete Flock House virus capsid under different conditions

Flock House virus (FHV) is an animal virus and considered a model system for non-enveloped viruses. It has a small, icosahedral capsid (T=3) and a bipartite positive-sense RNA genome. We present an extensive study of the FHV capsid dynamics from all-atom molecular dynamics simulations of the complete capsid. The simulations explore different biologically relevant conditions (neutral/low pH, with/without RNA in the capsid) using the CHARMM force field. The results show that low pH destabilizes the capsid, causing radial expansion, and RNA stabilizes the capsid. The finding of low pH destabilization is biologically relevant because the capsid is exposed to low pH in the endosome, where conformational changes occur leading to genome release. We also observe structural changes at the fivefold and twofold symmetry axes that likely relate to the externalization of membrane active γ peptides through the fivefold vertex and extrusion of RNA at the twofold axis. Simulations using the Amber force field at neutral pH are also performed and display similar characteristics to the CHARMM simulations.

Crystal Polymorph Selection Mechanism of Hard Spheres Hidden in the Fluid.

Nucleation plays a critical role in the birth of crystals and is associated with a vast array of phenomena, such as protein crystallization and ice formation in clouds. Despite numerous experimental and theoretical studies, many aspects of the nucleation process, such as the polymorph selection mechanism in the early stages, are far from being understood. Here, we show that the hitherto unexplained excess of particles in a face-centered-cubic (fcc)-like environment, as compared to those in a hexagonal-close-packed (hcp)-like environment, in a crystal nucleus of hard spheres can be explained by the higher order structure in the fluid phase. We show using both simulations and experiments that in the metastable fluid phase, pentagonal bipyramids, clusters with fivefold symmetry known to be inhibitors of crystal nucleation, transform into a different cluster, Siamese dodecahedra. These clusters are closely similar to an fcc subunit, which explains the higher propensity to grow fcc than hcp in hard spheres. We show that our crystallization and polymorph selection mechanism is generic for crystal nucleation from a dense, strongly correlated fluid phase.

Decahedra and Icosahedra Everywhere: The Anomalous Crystallization of Au and Other Metals at the Nanoscale (Crystal Research and Technology 4/2023)

Crystal Research and TechnologyVolume 58, Issue 4 2370007 Cover PictureFree Access Decahedra and Icosahedra Everywhere: The Anomalous Crystallization of Au and Other Metals at the Nanoscale (Crystal Research and Technology 4/2023) First published: 06 April 2023 https://doi.org/10.1002/crat.202370007AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Graphical Abstract The cover image of this issue refers to the Review article by Miguel José Yacaman and co-workers (article number 2200259). Micrographs of nanoparticles and images of natural objects with fivefold symmetry are arranged in juxtaposition to reveal striking similarities between the natural and the nano world. Although millions of times smaller than life, these particles somehow appear to belong in the natural world. The Review discusses several reasons for the stability of nanoparticles with fivefold symmetry, including the formation of twin boundaries, surface reconstruction faceting, and other factors. Volume58, Issue4April 20232370007 RelatedInformation

Effects of cooling rate on the glass formation process and the microstructural evolution of Silver mono-component metallic glass

In this study, using molecular dynamics simulations in combination with the embedded-atom approach, we investigate the effect of cooling rate on the microstructural evolution and the glass formation process of Silver monatomic metallic glass. In order to accomplish our investigation, we have utilised a variety of analytical techniques, including the pair distribution function, the bond angle distribution, the Voronoi tessellation analysis, the coordination number, and the five-fold symmetry. The splitting of the second peak in the pair distribution function during the cooling process confirms that glass formation occurs. Via the Went-Abraham parameter, we have found that a faster cooling rate leads to a higher glass transition temperature Tg, and a less relaxed glass has a lower density due to its greater free volume and disordered structure. In the same context, the bond angle distribution revealed that the cooling rate clearly influences the icosahedral short-range order in the quenched system, and the Voronoi tessellation analysis indicated that the percentage of mixed-like and icosahedral-like clusters grows as the cooling rate increases. Furthermore, the coordination number indicated that when the temperature drops throughout the cooling process, the local environment and topological structure of the amorphous Silver change. Lastly, we have also revealed that the five-fold symmetry controls the formation of the amorphous structure and that the highest cooling rate yields the greatest amount of icosahedral-like clusters in the vitreous phase, implying that fast cooling rates subserve the formation of glassy states with icosahedral-like features.

First-principles study of the initial stage of Pentacene adsorption on the twofold surface of the Ag-In-Yb quasicrystal

The adsorption of the pentacene (Pn) molecule on the twofold surface of icosahedral (i)-Ag-In-Yb Quasicrystal (QC) have been studied by means of density functional theory (DFT) calculations. We calculate the adsorption energy of Pn at various positions with the molecular axis parallel to the surface and aligned along the fivefold or twofold symmetry axes directions. Pn is stabilised on a Yb trapezoid site from the acute rhombohedron units located between the rhombic triacontahedral clusters. The calculated adsorption energies for different molecular orientations can explain a recent experimental observation.

Asynchronising five-fold symmetry sequence for better homonuclear polarisation transfer in magic-angle-spinning solid-state NMR

Recoupling, decoupling, and multidimensional correlation experiments in magic-angle-spinning (MAS) solid-state NMR can be designed by exploiting the symmetry of internal spin interactions. One such scheme, namely, C521, and its supercycled version SPC521, notated as a five-fold symmetry sequence, is widely used for double-quantum dipole-dipole recoupling. Such schemes are generally rotor synchronised by design. We demonstrate an asynchronous implementation of the SPC521 sequence leading to higher double-quantum homonuclear polarisation transfer efficiency compared to the normal synchronous implementation. Rotor-synchronisation is broken in two different ways: lengthening the duration of one of the pulses, denoted as pulse-width variation (PWV), and mismatching the MAS frequency denoted as MAS variation (MASV). The application of this asynchronous sequence is shown on three different samples, namely, U–13C-alanine and 1,4-13C-labelled ammonium phthalate which include 13Cα-13Cβ, 13Cα-13Co, and 13Co–13Co spin systems, and adenosine 5′- triphosphate disodium salt trihydrate (ATP⋅3H2O). We show that the asynchronous version performs better for spin pairs with small dipole-dipole couplings and large chemical-shift anisotropies, for example, 13Co–13Co. Simulations and experiments are shown to corroborate the results.

Decahedra and Icosahedra Everywhere: The Anomalous Crystallization of Au and Other Metals at the Nanoscale

AbstractThroughout history, objects with fivefold symmetry have been a popular topic of interest for artists, philosophers, and scientists. This may be because fivefold symmetry is very conspicuous in nature. In the case of crystals, fivefold rotational symmetry is mathematically forbidden, and macroscopic crystals exhibiting fivefold symmetry have never been shown to exist. Nevertheless, in the nanoworld, nanoparticles are often found with decahedral and icosahedral shapes that have an overall pseudo‐fivefold symmetry. These structures are observed at many length scales, from 1 nm up to 1 µm. In this review, several reasons for the stability of fivefold nanoparticles are discussed. These include the formation of twin boundaries, surface reconstruction faceting, and other factors.

Structure formation processes in fullerene mixtures

Glass formation processes in condensed matter are characterized by some specific short-range order changes in the arrangement of particles (atoms/molecules/ions). So, the short-range structural order in supercooled liquids and glasses is characterized by fivefold symmetry in the arrangement of particles, often referred to as icosahedral (ideal or distorted) short-range order. This article is devoted to the study of local structural features of the supercooled melt of the A20B80 fullerene mixture (where A = C60 and B = C70) obtained under various cooling protocols in order to elucidate the mechanism of formation of the icosahedral short-range order in binary molecular liquids. Comprehensive studies of the properties of a fullerene mixture melt were carried out using large-scale molecular dynamics simulations followed by structural and cluster analysis. The crystallization temperature and the critical glass transition temperature of the system were calculated to be T_m~1439 K and T_c~1238 K, respectively. It has been established that the crystallization of a binary fullerene mixture proceeds according to the polycrystalline scenario with the formation of clusters with fcc and hcp symmetries. It is shown that in a supercooled fullerene mixture, the short-range icosahedral order is formed by an insignificant number of ideal icosahedral clusters and a certain set of distorted icosahedral clusters, the fraction of which remains practically unchanged at temperatures below the critical glass transition temperature. Keywords: molecular dynamics, fullerenes, short-range order, structural ordering.

Процессы структурообразования в фуллереновых смесях

Glass formation processes in condensed matter are characterized by some specific short-range order changes in the arrangement of particles (atoms/molecules/ions). So, the short-range structural order in supercooled liquids and glasses is characterized by fivefold symmetry in the arrangement of particles, often referred to as icosahedral (ideal or distorted) short-range order. This article is devoted to the study of local structural features of the supercooled melt of the A20B80 fullerene mixture (where A = C60 and B = C70) obtained under various cooling protocols in order to elucidate the mechanism of formation of the icosahedral short-range order in binary molecular liquids. Comprehensive studies of the properties of a fullerene mixture melt were carried out using large-scale molecular dynamics simulations followed by structural and cluster analysis. The crystallization temperature and the critical glass transition temperature of the system were calculated to be Tm ≈ 1439 K and Tc ≈ 1238 K, respectively. It has been established that the crystallization of a binary fullerene mixture proceeds according to the polycrystalline scenario with the formation of clusters with fcc and hcp symmetries. It is shown that in a supercooled fullerene mixture, the short-range icosahedral order is formed by an insignificant number of ideal icosahedral clusters and a certain set of distorted icosahedral clusters, the fraction of which remains practically unchanged at temperatures below the critical glass transition temperature.

A 3D characterization of equiaxed grains induced by mediated nucleation in additively manufactured Inconel 718

In additive manufacturing of Ni-based alloy IN718, what causes Icosahedral Short-Range Order (ISRO) or iQC mediated nucleation of equiaxed grains is still not understood. In order to have a better comprehension of the microstructure formation, a more comprehensive characterization both on grain structure and chemical heterogeneities must be achieved. In this work, a scanning electron microscope equipped with a focused ion beam (FIB) allowed to perform a 3D EDS chemical analysis and EBSD orientation mapping of the volume in an equiaxed grain zone. After the 3D reconstruction of the equiaxed grains has been performed, grain-to-grain orientation analysis allowed to analyze multiple twin boundaries orientation relationships in a volume containing hundreds of grains. Chemical mapping using EDS allowed to identify TiC inclusions from which a five-fold symmetry axis seem to emerge, indicating a potential nucleation site. Such areas were analyzed in transmission electron microscopy (TEM) to investigate the different present phases. The nucleation sequence and potential origin of mediated nucleation are further discussed, opening new prospects for grain refinement in additively manufactured nickel-based alloys.

Heredity of clusters in liquid Ta rapid solidification process and its correlation with local symmetry

Metallic glass (MG) has received intensive attention in the fields of amorphous physics and materials science, owing to its excellent mechanical properties, good corrosion resistance, and large elastic deformation limit. Comparing with traditional oxide glass, the limited glass-forming ability (GFA) seriously restricts the application of MG in engineering. Therefore, the GFA has been a hot scientific issue in the field of amorphous material research. Recently, scientists have fully realized that GFA is closely related to the local atomic structure in liquid as well as its evolution features. Since the MG is called the “freezing” liquid, exploring the correlation of local atomic structures between liquid phase and solid phase under rapid solidification conditions is helpful in understanding the microstructural mechanism of GFA. Therefore, the rapid solidification process of liquid Ta is investigated via molecular dynamics simulation. The pair correlation function (PDF), the largest standard cluster (LSC), and the reverse atomic trajectory tracking methods are used to characterize and analyze the microstructure and its evolution during the rapid solicitation of liquid Ta. The results show that the local atomic configurations of the rapidly solidified Ta are various Kasper clusters as well as their distorted configurations, among of which [1/444, 10/555, 2/666] deformed icosahedron (or Z13 cluster) accounts for the highest proportion. The trend of hereditary ability of clusters revealed by the onset temperature of continuous heredity is consistent well with that by the fraction of staged heredity. The geometric symmetry of clusters can be quantitatively characterized by using the local symmetry parameter (LSP). The hereditary ability of clusters is closely related to their LSP. The local five-fold symmetry is beneficial to enhancing hereditary ability, while local four- and six-fold symmetry are disadvantageous for that. The probability of clusters with the same LSC index emerging in the energy range follows the Gaussian distribution, and the expected average atomic potential energy <inline-formula><tex-math id="M3">\begin{document}$ {E}_{\rm exp}^{j} $\end{document}</tex-math><alternatives><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="24-20231153_M3.jpg"/><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="24-20231153_M3.png"/></alternatives></inline-formula> is almost linearly related to the LSP, and <inline-formula><tex-math id="M4">\begin{document}$ {E}_{\rm exp}^{j} $\end{document}</tex-math><alternatives><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="24-20231153_M4.jpg"/><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="24-20231153_M4.png"/></alternatives></inline-formula> decreases with the increase of LSP<sub>5</sub>. The high local five-fold symmetry reduces the average atomic potential energy of LSC, thereby enhancing its configurational heredity. These findings have guiding significance in improving GFA through regulating the local symmetry of liquid monatomic metals or alloys.

A fractal structural feature related to dynamic crossover in metallic glass-forming liquids.

The dynamic crossover in supercooled liquids initially predicted by model coupling theory has been widely accepted, but its underlying structural origin is still an open issue for glass-forming liquids. By molecular dynamics simulations of binary CuZr liquids, the present work verifies that high pressure could enhance this crossover, facilitating the studies on the structural features at the crossover temperature Tc. We discover that the topological connectivity of icosahedral clusters is responsible for this dynamic crossover, rather than all clusters. Tc is the temperature at which the connectivity degree between these clusters reaches a maximum and the dynamic heterogeneity begins to keep stable. Below Tc, the fractal topological structures appear in the medium-range order scale. The icosahedral clusters with a certain connectivity pattern can be regarded as a fractal structural unit. By employing the established fractal analysis method, the fractal dimension D of the icosahedral network is calculated. Our results indicate that the D value increases monotonically with increasing pressure and the fractal behavior of the icosahedral network is an inherent feature of metallic glasses. We also find similar fractal behavior in clusters with high local five-fold symmetry. Our findings shed light on the origin of a dynamic crossover in the deep supercooled region of metallic glasses and also demonstrate the important role of icosahedral clusters in uncovering the fractal behavior of metallic glass.