Icosahedral Shape Research Articles

Incidence of mud crab reovirus (MCRV) outbreak in polyculture ponds of Andhra Pradesh, south east coast of India

Reovirus designated as Mud crab reovirus (MCRV) is associated with the mass mortalities of mud crabs resulting in significant economic loss to crab and shrimp-mud crab polyculture farmers in the Nagayalanka, Krishna district, Andhra Pradesh. The 100 % chronic mass mortalities have been attributed to the outbreak of Mud crab reovirus (MCRV) in the polyculture farms. The moribund crabs showed autotomy, discoloration of carapace, loss of appetite, slow movement and loose gills. Histopathological observations of the infected mud crabs showed an atrophied hepatopancreas, complete degeneration of tissues along with viral inclusions in hepatopancreas, gills and muscles. Further analysis using Transmission electron microscopy (TEM), showed that the viral particles had a diameter of 70 nm and exhibited a non-enveloped, icosahedral shape arranged in a crystalline manner. The virus mainly infects the connective tissue of hepatopancreas, gills, muscle and develops in the cytoplasm. RT-PCR reconfirmed the presence of reovirus in the hepatopancreas of spontaneously infected mud crab Scylla serrata. The current study shows the importance of monitoring the MCRV prevalence in polyculture farms to minimize its spread and precautionary measures can be taken by screening the brooders from the crab hatchery and stocking of wild crabs without screening should be avoided in order to prevent MCRV outbreak.

Hierarchical self-assembly of Au-nanoparticles into filaments: evolution and break.

We compare the assembly of individual Au nanoparticles in a vacuum and between two Au(111) surfaces via classical molecular dynamics on a timescale of 100 ns. In a vacuum, the assembly of three nanoparticles used as seeds, initially showing decahedral, truncated octahedral and icosahedral shapes with a diameter of 1.5-1.7 nm, evolves into a spherical object with about 10-12 layers and a gyration radius ∼2.5-2.8 nm. In a vacuum, 42% show just one 5-fold symmetry axis, 33% adopt a defected icosahedral arrangement, and 25% lose all 5-fold symmetry and display a face-centred-cubic shape with several parallel stacking faults. We model a constrained version of the same assembly that takes place between two Au(111) surfaces. During the dynamics, the two Au(111) surfaces are kept fixed at distances of 55 Å, 55.5 Å, 56 Å, and 56.5 Å. The latter distance accommodates 24 Au layers with no strain, while the others correspond to nominal strains of 1.5%, 2.4%, and 3.3%, respectively. In the constrained assembly, each individual seed tends to reorganize into a layered configuration, but the filament may break. The probability of breaking the assembled nanofilament depends on the individual morphology of the seeds. It is more likely to break at the decahedron/icosahedron interface, whilst it is more likely to layer with respect to the (111) orientation when a truncated octahedron sits between the decahedron and the icosahedron. We further observe that nanofilaments between surfaces at 56 Å have a >90% probability of breaking, which decreases to 8% when the surfaces are 55 Å apart. We attribute the dramatic change in probability of breaking to the peculiar decahedron/icosahedron interface and the higher average atomic strain in the nanofilaments. This in silico experiment can shed light on the understanding and control of the formation of metallic nanowires and nanoparticle-assembled networks, which find applications in next-generation electronic devices, such as resistive random access memories and neuromorphic devices.

Size and shape effects on chemical ordering in Ni-Pt nanoalloys.

The atomic structure and chemical ordering of Ni-Pt nanoalloys of different sizes and shapes are studied by numerical simulations using Monte Carlo methods and a realistic interatomic potential. The bulk Ni-Pt ordering tendency remains in fcc nanoparticles but we show some chemical ordering frustrations linked to surface reconstructions depending on the cluster size and shape. A reversed temperature dependence of Pt surface segregation is also established. In the particular case of fivefold symmetry as in icosahedra, ordering is observed in the core and on the facets at low temperatures with segregation of the smaller element (Ni) in the core because of atomic strain. We show that the icosahedral shape favors Pt surface segregation in comparison with octahedral and truncated octahedral structures.

Viruses participate in the organomineralization of travertines

Travertines, which precipitate from high temperature water saturated with calcium carbonate, are generally considered to be dominated by physico-chemical and microbial precipitates. Here, as an additional influence on organomineral formation, metagenomic data and microscopic analyses clearly demonstrate that highly diverse viral, bacterial and archaeal communities occur in the biofilms associated with several modern classic travertine sites in Europe and Asia, along with virus-like particles. Metagenomic analysis reveals that bacteriophages (bacterial viruses) containing icosahedral capsids and belonging to the Siphoviridae, Myoviridae and Podoviridae families are the most abundant of all viral strains, although the bacteriophage distribution does vary across the sampling sites. Icosahedral shapes of capsids are also the most frequently observed under the microscope, occurring as non-mineralized through to mineralized viruses and virus-like particles. Viruses are initially mineralized by Ca-Si amorphous precipitates with subordinate Mg and Al contents; these then alter to nanospheroids composed of Ca carbonate with minor silicate 80–300 nm in diameter. Understanding the roles of bacteriophages in modern carbonate-saturated settings and related organomineralization processes is critical for their broader inclusion in the geological record and ecosystem models.

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.

Atomic strain and catalytic properties of formate oxidation and dehydrogenation in AgPd nanoalloys.

Formate is a promising hydrogen carrier for safe storage and transport and a fuel for direct formate fuel cells. However, the sluggish kinetics of catalysts for formate dehydrogenation (FDH) and oxidation reactions (FORs) significantly limit the potential applications of formate. Strain effects can effectively modulate catalytic properties by altering the electronic structure. Nevertheless, the lack of theoretical principles to quantify atomic strain and its effects on FDH and FOR catalytic activity has made experimental efforts laborious. In this work, we establish a database of atomic strain distributions for AgPd nanoalloys, reveals that the presence of compressive strain at the edges and corners and compressive strain exerted on the surface of Ag@Pd nanoalloys, particularly the one with an icosahedral shape, boost the FDH and FOR catalytic activity by shifting down the d-band center, thus weakening the adsorption of key intermediate Had. This study provides a theoretical perspective on the development and use of formate as a hydrogen carrier and fuel.

A Fluorescein-Substituted Perbrominated Dodecaborate Cluster as an Anchor Dye for Large Macrocyclic Hosts and Its Application in Indicator Displacement Assays.

Perhalogenated boron clusters derived from B12Br122-, a superchaotropic dianion with a globular icosahedral shape, serve as inorganic cavity binders for cyclodextrins (CDs), in particular for large CDs (γ-CD and δ-CD), with high binding affinity (Ka > 106 M-1) in aqueous solution. This opens the door for applications of this anchoring moiety by linking it to organic residues, prominently fluorescent dyes. We report here the synthesis of a novel fluorescein-substituted perbrominated dodecaborate cluster by a copper(I)-catalyzed azide-alkyne click reaction. The formation of host-guest inclusion complexes between the dodecaborate-modified fluorescein dye and CDs can be readily followed by optical titrations, which afforded a binding constant of ∼1 × 104 M-1 with γ-CD; that is, the cluster functionalization allows binding of an otherwise nonbinding dye to the macrocycle ("anchor dye"). The formation of the 1:1 host-guest inclusion complex between the dye and γ-CD occurs over a broad range of pH values, which allows its application as a sensitive reporter pair according to the indicator displacement method, e.g., for drug detection. In addition, the substituted dye shows outer-wall binding to cucurbiturils through the dodecaborate moiety, leading to the formation of aggregates and significant fluorescence quenching of the dye.

Volume of intersection of sphere with pentagonal pyramid: Case of special practical interest for nano-grained composites

Volume of intersection of sphere with pentagonal pyramid: Case of special practical interest for nano-grained composites. / L. Chkhartishvili, O. Tsagareishvili, J. Khantadze. / Nano Studies. – 2020. – # 20. – pp. 19-24. – eng. Nanocomposite materials are built up from crystalline nanoparticles of different phases. As nanocrystallites often take icosahedral shape the structural model for a bifractional nanocomposite leads to the geometric task: to determine the volume cut out from the sphere by the lateral facets planes of a pentagonal pyramid, top of which coincides with the sphere center. In the paper, this problem is resolved analytically. Based on this result, it is possible to estimate quntitively the density of bufractional nanocomposites. Fig. 8, Ref. 4.

Effects of orientational order on modulated cylindrical interfaces.

Cylindrical interfaces occur in sheared or deformed emulsions and as biological or technological lipid monolayer or bilayer tubules. Like the corresponding spherical droplets and vesicles, these cylinderlike surfaces may host orientational order with n-fold rotational symmetry, for example in the positions of lipid molecules or of spherical nanoparticles. We examine how that order interacts with and induces shape modulations of cylindrical interfaces. While on spherical droplets 2n topological defects necessarily exist and can induce icosahedral droplet shapes, the cylindrical topology is compatible with a defect-free patterning. Nevertheless, once a modulation is introduced by a mechanism such as spontaneous curvature, nontrivial patterns of order, including ones with excess defects, emerge and have nonlinear effects on the shape of the tube. By examining the equilibrium energetics of the system analytically and with a lattice-based Markov chain Monte Carlo simulation, we predict low-temperature morphologies of modulated cylindrical interfaces hosting orientational order. A shape modulation induces a banded pattern of alternatingly isotropic and ordered interfacial material. Furthermore, cylindrical systems can be divided into type I, without defects, and type II, which go through a spectrum of defect states with up to 4n excess defects. The character of the curvature-induced shape transition from unmodulated to modulated cylinders is continuous or discontinuous accordingly.

N-Heterocyclic Carbene-Stabilized Hydrido Au24 Nanoclusters: Synthesis, Structure, and Electrocatalytic Reduction of CO2.

Atomically precise hydrido gold nanoclusters are extremely rare but interesting due to their potential applications in catalysis. By optimization of molecular precursors, we have prepared an unprecedented N-heterocyclic carbene-stabilized hydrido gold nanocluster, [Au24(NHC)14Cl2H3]3+. This cluster comprises a dimer of two Au12 kernels, each adopting an icosahedral shape with one missing vertex. The two kernels are joined through triangular faces, which are capped with a total of three hydrides. The hydrides are detected by electrospray ionization mass spectrometry and nuclear magnetic resonance spectroscopy, with density functional theory calculations supporting their position bridging the six uncoordinated gold sites. The reactivity of this Au24H3 cluster in the electrocatalytic reduction of CO2 is demonstrated and benchmarked against related catalysts.

Golden Quartic Polynomial and Moebius-Ball Electron

A symmetrical quartic polynomial, named golden one, can be connected to coefficients of the icosahedron equation as well as to the gyromagnetic correction of the electron and to number 137. This number is not a mystic one, but is connected with the inverse of Sommerfeld’s fine-structure constant and this way again connected with the electron. From number-theoretical realities, including the reciprocity relation of the golden ratio as effective pre-calculator of nature’s creativeness, a proposed closeness to the icosahedron may point towards the structure of the electron, thought off as a single-strand compacted helically self-confined charged elemantary particle of less spherical but assumed blunted icosahedral shape generated from a high energy double-helix photon. We constructed a chiral Moebius “ball” from a 13 times 180˚ twisted double helix strand, where the turning points of 12 generated slings were arranged towards the vertices of a regular icosahedron, belonging to the non-centrosymmetric rotation group I532. Mathematically put, we convert the helical motion of an energy quantum into a stationary motion on a Moebius stripe structure. The radius of the ball is about the Compton radius. This chiral closed circuit Moebius ball motion profile can be tentatively thought off as the dominant quantum vortex structure of the electron, and the model may be named CEWMB (Charged Electromagnetic Wave Moebius Ball). Also the gyromagnetic factor of the electron (ge = 2.002319) can be traced back to this special structure. However, nature’s energy infinity principle would suggest a superposition with additional less dominant (secondary) structures, governed also by the golden mean. A suggestion about the possible structure of delocalized hole carriers in the superconducting state is given.

Human Adenovirus Serotypes Efficiently Transducing HEK293 Cells: An In Vitro Propagation of HAdv

Generally, a gene which is inserted directly into a cell does not operate independently. Instead, the transmission of the gene is genetically modified by a biological messenger called a vector, consists of a transgene and a large DNA sequence as a backbone. Since they can deliver the new gene by infecting the cell, such viruses are also used as vectors. The adenovirus is a non-enveloped virus that can be tailored to transfer DNA to target cells, and it has sparked a lot of interest in the field, particularly in clinical trial therapy techniques. For the new age production of COVID-19 vaccine, development of different mammalian cell lines like HEK293 (most reliable growth and prosperity for transfection) and recombinant adenoviral vectors have become the first priority for biopharmaceutical giants and globally approved vaccine manufacturers to scale up their vaccine production. Adenoviruses have an icosahedral shape, with a protein coat encasing the viral double-stranded DNA genome. Because the adenovirus genome is relatively small, it's a good candidate for insertion of foreign DNA. The adenovirus E1A gene is deleted, and the virus loses its capacity to replicate. This ability can be restored during cell culture propagation by employing cells that produce the E1A protein, for example. Hence, in this mini research, I have shared an overview of the propagation of adenoviral vectors, i.e. recombinant adenovirus SARS CoV-2 vector in HEK-293 cell suspension culture.

Abstract P-40: The Shape and Size of the Recombinant Virus-like Particles Were Checked by Means of Electron Microscope

Background: Nucleocapsid protein of hepatitis-B virus (HBcAg) recombinantly synthesized in prokaryotic and eukaryotic cells is known to be capable to self-assemble into highly immunogenic stable viral-like particles (VLP) of icosahedral shape with a characteristic size of 32 nm (Schödel et al., 1994; Murray and Shiau, 1999). The VLP formation is tolerant to the insertion of some artificial epitopes to N- and C-termini of HBcAg monomer and also into major insertion region (MIR), forming a spike on the surface of VLP (Tordjeman et al., 1993, Peyret et al., 2015). Methods: We have investigated the possibility of heterologous expression of de novo designed gene coding the first 148 amino acid residues of HBcAg (Pumpens and Grens, 1999). The gene was specially designed to be suitable for the insertions of genes coding fluorescent proteins, which are desired for the studies of VLP distribution in tissues by confocal microscopy. Gene was optimized for overexpression in E. coli producer strains and special attention was taken to obtain a simple purification scheme, which reliably reduces the amount of pyrogens in purified VLP. The MIPT scientific platform of electron microscopy equipped with the transmission electron microscope Tecnai Polara G2 (Thermo Scientific (FEI)) was used. Carbon-coated (Lacey Carbon and 10 nm thin carbon) copper 200 mesh grids were treated with glow-discharge and coated with VLP suspension in deionized water. The samples were stained with uranyl acetate solution, air-dried, and inspected at the accelerating voltage of 300 kV. Results: The 32 nm size of heterologously synthesized VLP was successfully proved, and spherical shape was seen using negative contrasting.

Thermal conductivity dependence on shape and size in nanomaterials

Abstract In the present paper, we have studied the dependence of thermal conductivity on shape, size and dimension of nanomaterial. By using the quantitative expression of melting temperature, the expression for thermal conductivity is deduced in this work. Kapitza resistance term is also considered in the study to better explain the thermal conductivity variation in nanomaterials with scattering effect on thermal properties. The thermal conductivity is found to decreased as size of nanomaterials decease. The variation in thermal conductivity with size is calculated for nanowire, nanofilm, spherical, regular tetrahedral particle, regular octahedral particle, and regular icosahedral particle shapes. The results calculated in the present work are compared with the available experimental results to judge the validity of the present model.

The binary aluminum scandium clusters Al x Sc y with x + y = 13: when is the icosahedron retained?

Geometrical and electronic structures of the 13-atom clusters AlxScy with x + y = 13, as well as their thermodynamic stabilities were investigated using DFT calculations. Both anionic and neutral isomers of AlxScy were found to retain an icosahedral shape of both Al13 and Sc13 systems in which an Al atom occupies the endohedral central position of the icosahedral cage, irrespective of the number of Al atoms present. Such a phenomenon occurs to maximize the number of stronger Al–Al and Sc–Al bonds instead of the weaker Sc–Sc bonds. NBO analyses were applied to examine their electron configurations and rationalize the large number of open shells and thereby high multiplicities of the mixed clusters having more than three Sc atoms. The SOMOs are the molecular orbitals belonged to the irreducible representations of the symmetry point group of the clusters studied, rather than to the cluster electron shells. Evaluation of the average binding energies showed that the thermodynamic stability of AlxScy clusters is insignificantly altered as the number y goes from 0 to 7 and then steadily decreases when y attains the 7–13 range. Increase of the Sc atom number also reduces the electron affinities of the binary AlxScy clusters, and thus they gradually lose the superhalogen characteristics with respect to the pure Al13.

Two birds with one stone: oyster mushroom mediated bimetallic Au-Pt nanoparticles for agro-waste management and anticancer activity.

Agriculture has the most significant contribution in fulfilling the basic human need, sustaining life, and strengthening the economy of any country. To feed the exploding population of the world, there has been a quantum jump in the production of agricultural commodities, which has led to the production of a substantial considerable quantity of agricultural and agro-industrial wastes. The bulks of these wastes are lignocellulosic in nature and consist of three main polymeric constituents, i.e., cellulose, hemicellulose, and lignin, which are recalcitrant. The primary significant portions of these remain unutilized and are burnt in the field, leading to severe environmental aggression and wastage of resource. Farmers across the globe, including India, burn these agricultural wastes in their thousands of acre land, which contribute to spoiling the air quality index (AQI). This is very harmful, especially to children, pregnant women, old adults, and for patients suffering from respiratory diseases. The current manuscript sets up an agro-waste management platform by using paddy straw as a substrate for the production of nutritionally and medically rich oyster mushroom, Pleurotus florida (Pf) and which is further used in the green synthesis of bimetallic (gold-platinum) Au-Pt nanoparticle. Yield performance and biological efficiency of Pf were calculated from the degraded paddy straw. The green synthesized Au-Pt NPs were structurally characterized by ultraviolet-visible (UV-Vis), X-ray diffraction (XRD), transmission electron microscopy (TEM), energy dispersive spectroscopy (EDS), and zeta potential analysis. The prepared NPs showed a face-centered cubic crystal structure, icosahedral shape with a mean particle size of 16nm. Furthermore, we examined the cytotoxic activity of Au-Pt NPs using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay, intracellular reactive oxygen species (ROS) generation, and apoptosis by propidium iodide assay. We found that Au-Pt NPs exerted apoptotic activity on the human colon cancer cell line (HCT 116) in a dose-dependent manner from 12.5 to 200μg/mL. Overall, our findings create a prototype and open a new door to synthesizing functional nanoparticle by using oyster mushroom as the substrate for paddy straw agro-waste management and the applicability of Pf in the synthesis of eco-friendly Au-Pt NPs. This is the first kind of approach that kills two birds with one stone.

Light scattering and plasmonic response of Au–Fe3O4 nanoparticles

Surface plasmon (SP) response of nanoparticles (NP) has an unique path in the field of sensing, with specific developments in instrumentation and having a wide range of applications. Here it is described the light scattering process of NPs formed by magnetite core and gold shell (Au– $$\hbox {Fe}_{3}\hbox {O}_{4}$$ ). Those were synthesized by the co-precipitation method, resulting in a quasi-spherical (icosahedral) shape of an average of 37.5 nm. It was found a plasmonic behaviour from UV-visible spectra, exhibiting a SP peak around 560 nm, this response is strongly dependent on NP size and shape. To describe its plasmonic response, it was employed the Rayleigh scattering and Mie theory for a metal-dielectric shell-core. The numerical solutions of these models confirms the SP response and that there is a correlation between the size and shape of NPs due to scattering of light from them.

The Role of Tape Measure Protein in Nucleocytoplasmic Large DNA Virus Capsid Assembly.

Nucleocytoplasmic large DNA viruses (NCLDVs) are a group of large viruses that infect a wide range of hosts, from animals to protists. These viruses are grouped together in NCLDV based on genomic sequence analyses. They share a set of essential genes for virion morphogenesis and replication. Most NCLDVs generally have large physical sizes while their morphologies vary in different families, such as icosahedral, brick, or oval shape, raising the question of the possible regulatory factor on their morphogenesis. The capsids of icosahedral NCLDVs are assembled from small building blocks, named capsomers, which are the trimeric form of the major capsid proteins. Note that the capsids of immature poxvirus are spherical even though they are assembled from capsomers that share high structural conservation with those icosahedral NCLDVs. The recently published high resolution structure of NCLDVs, Paramecium bursaria Chlorella virus 1 and African swine fever virus, described the intensive network of minor capsid proteins that are located underneath the capsomers. Among these minor proteins is the elongated tape measure protein (TmP) that spans from one icosahedral fivefold vertex to another. In this study, we focused on the critical roles that TmP plays in the assembly of icosahedral NCLDV capsids, answering a question raised in a previously proposed spiral mechanism. Interestingly, basic local alignment search on the TmPs showed no significant hits in poxviruses, which might be the factor that differentiates poxviruses and icosahedral NCLDVs in their morphogenesis.

Identification and characterization of Miscanthus yellow fleck virus, a new polerovirus infecting Miscanthus sinensis.

Miscanthus sinensis is a grass used for sugarcane breeding and bioenergy production. Using high throughput sequencing technologies, we identified a new viral genome in infected M. sinensis leaf tissue displaying yellow fleck symptoms. This virus is most related to members of the genus Polerovirus in the family Luteoviridae. The canonical ORFs were computationally identified, the P3 coat protein was expressed, and virus-like particles were purified and found to conform to icosahedral shapes, characteristic of the family Luteoviridae. We propose the name Miscanthus yellow fleck virus for this new virus.

Polyhedral Effects on the Mass Activity of Platinum Nanoclusters

We use a coordination-based kinetics model to look at the kinetics of the turnover frequency (TOF) for the oxygen reduction reaction (ORR) for platinum nanoclusters. Clusters of octahedral, cuboctahedral, cubic, and icosahedral shape and size demonstrate the validity of the coordination-based approach. The Gibbs adsorption energy is computed using an empirical energy model based on density functional theory (DFT), statistical mechanics, and thermodynamics. We calculate the coordination and size dependence of the Gibbs adsorption energy and apply it to the analysis of the TOF. The platinum ORR follows a Langmuir–Hinshelwood mechanism, and we model the kinetics using a thermodynamic approach. Our modeling indicates that the coordination, shape, and the Gibbs energy of adsorption all are important factors in replicating an experimental TOF. We investigate the effects of size and shape of some platinum polyhedra on the oxygen reduction reaction (ORR) and the effect on the mass activity. The data are modeled quantitatively using lognormal distributions. We provide guidance on how to account for the effects of different distributions due to shape when determining the TOF.