INFLUENCE OF THE SIZE EFFECT ON THE REGULARITIES OF THE STRUCTURE FORMATION IN BIMETALLIC Au-Co NANOPARTICLES

В данной работе методом молекулярной динамики с использованием потенциала сильной связи исследовались биметаллические наночастицы Au - Co трёх стехиометрических составов различного размера. Установлены закономерности структурообразования, описаны их характерные особенности. В частности, в составах с 50ат.% и 75ат.% содержанием Au образуются множественные малые ядра локальной икосаэдрической симметрии. Только в составе Co -25ат.% Au с увеличением размера частиц преобладают кристаллические фазы. Выявлены составы, в которых внутренняя симметрия наночастицы определена наличием одного икосаэдра, либо сверхструктуры из нескольких икосаэдров. Рассчитаны концентрационные зависимости энергии смешения биметаллической наночастицы Au - Co. Показано, что в определённом диапазоне размеров существуют концентрационные составы, при которых биметаллический наносплав может проявлять нестабильность. С использованием калорических кривых потенциальной части внутренней энергии определены температуры кристаллизации. Установлено, что температура кристаллизации демонстрирует умеренный, либо существенный, в зависимости от состава, рост с увеличением размера биметаллических наночастиц Au - Co. This work studied bimetallic Au - Co nanoparticles of three stoichiometric compositions of various sizes by the molecular dynamics method using the tight-binding potential. The regularities of structure formation are established, their characteristic features are described. In particular, in compositions with 50at% and 75at% Au content, multiple small nuclei of local icosahedral symmetry are formed. Crystalline phases prevail only in the Co - 25 at% Au composition with an increase in the particle size. Compositions are revealed in which the internal symmetry of a nanoparticle is determined by the presence of one icosahedron or a superstructure of several icosahedrons. The concentration dependences of the mixing energy of a bimetallic Au - Co nanoparticle are calculated. It is shown that there are concentrations of compositions at which bimetallic nanoalloys can exhibit instability in a certain size range. Crystallization temperatures were determined using the caloric curves of the potential part of the internal energy. It was found that the crystallization temperature demonstrates a moderate or significant, depending on the composition as well as growth with an increase in the size of bimetallic Au - Co nanoparticles.

How One can Repair Non-integrable Kahan Discretizations. II. A Planar System with Invariant Curves of Degree 6

We find a novel one-parameter family of integrable quadratic Cremona maps of the plane preserving a pencil of curves of degree 6 and of genus 1. They turn out to serve as Kahan-type discretizations of a novel family of quadratic vector fields possessing a polynomial integral of degree 6 whose level curves are of genus 1, as well. These vector fields are non-homogeneous generalizations of reduced Nahm systems for magnetic monopoles with icosahedral symmetry, introduced by Hitchin, Manton and Murray. The straightforward Kahan discretization of these novel non-homogeneous systems is non-integrable. However, this drawback is repaired by introducing adjustments of order $$O(\epsilon ^2)$$ O ( ϵ 2 ) in the coefficients of the discretization, where $$\epsilon $$ ϵ is the stepsize.

High Resolution Structure of the Mature Capsid of Ralstonia Solanacearum Bacteriophage ϕRSA1 by Cryo-Electron Microscopy

The ϕRSA1 bacteriophage has been isolated from Ralstonia solanacearum, a gram negative bacteria having a significant economic impact on many important crops. We solved the three-dimensional structure of the ϕRSA1 mature capsid to 3.9 Å resolution by cryo-electron microscopy. The capsid shell, that contains the 39 kbp of dsDNA genome, has an icosahedral symmetry characterized by an unusual triangulation number of T = 7, dextro. The ϕRSA1 capsid is composed solely of the polymerization of the major capsid protein, gp8, which exhibits the typical “Johnson” fold first characterized in E. coli bacteriophage HK97. As opposed to the latter, the ϕRSA1 mature capsid is not stabilized by covalent crosslinking between its subunits, nor by the addition of a decoration protein. We further describe the molecular interactions occurring between the subunits of the ϕRSA1 capsid and their relationships with the other known bacteriophages.

Foot and mouth disease virus: A review

As seen by prior tragic outbreaks in many places throughout the world, the foot and mouth disease virus, or "FMDV," is one of the most critical challenges in animal health. In this review, the major features of FMDV, as well as aspects of its interactions with cells and hosts, were discussed. On the other hand, present and upcoming FMD treatment approaches. The first vertebrate virus found was the foot-and-mouth disease virus (FMDV). A capsid protein and the viral genome (+ve sense single strand RNA) make up FMDV. The icosahedral symmetry of the viral structure is made up of structural proteins (VP1, VP2, VP3, and VP4) as well as non-structural proteins (L, 1A, 1B, 1C, 1D, 2A, 2B, 2C, 3A, 3B, 3C, and 3D). The viral replication takes place in the cytoplasm of the cell. Because FMDV has a short incubation period, it spreads quickly. Direct contact is the most often used method of FMDV transmission. The occurrence of direct contact via aerosol and mechanical transmission (fomites, feed, and water). The immunological response is stimulated by the infection with FMD. However, due to virus antigenic diversity, the immune response does not always protect against FMD (antigenic shift). FMDV is divided into seven serotypes based on antigenic variation. O, A, C, SAT-1, SAT-2, SAT-3, and Asia-1 are the serotypes in question. O is the most frequent serotype.

iPVP-MCV: A Multi-Classifier Voting Model for the Accurate Identification of Phage Virion Proteins

The classic structure of a bacteriophage is commonly characterized by complex symmetry. The head of the structure features icosahedral symmetry, whereas the tail features helical symmetry. The phage virion protein (PVP), a type of bacteriophage structural protein, is an essential material of the infectious viral particles and is responsible for multiple biological functions. Accurate identification of PVPs is of great significance for comprehending the interaction between phages and host bacteria and developing new antimicrobial drugs or antibiotics. However, traditional experimental approaches for identifying PVPs are often time-consuming and laborious. Therefore, the development of computational methods that can efficiently and accurately identify PVPs is desired. In this study, we proposed a multi-classifier voting model called iPVP-MCV to enhance the predictive performance of PVPs based on their amino acid sequences. First, three types of evolutionary features were extracted from the position-specific scoring matrix (PSSM) profiles to represent PVPs and non-PVPs. Then, a set of baseline models were trained based on the support vector machine (SVM) algorithm combined with each type of feature descriptors. Finally, the outputs of these baseline models were integrated to construct the proposed method iPVP-MCV by using the majority voting strategy. Our results demonstrated that the proposed iPVP-MCV model was superior to existing methods when performing the rigorous independent dataset test.

Framboid Self-Assembly and Self-Organization

The formation of framboids involves two distinct processes. First, pyrite microcrystals aggregate into spherical groups through surface free energy minimization. The self-assembly of framboid microcrystals to form framboids is consistent with estimations based on the classical Derjaguin-Landau-Verwey-Overbeek (DVLO) theory, which balances the attraction between particles due to the van der Waals forces against the interparticle electrostatic repulsive force. Second, the microcrystals rearrange themselves into ordered domains through entropy maximization. Icosahedral symmetry tends to minimize short-range attractive interactions and maximize entropy. The physical processes which facilitate this rearrangement are Brownian motion and surface interactions. Curved framboid interface enforce deviation from the cubic close packed structure. In the absence of a curved surface, weakly interacting colloidal particles preferentially self-assemble into a cubic close packed structure, and this is observed in irregular, non-framboidal aggregates of pyrite micro- and nanocrystals.

Crystal structure of the potato leafroll virus coat protein and implications for viral assembly

Luteoviruses, poleroviruses, and enamoviruses are insect-transmitted, agricultural pathogens that infect a wide array of staple food crops. Previous cryo-electron microscopy studies of virus-like particles indicate that luteovirid viral capsids are built from a structural coat protein that organizes with T=3 icosahedral symmetry. Here we present the crystal structure of a truncated version of the coat protein monomer from potato leafroll virus at 1.57-Å resolution. In the crystal lattice, monomers pack into flat sheets that preserve the two-fold and three-fold axes of icosahedral symmetry and show minimal structural deviations when compared to the full-length subunits of the assembled virus-like particle. These observations have important implications in viral assembly and maturation, suggesting that the CP N-terminus and its interactions with RNA serve as a key driver for generating capsid curvature.

On symmetry breaking of dual polyhedra of non-crystallographic group H 3

The study of the polyhedra described in this paper is relevant to the icosahedral symmetry in the assembly of various spherical molecules, biomolecules and viruses. A symmetry-breaking mechanism is applied to the family of polytopes {\cal V}_{H_{3}}(\lambda) constructed for each type of dominant point λ. Here a polytope {\cal V}_{H_{3}}(\lambda) is considered as a dual of a {\cal D}_{H_{3}}(\lambda) polytope obtained from the action of the Coxeter group H 3 on a single point \lambda\in{\bb R}^{3}. The H 3 symmetry is reduced to the symmetry of its two-dimensional subgroups H 2, A 1 × A 1 and A 2 that are used to examine the geometric structure of {\cal V}_{H_{3}}(\lambda) polytopes. The latter is presented as a stack of parallel circular/polygonal orbits known as the `pancake' structure of a polytope. Inserting more orbits into an orbit decomposition results in the extension of the {\cal V}_{H_{3}}(\lambda) structure into various nanotubes. Moreover, since a {\cal V}_{H_{3}}(\lambda) polytope may contain the orbits obtained by the action of H 3 on the seed points (a, 0, 0), (0, b, 0) and (0, 0, c) within its structure, the stellations of flat-faced {\cal V}_{H_{3}}(\lambda) polytopes are constructed whenever the radii of such orbits are appropriately scaled. Finally, since the fullerene C20 has the dodecahedral structure of {\cal V}_{H_{3}}(a,0,0), the construction of the smallest fullerenes C24, C26, C28, C30 together with the nanotubes C20+6N , C20+10N is presented.

Abstract OR-7: Genome Release Mechanism of Picorna-Like Viruses

Protein capsids protect the genomes of viruses from degradation in the extracellular environment. However, virus capsids must release genomes into a host cell to initiate infection. We used cryo-electron microscopy to characterize the genome release of viruses from the order Picornavirales: picornaviruses, dicistroviruses, and iflaviruses. These virus families include numerous human and animal pathogens. The viruses have non-enveloped virions and capsids organized with icosahedral symmetry. Their genome release can be induced in vitro by exposure to acidic pH, mimicking conditions in endosomes. We show that conformational changes of capsids and expansion of viral RNA genomes, which are induced by acidic pH, trigger the opening of picorna-like virus particles. The capsids of the studied viruses crack into pieces or open like flowers to release their genomes. The large openings of capsids enable the virus genomes to exit within microseconds, which limits the probability of their degradation by the RNases. Characterization of the virus genome release is the first step towards developing inhibitors of the process.

Long-range magnetic order in real icosahedral quasicrystals

Quasicrystals (QCs), first discovered in 1984, generally do not exhibit long-range magnetic order. Here, we report on long-range magnetic order in the real icosahedral quasicrystals (i QCs) Au–Ga–Gd and Au–Ga–Tb. The Au65Ga20Gd15 i QC exhibits a ferromagnetic transition at TC = 23 K, manifested as a sharp anomaly in both magnetic-susceptibility and specific-heat measurements. Quick magnetic saturation to almost the full moment (7μB/Gd3+) is observed under 100 Oe at 2 K. This is the first observation of long-range magnetic order in a real quasicrystal, in contrast to the spin-glass-like behaviours observed for the other magnetic quasicrystals found to date. Moreover, when Gd is replaced by Tb, i.e. for the Au65Ga20Tb15 i QC, a ferromagnetic behaviour is still retained with TC = 16 K. Although the sharp anomaly in the specific heat observed for the Au65Ga20Gd15 i QC is significantly broadened upon Tb substitution, neutron-diffraction experiments clearly show the marked development of magnetic Bragg peaks below TC, indicating long-range magnetic order for the Au65Ga20Tb15 i QC also. Our findings can contribute to the further investigation of exotic magnetic orders formed on real quasiperiodic lattices with unprecedented highest global symmetry, i.e. icosahedral symmetry.