Quasicrystals at extreme conditions: The role of pressure in stabilizing icosahedral Al 63Cu 24Fe 13 at high temperature

DOE PAGES

Stagno, Vincenzo; Bindi, Luca; Park, Changyong; ...

2015-11-20

Icosahedrite, the first natural quasicrystal with composition Al 63Cu 24Fe 13, was discovered in several grains of the Khatyrka meteorite, a unique CV3 carbonaceous chondrite. The presence in the meteorite fragments of icosahedrite strictly associated with high-pressure phases like ahrensite and stishovite indicates a formation conditions at high pressures and temperatures, likely during an impact-induced shock occurred in contact with the reducing solar nebula gas. In contrast, previous experimental studies on the stability of synthetic icosahedral AlCuFe, which were limited to ambient pressure, indicated incongruent melting at ~1123 K, while high-pressure experiments carried out at room temperature showed structural stabilitymore » up to about 35 GPa. These data are insufficient to experimentally constrain the formation and stability of icosahedrite under extreme conditions. Here we present the results of in situ high pressure experiments using diamond anvil cells of the compressional behavior of synthetic icosahedrite up to ~50 GPa at room temperature. Simultaneous high P-T experiments have been also carried out using both laser-heated diamond anvil cells combined with in situ synchrotron X-ray diffraction (at ~42 GPa) and multi-anvil apparatus (at 21 GPa) to investigate the structural evolution of icosahedral Al 63Cu 24Fe 13 and crystallization of possible coexisting phases. The results demonstrate that the quasiperiodic symmetry of icosahedrite is retained over the entire experimental pressure range explored. In addition, we show that pressure acts to stabilize the icosahedral symmetry at temperatures much higher than previously reported. Based on our experimental study, direct crystallization of Al-Cu-Fe quasicrystals from an unusual Al-Cu-rich melt would be possible but limited to a narrow temperature range beyond which crystalline phases would form, like those observed in the Khatyrka meteorite. Here, an alternative mechanism would consist in late

Icosahedral and decagonal quasicrystals of intermetallic compounds are multiple twins of cubic or orthorhombic crystals composed of very large atomic complexes with icosahedral point-group symmetry in cubic close packing or body-centered packing: Structure of decagonal Al6Pd

PubMed Central

Pauling, Linus

1989-01-01

A doubly icosahedral complex involves roughly spherical clusters of atoms with icosahedral point-group symmetry, which are themselves, in parallel orientation, icosahedrally packed. These complexes may form cubic crystallites; three structures of this sort have been identified. Analysis of electron diffraction photographs of the decagonal quasicrystal Al6Pd has led to its description as involving pentagonal twinning of an orthorhombic crystal with a = 51.6 Å, b = 37.6 Å, and c = 33.24 Å, with about 4202 atoms in the unit, comprising two 1980-atom doubly icosahedral complexes, each involving icosahedral packing of 45 44-atom icosahedral complexes (at 0 0 0 and 1/2 1/2 1/2) and 242 interstitial atoms. The complexes and clusters are oriented with one of their fivefold axes in the c-axis direction. Images PMID:16594092

Icosahedral and decagonal quasicrystals of intermetallic compounds are multiple twins of cubic or orthorhombic crystals composed of very large atomic complexes with icosahedral point-group symmetry in cubic close packing or body-centered packing: Structure of decagonal Al(6)Pd.

PubMed

Pauling, L

1989-12-01

A doubly icosahedral complex involves roughly spherical clusters of atoms with icosahedral point-group symmetry, which are themselves, in parallel orientation, icosahedrally packed. These complexes may form cubic crystallites; three structures of this sort have been identified. Analysis of electron diffraction photographs of the decagonal quasicrystal Al(6)Pd has led to its description as involving pentagonal twinning of an orthorhombic crystal with a = 51.6 A, b = 37.6 A, and c = 33.24 A, with about 4202 atoms in the unit, comprising two 1980-atom doubly icosahedral complexes, each involving icosahedral packing of 45 44-atom icosahedral complexes (at 0 0 0 and 1/2 1/2 1/2) and 242 interstitial atoms. The complexes and clusters are oriented with one of their fivefold axes in the c-axis direction.

Diffuse Scattering in the Icosahedral AL-Li-Cu Quasicrystal

NASA Astrophysics Data System (ADS)

Proult, A.; Donnadieu, P.; Wang, K.; Garoche, P.

1995-12-01

Electron diffraction patterns of icosahedral quasicrystals frequently exhibit diffuse scattering features. We report a detailed analysis of diffuse scattering in Al{6}Li{3}Cu (T2) quasicrystalline samples. The samples have been specifically heat-treated which allows to observe pronounced diffuse effects. Diffuse streaks are observed along the 5-fold and 2-fold symmetry axes and are elongated perpendicularly to these directions. These streaks are due to discs in the 3-dimensional reciprocal space. The diffuse disc positions are only indexable in the 6-dimensional hyperspace but the disc intensities do not agree with the ones predicted by the Cut-and-Project method. The diffuse discs we observed seem to be related to an original quasicrystalline phenomenon overlapping with the icosahedral phase. Les diagrammes de diffraction électronique des quasicristaux icosaédriques présentent fréquemment des diffusions diffuses. Nous les analysons ici en détails sur des échantillons de phase quasicristalline Al{6}Li{3}Cu (T2) traités thermiquement dans lesquels les diffusions diffuses sont trés prononcées. Les intensités diffuses forment des batônnets centrés sur des positions appartenant aux rangées réciproques d'ordre 5 et d'ordre 2 et allongés perpendiculairement à ces directions. On montre qu'il s'agit en fait de disques diffus. dans le réseau réciproque à 3 dimensions, dont les positions ne peuvent s'indexer que sur le réseau à 6 dimensions. Toutefois, les intensités ne correspondent pas à celle prédites par l'algorithme de Coupe-et-Projection. Les disques de diffusion diffuse semblent relever d'une organisation quasicristalline originale se superposant à la phase icosaédrique.

Analysis of pulsed-neutron powder diffraction patterns of the icosahedral quasicrystals Pd3Siu and AlCuLiMg (three alloys) as twinned cubic crystals with large units.

PubMed Central

Pauling, L

1991-01-01

The low-Q peaks on three pulsed-neutron powder patterns (total, U differential, and Pd differential) of the icosahedral quasicrystal Pd3SiU have been indexed on the basis of an assumed cubic structure of the crystals that by icosahedral twinning form the quasicrystal. The primitive unit cube is found to have edge length 56.20 A and to contain approximately 12,100 atoms. Similar analyses of pulsed-neutron patterns of Al55Cu10Li35, Al55Cu10Li30Mg5, and Al510Cu125Li235Mg130 give values of the cube edge length 58.3, 58.5, and 58.4 A, respectively, with approximately 11,650 atoms in the unit cube. It is suggested that the unit contains eight complexes in the beta-W positions, plus some small interstitial groups of atoms, with each complex consisting of a centered icosahedron of 13 clusters, each of 116 atoms with the icosahedral structure found in the body-centered cubic crystal Mg32(Al,Zn)49. PMID:11607201

Analysis of pulsed-neutron powder diffraction patterns of the icosahedral quasicrystals Pd3Siu and AlCuLiMg (three alloys) as twinned cubic crystals with large units.

PubMed

Pauling, L

1991-08-01

The low-Q peaks on three pulsed-neutron powder patterns (total, U differential, and Pd differential) of the icosahedral quasicrystal Pd3SiU have been indexed on the basis of an assumed cubic structure of the crystals that by icosahedral twinning form the quasicrystal. The primitive unit cube is found to have edge length 56.20 A and to contain approximately 12,100 atoms. Similar analyses of pulsed-neutron patterns of Al55Cu10Li35, Al55Cu10Li30Mg5, and Al510Cu125Li235Mg130 give values of the cube edge length 58.3, 58.5, and 58.4 A, respectively, with approximately 11,650 atoms in the unit cube. It is suggested that the unit contains eight complexes in the beta-W positions, plus some small interstitial groups of atoms, with each complex consisting of a centered icosahedron of 13 clusters, each of 116 atoms with the icosahedral structure found in the body-centered cubic crystal Mg32(Al,Zn)49.

Influence of leaching on surface composition, microstructure, and valence band of single grain icosahedral Al-Cu-Fe quasicrystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lowe, M.; McGrath, R.; Sharma, H. R.

The use of quasicrystals as precursors to catalysts for the steam reforming of methanol is potentially one of the most important applications of these new materials. To develop application as a technology requires a detailed understanding of the microscopic behavior of the catalyst. Here, we report the effect of leaching treatments on the surface microstructure, chemical composition, and valence band of the icosahedral (i-) Al-Cu-Fe quasicrystal in an attempt to prepare a model catalyst. The high symmetry fivefold surface of a single grain i-Al-Cu-Fe quasicrystal was leached with NaOH solution for varying times, and the resulting surface was characterized bymore » x-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), scanning electron microscopy (SEM), and atomic force microscopy (AFM). The leaching treatments preferentially remove Al producing a capping layer consisting of Fe and Cu oxides. The subsurface layer contains elemental Fe and Cu in addition to the oxides. The quasicrystalline bulk structure beneath remains unchanged. The subsurface gradually becomes Fe{sub 3}O{sub 4} rich with increasing leaching time. The surface after leaching exhibits micron sized dodecahedral cavities due to preferential leaching along the fivefold axis. Nanoparticles of the transition metals and their oxides are precipitated on the surface after leaching. The size of the nanoparticles is estimated by high resolution transmission microscopy to be 5-20 nm, which is in agreement with the AFM results. Selected area electron diffraction (SAED) confirms the crystalline nature of the nanoparticles. SAED further reveals the formation of an interface between the high atomic density lattice planes of nanoparticles and the quasicrystal. These results provide an important insight into the preparation of model catalysts of nanoparticles for steam reforming of methanol.« less

The deviations of the Al6Li3Cu quasicrystal from icosahedral symmetry : a reminiscence of a cubic crystal

NASA Astrophysics Data System (ADS)

Donnadieu, Patricia

1994-05-01

The (Al6Li3Cu) (T2) quasicrystals are known to exhibit large deviations from the icosahedral symmetry. Series of electron diffraction patterns are used to investigate these imperfections in as-cast T, samples. A detailed analysis of the 5-fold and 3-fold symmetry diffraction patterns shows that they are compatible with the m3 point group instead of the m35 icosahedral group. This symmetry reduction is interprétéd as reminiscent of the cubic approximant phase (R-Al5Li3Cu) rather than of higher order approximant phases. This interpretation is supported by previous observations on crystal/quasicrystal phase transformation in the AlLiCu system. Les quasicristaux de phase T2(Al6Li3Cu) montrent d'importantes déviations à la symétrie icosaédrique. Ces imperfections sont mises en évidence par diffraction électronique dans des échantillons de phase T2 brut de coulée. Un examen détaillé des diagrammes de diffraction de symétrie d'ordre 3 et 5 révèle qu'ils sont compatibles avec le groupe ponctuel m3 au lieu du groupe de l'icosaèdre (m35). Cette réduction de symétrie est interprétée comme une réminiscence de la phase cubique approximante (R-Al5Li3Cu) et non l'apparition d'approximant d'ordre plus élevé. Cette interprétation est suggérée par des observations antérieures sur la transformation cristal/quasicristal dans le système AlLiCu.

Quasicrystal structure and growth models: discussion of the status quo and the still open questions

NASA Astrophysics Data System (ADS)

Steurer, Walter

2017-02-01

Where are we now in quasicrystal (QC) research more than three decades after Dan Shechtman’s discovery? Do we fully understand the origin of quasiperiodicity, the formation, growth, thermodynamic stability, structure and properties of quasicrystals? First, I will shortly present the status quo, then I will address the still open questions, and identify potential focus areas for future research. Because of the limited space, I will focus on decagonal quasicrystals (DQCs); the status quo for research on icosahedral quasicrystals (IQCs) is comparable.

Collisions in outer space produced an icosahedral phase in the Khatyrka meteorite never observed previously in the laboratory.

PubMed

Bindi, Luca; Lin, Chaney; Ma, Chi; Steinhardt, Paul J

2016-12-08

We report the first occurrence of an icosahedral quasicrystal with composition Al 62.0(8) Cu 31.2(8) Fe 6.8(4) , outside the measured equilibrium stability field at standard pressure of the previously reported Al-Cu-Fe quasicrystal (Al x Cu y Fe z , 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 (Al 63 Cu 24 Fe 13 ), 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.

Collisions in outer space produced an icosahedral phase in the Khatyrka meteorite never observed previously in the laboratory

PubMed Central

Bindi, Luca; Lin, Chaney; Ma, Chi; Steinhardt, Paul J.

2016-01-01

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. PMID:27929519

Shock synthesis of quasicrystals with implications for their origin in asteroid collisions.

PubMed

Asimow, Paul D; Lin, Chaney; Bindi, Luca; Ma, Chi; Tschauner, Oliver; Hollister, Lincoln S; Steinhardt, Paul J

2016-06-28

We designed a plate impact shock recovery experiment to simulate the starting materials and shock conditions associated with the only known natural quasicrystals, in the Khatyrka meteorite. At the boundaries among CuAl5, (Mg0.75Fe(2+) 0.25)2SiO4 olivine, and the stainless steel chamber walls, the recovered specimen contains numerous micron-scale grains of a quasicrystalline phase displaying face-centered icosahedral symmetry and low phason strain. The compositional range of the icosahedral phase is Al68-73Fe11-16Cu10-12Cr1-4Ni1-2 and extends toward higher Al/(Cu+Fe) and Fe/Cu ratios than those reported for natural icosahedrite or for any previously known synthetic quasicrystal in the Al-Cu-Fe system. The shock-induced synthesis demonstrated in this experiment reinforces the evidence that natural quasicrystals formed during a shock event but leaves open the question of whether this synthesis pathway is attributable to the expanded thermodynamic stability range of the quasicrystalline phase at high pressure, to a favorable kinetic pathway that exists under shock conditions, or to both thermodynamic and kinetic factors.

Shock synthesis of quasicrystals with implications for their origin in asteroid collisions

NASA Astrophysics Data System (ADS)

Asimow, Paul D.; Lin, Chaney; Bindi, Luca; Ma, Chi; Tschauner, Oliver; Hollister, Lincoln S.; Steinhardt, Paul J.

2016-06-01

We designed a plate impact shock recovery experiment to simulate the starting materials and shock conditions associated with the only known natural quasicrystals, in the Khatyrka meteorite. At the boundaries among CuAl5, (Mg0.75Fe2+0.25)2SiO4 olivine, and the stainless steel chamber walls, the recovered specimen contains numerous micron-scale grains of a quasicrystalline phase displaying face-centered icosahedral symmetry and low phason strain. The compositional range of the icosahedral phase is Al68-73Fe11-16Cu10-12Cr1-4Ni1-2 and extends toward higher Al/(Cu+Fe) and Fe/Cu ratios than those reported for natural icosahedrite or for any previously known synthetic quasicrystal in the Al-Cu-Fe system. The shock-induced synthesis demonstrated in this experiment reinforces the evidence that natural quasicrystals formed during a shock event but leaves open the question of whether this synthesis pathway is attributable to the expanded thermodynamic stability range of the quasicrystalline phase at high pressure, to a favorable kinetic pathway that exists under shock conditions, or to both thermodynamic and kinetic factors.

Icosahedral quasicrystalline (Ti1.6V0.4Ni)100-xScx alloys: Synthesis, structure and their application in Ni-MH batteries

NASA Astrophysics Data System (ADS)

Hu, Wen; Yi, Jianhong; Zheng, Biju; Wang, Limin

2013-06-01

Thanks to the revolutionary discovery of 5-fold symmetry contributed by Shechtman, quasicrystal is now recognized as another solid-state existing form. As the second largest class of quasicrystals, titanium-based icosahedral quasicrystals are very promising for hydrogen storage applications owing to their inherent abundant interstitial sites and favorable hydrogen-metal chemistry. In this context, (Ti1.6V0.4Ni)100-xScx (x=0.5-6) quaternary icosahedral quasicrystals have been successfully synthesized via arc-melting and subsequent melt-spinning techniques, and then their electrochemical performance toward hydrogen is explored. When the molar ratio of Sc addition is under 1%, a maximum discharge capacity of about 270 mA h g-1 can be delivered. With further increasing Sc amount to 6%, good cycling stability as well as significantly retarded self-discharge rate (capacity retention 94% after 24 h relaxation) is observed. But meanwhile, the discharge capacities fall into 250-240 mA h g-1, and the electrocatalytic activity improvement is highly demanded.

Bronze-mean hexagonal quasicrystal

NASA Astrophysics Data System (ADS)

Dotera, Tomonari; Bekku, Shinichi; Ziherl, Primož

2017-10-01

The most striking feature of conventional quasicrystals is their non-traditional symmetry characterized by icosahedral, dodecagonal, decagonal or octagonal axes. The symmetry and the aperiodicity of these materials stem from an irrational ratio of two or more length scales controlling their structure, the best-known examples being the Penrose and the Ammann-Beenker tiling as two-dimensional models related to the golden and the silver mean, respectively. Surprisingly, no other metallic-mean tilings have been discovered so far. Here we propose a self-similar bronze-mean hexagonal pattern, which may be viewed as a projection of a higher-dimensional periodic lattice with a Koch-like snowflake projection window. We use numerical simulations to demonstrate that a disordered variant of this quasicrystal can be materialized in soft polymeric colloidal particles with a core-shell architecture. Moreover, by varying the geometry of the pattern we generate a continuous sequence of structures, which provide an alternative interpretation of quasicrystalline approximants observed in several metal-silicon alloys.

Inelastic neutron scattering study of icosahedral AlFeCu quasicrystal

NASA Astrophysics Data System (ADS)

Quilichini, M.; Hennion, B.; Heger, G.; Lefebvre, S.; Quivy, A.

1992-02-01

Dynamical properties of quasiperiodic structures are rather tricky and far from being understood. For quasicrystals only little information is available both theoretically and experimentally. In this paper we present new experimental results obtained by inelastic neutron scattering on a monodomain quasicrystal of Al{63}Cu{25}Fe{12} already investigated in a previous study [1]. In section 1 we recall the basic features of the quasiperiodic structures and briefly review theoretical works on the dynamics of quasicrystals which can be of some help to appreciate the experimental data presented in section 2 and discussed in section 3. Les propriétés dynamiques des structures quasipériodiques sont complexes et pas encore complètement comprises. Pour les quasicristaux on ne possède que peu d'études dynamiques tant du point de vue théorique qu'expérimental. Dans cette lettre nous présentons des nouveaux résultats obtenus par diffusion inélastique de neutrons avec un quasicristal monodomaine de Al{63}Cu{25}Fe{12} que nous avions déjà étudié [1]. Dans la partie 1 nous rappelons quelques propriétés spécifiques des structures quasipériodiques et nous résumons brièvement les travaux théoriques qui nous permettent une interprétation qualitative des données expérimentales présentées dans la partie 2 et discutées dans la partie 3.

High-resolution electron microscopy observation of a new crystalline approximant W' of Mg-Zn-Y icosahedral quasicrystal

PubMed

Luo; Hashimoto

2000-10-01

A new ordered structure W' with a lattice parameter (a = 2.05 nm) about three times as large as that of the fundamental face-centered cubic W phase (a = 0.6848 nm) has been found in the Mg-Zn-Y system by means of transmission electron microscopy. The W' and W phases have the cube-to-cube orientation relationship. Moreover, the strong electron diffraction spots of the W' phase showed pseudoicosahedral symmetry, implying that it is a crystalline approximant of the Mg-Zn-Y icosahedral quasicrystal. In the high-resolution electron microscopic images of the W' phase, Penrose tiles of pentagons and boats with an edge length of a(p) = 0.481 nm can be identified. A binary tile of crown subunit has also been deduced from such a tiling. Translation domains of the W' phase have also been observed and the translation vectors at the domain boundary are: a(p), tau x a(p) and (1 + tau) x a(p), respectively, where (1 + tau) x a(p) equals to the edge length a(r) of the big obtuse rhombus of the W' phase and tau = (1 + square root of 5)/2, is the golden ratio.

Shear localization and size-dependent strength of YCd 6 quasicrystal approximant at the micrometer length scale

DOE PAGES

Song, Gyuho; Kong, Tai; Dusoe, Keith J.; ...

2018-01-24

Mechanical properties of materials are strongly dependent of their atomic arrangement as well as the sample dimension, particularly at the micrometer length scale. Here in this study, we investigated the small-scale mechanical properties of single-crystalline YCd 6, which is a rational approximant of the icosahedral Y-Cd quasicrystal. In situ microcompression tests revealed that shear localization always occurs on {101} planes, but the shear direction is not constrained to any particular crystallographic directions. Furthermore, the yield strengths show the size dependence with a power law exponent of 0.4. Shear localization on {101} planes and size-dependent yield strength are explained in termsmore » of a large interplanar spacing between {101} planes and the energetics of shear localization process, respectively. The mechanical behavior of the icosahedral Y-Cd quasicrystal is also compared to understand the influence of translational symmetry on the shear localization process in both YCd 6 and Y-Cd quasicrystal micropillars. Finally, the results of this study will provide an important insight in a fundamental understanding of shear localization process in novel complex intermetallic compounds.« less

Shear localization and size-dependent strength of YCd 6 quasicrystal approximant at the micrometer length scale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Gyuho; Kong, Tai; Dusoe, Keith J.

Mechanical properties of materials are strongly dependent of their atomic arrangement as well as the sample dimension, particularly at the micrometer length scale. Here in this study, we investigated the small-scale mechanical properties of single-crystalline YCd 6, which is a rational approximant of the icosahedral Y-Cd quasicrystal. In situ microcompression tests revealed that shear localization always occurs on {101} planes, but the shear direction is not constrained to any particular crystallographic directions. Furthermore, the yield strengths show the size dependence with a power law exponent of 0.4. Shear localization on {101} planes and size-dependent yield strength are explained in termsmore » of a large interplanar spacing between {101} planes and the energetics of shear localization process, respectively. The mechanical behavior of the icosahedral Y-Cd quasicrystal is also compared to understand the influence of translational symmetry on the shear localization process in both YCd 6 and Y-Cd quasicrystal micropillars. Finally, the results of this study will provide an important insight in a fundamental understanding of shear localization process in novel complex intermetallic compounds.« less

Evolution of Nano-structured Quasicrystals from Amorphous alloys

NASA Astrophysics Data System (ADS)

Xing, L. Q.; Kelton, K. F.

2002-03-01

Ta shows a significant effect on the precipitation of quasicrystals in (Zr_1-xTa_x)_64Cu_18Ni_8Al_10 amorphous alloys. The amorphous alloy made without Ta forms precipitates of tetragonal Zr_2Cu primary phases upon annealing. The addition of a small amount of Ta ( ~ 3 at%) to the alloy initiates the precipitation of primary icosahedral quasicrystal phases. Moreover, as the Ta concentration increases, the size of the precipitates decreases dramatically. To study the effect of Ta in this alloy system and to understand the mechanism for the precipitation of nano-structured quasicrystals, we have investigated the crystallization characteristics of the alloys made with different Ta concentration using DSC, checked the structures of the annealed samples with TEM and X-ray diffraction, and analyzed the kinetics of the crystallization processes. The kinetic parameter and the measured crystal size distribution will be compared with theoretical predictions from conventional nucleation and growth model and from a new model for nucleation that couples the long-range diffusion flux with the interfacial attachment processes.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Unal, B.; Jenks, C.J.; Thiel, P.A.

From other work, two preferred sites have been suggested for metals and semimetals adsorbed on the fivefold surfaces of icosahedral, Al-based quasicrystals. Because of their appearance in scanning tunneling microscopy (STM) images, these sites are known as dark stars and white flowers. In this paper, we analyze four bulk structural models in physical space to determine the types, chemical decorations, and densities of the dark star - and, to a lesser extent, the white flower - adsorption sites for the fivefold planes of icosahedral Al-Pd-Mn. We find that the chemical decorations of these sites are heterogeneous, even within a singlemore » model. Both features are also structurally heterogeneous, according to STM measurements, and the structural variation is consistent with the bulk structure models. Finally, from the models, the density of dark stars in the planes correlates with the step height. This may explain previous experimental observations of different properties for different terraces.« less

Atomic model of anti-phase boundaries in a face-centred icosahedral Zn Mg Dy quasicrystal

NASA Astrophysics Data System (ADS)

Wang, Jianbo; Yang, Wenge; Wang, Renhui

2003-03-01

An atomic model in the physical space for an anti-phase boundary (APB) in the ordered face-centred icosahedral Zn-Mg-Dy quasicrystal phase is presented, based on a six-dimensional model suggested by Ishimasa and Shimizu (2000 Mater. Sci. Eng. A 294-296 232, Ishimasa 2001 private communication). The physical space atomic positions of the defected structure were used for the calculation of the corresponding exit-plane wavefunction and high-resolution transmission electron microscopy images. The analysis of the defect by inverse Fourier transformation reveals that when superstructure reflection spots are used for back-transformation, then at the APB, bright lattice fringes are found to turn into dark ones, and vice versa. When fundamental reflections are used, the APB is not visible. This phenomenon is the same as the corresponding experimental study recently published by Heggen et al(2001a Phys. Rev. B 64 014202). Based on this atomic model it is found that the APB perpendicular to a fivefold axis A5 (APB-A5) is a non-conservative boundary, while the APB perpendicular to a pseudo-twofold axis A2P (APB-A2P) is a conservative one. This fact is consistent with the experimental observation (Heggen et al2002 J. Alloys Compounds 342 330) that the frequency of occurrence of APB-A5 is 90% in the heat-treated samples compared with that in the deformed samples (45%), while the frequency of occurrence of APB-A2P is 34% in the deformed samples compared with that in the heat-treated samples.

Shock synthesis of quasicrystals with implications for their origin in asteroid collisions

DOE PAGES

Asimow, Paul D.; Lin, Chaney; Bindi, Luca; ...

2016-06-28

Here, we designed a plate impact shock recovery experiment to simulate the starting materials and shock conditions associated with the only known natural quasicrystals, in the Khatyrka meteorite. At the boundaries among CuAl5, (Mg 0.75Fe 0.25 2+) 2SiO 4 olivine, and the stainless steel chamber walls, the recovered specimen contains numerous micron-scale grains of a quasicrystalline phase displaying face-centered icosahedral symmetry and low phason strain. The compositional range of the icosahedral phase is Al 68-73Fe 11-16Cu 10-12Cr 1-4Ni 1-2 and extends toward higher Al/(Cu+Fe) and Fe/Cu ratios than those reported for natural icosahedrite or for any previously known synthetic quasicrystalmore » in the Al-Cu-Fe system. The shock-induced synthesis demonstrated in this experiment reinforces the evidence that natural quasicrystals formed during a shock event but leaves open the question of whether this synthesis pathway is attributable to the expanded thermodynamic stability range of the quasicrystalline phase at high pressure, to a favorable kinetic pathway that exists under shock conditions, or to both thermodynamic and kinetic factors.« less

Shock synthesis of quasicrystals with implications for their origin in asteroid collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Asimow, Paul D.; Lin, Chaney; Bindi, Luca

Here, we designed a plate impact shock recovery experiment to simulate the starting materials and shock conditions associated with the only known natural quasicrystals, in the Khatyrka meteorite. At the boundaries among CuAl5, (Mg 0.75Fe 0.25 2+) 2SiO 4 olivine, and the stainless steel chamber walls, the recovered specimen contains numerous micron-scale grains of a quasicrystalline phase displaying face-centered icosahedral symmetry and low phason strain. The compositional range of the icosahedral phase is Al 68-73Fe 11-16Cu 10-12Cr 1-4Ni 1-2 and extends toward higher Al/(Cu+Fe) and Fe/Cu ratios than those reported for natural icosahedrite or for any previously known synthetic quasicrystalmore » in the Al-Cu-Fe system. The shock-induced synthesis demonstrated in this experiment reinforces the evidence that natural quasicrystals formed during a shock event but leaves open the question of whether this synthesis pathway is attributable to the expanded thermodynamic stability range of the quasicrystalline phase at high pressure, to a favorable kinetic pathway that exists under shock conditions, or to both thermodynamic and kinetic factors.« less

Icosahedral quasicrystalline (Ti₁.₆V₀.₄Ni)₁₀₀₋xScx alloys: Synthesis, structure and their application in Ni-MH batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Wen; State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, CAS, Changchun 130022, Jilin; Yi, Jianhong

2013-06-01

Thanks to the revolutionary discovery of 5-fold symmetry contributed by Shechtman, quasicrystal is now recognized as another solid-state existing form. As the second largest class of quasicrystals, titanium-based icosahedral quasicrystals are very promising for hydrogen storage applications owing to their inherent abundant interstitial sites and favorable hydrogen-metal chemistry. In this context, (Ti₁.₆V₀.₄Ni)₁₀₀₋xScx (x=0.5–6) quaternary icosahedral quasicrystals have been successfully synthesized via arc-melting and subsequent melt-spinning techniques, and then their electrochemical performance toward hydrogen is explored. When the molar ratio of Sc addition is under 1%, a maximum discharge capacity of about 270 mA h g⁻¹ can be delivered. With furthermore » increasing Sc amount to 6%, good cycling stability as well as significantly retarded self-discharge rate (capacity retention 94% after 24 h relaxation) is observed. But meanwhile, the discharge capacities fall into 250-240 mA h g⁻¹, and the electrocatalytic activity improvement is highly demanded. - Graphical abstract: Quasicrystalline Ti–V–Ni–Sc hydrogen storage materials: Sc addition into Ti₁.₆V₀.₄Ni alloy forms the icosahedral phase (see picture). With optimal Sc dosage, the anodic cycling stability and self-discharge property are greatly enhanced. - Highlights: • Crystalline disallowed 5-fold symmetry is present in (Ti₁.₆V₀.₄Ni)₁₀₀₋xScx alloys. • Ti-based metastable quasicrystalline alloys can store hydrogen electrochemically. • A maximum discharge capacity of 270 mA h g⁻¹ can be delivered. • Advantageous cycle stability and self-discharge property benefit from Sc addition. • Ti and V dissolution is suppressed by an oxide layer resulting from Sc corrosion.« less

Critical Slowing Down in Zn-Mg-Ho Quasicrystal

NASA Astrophysics Data System (ADS)

Sugiyama, Jun; Nozaki, Hiroshi; Ansaldo, Eduardo J.; Morris, Gerald D.; Brewer, Jess H.; Sato, Taku J.

By means of longitudinal field muon-spin spectroscopy, we have found a clear critical slowing down caused by spin fluctuation of Ho moments in the icosahedral quasicrystal (QC), i-ZnMgHo, with freezing temperature (Tf =1.95 K), for which the susceptibility showed an anomaly at5K. The difference is attributed to crystalline elec-tric field (CEF) effects. The muons experience a broad, fluctuating, field distribution, of width Δ ∼6.3Taround Tf . The effect of the CEF is also apparent in zero field and weak applied transverse field measurements, with an onset around 60 K. For the Cd-based QCs (CdMgHo and CdMgGd), which exhibited two freezing temperatures in the susceptibility, the change in fluctuation rate, i.e. freezing, occurs at the lower Tf .

Evidence for the extraterrestrial origin of a natural quasicrystal.

PubMed

Bindi, Luca; Eiler, John M; Guan, Yunbin; Hollister, Lincoln S; MacPherson, Glenn; Steinhardt, Paul J; Yao, Nan

2012-01-31

We present evidence that a rock sample found in the Koryak Mountains in Russia and containing icosahedrite, an icosahedral quasicrystalline phase with composition Al(63)Cu(24)Fe(13), is part of a meteorite, likely formed in the early solar system about 4.5 Gya. The quasicrystal grains are intergrown with diopside, forsterite, stishovite, and additional metallic phases [khatyrkite (CuAl(2)), cupalite (CuAl), and β-phase (AlCuFe)]. This assemblage, in turn, is enclosed in a white rind consisting of diopside, hedenbergite, spinel (MgAl(2)O(4)), nepheline, and forsterite. Particularly notable is a grain of stishovite (from the interior), a tetragonal polymorph of silica that only occurs at ultrahigh pressures (≥ 10 Gpa), that contains an inclusion of quasicrystal. An extraterrestrial origin is inferred from secondary ion mass spectrometry (18)O/(16)O and (17)O/(16)O measurements of the pyroxene and olivine intergrown with the metal that show them to have isotopic compositions unlike any terrestrial minerals and instead overlap those of anhydrous phases in carbonaceous chondrite meteorites. The spinel from the white rind has an isotopic composition suggesting that it was part of a calcium-aluminum-rich inclusion similar to those found in CV3 chondrites. The mechanism that produced this exotic assemblage is not yet understood. The assemblage (metallic copper-aluminum alloy) is extremely reduced, and the close association of aluminum (high temperature refractory lithophile) with copper (low temperature chalcophile) is unexpected. Nevertheless, our evidence indicates that quasicrystals can form naturally under astrophysical conditions and remain stable over cosmic timescales, giving unique insights on their existence in nature and stability.

Evidence for the extraterrestrial origin of a natural quasicrystal

PubMed Central

Bindi, Luca; Eiler, John M.; Guan, Yunbin; Hollister, Lincoln S.; MacPherson, Glenn; Steinhardt, Paul J.; Yao, Nan

2012-01-01

We present evidence that a rock sample found in the Koryak Mountains in Russia and containing icosahedrite, an icosahedral quasicrystalline phase with composition Al63Cu24Fe13, is part of a meteorite, likely formed in the early solar system about 4.5 Gya. The quasicrystal grains are intergrown with diopside, forsterite, stishovite, and additional metallic phases [khatyrkite (CuAl2), cupalite (CuAl), and β-phase (AlCuFe)]. This assemblage, in turn, is enclosed in a white rind consisting of diopside, hedenbergite, spinel (MgAl2O4), nepheline, and forsterite. Particularly notable is a grain of stishovite (from the interior), a tetragonal polymorph of silica that only occurs at ultrahigh pressures (≥10 Gpa), that contains an inclusion of quasicrystal. An extraterrestrial origin is inferred from secondary ion mass spectrometry 18O/16O and 17O/16O measurements of the pyroxene and olivine intergrown with the metal that show them to have isotopic compositions unlike any terrestrial minerals and instead overlap those of anhydrous phases in carbonaceous chondrite meteorites. The spinel from the white rind has an isotopic composition suggesting that it was part of a calcium-aluminum-rich inclusion similar to those found in CV3 chondrites. The mechanism that produced this exotic assemblage is not yet understood. The assemblage (metallic copper-aluminum alloy) is extremely reduced, and the close association of aluminum (high temperature refractory lithophile) with copper (low temperature chalcophile) is unexpected. Nevertheless, our evidence indicates that quasicrystals can form naturally under astrophysical conditions and remain stable over cosmic timescales, giving unique insights on their existence in nature and stability. PMID:22215583

Al{sub 70}Pd{sub 21.5}Mn{sub 8.5}: A quasicrystal showing the de haas-van Alphen effect

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haanappel, E.G.; Kycia, S.W.; Harmon, B.N.

1995-07-01

We have measured the de Haas-van Alphen effect in the icosahedral quasicrystal Al{sub 70}Pd{sub 21.5}Mn{sub 8.5}. We have found two well-defined frequencies with the magnetic field parallel to a five-fold axis, and two different ones with the field parallel to a two-fold axis. On increasing the temperature, the amplitude of the oscillations substantially decreased, suggesting that the carriers have large masses.

Icosahedral quasicrystal Al71Pd21Mn08 and its ξ' approximant: Linear expansivity, specific heat, magnetic susceptibility, electrical resistivity, and elastic constants

NASA Astrophysics Data System (ADS)

Swenson, C. A.; Fisher, I. R.; Anderson, N. E.; Canfield, P. C.; Migliori, A.

2002-05-01

Linear thermal expansivity (α, 1-300 K), heat capacity (Cp, 1-108 K), magnetic susceptibility (χ, 1-300 K), and electrical resistivity (ρ, 1-300 K) measurements are reported for a single-grain i-Al71Pd21Mn08 quasicrystal and its Al72Pd25Mn03 approximant, and 300 K elastic constants for the quasicrystal. The approximant α (αAp) and Cp (CpAp) data show ``metallic'' behavior, while the previously reported onset of a transition to a spin-glass state (Tf<1.8 K) dominates αQ and CpQ below 11 K. CpAp and CpQ superimpose above 16 K when plotted vs T/Θ0 using the experimental Θ0Ap=455(3) K and an adjusted Θ0ApQ=480(4) K. The 300 K elastic constants extrapolated to T=0 give Θel0Q=505(1) K, suggesting that the normalization is valid only above 16 K. The lattice contribution to CpAp (and, indirectly, CpQ) shows strong (unique) deviations from Debye-like behavior (+3% at 0.84 K for the CpAp data fit). The various Grüneisen parameters (Γ) that are calculated from these data all are positive and normal in magnitude except for a large limiting approximant lattice value, Γlat0Ap=11.3, which may be related to the large dispersion effects in Cp. For the approximant, the combination of anisotropic and large resistivities, a small diamagnetic susceptibility, and a ``large'' linear (electronic) contribution to CpAp (γAp=0.794 mJ/mol K2) suggests the existence of a pseudogap in the electronic density of states. The unusually large, highly volume dependent, dispersion at low temperatures for the quasicrystal and its approximant are not consistent with inelastic neutron scattering and other data, and raise questions about the role of phonons in quasicrystals. The present 300 K resistivities can be used with a published correlation to estimate γQ~0.25 mJ/mol K2.

Discovery of superconductivity in quasicrystal.

PubMed

Kamiya, K; Takeuchi, T; Kabeya, N; Wada, N; Ishimasa, T; Ochiai, A; Deguchi, K; Imura, K; Sato, N K

2018-01-11

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.

Phase equilibria in the nominally Al65Cu23Fe12 system at 3, 5 and 21 GPa: Implications for the quasicrystal-bearing Khatyrka meteorite

NASA Astrophysics Data System (ADS)

Stagno, Vincenzo; Bindi, Luca; Steinhardt, Paul J.; Fei, Yingwei

2017-10-01

Two of the three natural quasiperiodic crystals found in the Khatyrka meteorite show a composition within the Al-Cu-Fe system. Icosahedrite, with formula Al63Cu24Fe13, coexists with the new Al62Cu31Fe7 quasicrystal plus additional Al-metallic minerals such as stolperite (AlCu), kryachkoite [(Al,Cu)6(Fe,Cu)], hollisterite (AlFe3), khatyrkite (Al2Cu) and cupalite (AlCu), associated to high-pressure phases like ringwoodite/ahrensite, coesite, and stishovite. These high-pressure minerals represent the evidence that most of the Khatyrka meteoritic fragments formed at least at 5 GPa and 1200 °C, if not at more extreme conditions. On the other hand, experimental studies on phase equilibria within the representative Al-Cu-Fe system appear mostly limited to ambient pressure conditions, yet. This makes the interpretation of the coexisting mineral phases in the meteoritic sample quite difficult. We performed experiments at 3, 5 and 21 GPa and temperatures of 800-1500 °C using the multi-anvil apparatus to investigate the phase equilibria in the Al65Cu23Fe12 system representative of the first natural quasicrystal, icosahedrite. Our results, supported by single-crystal X-ray diffraction and analyses by scanning electron microscopy, confirm the stability of icosahedrite at high pressure and temperature along with additional coexisting Al-bearing phases representative of khatyrkite and stolperite as those found in the natural meteorite. One reversal experiment performed at 5 GPa and 1200 °C shows the formation of the icosahedral quasicrystal from a pure Al, Cu and Fe mixture, a first experimental synthesis of icosahedrite under those conditions. Pressure appears to not play a major role in the distribution of Al, Cu and Fe between the coexisting phases, icosahedrite in particular. Results from this study extend our knowledge on the stability of icosahedral AlCuFe at higher temperature and pressure than previously examined, and provide a new constraint on the stability of

Natural quasicrystal with decagonal symmetry

NASA Astrophysics Data System (ADS)

Bindi, Luca; Yao, Nan; Lin, Chaney; Hollister, Lincoln S.; Andronicos, Christopher L.; Distler, Vadim V.; Eddy, Michael P.; Kostin, Alexander; Kryachko, Valery; MacPherson, Glenn J.; Steinhardt, William M.; Yudovskaya, Marina; Steinhardt, Paul J.

2015-03-01

We report the first occurrence of a natural quasicrystal with decagonal symmetry. The quasicrystal, with composition Al71Ni24Fe5, was discovered in the Khatyrka meteorite, a recently described CV3 carbonaceous chondrite. Icosahedrite, Al63Cu24Fe13, the first natural quasicrystal to be identified, was found in the same meteorite. The new quasicrystal was found associated with steinhardtite (Al38Ni32Fe30), Fe-poor steinhardtite (Al50Ni40Fe10), Al-bearing trevorite (NiFe2O4) and Al-bearing taenite (FeNi). Laboratory studies of decagonal Al71Ni24Fe5 have shown that it is stable over a narrow range of temperatures, 1120 K to 1200 K at standard pressure, providing support for our earlier conclusion that the Khatyrka meteorite reached heterogeneous high temperatures [1100 < T(K) <= 1500] and then rapidly cooled after being heated during an impact-induced shock that occurred in outer space 4.5 Gya. The occurrences of metallic Al alloyed with Cu, Ni, and Fe raises new questions regarding conditions that can be achieved in the early solar nebula.

As-Cast Icosashedral Quasicrystals in Ti-Zr-Ni Alloys

NASA Astrophysics Data System (ADS)

Lee, Geun Woo; Gangopadhyay, Anup K.; Kelton, Kenneth F.

2002-03-01

Most Ti-based icosahedral quasicrystals (i-phase) obtained by rapid quenching from the melt are metastable and disordered. In contrast, the Ti-Zr-Ni i-phase prepared by low temperature annealing is stable and better ordered. This i-phase is formed by a solid-state transformation from C14 Laves phase and α (Ti/Zr) solid-solution phase. It has not been possible previously to grow this i-phase directly from the liquid. Here, the nucleation and growth of the i-phase from the liquid in as-cast Ti-Zr-Ni alloys is reported. Pentagonal growth ledges in as-cast Ti-Zr-Ni ingots are clearly observed. Transmission electron microscopy and x-ray diffraction studies confirm the phase identity. Differential scanning calorimetry measurements show an endothermic transformation from the i-phase to a phase mixture of the C14 Laves and solid-solution phases, demonstrating that this i-phase is also stable. The short time that the liquid remains in the Laves phase-forming-field and the higher nucleation rate of the i-phase, owing to the presumed similarity between the local atomic structures of the i-phase and liquid, allows the i-phase to nucleate and grow directly from the liquid. Container-less solidification studies using electrostatic levitation (ESL) techniques support this conclusion.

Fine Structure of Diffuse Scattering Rings in Al-Li-Cu Quasicrystal: A Comparative X-ray and Electron Diffraction Study

NASA Astrophysics Data System (ADS)

Donnadieu, P.; Dénoyer, F.

1996-11-01

A comparative X-ray and electron diffraction study has been performed on Al-Li-Cu icosahedral quasicrystal in order to investigate the diffuse scattering rings revealed by a previous work. Electron diffraction confirms the existence of rings but shows that the rings have a fine structure. The diffuse aspect on the X-ray diffraction patterns is then due to an averaging effect. Recent simulations based on the model of canonical cells related to the icosahedral packing give diffractions patterns in agreement with this fine structure effect. Nous comparons les diagrammes de diffraction des rayon-X et des électrons obtenus sur les mêmes échantillons du quasicristal icosaèdrique Al-Li-Cu. Notre but est d'étudier les anneaux de diffusion diffuse mis en évidence par un travail précédent. Les diagrammes de diffraction électronique confirment la présence des anneaux mais ils montrent aussi que ces anneaux possèdent une structure fine. L'aspect diffus des anneaux révélés par la diffraction des rayons X est dû à un effet de moyenne. Des simulations récentes basées sur la décomposition en cellules canoniques de l'empilement icosaédrique produisent des diagrammes de diffraction en accord avec ces effects de structure fine.

Photonic quasi-crystal terahertz lasers

PubMed Central

Vitiello, Miriam Serena; Nobile, Michele; Ronzani, Alberto; Tredicucci, Alessandro; Castellano, Fabrizio; Talora, Valerio; Li, Lianhe; Linfield, Edmund H.; Davies, A. Giles

2014-01-01

Quasi-crystal structures do not present a full spatial periodicity but are nevertheless constructed starting from deterministic generation rules. When made of different dielectric materials, they often possess fascinating optical properties, which lie between those of periodic photonic crystals and those of a random arrangement of scatterers. Indeed, they can support extended band-like states with pseudogaps in the energy spectrum, but lacking translational invariance, they also intrinsically feature a pattern of ‘defects’, which can give rise to critically localized modes confined in space, similar to Anderson modes in random structures. If used as laser resonators, photonic quasi-crystals open up design possibilities that are simply not possible in a conventional periodic photonic crystal. In this letter, we exploit the concept of a 2D photonic quasi crystal in an electrically injected laser; specifically, we pattern the top surface of a terahertz quantum-cascade laser with a Penrose tiling of pentagonal rotational symmetry, reaching 0.1–0.2% wall-plug efficiencies and 65 mW peak output powers with characteristic surface-emitting conical beam profiles, result of the rich quasi-crystal Fourier spectrum. PMID:25523102

Photonic quasi-crystal terahertz lasers

NASA Astrophysics Data System (ADS)

Vitiello, Miriam Serena; Nobile, Michele; Ronzani, Alberto; Tredicucci, Alessandro; Castellano, Fabrizio; Talora, Valerio; Li, Lianhe; Linfield, Edmund H.; Davies, A. Giles

2014-12-01

Quasi-crystal structures do not present a full spatial periodicity but are nevertheless constructed starting from deterministic generation rules. When made of different dielectric materials, they often possess fascinating optical properties, which lie between those of periodic photonic crystals and those of a random arrangement of scatterers. Indeed, they can support extended band-like states with pseudogaps in the energy spectrum, but lacking translational invariance, they also intrinsically feature a pattern of ‘defects’, which can give rise to critically localized modes confined in space, similar to Anderson modes in random structures. If used as laser resonators, photonic quasi-crystals open up design possibilities that are simply not possible in a conventional periodic photonic crystal. In this letter, we exploit the concept of a 2D photonic quasi crystal in an electrically injected laser; specifically, we pattern the top surface of a terahertz quantum-cascade laser with a Penrose tiling of pentagonal rotational symmetry, reaching 0.1-0.2% wall-plug efficiencies and 65 mW peak output powers with characteristic surface-emitting conical beam profiles, result of the rich quasi-crystal Fourier spectrum.

Photonic quasi-crystal terahertz lasers.

PubMed

Vitiello, Miriam Serena; Nobile, Michele; Ronzani, Alberto; Tredicucci, Alessandro; Castellano, Fabrizio; Talora, Valerio; Li, Lianhe; Linfield, Edmund H; Davies, A Giles

2014-12-19

Quasi-crystal structures do not present a full spatial periodicity but are nevertheless constructed starting from deterministic generation rules. When made of different dielectric materials, they often possess fascinating optical properties, which lie between those of periodic photonic crystals and those of a random arrangement of scatterers. Indeed, they can support extended band-like states with pseudogaps in the energy spectrum, but lacking translational invariance, they also intrinsically feature a pattern of 'defects', which can give rise to critically localized modes confined in space, similar to Anderson modes in random structures. If used as laser resonators, photonic quasi-crystals open up design possibilities that are simply not possible in a conventional periodic photonic crystal. In this letter, we exploit the concept of a 2D photonic quasi crystal in an electrically injected laser; specifically, we pattern the top surface of a terahertz quantum-cascade laser with a Penrose tiling of pentagonal rotational symmetry, reaching 0.1-0.2% wall-plug efficiencies and 65 mW peak output powers with characteristic surface-emitting conical beam profiles, result of the rich quasi-crystal Fourier spectrum.

Quasicrystals: Making invisible materials

NASA Astrophysics Data System (ADS)

Boriskina, Svetlana V.

2015-07-01

All-dielectric photonic quasicrystals may act as zero-refractive-index homogeneous materials despite their lack of translational symmetry and periodicity, stretching wavelengths to infinity and offering applications in light wavefront sculpting and optical cloaking.

From Quasicrystals to Crystals with Interpenetrating Icosahedra in Ca–Au–Al: In Situ Variable-Temperature Transformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pham, Joyce; Meng, Fanqiang; Lynn, Matthew J.

The irreversible transformation from an icosahedral quasicrystal (i-QC) CaAu 4.39Al 1.61 to its cubic 2/1 crystalline approximant (CA) Ca 13Au 56.31(3)Al 21.69 (CaAu 4.33(1)Al1.67, Pamore » $$\\bar{3}$$ (No. 205); Pearson symbol: cP728; a = 23.8934(4)), starting at ~570 °C and complete by ~650 °C, is discovered from in situ, high-energy, variable-temperature powder X-ray diffraction (PXRD), thereby providing direct experimental evidence for the relationship between QCs and their associated CAs. The new cubic phase crystallizes in a Tsai-type approximant structure under the broader classification of polar intermetallic compounds, in which atoms of different electronegativities, viz., electronegative Au + Al vs electropositive Ca, are arranged in concentric shells. From a structural chemical perspective, the outermost shell of this cubic approximant may be described as interpenetrating and edge-sharing icosahedra, a perspective that is obtained by splitting the traditional structural description of this shell as a 92-atom rhombic triacontahedron into an 80-vertex cage of primarily Au [Au 59.86(2)Al 17.14⟂ 3.00] and an icosahedral shell of only Al [Al 10.5⟂ 1.5]. Following the proposal that the cubic 2/1 CA approximates the structure of the i-QC and on the basis of the observed transformation, an atomic site analysis of the 2/1 CA, which shows a preference to maximize the number of heteroatomic Au–Al nearest neighbor contacts over homoatomic Al–Al contacts, implies a similar outcome for the i-QC structure. Analysis of the most intense reflections in the diffraction pattern of the cubic 2/1 CA that changed during the phase transformation shows correlations with icosahedral symmetry, and the stability of this cubic phase is assessed using valence electron counts. Finally, according to electronic structure calculations, a cubic 1/1 CA, “Ca 24Au 88Al 64” (CaAu 3.67Al 2.67) is proposed.« less

From Quasicrystals to Crystals with Interpenetrating Icosahedra in Ca–Au–Al: In Situ Variable-Temperature Transformation

DOE PAGES

Pham, Joyce; Meng, Fanqiang; Lynn, Matthew J.; ...

2017-12-29

The irreversible transformation from an icosahedral quasicrystal (i-QC) CaAu 4.39Al 1.61 to its cubic 2/1 crystalline approximant (CA) Ca 13Au 56.31(3)Al 21.69 (CaAu 4.33(1)Al1.67, Pamore » $$\\bar{3}$$ (No. 205); Pearson symbol: cP728; a = 23.8934(4)), starting at ~570 °C and complete by ~650 °C, is discovered from in situ, high-energy, variable-temperature powder X-ray diffraction (PXRD), thereby providing direct experimental evidence for the relationship between QCs and their associated CAs. The new cubic phase crystallizes in a Tsai-type approximant structure under the broader classification of polar intermetallic compounds, in which atoms of different electronegativities, viz., electronegative Au + Al vs electropositive Ca, are arranged in concentric shells. From a structural chemical perspective, the outermost shell of this cubic approximant may be described as interpenetrating and edge-sharing icosahedra, a perspective that is obtained by splitting the traditional structural description of this shell as a 92-atom rhombic triacontahedron into an 80-vertex cage of primarily Au [Au 59.86(2)Al 17.14⟂ 3.00] and an icosahedral shell of only Al [Al 10.5⟂ 1.5]. Following the proposal that the cubic 2/1 CA approximates the structure of the i-QC and on the basis of the observed transformation, an atomic site analysis of the 2/1 CA, which shows a preference to maximize the number of heteroatomic Au–Al nearest neighbor contacts over homoatomic Al–Al contacts, implies a similar outcome for the i-QC structure. Analysis of the most intense reflections in the diffraction pattern of the cubic 2/1 CA that changed during the phase transformation shows correlations with icosahedral symmetry, and the stability of this cubic phase is assessed using valence electron counts. Finally, according to electronic structure calculations, a cubic 1/1 CA, “Ca 24Au 88Al 64” (CaAu 3.67Al 2.67) is proposed.« less

Synthesis of an Al-Mn-Based Alloy Containing In Situ-Formed Quasicrystals and Evaluation of Its Mechanical and Corrosion Properties

NASA Astrophysics Data System (ADS)

Naglič, Iztok; Samardžija, Zoran; Delijić, Kemal; Kobe, Spomenka; Leskovar, Blaž; Markoli, Boštjan

2018-05-01

An Al-Mn alloy with additions of copper, magnesium, and silicon was prepared and cast into a copper mold. It contains in situ-formed icosahedral quasicrystals (iQCs), as confirmed by electron backscatter diffraction. The aim of this work is to present the mechanical and corrosion properties of this alloy and compare its properties with some conventional commercial materials. The compressive strength and compressive yield strength were 751 MPa and 377 MPa, while the compressive fracture strain was 19%. It was observed that intensive shearing caused the final fracture of the specimens and the fractured iQC dendrites still showed cohesion with the α-Al matrix. The polarization resistance and corrosion rate of the artificially aged alloy were 7.30 kΩ and 1.2 μm/year. The evaluated properties are comparable to conventional, discontinuously reinforced aluminum metal-matrix composites and structural wrought aluminum alloys.

Tamm-plasmon polaritons in one-dimensional photonic quasi-crystals.

PubMed

Shukla, Mukesh Kumar; Das, Ritwick

2018-02-01

We present an investigation to ascertain the existence of Tamm-plasmon-polariton-like modes in one-dimensional (1D) quasi-periodic photonic systems. Photonic bandgap formation in quasi-crystals is essentially a consequence of long-range periodicity exhibited by multilayers and, thus, it can be explained using the dispersion relation in the Brillouin zone. Defining a "Zak"-like topological phase in 1D quasi-crystals, we propose a recipe to ascertain the existence of Tamm-like photonic surface modes in a metal-terminated quasi-crystal lattice. Additionally, we also explore the conditions of efficient excitation of such surface modes along with their dispersion characteristics.

Photonic crystals, amorphous materials, and quasicrystals.

PubMed

Edagawa, Keiichi

2014-06-01

Photonic crystals consist of artificial periodic structures of dielectrics, which have attracted much attention because of their wide range of potential applications in the field of optics. We may also fabricate artificial amorphous or quasicrystalline structures of dielectrics, i.e. photonic amorphous materials or photonic quasicrystals. So far, both theoretical and experimental studies have been conducted to reveal the characteristic features of their optical properties, as compared with those of conventional photonic crystals. In this article, we review these studies and discuss various aspects of photonic amorphous materials and photonic quasicrystals, including photonic band gap formation, light propagation properties, and characteristic photonic states.

Film growth arising from the deposition of Au onto an i-Al Pd Mn quasicrystal: a medium energy ion scattering study

NASA Astrophysics Data System (ADS)

Noakes, T. C. Q.; Bailey, P.; Draxler, M.; McConville, C. F.; Ross, A. R.; Lograsso, T. A.; Leung, L.; Smerdon, J. A.; McGrath, R.

2006-06-01

The room temperature deposition of 7 ML of Au onto the fivefold symmetric surface of icosahedral Al-Pd-Mn leads to the formation of a several monolayers thick Au-Al alloy film. An AlAu film with 1:1 stoichiometry is formed, which shows no evidence of ordered structure, being either amorphous or polycrystalline. Annealing to 325 °C causes more Al to diffuse into the film, producing Al2Au but still with no indication of structure. Experiments using 0.5 ML of pre-deposited In demonstrated a surfactant effect as the In 'floated' on the surface during growth and produced a reduction in film roughness. However, contrary to previous findings the film was still either amorphous or polycrystalline, with no evidence of quasi-crystalline or aperiodic structure. Experiments were also conducted using smaller doses of Au to look for the formation of an epitaxial layer and, if formed, determine the registry with the substrate. However, no change in the Pd blocking curves for the surface could be seen, suggesting that the Au does not adsorb in well defined sites. This result is not surprising when considering that even for these low doses Al is drawn into the film, changing the composition and probably the structure of the topmost layers of the substrate, so that the potential adsorption sites on the clean surface may no longer exist.

Probing the growth and melting pathways of a decagonal quasicrystal in real-time

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Insung; Xiao, Xianghui; Shahani, Ashwin J.

How does a quasicrystal grow? Despite the decades of research that have been dedicated to this area of study, it remains one of the fundamental puzzles in the field of crystal growth. Although there has been no lack of theoretical studies on quasicrystal growth, there have been very few experimental investigations with which to test their various hypotheses. In particular, evidence of the in situ and three-dimensional (3D) growth of a quasicrystal from a parent liquid phase is lacking. To fill-in-the-gaps in our understanding of the solidification and melting pathways of quasicrystals, we performed synchrotron-based X-ray imaging experiments on amore » decagonal phase with composition of Al-15at%Ni-15at%Co. High-flux X-ray tomography enabled us to observe both growth and melting morphologies of the 3D quasicrystal at temperature. We determined that there is no time-reversal symmetry upon growth and melting of the decagonal quasicrystal. While quasicrystal growth is predominantly dominated by the attachment kinetics of atomic clusters in the liquid phase, melting is instead barrier-less and limited by buoyancy-driven convection. These experimental results provide the much-needed benchmark data that can be used to validate simulations of phase transformations involving this unique phase of matter.« less

Probing the growth and melting pathways of a decagonal quasicrystal in real-time

DOE PAGES

Han, Insung; Xiao, Xianghui; Shahani, Ashwin J.

2017-12-12

How does a quasicrystal grow? Despite the decades of research that have been dedicated to this area of study, it remains one of the fundamental puzzles in the field of crystal growth. Although there has been no lack of theoretical studies on quasicrystal growth, there have been very few experimental investigations with which to test their various hypotheses. In particular, evidence of the in situ and three-dimensional (3D) growth of a quasicrystal from a parent liquid phase is lacking. To fill-in-the-gaps in our understanding of the solidification and melting pathways of quasicrystals, we performed synchrotron-based X-ray imaging experiments on amore » decagonal phase with composition of Al-15at%Ni-15at%Co. High-flux X-ray tomography enabled us to observe both growth and melting morphologies of the 3D quasicrystal at temperature. We determined that there is no time-reversal symmetry upon growth and melting of the decagonal quasicrystal. While quasicrystal growth is predominantly dominated by the attachment kinetics of atomic clusters in the liquid phase, melting is instead barrier-less and limited by buoyancy-driven convection. These experimental results provide the much-needed benchmark data that can be used to validate simulations of phase transformations involving this unique phase of matter.« less

Photonic crystals, amorphous materials, and quasicrystals

PubMed Central

Edagawa, Keiichi

2014-01-01

Photonic crystals consist of artificial periodic structures of dielectrics, which have attracted much attention because of their wide range of potential applications in the field of optics. We may also fabricate artificial amorphous or quasicrystalline structures of dielectrics, i.e. photonic amorphous materials or photonic quasicrystals. So far, both theoretical and experimental studies have been conducted to reveal the characteristic features of their optical properties, as compared with those of conventional photonic crystals. In this article, we review these studies and discuss various aspects of photonic amorphous materials and photonic quasicrystals, including photonic band gap formation, light propagation properties, and characteristic photonic states. PMID:27877676

Raman effect in icosahedral boron-rich solids

PubMed Central

Werheit, Helmut; Filipov, Volodymyr; Kuhlmann, Udo; Schwarz, Ulrich; Armbrüster, Marc; Leithe-Jasper, Andreas; Tanaka, Takaho; Higashi, Iwami; Lundström, Torsten; Gurin, Vladimir N; Korsukova, Maria M

2010-01-01

We present Raman spectra of numerous icosahedral boron-rich solids having the structure of α-rhombohedral, β-rhombohedral, α-tetragonal, β-tetragonal, YB66, orthorhombic or amorphous boron. The spectra were newly measured and, in some cases, compared with reported data and discussed. We emphasize the importance of a high signal-to-noise ratio in the Raman spectra for detecting weak effects evoked by the modification of compounds, accommodation of interstitial atoms and other structural defects. Vibrations of the icosahedra, occurring in all the spectra, are interpreted using the description of modes in α-rhombohedral boron by Beckel et al. The Raman spectrum of boron carbide is largely clarified. Relative intra- and inter-icosahedral bonding forces are estimated for the different structural groups and for vanadium-doped β-rhombohedral boron. The validity of Badger's rule is demonstrated for the force constants of inter-icosahedral B–B bonds, whereas the agreement is less satisfactory for the intra-icosahedral B–B bonds. PMID:27877328

Multilayered sandwich-like architecture containing large-scale faceted Al–Cu–Fe quasicrystal grains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wei, Dongxia; He, Zhanbing, E-mail: hezhanbing@ustb.edu.cn

Faceted quasicrystals are structurally special compared with traditional crystals. Although the application of faceted quasicrystals has been expected, wide-scale application has not occurred owing to the limited exposure of the facets. Using a facile method of heat treatment, we synthesize a multilayered sandwich-like structure with each layer composed of large-scale pentagonal-dodecahedra of Al–Cu–Fe quasicrystals. Moreover, there are channels between the adjacent Al–Cu–Fe layers that serve to increase the exposure of the facets of quasicrystals. Scanning electron microscopy, transmission electron microscopy, and X-ray diffraction are used to characterize the multilayered architecture, and the generation mechanisms of this special structure are alsomore » discussed. - Highlights: • A multilayered sandwich-like structure is produced by a facile method. • Each layer is covered by large-scale faceted Al–Cu–Fe quasicrystals. • There are channels between the adjacent Al–Cu–Fe layers.« less

Properties- and applications of quasicrystals and complex metallic alloys.

PubMed

Dubois, Jean-Marie

2012-10-21

This article aims at an account of what is known about the potential for applications of quasicrystals and related compounds, the so-called family of Complex Metallic Alloys (CMAs‡). Attention is focused at aluminium-based CMAs, which comprise a large number of crystalline compounds and quasicrystals made of aluminium alloyed with transition metals (like Fe or Cu) or normal metals like Mg. Depending on composition, the structural complexity varies from a few atoms per unit cell up to thousands of atoms. Quasicrystals appear then as CMAs of ultimate complexity and exhibit a lattice that shows no periodicity anymore in the usual 3-dimensional space. Properties change dramatically with lattice complexity and turn the metal-type behaviour of simple Al-based crystals into a far more complex behaviour, with a fingerprint of semi-conductors that may be exploited in various applications, potential or realised. An account of the ones known to the author is given in the light of the relevant properties, namely light absorption, reduced adhesion and friction, heat insulation, reinforcement of composites for mechanical devices, and few more exotic ones. The role played by the search for applications of quasicrystals in the development of the field is briefly addressed in the concluding section.

Superior room-temperature ductility of typically brittle quasicrystals at small sizes

PubMed Central

Zou, Yu; Kuczera, Pawel; Sologubenko, Alla; Sumigawa, Takashi; Kitamura, Takayuki; Steurer, Walter; Spolenak, Ralph

2016-01-01

The discovery of quasicrystals three decades ago unveiled a class of matter that exhibits long-range order but lacks translational periodicity. Owing to their unique structures, quasicrystals possess many unusual properties. However, a well-known bottleneck that impedes their widespread application is their intrinsic brittleness: plastic deformation has been found to only be possible at high temperatures or under hydrostatic pressures, and their deformation mechanism at low temperatures is still unclear. Here, we report that typically brittle quasicrystals can exhibit remarkable ductility of over 50% strains and high strengths of ∼4.5 GPa at room temperature and sub-micrometer scales. In contrast to the generally accepted dominant deformation mechanism in quasicrystals—dislocation climb, our observation suggests that dislocation glide may govern plasticity under high-stress and low-temperature conditions. The ability to plastically deform quasicrystals at room temperature should lead to an improved understanding of their deformation mechanism and application in small-scale devices. PMID:27515779

Liquid Quasicrystals

NASA Astrophysics Data System (ADS)

Ungar, Goran

Following the discovery of quasicrystals by Shechtman and Cahn in 1984, for the following 20 years the new field of QCs was confined to metal alloys and atomic-scale structures. Then, with the discovery of a liquid crystal phase possessing dodecagonal QC symmetry], research interest has extended from metal alloys to those where the motifs were no longer single atoms but assemblies of many molecules. In dendron-based liquid quasicrystals (LQC) between 10-50 molecules form a supramolecular sphere with 103 - 104 atoms. In 2007 a 2-d quasiperiodic phase was found in three-arm star ABC polymers. In 2012 the first linear diblock copolymer was reported to form a sphere-based bulk QC phase, similar to that in dendrimer LQC but on a still larger scale. In the same year bulk QC domains were reported in ``hard'' nanoporous silica, produced however, again from a ``soft'' lyotropic template. The symmetry of all confirmed soft QCs so far is 12-fold. Another important development in soft QCs is the observation of complex QC approximants in a number of side-branched polyphilic LC honeycombs, described by multicolour tilings. In fact, recently we found a genuine dodecagonal QC in such systems, the first example of a 2D LQC. Furthermore, we succeeded in direct AFM imaging of the xy plane of a dendrimer LQC. The images confirm the ``half-step'' inflation rule, proposed earlier but not confirmed until now. Funding is acknowledged from Leverhulme Trust.

Quasicrystals and Quantum Computing

NASA Astrophysics Data System (ADS)

Berezin, Alexander A.

1997-03-01

In Quantum (Q) Computing qubits form Q-superpositions for macroscopic times. One scheme for ultra-fast (Q) computing can be based on quasicrystals. Ultrafast processing in Q-coherent structures (and the very existence of durable Q-superpositions) may be 'consequence' of presence of entire manifold of integer arithmetic (A0, aleph-naught of Georg Cantor) at any 4-point of space-time, furthermore, at any point of any multidimensional phase space of (any) N-particle Q-system. The latter, apart from quasicrystals, can include dispersed and/or diluted systems (Berezin, 1994). In such systems such alleged centrepieces of Q-Computing as ability for fast factorization of long integers can be processed by sheer virtue of the fact that entire infinite pattern of prime numbers is instantaneously available as 'free lunch' at any instant/point. Infinitely rich pattern of A0 (including pattern of primes and almost primes) acts as 'independent' physical effect which directly generates Q-dynamics (and physical world) 'out of nothing'. Thus Q-nonlocality can be ultimately based on instantaneous interconnectedness through ever- the-same structure of A0 ('Platonic field' of integers).

An Icosahedral Quasicrystal and Its 1/0 Crystalline Approximant in the Ca–Au–Al System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pham, Joyce; Kreyssig, Andreas; Goldman, Alan I.

2016-10-17

A new icosahedral quasicrystalline phase, CaAu4.5–xAl1.5+x [0.11 ≤ x ≤ 0.40(6); CaAu4.4Al1.6, aQC = 5.383(4) Å, and Pm35], and its lowest-order 1/0 cubic crystalline approximant phase, CaAu3+xAl1–x [0 ≤ x ≤ 0.31(1); a = 9.0766(5)–9.1261(8) Å, Pa3(No. 205), and Pearson symbol cP40], have been discovered in the Ca-poor region of the Ca–Au–Al system. In the crystalline approximant, eight [Au3–xAl1+x] tetrahedra fill the unit cell, and each tetrahedron is surrounded by four Ca atoms, thus forming a three-dimensional network of {Ca4/4[Au3–xAl1+x]} tetrahedral stars. A computational study of Au and Al site preferences concurs with the experimental results, which indicate a preferencemore » for near-neighbor Au–Al interactions over Au–Au and Al–Al interactions. Analysis of the electronic density of states and the associated crystal orbital Hamilton population curves was used to rationalize the descriptions of CaAu4.5–xAl1.5+x [0.11 ≤ x ≤ 0.46(6)] and CaAu3+xAl1–x [0 ≤ x ≤ 0.31(1)] as polar intermetallic species, whereby Ca atoms engage in polar covalent bonding with the electronegative, electron-deficient [Au3–xAl1+x] tetrahedral clusters and the observed phase width of the crystalline approximant.« less

Multiple-scale structures: from Faraday waves to soft-matter quasicrystals.

PubMed

Savitz, Samuel; Babadi, Mehrtash; Lifshitz, Ron

2018-05-01

For many years, quasicrystals were observed only as solid-state metallic alloys, yet current research is now actively exploring their formation in a variety of soft materials, including systems of macromolecules, nanoparticles and colloids. Much effort is being invested in understanding the thermodynamic properties of these soft-matter quasicrystals in order to predict and possibly control the structures that form, and hopefully to shed light on the broader yet unresolved general questions of quasicrystal formation and stability. Moreover, the ability to control the self-assembly of soft quasicrystals may contribute to the development of novel photonics or other applications based on self-assembled metamaterials. Here a path is followed, leading to quantitative stability predictions, that starts with a model developed two decades ago to treat the formation of multiple-scale quasiperiodic Faraday waves (standing wave patterns in vibrating fluid surfaces) and which was later mapped onto systems of soft particles, interacting via multiple-scale pair potentials. The article reviews, and substantially expands, the quantitative predictions of these models, while correcting a few discrepancies in earlier calculations, and presents new analytical methods for treating the models. In so doing, a number of new stable quasicrystalline structures are found with octagonal, octadecagonal and higher-order symmetries, some of which may, it is hoped, be observed in future experiments.

Studies of Nucleation and Growth, Specific Heat and Viscosity of Undercooled Melts of Quasicrystals and Polytetrehedral-Phase-Forming Alloys

NASA Technical Reports Server (NTRS)

2003-01-01

By investigating the properties of quasicrystals and quasicrystal-forming liquid alloys, we may determine the role of ordering of the liquid phase in the formation of quasicrystals, leading to a better fundamental understanding of both the quasicrystal and the liquid. A quasicrystal is solid characterized by a symmetric but non-periodic arrangement of atoms, usually in the form of an icosahedron (12 atoms, 20 triangular faces). It is theorized that the short-range order in liquids takes this same form. The degree of ordering depends on the temperature of the liquid, and affects many of the liquid s properties, including specific heat, viscosity, and electrical resistivity. The MSFC role in this project includes solidification studies, phase diagram determination, and thermophysical property measurements on the liquid quasicrystal-forming alloys, all by electrostatic levitation (ESL). The viscosity of liquid quasicrystal-forming alloys is measured by the oscillating drop method, both in the stable and undercooled liquid state. The specific heat of solid, undercooled liquid, and stable liquid are measured by the radiative cooling rate of the droplets.

Beta cell device using icosahedral boride compounds

DOEpatents

Aselage, Terrence L.; Emin, David

2002-01-01

A beta cell for converting beta-particle energies into electrical energy having a semiconductor junction that incorporates an icosahedral boride compound selected from B.sub.12 As.sub.2, B.sub.12 P.sub.2, elemental boron having an .alpha.-rhombohedral structure, elemental boron having a .beta.-rhombohedral structure, and boron carbides of the chemical formula B.sub.12-x C.sub.3-x, where 0.15icosahedral boride compound self-heals, resisting degradation from radiation damage.

Two-dimensional microsphere quasi-crystal: fabrication and properties

NASA Astrophysics Data System (ADS)

Noginova, Natalia E.; Venkateswarlu, Putcha; Kukhtarev, Nickolai V.; Sarkisov, Sergey S.; Noginov, Mikhail A.; Caulfield, H. John; Curley, Michael J.

1996-11-01

2D quasi-crystals were fabricated from polystyrene microspheres and characterized for their structural, diffraction, and non-linear optics properties. The quasi- crystals were produced with the method based on Langmuir- Blodgett thin film technique. Illuminating the crystal with the laser beam, we observed the diffraction pattern in the direction of the beam propagation and in the direction of the back scattering, similar to the x-ray Laue pattern observed in regular crystals with hexagonal structure. The absorption spectrum of the quasi-crystal demonstrated two series of regular maxima and minima, with the spacing inversely proportional to the microspheres diameter. Illumination of the dye-doped microspheres crystal with Q- switched radiation of Nd:YAG laser showed the enhancement of non-linear properties, in particular, second harmonic generation.

Growth of two-dimensional decagonal colloidal quasicrystals

NASA Astrophysics Data System (ADS)

Martinsons, M.; Schmiedeberg, M.

2018-06-01

The growth of quasicrystals, i.e. structures with long-range positional order but no periodic translational symmetry, is more complex than the growth of periodic crystals. By employing Brownian dynamics simulations in two dimensions for colloidal particles that interact according to an isotropic pair potential with two incommensurate lengths, we study the growth of quasicrystalline structures by sequentially depositing particles at their surface. We quantify the occurrence of quasicrystalline order as a function of the temperature and the rate of added particles. In addition, we explore defects like local triangular order or gaps within the quasicrystalline structure. Furthermore, we analyze the shapes of the surfaces in grown structures which tend to build straight lines along the symmetry axes of the quasicrystal. Finally, we identify phasonic flips which are rearrangements of the particles due to additional degrees of freedom. The number of phasonic flips decreases with the distance to the surface.

Spin waves in planar quasicrystal of Penrose tiling

NASA Astrophysics Data System (ADS)

Rychły, J.; Mieszczak, S.; Kłos, J. W.

2018-03-01

We investigated two-dimensional magnonic structures which are the counterparts of photonic quasicrystals forming Penrose tiling. We considered the slab composed of Ni (or Py) disks embedded in Fe (or Co) matrix. The disks are arranged in quasiperiodic Penrose-like structure. The infinite quasicrystal was approximated by its rectangular section with periodic boundary conditions applied. This approach allowed us to use the plane wave method to find the frequency spectrum of eigenmodes for spin waves and their spatial profiles. The calculated integrated density of states shows more distinctive magnonic gaps for the structure composed of materials of high magnetic contrast (Ni and Fe) and relatively high filling fraction. This proves the impact of quasiperiodic long-range order on the spectrum of spin waves. We also investigated the localization of spin wave eingenmodes resulting from the quasiperiodicity of the structure.

Synthesis of icosahedral gold nanocrystals: a thermal process strategy.

PubMed

Zhou, Min; Chen, Shenhao; Zhao, Shiyong

2006-03-16

We demonstrate a one-step thermal process route to the synthesis of icosahedral gold nanocrystals. By regulating the concentrations of poly(vinyl pyrrolidone) (PVP) and HAuCl4 or changing the temperature, we can readily access the shapes of icosahedral nanocrystals with good uniformity. These gold nanostructures, with unique geometrical shapes, might find use in areas that include photonics, optoelectronics, and optical sensing. We also observed that these gold nanocrystals have a strong tendency to be immobilized spontaneously on the glass substrate.

From Glass Formation to Icosahedral Ordering by Curving Three-Dimensional Space.

PubMed

Turci, Francesco; Tarjus, Gilles; Royall, C Patrick

2017-05-26

Geometric frustration describes the inability of a local molecular arrangement, such as icosahedra found in metallic glasses and in model atomic glass formers, to tile space. Local icosahedral order, however, is strongly frustrated in Euclidean space, which obscures any causal relationship with the observed dynamical slowdown. Here we relieve frustration in a model glass-forming liquid by curving three-dimensional space onto the surface of a 4-dimensional hypersphere. For sufficient curvature, frustration vanishes and the liquid "freezes" in a fully icosahedral structure via a sharp "transition." Frustration increases upon reducing the curvature, and the transition to the icosahedral state smoothens while glassy dynamics emerge. Decreasing the curvature leads to decoupling between dynamical and structural length scales and the decrease of kinetic fragility. This sheds light on the observed glass-forming behavior in Euclidean space.

Self-similarity and self-inversion of quasicrystals

NASA Astrophysics Data System (ADS)

Madison, A. E.

2014-08-01

The discovery of quasicrystals played a revolutionary role in the condensed matter science and forced to renounce the dogma of the classical crystallography that the regular filling of the space by identical blocks is reduced solely to the Fedorov space groups. It is shown that aperiodic crystals, apart from the similarity, exhibit the self-inversion property. In a broadened sense, the self-inversion implies the possible composition of the inversion with translations, rotations, and homothety, whereas pure reflection by itself in a circle can be absent as an independent symmetry element. It is demonstrated that the symmetry of aperiodic tilings is described by Schottky groups (which belong to a particular type of Kleinian groups generated by the linear fractional Möbius transformations); in the theory of aperiodic crystals, the Schottky groups play the same role that the Fedorov groups play in the theory of crystal lattices. The local matching rules for the Penrose fractal tiling are derived, the problem of choice of the fundamental region of the group of motions of a quasicrystal is discussed, and the relation between the symmetry of aperiodic tilings and the symmetry of constructive fractals is analyzed.

Emergent quasicrystals in strongly correlated systems

NASA Astrophysics Data System (ADS)

Sagi, Eran; Nussinov, Zohar

2016-07-01

Commensurability is of paramount importance in numerous strongly interacting electronic systems. In the fractional quantum Hall effect, a rich cascade of increasingly narrow plateaux appear at larger denominator filling fractions. Rich commensurate structures also emerge, at certain filling fractions, in high temperature superconductors and other electronic systems. A natural question concerns the character of these and other electronic systems at irrational filling fractions. Here we demonstrate that quasicrystalline structures naturally emerge in these situations, and trigger behaviors not typically expected of periodic systems. We first show that irrationally filled quantum Hall systems cross over into quasiperiodically ordered configuration in the thin-torus limit. Using known properties of quasicrystals, we argue that these states are unstable against the effects of disorder, in agreement with the existence of quantum Hall plateaux. We then study analogous physical situations in a system of cold Rydberg atoms placed on an optical lattice. Such an experimental setup is generally disorder free, and can therefore be used to detect the emergent quasicrystals we predict. We discuss similar situations in the Falicov-Kimball model, where known exact results can be used to establish quasicrystalline structures in one and two dimensions. We briefly speculate on possible relations between our theoretical findings and the existence of glassy dynamics and other features of strongly correlated electronic systems.

The Connection Between Local Icosahedral Order in Metallic Liquids and the Nucleation of Ordered Phases

NASA Technical Reports Server (NTRS)

Curreri, Peter A. (Technical Monitor); Kelton, K. F.; Gangopadhyay, A.; Lee, G. W.; Hyers, R. W.; Rathz, R. J.; Rogers, J.; Schenk, T.; Simonet, V.; Holland-Moritz, D.

2003-01-01

Over fifty years ago, David Turnbull showed that the temperature of many metallic liquids could be decreased far below their equilibrium melting temperature before crystallization occurred. To explain those surprising results, Charles Frank hypothesized that the local structures of undercooled metallic liquids are different from those of crystal phases, containing a significant degree of icosahedral order that is incompatible with extended periodicity. Such structural differences must create a barrier to the formation crystal phases, explaining the observed undercooling behavior. If true, the nucleation from the liquid of phases with extended icosahedral order should be easier. Icosahedral order is often favored in small clusters, as observed recently in liquid-like clusters of pure Pb on the (111) surface of Si, for example. However, it has never been shown that an increasing preference for icosahedral phase formation can be directly linked with the development of icosahedral order in the undercooled liquid. Owing to the combination of very recent advances in levitation techniques and the availability of synchrotron x-ray and high flux neutron facilities, this is shown here.

The Connection Between Local Icosahedral Order in Metallic Liquids and the Nucleation of Ordered Phases

NASA Technical Reports Server (NTRS)

Kelton, K. F.; Gangopadhyay, A. K.; Lee, G. W.; Hyers, R. W.; Rathz, T. J.; Rogers, J. R.; Robinson, M. B.; Schenk, T.; Simonet, V.; Holland-Moritz, D.;

On the stability of a quasicrystal and its crystalline approximant in a system of hard disks with a soft corona

NASA Astrophysics Data System (ADS)

Pattabhiraman, Harini; Gantapara, Anjan P.; Dijkstra, Marjolein

2015-10-01

Using computer simulations, we study the phase behavior of a model system of colloidal hard disks with a diameter σ and a soft corona of width 1.4σ. The particles interact with a hard core and a repulsive square-shoulder potential. We calculate the free energy of the random-tiling quasicrystal and its crystalline approximants using the Frenkel-Ladd method. We explicitly account for the configurational entropy associated with the number of distinct configurations of the random-tiling quasicrystal. We map out the phase diagram and find that the random tiling dodecagonal quasicrystal is stabilised by entropy at finite temperatures with respect to the crystalline approximants that we considered, and its stability region seems to extend to zero temperature as the energies of the defect-free quasicrystal and the crystalline approximants are equal within our statistical accuracy.

David Adler Lectureship Award in the Field of Materials Physics Talk: Surfaces of Quasicrystals

NASA Astrophysics Data System (ADS)

Thiel, Patricia

2010-03-01

Quasiperiodic order is recognized (in a utilitarian, rather than a mathematical sense) by the absence of periodicity, concurrent with a classically-forbidden rotational symmetry. It is quite beautiful, having captured the attention of scientists and artists alike. Following the discovery of quasiperiodic order in a real system,footnotetextD. Shechtman, I. Blech, D. Gratias, and J.W. Cahn, Phys. Rev. Lett. 53, 1951 (1984). many metallic alloys and intermetallics were found to exhibit this type of order on the atomic scale. More recently ``soft'' quasicrystals were discovered,footnotetextL. Bindi, P.J. Steinhardt, N. Yao, and P.J. Lu, Science 324, 1306 (2009). and nanocrystalline arrays were found to spontaneously adopt quasiperiodic order.footnotetextD.V. Talapin, E.V. Shevchenko, M.I. Bodnarchuk, X. Ye, J. Chen, and C.B. Murray, Nature 461 , 964 (2009). From a scientific perspective, quasicrystals are alluring because they allow us to test the relationship between atomic structure and physical properties. This talk deals with the ways in which our understanding of solid surfaces has been both enriched and challenged by these complex materials.footnotetextP. Thiel, Annu. Rev. Phys. Chem. (2008).^,footnotetextV. Fourn'ee, J. Ledieu, and P. Thiel, J. Phys: Condens. Matter. 20, 3310301 (2008). properties of the metallic quasicrystals originally generated interest because they were unusual.footnotetextJ.M. Dubois, Useful Quasicrystals(World Scientific, Singapore, 2005). For instance, among Al-rich alloys, the Al-based quasicrystalline phases exhibit puzzling resistance to surface oxidation. Also, Al-rich quasicrystals have surprisingly good and promising catalytic properties (e.g. for steam reforming of methanol).footnotetextA.P. Tsai and M. Yoshimura, Appl. Cat. A: General 214 , 237 (2001). Perhaps most famously, they exhibit low friction.^7 Comparisons with crystalline materials have established that these features are deeply related to the quasiperiodic atomic

Icosahedral plant viral nanoparticles - bioinspired synthesis of nanomaterials/nanostructures.

PubMed

Narayanan, Kannan Badri; Han, Sung Soo

2017-10-01

Viral nanotechnology utilizes virus nanoparticles (VNPs) and virus-like nanoparticles (VLPs) of plant viruses as highly versatile platforms for materials synthesis and molecular entrapment that can be used in the nanotechnological fields, such as in next-generation nanoelectronics, nanocatalysis, biosensing and optics, and biomedical applications, such as for targeting, therapeutic delivery, and non-invasive in vivo imaging with high specificity and selectivity. In particular, plant virus capsids provide biotemplates for the production of novel nanostructured materials with organic/inorganic moieties incorporated in a very precise and controlled manner. Interestingly, capsid proteins of spherical plant viruses can self-assemble into well-organized icosahedral three-dimensional (3D) nanoscale multivalent architectures with high monodispersity and structural symmetry. Using viral genetic and protein engineering of icosahedral viruses with a variety of sizes, the interior, exterior and the interfaces between coat protein (CP) subunits can be manipulated to fabricate materials with a wide range of desirable properties allowing for biomineralization, encapsulation, infusion, controlled self-assembly, and multivalent ligand display of nanoparticles or molecules for varied applications. In this review, we discuss the various functional nanomaterials/nanostructures developed using the VNPs and VLPs of different icosahedral plant viruses and their nano(bio)technological and nanomedical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Huogen; Chen, Liang

Ti-Zr-Ni quasicrystals have been demonstrated to store a large number of hydrogen atoms, which implies strong potential application in hydrogen energy field for them. However, the desorption of hydrogen atoms in the quasicrystals is quite difficult, with the indication of high desorption temperature and slow desorption rate. The shortage limits their use in the field to a large extent. But this kind of quasicrystals might be used in nuclear fusion energy field, because tritium as a coral fuel for nuclear fusion needs tight storage. However, equilibrium pressure at room temperature of Ti-Zr-Ni quasicrystals, important for their application in fusion energymore » field, has not been clear yet. In this work, we designed a gas-solid reaction system with the pressure resolution of 10{sup −8}Pa and carried out hydrogen desorption investigation at different temperatures on Ti{sub 36}Zr{sub 40}Ni{sub 20}Pd{sub 4} icosahedral quasicrystal. Based on three Pressure-Composition-Temperature desorption curves, we speculate according to Van’t Hoff theory about hydrogen storage that its equilibrium pressure at room temperature could be at the magnitude of 10{sup −6}Pa, displaying good stability of hydrogen in the quasicrystal and also implying application prospects in fusion energy field for quasicrystals of this type.« less

Growth of a decagonal Al 70Ni 15Co 15 single quasicrystal by the Czochralski method

NASA Astrophysics Data System (ADS)

Jeong, H. T.; Kim, S. H.; Kim, W. T.; Kim, D. H.; Inkson, B. J.

2000-07-01

Single decagonal quasicrystals of Al 70Ni 15Co 15 were grown by the Czochralski method at Ar atmosphere. The grown crystals were of single decagonal phase without any secondary phases due to the peritectic reaction and contained a large single quasicrystal of cm order size. The high quality and single quasicrystallinity of them were examined by the Laue transmission photography, single crystal X-ray diffraction, and high-resolution electron microscopy investigations.

Speckle in the diffraction patterns of Hendricks-Teller and icosahedral glass models

NASA Technical Reports Server (NTRS)

Garg, Anupam; Levine, Dov

1988-01-01

It is shown that the X-ray diffraction patterns from the Hendricks-Teller model for layered systems and the icosahedral glass models for the icosahedral phases show large fluctuations between nearby scattering wave vectors and from sample to sample, that are quite analogous to laser speckle. The statistics of these fluctuations are studied analytically for the first model and via computer simulations for the second. The observability of these effects is discussed briefly.

The Connection Between Local Icosahedral Order in Metallic Liquids and the Nucleation Behavior of Ordered Phases

NASA Technical Reports Server (NTRS)

Kelton, K. F.; Gangopadhyay, A. K.; Lee, G. W.; Hyers, R. W.; Rathz, T. J.; Rogers, J. R.; Robinson, M. B.; Schenk, T.; Simonet, V.

2003-01-01

Over fifty years ago, David Turnbull showed that the temperature of many metallic liquids could be decreased far below their equilibrium melting temperature before crystallization occurred. To explain those surprising results, Charles Frank hypothesized that the local structures of undercooled metallic liquids are different from those of crystal phases, containing a significant degree of icosahedral order that is incompatible with extended periodicity. Such structural differences must create a barrier to the formation crystal phases, explaining the observed undercooling behavior. If true, the nucleation from the liquid of phases with extended icosahedral order should be easier. Icosahedral order is often favored in small clusters, as observed recently in liquid-like clusters of pure Pb on the (111) surface of Si[3], for example. However, it has never been shown that an increasing preference for icosahedral phase formation can be directly linked with the development of icosahedral order in the undercooled liquid. Owing to the combination of very recent advances in levitation techniques and the availability of synchrotron x-ray and high flux neutron facilities, this is shown here.

Forging Unsupported Metal-Boryl Bonds with Icosahedral Carboranes.

PubMed

Saleh, Liban M A; Dziedzic, Rafal M; Khan, Saeed I; Spokoyny, Alexander M

2016-06-13

In contrast to the plethora of metal-catalyzed cross-coupling methods available for the installation of functional groups on aromatic hydrocarbons, a comparable variety of methods are currently not available for icosahedral carboranes, which are boron-rich three-dimensional aromatic analogues of aryl groups. Part of this is due to the limited understanding of the elementary steps for cross-coupling involving carboranes. Here, we report our efforts in isolating metal-boryl complexes to further our understanding of one of these elementary steps, oxidative addition. Structurally characterized examples of group 10 M-B bonds featuring icosahedral carboranes are completely unknown. Use of mercurocarboranes as a reagent to deliver M-B bonds saw divergent reactivity for platinum and palladium, with a Pt-B bond being isolated for the former, and a rare Pd-Hg bond being formed for the latter. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Real-space observation of magnetic excitations and avalanche behavior in artificial quasicrystal lattices

DOE PAGES

Brajuskovic, V.; Barrows, F.; Phatak, C.; ...

2016-10-03

Artificial spin ice lattices have emerged as model systems for studying magnetic frustration in recent years. Most work to date has looked at periodic artificial spin ice lattices. In this paper, we observe frustration effects in quasicrystal artificial spin ice lattices that lack translational symmetry and contain vertices with different numbers of interacting elements. We find that as the lattice state changes following demagnetizing and annealing, specific vertex motifs retain low-energy configurations, which excites other motifs into higher energy configurations. In addition, we find that unlike the magnetization reversal process for periodic artificial spin ice lattices, which occurs through 1Dmore » avalanches, quasicrystal lattices undergo reversal through a dendritic 2D avalanche mechanism.« less

Real-space observation of magnetic excitations and avalanche behavior in artificial quasicrystal lattices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brajuskovic, V.; Barrows, F.; Phatak, C.

Artificial spin ice lattices have emerged as model systems for studying magnetic frustration in recent years. Most work to date has looked at periodic artificial spin ice lattices. In this paper, we observe frustration effects in quasicrystal artificial spin ice lattices that lack translational symmetry and contain vertices with different numbers of interacting elements. We find that as the lattice state changes following demagnetizing and annealing, specific vertex motifs retain low-energy configurations, which excites other motifs into higher energy configurations. In addition, we find that unlike the magnetization reversal process for periodic artificial spin ice lattices, which occurs through 1Dmore » avalanches, quasicrystal lattices undergo reversal through a dendritic 2D avalanche mechanism.« less

Method of making an icosahedral boride structure

DOEpatents

Hersee, Stephen D.; Wang, Ronghua; Zubia, David; Aselage, Terrance L.; Emin, David

2005-01-11

A method for fabricating thin films of an icosahedral boride on a silicon carbide (SiC) substrate is provided. Preferably the icosahedral boride layer is comprised of either boron phosphide (B.sub.12 P.sub.2) or boron arsenide (B.sub.12 As.sub.2). The provided method achieves improved film crystallinity and lowered impurity concentrations. In one aspect, an epitaxially grown layer of B.sub.12 P.sub.2 with a base layer or substrate of SiC is provided. In another aspect, an epitaxially grown layer of B.sub.12 As.sub.2 with a base layer or substrate of SiC is provided. In yet another aspect, thin films of B.sub.12 P.sub.2 or B.sub.12 As.sub.2 are formed on SiC using CVD or other vapor deposition means. If CVD techniques are employed, preferably the deposition temperature is above 1050.degree. C., more preferably in the range of 1100.degree. C. to 1400.degree. C., and still more preferably approximately 1150.degree. C.

Fibonacci, quasicrystals and the beauty of flowers.

PubMed

Gardiner, John

2012-12-01

The appearance of Fibonacci sequences and the golden ratio in plant structures is one of the great outstanding puzzles of biology. Here I suggest that quasicrystals, which naturally pack in the golden ratio, may be ubiquitous in biological systems and introduce the golden ratio into plant phyllotaxy. The appearance of golden ratio-based structures as beautiful indicates that the golden ratio may play a role in the development of consciousness and lead to the aesthetic natural selection of flowering plants.

Breaking Symmetry in Viral Icosahedral Capsids as Seen through the Lenses of X-ray Crystallography and Cryo-Electron Microscopy

PubMed Central

Parent, Kristin N.; Schrad, Jason R.; Cingolani, Gino

2018-01-01

The majority of viruses on Earth form capsids built by multiple copies of one or more types of a coat protein arranged with 532 symmetry, generating an icosahedral shell. This highly repetitive structure is ideal to closely pack identical protein subunits and to enclose the nucleic acid genomes. However, the icosahedral capsid is not merely a passive cage but undergoes dynamic events to promote packaging, maturation and the transfer of the viral genome into the host. These essential processes are often mediated by proteinaceous complexes that interrupt the shell’s icosahedral symmetry, providing a gateway through the capsid. In this review, we take an inventory of molecular structures observed either internally, or at the 5-fold vertices of icosahedral DNA viruses that infect bacteria, archea and eukaryotes. Taking advantage of the recent revolution in cryo-electron microscopy (cryo-EM) and building upon a wealth of crystallographic structures of individual components, we review the design principles of non-icosahedral structural components that interrupt icosahedral symmetry and discuss how these macromolecules play vital roles in genome packaging, ejection and host receptor-binding. PMID:29414851

May quasicrystals be good thermoelectric materials?

NASA Astrophysics Data System (ADS)

Maciá, Enrique

2000-11-01

We present a theoretical analysis of quasicrystals (QCs) as potential thermoelectric materials. We consider a self-similar density of states model and extend the framework introduced in [G. D. Mahan and J. O. Sofo, Proc. Natl. Acad. Sci. U.S.A. 93, 7436 (1996)] to systems exhibiting correlated features in their electronic structure. We show that relatively high values of the thermoelectric figure of merit, ranging from 0.01 up to 1.6 at room temperature, may be expected for these systems. We compare our results with available experimental data on transport properties of QCs and suggest some potential candidates for thermoelectric applications.

Metal-organic framework materials based on icosahedral boranes and carboranes

DOEpatents

Mirkin, Chad A.; Hupp, Joseph T.; Farha, Omar K.; Spokoyny, Alexander M.; Mulfort, Karen L.

2010-11-02

Disclosed herein are metal-organic frameworks of metals and boron rich ligands, such as carboranes and icosahedral boranes. Methods of synthesizing and using these materials in gas uptake are disclosed.

Icosahedral (A5) family symmetry and the golden ratio prediction for solar neutrino mixing

NASA Astrophysics Data System (ADS)

Everett, Lisa L.; Stuart, Alexander J.

2009-04-01

We investigate the possibility of using icosahedral symmetry as a family symmetry group in the lepton sector. The rotational icosahedral group, which is isomorphic to A5, the alternating group of five elements, provides a natural context in which to explore (among other possibilities) the intriguing hypothesis that the solar neutrino mixing angle is governed by the golden ratio, ϕ=(1+5)/2. We present a basic toolbox for model building using icosahedral symmetry, including explicit representation matrices and tensor product rules. As a simple application, we construct a minimal model at tree level in which the solar angle is related to the golden ratio, the atmospheric angle is maximal, and the reactor angle vanishes to leading order. The approach provides a rich setting in which to investigate the flavor puzzle of the standard model.

Microstructures evolution and physical properties of laser induced NbC modified nanocrystalline composites

NASA Astrophysics Data System (ADS)

Li, Jianing; Liu, Kegao; Yuan, Xingdong; Shan, Feihu; Zhang, Bolun; Wang, Zhe; Xu, Wenzhuo; Zhang, Zheng; An, Xiangchen

2017-10-01

The nanoscale quasicrystals (NQs), amorphous and ultrafine nanocrystals (UNs) modified hard composites are produced by laser cladding (LC) of the Ni60A-TiC-NbC-Sb mixed powders on the additive manufacturing (AM) TA1 titanium alloy. The LC technique is favorable to formations of icosahedral quasicrystals (I-phase) with five-fold symmetry due to its rapid cooling and solidification characteristics. The formation mechanism of this I-phase is explained here. Under the actions of NQs, amorphous and UNs, such LC composites exhibited an extremely high micro-hardness. UNs may also intertwin with amorphous, forming yarn-shape materials. This research provides essential theoretical basis to improve the quality of laser-treated composites.

Phason space analysis and structure modelling of 100 Å-scale dodecagonal quasicrystal in Mn-based alloy

NASA Astrophysics Data System (ADS)

Ishimasa, Tsutomu; Iwami, Shuhei; Sakaguchi, Norihito; Oota, Ryo; Mihalkovič, Marek

2015-11-01

The dodecagonal quasicrystal classified into the five-dimensional space group P126/mmc, recently discovered in a Mn-Cr-Ni-Si alloy, has been analysed using atomic-resolution spherical aberration-corrected electron microscopy, i.e. high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) and conventional transmission electron microscopy. By observing along the 12-fold axis, non-periodic tiling consisting of an equilateral triangle and a square has been revealed, of which common edge length is a = 4.560 Å. These tiles tend to form a network of dodecagons of which size is ?a ≈ 17 Å in diameter. The tiling was interpreted as an aggregate of 100 Å-scale oriented domains of high- and low-quality quasicrystals with small crystallites appearing at their boundaries. The quasicrystal domains exhibited a densely filled circular acceptance region in the phason space. This is the first observation of the acceptance region in an actual dodecagonal quasicrystal. Atomic structure model consistent with the electron microscopy images is a standard Frank-Kasper decoration of the triangle and square tiles that can be inferred from the crystal structures of Zr4Al3 and Cr3Si. Four kinds of layers located at z = 0, ±1/4 and 1/2 are stacked periodically along the 12-fold axis, and the atoms at z = 0 and 1/2 form hexagonal anti-prisms consistently with the 126-screw axis. The validity of this structure model was examined by means of powder X-ray diffraction.

HCIV-1 and Other Tailless Icosahedral Internal Membrane-Containing Viruses of the Family Sphaerolipoviridae.

PubMed

Demina, Tatiana A; Pietilä, Maija K; Svirskaitė, Julija; Ravantti, Janne J; Atanasova, Nina S; Bamford, Dennis H; Oksanen, Hanna M

2017-02-18

Members of the virus family Sphaerolipoviridae include both archaeal viruses and bacteriophages that possess a tailless icosahedral capsid with an internal membrane. The genera Alpha- and Betasphaerolipovirus comprise viruses that infect halophilic euryarchaea, whereas viruses of thermophilic Thermus bacteria belong to the genus Gammasphaerolipovirus . Both sequence-based and structural clustering of the major capsid proteins and ATPases of sphaerolipoviruses yield three distinct clades corresponding to these three genera. Conserved virion architectural principles observed in sphaerolipoviruses suggest that these viruses belong to the PRD1-adenovirus structural lineage. Here we focus on archaeal alphasphaerolipoviruses and their related putative proviruses. The highest sequence similarities among alphasphaerolipoviruses are observed in the core structural elements of their virions: the two major capsid proteins, the major membrane protein, and a putative packaging ATPase. A recently described tailless icosahedral haloarchaeal virus, Haloarcula californiae icosahedral virus 1 (HCIV-1), has a double-stranded DNA genome and an internal membrane lining the capsid. HCIV-1 shares significant similarities with the other tailless icosahedral internal membrane-containing haloarchaeal viruses of the family Sphaerolipoviridae . The proposal to include a new virus species, Haloarcula virus HCIV1 , into the genus Alphasphaerolipovirus was submitted to the International Committee on Taxonomy of Viruses (ICTV) in 2016.

Observation of a Time Quasicrystal and Its Transition to a Superfluid Time Crystal.

PubMed

Autti, S; Eltsov, V B; Volovik, G E

2018-05-25

We report experimental realization of a quantum time quasicrystal and its transformation to a quantum time crystal. We study Bose-Einstein condensation of magnons, associated with coherent spin precession, created in a flexible trap in superfluid ^{3}He-B. Under a periodic drive with an oscillating magnetic field, the coherent spin precession is stabilized at a frequency smaller than that of the drive, demonstrating spontaneous breaking of discrete time translation symmetry. The induced precession frequency is incommensurate with the drive, and hence, the obtained state is a time quasicrystal. When the drive is turned off, the self-sustained coherent precession lives a macroscopically long time, now representing a time crystal with broken symmetry with respect to continuous time translations. Additionally, the magnon condensate manifests spin superfluidity, justifying calling the obtained state a time supersolid or a time supercrystal.

Observation of a Time Quasicrystal and Its Transition to a Superfluid Time Crystal

NASA Astrophysics Data System (ADS)

Autti, S.; Eltsov, V. B.; Volovik, G. E.

2018-05-01

We report experimental realization of a quantum time quasicrystal and its transformation to a quantum time crystal. We study Bose-Einstein condensation of magnons, associated with coherent spin precession, created in a flexible trap in superfluid 3He-B . Under a periodic drive with an oscillating magnetic field, the coherent spin precession is stabilized at a frequency smaller than that of the drive, demonstrating spontaneous breaking of discrete time translation symmetry. The induced precession frequency is incommensurate with the drive, and hence, the obtained state is a time quasicrystal. When the drive is turned off, the self-sustained coherent precession lives a macroscopically long time, now representing a time crystal with broken symmetry with respect to continuous time translations. Additionally, the magnon condensate manifests spin superfluidity, justifying calling the obtained state a time supersolid or a time supercrystal.

Effects of crystalline electronic field and onsite interorbital interaction in Yb-based quasicrystal and approximant crystal.

PubMed

Watanabe, Shinji; Miyake, Kazumasa

2018-05-10

To get an insight into a new type of quantum critical phenomena recently discovered in the quasicrystal Yb 15 Al 34 Au 51 and approximant crystal (AC) Yb 14 Al 35 Au 51 under pressure, we discuss the property of the crystalline electronic field (CEF) at Yb in the AC and show that uneven CEF levels at each Yb site can appear because of the Al/Au mixed sites. Then we construct the minimal model for the electronic state on the AC by introducing the onsite Coulomb repulsion between the 4f and 5d orbitals at Yb. Numerical calculations for the ground state shows that the lattice constant dependence of the Yb valence well explains the recent measurement done by systematic substitution of elements of Al and Au in the quasicrystal and AC, where the quasicrystal Yb 15 Al 34 Au 51 is just located at the point from where the Yb-valence starts to change drastically. Our calculation convincingly demonstrates that this is indeed the evidence that this material is just located at the quantum critical point of the Yb-valence transition.

Effects of crystalline electronic field and onsite interorbital interaction in Yb-based quasicrystal and approximant crystal

NASA Astrophysics Data System (ADS)

Watanabe, Shinji; Miyake, Kazumasa

2018-05-01

To get an insight into a new type of quantum critical phenomena recently discovered in the quasicrystal Yb15Al34Au51 and approximant crystal (AC) Yb14Al35Au51 under pressure, we discuss the property of the crystalline electronic field (CEF) at Yb in the AC and show that uneven CEF levels at each Yb site can appear because of the Al/Au mixed sites. Then we construct the minimal model for the electronic state on the AC by introducing the onsite Coulomb repulsion between the 4f and 5d orbitals at Yb. Numerical calculations for the ground state shows that the lattice constant dependence of the Yb valence well explains the recent measurement done by systematic substitution of elements of Al and Au in the quasicrystal and AC, where the quasicrystal Yb15Al34Au51 is just located at the point from where the Yb-valence starts to change drastically. Our calculation convincingly demonstrates that this is indeed the evidence that this material is just located at the quantum critical point of the Yb-valence transition.

Pseudo-icosahedral Cr 55 Al 232 - δ as a high-temperature protective material

DOE PAGES

Rosa, R.; Bhattacharya, S.; Pabla, J.; ...

2018-03-19

In this paper, we report here a course of basic research into the potential suitability of a pseudo-icosahedral Cr aluminide as a material for high temperature protective coatings. Cr 55Al 232-δ [δ = 2.70(6)] exhibits high hardness at room temperature as well as low thermal conductivity and excellent oxidation resistance at 973 K, with an oxidation rate comparable to those of softer, denser benchmark materials. Lastly, the origin of these promising properties can be traced to competing long-range and short-range symmetries within the pseudo-icosahedral crystal structure, suggesting new criteria for future materials research.

Pseudo-icosahedral Cr55Al232 -δ as a high-temperature protective material

NASA Astrophysics Data System (ADS)

Rosa, R.; Bhattacharya, S.; Pabla, J.; He, H.; Misuraca, J.; Nakajima, Y.; Bender, A. D.; Antonacci, A. K.; Adrip, W.; McNally, D. E.; Zebro, A.; Kamenov, P.; Geschwind, G.; Ghose, S.; Dooryhee, E.; Ibrahim, A.; Tritt, T. M.; Aronson, M. C.; Simonson, J. W.

2018-03-01

We report here a course of basic research into the potential suitability of a pseudo-icosahedral Cr aluminide as a material for high-temperature protective coatings. Cr55Al232 -δ [ δ =2.70 (6 ) ] exhibits high hardness at room temperature as well as low thermal conductivity and excellent oxidation resistance at 973 K, with an oxidation rate comparable to those of softer, denser benchmark materials. The origin of these promising properties can be traced to competing long-range and short-range symmetries within the pseudo-icosahedral crystal structure, suggesting new criteria for future materials research.

Pseudo-icosahedral Cr 55 Al 232 - δ as a high-temperature protective material

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosa, R.; Bhattacharya, S.; Pabla, J.

In this paper, we report here a course of basic research into the potential suitability of a pseudo-icosahedral Cr aluminide as a material for high temperature protective coatings. Cr 55Al 232-δ [δ = 2.70(6)] exhibits high hardness at room temperature as well as low thermal conductivity and excellent oxidation resistance at 973 K, with an oxidation rate comparable to those of softer, denser benchmark materials. Lastly, the origin of these promising properties can be traced to competing long-range and short-range symmetries within the pseudo-icosahedral crystal structure, suggesting new criteria for future materials research.

Virus templated plasmonic nanoclusters with icosahedral symmetry via directed assembly

NASA Astrophysics Data System (ADS)

Ratna, Banahalli; Fontana, Jake; Dressick, Walter; Phelps, Jamie; Johnson, John; Sampson, Travian; Rendell, Ronald; Soto, Carissa

2015-03-01

Controlling the spatial and orientational order of plasmonic nanoparticles may lead to structures with novel electromagnetic properties and applications such as sub-wavelength imaging and ultra-sensitive chemical sensors. Here we report the directed assembly of three-dimensional, icosahedral plasmonic nanoclusters with resonances at visible wavelengths. We show using transmission electron microcopy and in situ dynamic light scattering the nanoclusters consist of twelve gold nanospheres attached to thiol groups at predefined locations on the surface of a genetically engineered cowpea mosaic virus with icosahedral symmetry. We measured the bulk absorbance from aqueous suspensions of nanoclusters and reproduced the major features of the spectrum using finite-element simulations. Furthermore, because the viruses are easily produced in gram quantities the directed assembly approach is capable of high-throughput, providing a strategy to realize large quantities for applications. NRL summer intern under the HBCU/MI Summer Research Program.

A 3-D Finite-Volume Non-hydrostatic Icosahedral Model (NIM)

NASA Astrophysics Data System (ADS)

Lee, Jin

2014-05-01

The Nonhydrostatic Icosahedral Model (NIM) formulates the latest numerical innovation of the three-dimensional finite-volume control volume on the quasi-uniform icosahedral grid suitable for ultra-high resolution simulations. NIM's modeling goal is to improve numerical accuracy for weather and climate simulations as well as to utilize the state-of-art computing architecture such as massive parallel CPUs and GPUs to deliver routine high-resolution forecasts in timely manner. NIM dynamic corel innovations include: * A local coordinate system remapped spherical surface to plane for numerical accuracy (Lee and MacDonald, 2009), * Grid points in a table-driven horizontal loop that allow any horizontal point sequence (A.E. MacDonald, et al., 2010), * Flux-Corrected Transport formulated on finite-volume operators to maintain conservative positive definite transport (J.-L, Lee, ET. Al., 2010), *Icosahedral grid optimization (Wang and Lee, 2011), * All differentials evaluated as three-dimensional finite-volume integrals around the control volume. The three-dimensional finite-volume solver in NIM is designed to improve pressure gradient calculation and orographic precipitation over complex terrain. NIM dynamical core has been successfully verified with various non-hydrostatic benchmark test cases such as internal gravity wave, and mountain waves in Dynamical Cores Model Inter-comparisons Projects (DCMIP). Physical parameterizations suitable for NWP are incorporated into NIM dynamical core and successfully tested with multimonth aqua-planet simulations. Recently, NIM has started real data simulations using GFS initial conditions. Results from the idealized tests as well as real-data simulations will be shown in the conference.

Semiclassical dynamics, Berry curvature, and spiral holonomy in optical quasicrystals

NASA Astrophysics Data System (ADS)

Spurrier, Stephen; Cooper, Nigel R.

2018-04-01

We describe the theory of the dynamics of atoms in two-dimensional quasicrystalline optical lattices. We focus on a regime of shallow lattice depths under which the applied force can cause Landau-Zener tunneling past a dense hierarchy of gaps in the quasiperiodic energy spectrum. We derive conditions on the external force that allow for a "semiadiabatic" regime in which semiclassical equations of motion can apply, leading to Bloch oscillations between the edges of a pseudo-Brillouin-zone. We verify this semiclassical theory by comparing to the results of an exact numerical solution. Interesting features appear in the semiclassical dynamics for the quasicrystal for a particle driven in a cyclic trajectory around the corner of the pseudo-Brillouin-zone: The particle fails to return to its initial state, providing a realization of a "spiral holonomy" in the dynamics. We show that there can appear anomalous velocity contributions, associated with nonzero Berry curvature. We relate these to the Berry phase associated with the spiral holonomy, and show how the Berry curvature can be accessed from the semiclassical dynamics. Finally, by identifying the pseudo-Brillouin-zone as a higher genus surface, we show that the Chern number classification for periodic systems can be extended to a quasicrystal, thereby determining a topological index for the system.

Soft materials design via self assembly of functionalized icosahedral particles

NASA Astrophysics Data System (ADS)

Muthukumar, Vidyalakshmi Chockalingam

In this work we simulate self assembly of icosahedral building blocks using a coarse grained model of the icosahedral capsid of virus 1m1c. With significant advancements in site-directed functionalization of these macromolecules [1], we propose possible application of such self-assembled materials for drug delivery. While there have been some reports on organization of viral particles in solution through functionalization, exploiting this behaviour for obtaining well-ordered stoichiometric structures has not yet been explored. Our work is in well agreement with the earlier simulation studies of icosahedral gold nanocrystals, giving chain like patterns [5] and also broadly in agreement with the wet lab works of Finn, M.G. et al., who have shown small predominantly chain-like aggregates with mannose-decorated Cowpea Mosaic Virus (CPMV) [22] and small two dimensional aggregates with oligonucleotide functionalization on the CPMV capsid [1]. To quantify the results of our Coarse Grained Molecular Dynamics Simulations I developed analysis routines in MATLAB using which we found the most preferable nearest neighbour distances (from the radial distribution function (RDF) calculations) for different lengths of the functional groups and under different implicit solvent conditions, and the most frequent coordination number for a virus particle (histogram plots further using the information from RDF). Visual inspection suggests that our results most likely span the low temperature limits explored in the works of Finn, M.G. et al., and show a good degree of agreement with the experimental results in [1] at an annealing temperature of 4°C. Our work also reveals the possibility of novel stoichiometric N-mer type aggregates which could be synthesized using these capsids with appropriate functionalization and solvent conditions.

Archaeal Haloarcula californiae Icosahedral Virus 1 Highlights Conserved Elements in Icosahedral Membrane-Containing DNA Viruses from Extreme Environments.

PubMed

Demina, Tatiana A; Pietilä, Maija K; Svirskaitė, Julija; Ravantti, Janne J; Atanasova, Nina S; Bamford, Dennis H; Oksanen, Hanna M

2016-07-19

Despite their high genomic diversity, all known viruses are structurally constrained to a limited number of virion morphotypes. One morphotype of viruses infecting bacteria, archaea, and eukaryotes is the tailless icosahedral morphotype with an internal membrane. Although it is considered an abundant morphotype in extreme environments, only seven such archaeal viruses are known. Here, we introduce Haloarcula californiae icosahedral virus 1 (HCIV-1), a halophilic euryarchaeal virus originating from salt crystals. HCIV-1 also retains its infectivity under low-salinity conditions, showing that it is able to adapt to environmental changes. The release of progeny virions resulting from cell lysis was evidenced by reduced cellular oxygen consumption, leakage of intracellular ATP, and binding of an indicator ion to ruptured cell membranes. The virion contains at least 12 different protein species, lipids selectively acquired from the host cell membrane, and a 31,314-bp-long linear double-stranded DNA (dsDNA). The overall genome organization and sequence show high similarity to the genomes of archaeal viruses in the Sphaerolipoviridae family. Phylogenetic analysis based on the major conserved components needed for virion assembly-the major capsid proteins and the packaging ATPase-placed HCIV-1 along with the alphasphaerolipoviruses in a distinct, well-supported clade. On the basis of its virion morphology and sequence similarities, most notably, those of its core virion components, we propose that HCIV-1 is a member of the PRD1-adenovirus structure-based lineage together with other sphaerolipoviruses. This addition to the lineage reinforces the notion of the ancient evolutionary links observed between the viruses and further highlights the limits of the choices found in nature for formation of a virion. Under conditions of extreme salinity, the majority of the organisms present are archaea, which encounter substantial selective pressure, being constantly attacked by

Crystallography of decahedral and icosahedral particles. II - High symmetry orientations

NASA Technical Reports Server (NTRS)

Yang, C. Y.; Yacaman, M. J.; Heinemann, K.

1979-01-01

Based on the exact crystal structure of decahedral and icosahedral particles, high energy electron diffraction patterns and image profiles have been derived for various high symmetry orientations of the particles with respect to the incident beam. These results form a basis for the identification of small metal particle structures with advanced methods of transmission electron microscopy.

Controlling the Growth of Au on Icosahedral Seeds of Pd by Manipulating the Reduction Kinetics

DOE PAGES

Lv, Tian; Yang, Xuan; Zheng, Yiqun; ...

2016-03-29

This article reports a systematic study of how Au atoms nucleate and grow on Pd icosahedral seeds with a multiply twinned structure. By manipulating the reduction kinetics, we obtained Pd–Au bimetallic nanocrystals with two distinct shapes and structures. Specifically, Pd@Au core–shell icosahedra were formed when a relatively fast reduction rate was used for the HAuCl 4 precursor. At a slow reduction rate, in contrast, the nucleation and growth of Au atoms were mainly confined to one of the vertices of a Pd icosahedral seed, resulting in the formation of a Au icosahedron by sharing five adjacent faces with the Pdmore » seed. The same growth pattern was observed for Pd icosahedral seeds with both sizes of 32 and 20 nm. Also, we have also investigated the effects of other kinetic parameters, including the concentration of reducing agent and reaction temperature, on the growth pathway undertaken by the Au atoms. In conclusion, we believe that the mechanistic insights obtained from this study can be extended to other systems, including the involvement of different metals and/or seeds with different morphologies.« less

Antiferromagnetic order and the structural order-disorder transition in the Cd6Ho quasicrystal approximant

NASA Astrophysics Data System (ADS)

Kreyssig, Andreas; Beutier, Guillaume; Hiroto, Takanobu; Kim, Min Gyu; Tucker, Gregory S.; de Boissieu, Marc; Tamura, Ryuji; Goldman, Alan I.

2013-09-01

It has generally been accepted that the orientational ordering of the Cd4 tetrahedron within the Cd6 R quasicrystal approximants is kinetically inhibited for R = Ho, Er, Tm and Lu by steric constraints. Our high-resolution X-ray scattering measurements of the Cd6Ho quasicrystal approximant, however, reveal an abrupt (first-order) transition to a monoclinic structure below T S = 178 K for samples that have 'aged' at room temperature for approximately one year, reopening this question. Using X-ray resonant magnetic scattering at the Ho L 3-edge we have elucidated the nature of the antiferromagnetic ordering below T N = 8.5 K in Cd6Ho. The magnetic Bragg peaks are found at the charge forbidden H + K + L = 2n + 1 positions, referenced to the high-temperature body-centred cubic structure. In general terms, this corresponds to antiferromagnetic arrangements of the Ho moments on adjacent clusters in the unit cell as previously found for Cd6Tb.

Studies of Nucleation, Growth, Specific Heat, and Viscosity of Undercooled Melts of Quasicrystals and Polytetrahedral-Phase-Forming Alloys

NASA Technical Reports Server (NTRS)

Kelton, K. F.; Croat, T. K.; Gangopadhyay, A.; Holland-Moritz, D.; Hyers, Robert W.; Rathz, Thomas J.; Robinson, Michael B.; Rogers, Jan R.

2001-01-01

Undercooling experiments and thermal physical property measurements of metallic alloys on the International Space Station (ISS) are planned. This recently-funded research focuses on fundamental issues of the formation and structure of highly-ordered non-crystallographic phases (quasicrystals) and related crystal phases (crystal approximants), and the connections between the atomic structures of these phases and those of liquids and glasses. It extends studies made previously by us of the composition dependence of crystal nucleation processes in silicate and metallic glasses, to the case of nucleation from the liquid phase. Motivating results from rf-levitation and drop-tube measurements of the undercooling of Ti/Zr-based liquids that form quasicrystals and crystal approximants are discussed. Preliminary measurements by electrostatic levitation (ESL) are presented.

Cooperative Formation of Icosahedral Proline Clusters from Dimers

NASA Astrophysics Data System (ADS)

Jacobs, Alexander D.; Jovan Jose, K. V.; Horness, Rachel; Raghavachari, Krishnan; Thielges, Megan C.; Clemmer, David E.

2018-01-01

Ion mobility spectrometry-mass spectrometry and Fourier transform infrared spectroscopy (FTIR) techniques were combined with quantum chemical calculations to examine the origin of icosahedral clusters of the amino acid proline. When enantiopure proline solutions are electrosprayed (using nanospray) from 100 mM ammonium acetate, only three peaks are observed in the mass spectrum across a concentration range of five orders of magnitude: a monomer [Pro+H]+ species, favored from 0.001 to 0.01 mM proline concentrations; a dimer [2Pro+H]+ species, the most abundant species for proline concentrations above 0.01 mM; and, the dimer and dodecamer [12Pro+2H]2+ for 1.0 mM and more concentrated proline solutions. Electrospraying racemic D/ L-proline solutions from 100 mM ammonium acetate leads to a monomer at low proline concentrations (0.001 to 0.1 mM), and a dimer at higher concentrations (>0.09 mM), as well as a very small population of 8 to 15 Pro clusters that comprise <0.1% of the total ion signals even at the highest proline concentration. Solution FTIR studies show unique features that increase in intensity in the enantiopure proline solutions, consistent with clustering, presumably from the icosahedral geometry in bulk solution. When normalized for the total proline, these results are indicative of a cooperative formation of the enantiopure 12Pro species from 2Pro. [Figure not available: see fulltext.

Nonhydrostatic icosahedral atmospheric model (NICAM) for global cloud resolving simulations

NASA Astrophysics Data System (ADS)

Satoh, M.; Matsuno, T.; Tomita, H.; Miura, H.; Nasuno, T.; Iga, S.

2008-03-01

A new type of ultra-high resolution atmospheric global circulation model is developed. The new model is designed to perform "cloud resolving simulations" by directly calculating deep convection and meso-scale circulations, which play key roles not only in the tropical circulations but in the global circulations of the atmosphere. Since cores of deep convection have a few km in horizontal size, they have not directly been resolved by existing atmospheric general circulation models (AGCMs). In order to drastically enhance horizontal resolution, a new framework of a global atmospheric model is required; we adopted nonhydrostatic governing equations and icosahedral grids to the new model, and call it Nonhydrostatic ICosahedral Atmospheric Model (NICAM). In this article, we review governing equations and numerical techniques employed, and present the results from the unique 3.5-km mesh global experiments—with O(10 9) computational nodes—using realistic topography and land/ocean surface thermal forcing. The results show realistic behaviors of multi-scale convective systems in the tropics, which have not been captured by AGCMs. We also argue future perspective of the roles of the new model in the next generation atmospheric sciences.

Simulations of polymorphic icosahedral shells assembling around many cargo molecules

NASA Astrophysics Data System (ADS)

Mohajerani, Farzaneh; Perlmutter, Jason; Hagan, Michael

Bacterial microcompartments (BMCs) are large icosahedral shells that sequester the enzymes and reactants responsible for particular metabolic pathways in bacteria. Although different BMCs vary in size and encapsulate different cargoes, they are constructed from similar pentameric and hexameric shell proteins. Despite recent groundbreaking experiments which visualized the formation of individual BMCs, the detailed assembly pathways and the factors which control shell size remain unclear. In this talk, we describe theoretical and computational models that describe the dynamical encapsulation of hundreds of cargo molecules by self-assembling icosahedral shells. We present phase diagrams and analysis of dynamical simulation trajectories showing how the thermodynamics, assembly pathways, and emergent structures depend on the interactions among shell proteins and cargo molecules. Our model suggests a mechanism for controlling insertion of the 12 pentamers required for a closed shell topology, and the relationship between assembly pathway and BMC size polydispersity. In addition to elucidating how native BMCs assemble,our results establish principles for reengineering BMCs or viral capsids as customizable nanoreactors that can assemble around a programmable set of enzymes and reactants. Supported by NIH R01GM108021 and Brandeis MRSEC DMR-1420382.

Interactions among K+-Ca2+ exchange, sorption of m-dinitrobenzene, and smectite quasicrystal dynamics.

PubMed

Chatterjee, Ritushree; Laird, David A; Thompson, Michael L

2008-12-15

The fate of organic contaminants in soils and sediments is influenced by sorption of the compounds to surfaces of soil materials. We investigated the interaction among sorption of an organic compound, cation exchange reactions, and both the size and swelling of smectite quasicrystals. Two reference smectites that vary in location and amount of layer charge, SPV (a Wyoming bentonite) and SAz-1 were initially Ca- and K-saturated and then equilibrated with mixed 0.01 M KCl and 0.005 M CaCl2 salt solutions both with and without the presence of 200 mg L(-1) m-dinitrobenzene (m-DNB). In general, sorption of m-DNB increased with the amount of K+ in the system for both clays, and the SPV sorbed more m-DNB than the SAz-1. Sorption of m-DNB increased the preference of Ca-SPV for K+ relative to Ca2+ but had little effect on K+-Ca2+ selectivity for K-SPV. Selectivity for K+ relative to Ca2+ was slightly higher for both K-SAz-1 and Ca-SAz-1 in the presence of m-DNB than in its absence. Distinct hysteresis loops were observed for the K+-Ca2+ cation exchange reactions for both clays, and the legacy of having been initially Ca- or K-saturated influenced sorption of m-DNB by SPV but had little effect for SAz-1. Suspension X-ray diffraction was used to measure changes in d-spacing and the relative thickness of smectite quasicrystals during the cation exchange and m-DNB sorption reactions. The results suggest that interactions among cation exchange and organic sorption reactions are controlled byan inherently hysteretic complex feedback process that is regulated by changes in the size and extent of swelling of smectite quasicrystals.

Ionic strength-induced formation of smectite quasicrystals enhances nitroaromatic compound sorption.

PubMed

Li, Hui; Pereira, Tanya R; Teppen, Brian J; Laird, David A; Johnston, Cliff T; Boyd, Stephen A

2007-02-15

Sorption of organic contaminants by soils is a determinant controlling their transport and fate in the environment. The influence of ionic strength on nitroaromatic compound sorption by K+- and Ca2+ -saturated smectite was examined. Sorption of 1,3-dinitrobenzene by K-smectite increased as KCl ionic strength increased from 0.01 to 0.30 M. In contrast, sorption by Ca-smectite at CaCl2 ionic strengths of 0.015 and 0.15 M remained essentially the same. The "salting-out" effect on the decrease of 1,3-dinitrobenzene aqueous solubility within this ionic strength range was <1.5% relative to the solubility in pure water. This decrease of solubility is insufficient to account for the observed increase of sorption by K-smectite with increasing KCl ionic strength. X-ray diffraction patterns and light absorbance of K-clay suspensions indicated the aggregation of clay particles and the formation of quasicrystal structures as KCI ionic strength increased. Sorption enhancement is attributed to the formation of better-ordered K-clay quasicrystals with reduced interlayer distances rather than to the salting-out effect. Dehydration of 1,3-dinitrobenzene is apparently a significant driving force for sorption, and we show for the first time that sorption of small, planar, neutral organic molecules, namely, 1,3-dinitrobenzene, causes previously expanded clay interlayers to dehydrate and collapse in aqueous suspension.

Two- and three-dimensional growth of Bi on i -Al-Pd-Mn studied using medium-energy ion scattering

NASA Astrophysics Data System (ADS)

Noakes, T. C. Q.; Bailey, P.; McConville, C. F.; Draxler, M.; Walker, M.; Brown, M. G.; Hentz, A.; Woodruff, D. P.; Lograsso, T. A.; Ross, A. R.; Smerdon, J. A.; Leung, L.; McGrath, R.

2010-11-01

Recent work on the growth of thin metal films on quasicrystalline substrates has indicated the formation of so-called “magic height” islands with multiples of 4 atomic layers (AL) arising as a result of quantum size effects, which lead to enhanced stability. Here the results of a study are reported of Bi deposition on i -Al-Pd-Mn using medium-energy ion scattering to characterize the island thickness and the structural arrangement of Bi atoms within the islands. In addition, data were taken from annealed surfaces after Bi cluster desorption to leave a single aperiodic monolayer of Bi at the surface. Scattered-ion energy spectra from the Bi islands are consistent with a single Bi monolayer covered with mainly 4 AL islands for both 1.8 and 3.2 monolayer equivalent coverages but with some occupation of 2 and 8 Al islands as well. The angular dependence of the scattered-ion intensity (“blocking curve”) from Bi has been compared with simulations for various models of both rhombohedral Bi and a distorted “black-phosphorus”-like structure. The data demonstrate bilayer formation within the Bi islands. In the case of the aperiodic Bi monolayer, the blocking curves from substrate scattering are found to be inconsistent with two high-symmetry sites on the quasicrystalline surface that theory indicates are energetically favorable but do not exclude the formation of pentagonal arrangements of Bi atoms as seen in other recent experimental work.

Analysis of phases in the structure determination of an icosahedral virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plevka, Pavel; Kaufmann, Bärbel; Rossmann, Michael G.

2012-03-15

The constraints imposed on structure-factor phases by noncrystallographic symmetry (NCS) allow phase improvement, phase extension to higher resolution and hence ab initio phase determination. The more numerous the NCS redundancy and the greater the volume used for solvent flattening, the greater the power for phase determination. In a case analyzed here the icosahedral NCS phasing appeared to have broken down, although later successful phase extension was possible when the envelope around the NCS region was tightened. The phases from the failed phase-determination attempt fell into four classes, all of which satisfied the NCS constraints. These four classes corresponded to themore » correct solution, opposite enantiomorph, Babinet inversion and opposite enantiomorph with Babinet inversion. These incorrect solutions can be seeded from structure factors belonging to reciprocal-space volumes that lie close to icosahedral NCS axes where the structure amplitudes tend to be large and the phases tend to be 0 or {pi}. Furthermore, the false solutions can spread more easily if there are large errors in defining the envelope designating the region in which NCS averaging is performed.« less

Analysis of phases in the structure determination of an icosahedral virus

PubMed Central

Plevka, Pavel; Kaufmann, Bärbel; Rossmann, Michael G.

2011-01-01

The constraints imposed on structure-factor phases by non­crystallographic symmetry (NCS) allow phase improvement, phase extension to higher resolution and hence ab initio phase determination. The more numerous the NCS redundancy and the greater the volume used for solvent flattening, the greater the power for phase determination. In a case analyzed here the icosahedral NCS phasing appeared to have broken down, although later successful phase extension was possible when the envelope around the NCS region was tightened. The phases from the failed phase-determination attempt fell into four classes, all of which satisfied the NCS constraints. These four classes corresponded to the correct solution, opposite enantiomorph, Babinet inversion and opposite enantiomorph with Babinet inversion. These incorrect solutions can be seeded from structure factors belonging to reciprocal-space volumes that lie close to icosahedral NCS axes where the structure amplitudes tend to be large and the phases tend to be 0 or π. Furthermore, the false solutions can spread more easily if there are large errors in defining the envelope designating the region in which NCS averaging is performed. PMID:21636897

Crystallography of decahedral and icosahedral particles. I - Geometry of twinning

NASA Technical Reports Server (NTRS)

Yang, C. Y.

1979-01-01

The crystal structure of the tetrahedral twins in multiply-twinned particles with decahedral and icosahedral point group symmetries has been examined and correlated with the face-centered cubic structure. Details on the crystal structure as well as the geometrical relationships among twins in each particle are presented. These crystallographic facts serve as a basis for the interpretation of small particle images obtained with advanced methods of transmission electron microscopy.

A Vertically Flow-Following, Icosahedral Grid Model for Medium-Range and Seasonal Prediction. Part 1: Model Description

NASA Technical Reports Server (NTRS)

Bleck, Rainer; Bao, Jian-Wen; Benjamin, Stanley G.; Brown, John M.; Fiorino, Michael; Henderson, Thomas B.; Lee, Jin-Luen; MacDonald, Alexander E.; Madden, Paul; Middlecoff, Jacques;

Towards physical implementation of an optical add-drop multiplexer (OADM) based upon properties of 12-fold photonic quasicrystals

NASA Astrophysics Data System (ADS)

Gauthier, Robert C.; Mnaymneh, Khaled

2005-09-01

The key feature that gives photonic crystals (PhCs) their ability to form photonic band gaps (PBGs) analogous to electronic band gaps of semiconductors is their translation symmetries. In recent years, however, it has been found that structures that possess only rotational symmetries can also have PBGs. In addition, these structures, known as Photonic Quasicrystals (PhQs), have other interesting qualities that set them apart of their translational cousins. One interesting feature is how defect states can be created in PhQs. If the rotational symmetry is disturbed, defect states analogous to defects states that are created in PhCs can be obtained. Simulation results of these defect states and other propagation properties of planar 12-fold photonic quasicrystal patterns, and its physical implementations in Silicon-On-Insulator (SOI) are presented. The main mechanisms required to make any optical multiplexing system is propagation; stop bands and add/drop ports. With the rotationally symmetry of the PhQ causing the stop bands, line defects facilitating propagation and now these specially design defect states acting as add/drop ports, a physical implementation of an OADM can be presented. Theoretical, practical and manufacturing benefits of PhQs are discussed. Simulated transmission plots are shown for various fill factors, dielectric contrast and propagation direction. It is shown that low index waveguides can be produced using the quasi-crystal photonic crystal pattern. Fabrication steps and results are shown.

Origin of Quantum Criticality in Yb-Al-Au Approximant Crystal and Quasicrystal

NASA Astrophysics Data System (ADS)

Watanabe, Shinji; Miyake, Kazumasa

2016-06-01

To get insight into the mechanism of emergence of unconventional quantum criticality observed in quasicrystal Yb15Al34Au51, the approximant crystal Yb14Al35Au51 is analyzed theoretically. By constructing a minimal model for the approximant crystal, the heavy quasiparticle band is shown to emerge near the Fermi level because of strong correlation of 4f electrons at Yb. We find that charge-transfer mode between 4f electron at Yb on the 3rd shell and 3p electron at Al on the 4th shell in Tsai-type cluster is considerably enhanced with almost flat momentum dependence. The mode-coupling theory shows that magnetic as well as valence susceptibility exhibits χ ˜ T-0.5 for zero-field limit and is expressed as a single scaling function of the ratio of temperature to magnetic field T/B over four decades even in the approximant crystal when some condition is satisfied by varying parameters, e.g., by applying pressure. The key origin is clarified to be due to strong locality of the critical Yb-valence fluctuation and small Brillouin zone reflecting the large unit cell, giving rise to the extremely-small characteristic energy scale. This also gives a natural explanation for the quantum criticality in the quasicrystal corresponding to the infinite limit of the unit-cell size.

Extra-electron induced covalent strengthening and generalization of intrinsic ductile-to-brittle criterion

PubMed Central

Niu, Haiyang; Chen, Xing-Qiu; Liu, Peitao; Xing, Weiwei; Cheng, Xiyue; Li, Dianzhong; Li, Yiyi

2012-01-01

Traditional strengthening ways, such as strain, precipitation, and solid-solution, come into effect by pinning the motion of dislocation. Here, through first-principles calculations we report on an extra-electron induced covalent strengthening mechanism, which alters chemical bonding upon the introduction of extra-valence electrons in the matrix of parent materials. It is responsible for the brittle and high-strength properties of Al12W-type compounds featured by the typical fivefold icosahedral cages, which are common for quasicrystals and bulk metallic glasses (BMGs). In combination with this mechanism, we generalize ductile-to-brittle criterion in a universal hyperbolic form by integrating the classical Pettifor's Cauchy pressure with Pugh's modulus ratio for a wide variety of materials with cubic lattices. This study provides compelling evidence to correlate Pugh's modulus ratio with hardness of materials and may have implication for understanding the intrinsic brittleness of quasicrystals and BMGs. PMID:23056910

Extra-electron induced covalent strengthening and generalization of intrinsic ductile-to-brittle criterion.

PubMed

Niu, Haiyang; Chen, Xing-Qiu; Liu, Peitao; Xing, Weiwei; Cheng, Xiyue; Li, Dianzhong; Li, Yiyi

2012-01-01

Traditional strengthening ways, such as strain, precipitation, and solid-solution, come into effect by pinning the motion of dislocation. Here, through first-principles calculations we report on an extra-electron induced covalent strengthening mechanism, which alters chemical bonding upon the introduction of extra-valence electrons in the matrix of parent materials. It is responsible for the brittle and high-strength properties of Al(12)W-type compounds featured by the typical fivefold icosahedral cages, which are common for quasicrystals and bulk metallic glasses (BMGs). In combination with this mechanism, we generalize ductile-to-brittle criterion in a universal hyperbolic form by integrating the classical Pettifor's Cauchy pressure with Pugh's modulus ratio for a wide variety of materials with cubic lattices. This study provides compelling evidence to correlate Pugh's modulus ratio with hardness of materials and may have implication for understanding the intrinsic brittleness of quasicrystals and BMGs.

Cosmic history and a candidate parent asteroid for the quasicrystal-bearing meteorite Khatyrka

NASA Astrophysics Data System (ADS)

Meier, Matthias M. M.; Bindi, Luca; Heck, Philipp R.; Neander, April I.; Spring, Nicole H.; Riebe, My E. I.; Maden, Colin; Baur, Heinrich; Steinhardt, Paul J.; Wieler, Rainer; Busemann, Henner

2018-05-01

The unique CV-type meteorite Khatyrka is the only natural sample in which "quasicrystals" and associated crystalline Cu, Al-alloys, including khatyrkite and cupalite, have been found. They are suspected to have formed in the early Solar System. To better understand the origin of these exotic phases, and the relationship of Khatyrka to other CV chondrites, we have measured He and Ne in six individual, ∼40-μm-sized olivine grains from Khatyrka. We find a cosmic-ray exposure age of about 2-4 Ma (if the meteoroid was <3 m in diameter, more if it was larger). The U, Th-He ages of the olivine grains suggest that Khatyrka experienced a relatively recent (<600 Ma) shock event, which created pressure and temperature conditions sufficient to form both the quasicrystals and the high-pressure phases found in the meteorite. We propose that the parent body of Khatyrka is the large K-type asteroid 89 Julia, based on its peculiar, but matching reflectance spectrum, evidence for an impact/shock event within the last few 100 Ma (which formed the Julia family), and its location close to strong orbital resonances, so that the Khatyrka meteoroid could plausibly have reached Earth within its rather short cosmic-ray exposure age.

Analysis of phases in the structure determination of an icosahedral virus.

PubMed

Plevka, Pavel; Kaufmann, Bärbel; Rossmann, Michael G

2011-06-01

The constraints imposed on structure-factor phases by noncrystallographic symmetry (NCS) allow phase improvement, phase extension to higher resolution and hence ab initio phase determination. The more numerous the NCS redundancy and the greater the volume used for solvent flattening, the greater the power for phase determination. In a case analyzed here the icosahedral NCS phasing appeared to have broken down, although later successful phase extension was possible when the envelope around the NCS region was tightened. The phases from the failed phase-determination attempt fell into four classes, all of which satisfied the NCS constraints. These four classes corresponded to the correct solution, opposite enantiomorph, Babinet inversion and opposite enantiomorph with Babinet inversion. These incorrect solutions can be seeded from structure factors belonging to reciprocal-space volumes that lie close to icosahedral NCS axes where the structure amplitudes tend to be large and the phases tend to be 0 or π. Furthermore, the false solutions can spread more easily if there are large errors in defining the envelope designating the region in which NCS averaging is performed. © 2011 International Union of Crystallography

Icosahedral stereographic projections in three dimensions for use in dark field TEM.

PubMed

Bourdillon, Antony J

2013-08-01

Thermodynamics require that rapidly cooled crystals and quasicrystals are relatively defective. Yet, without convenient 3-dimensional indexation both at crystal poles and in diffraction planes, or Kikuchi maps, it is difficult to identify the defects by dark field transmission electron microscopy. For two phase Al6Mn, these maps are derived. They relate i-Al6Mn to the standard face centered cubic, matrix crystals. An example of their usefulness in determining interfacial characteristics is described. Indices are integral powers on an irrational number. Copyright © 2013 Elsevier Ltd. All rights reserved.

Atomistic simulation of frictional anisotropy on quasicrystal approximant surfaces

DOE PAGES

Ye, Zhijiang; Martini, Ashlie; Thiel, Patricia; ...

2016-06-23

J. Y. Park et al. [Science 309, 1354 (2005)] have reported eight times greater atomic-scale friction in the periodic than in the quasiperiodic direction on the twofold face of a decagonal Al-Ni-Co quasicrystal. Here we present results of molecular-dynamics simulations intended to elucidate mechanisms behind this giant frictional anisotropy. Simulations of a bare atomic-force-microscope tip on several model substrates and under a variety of conditions failed to reproduce experimental results. On the other hand, including the experimental passivation of the tip with chains of hexadecane thiol, we reproduce qualitatively the experimental anisotropy in friction, finding evidence for entrainment of themore » organic chains in surface furrows parallel to the periodic direction.« less

Quasicrystal-reinforced Mg alloys.

PubMed

Kyun Kim, Young; Tae Kim, Won; Hyang Kim, Do

2014-04-01

The formation of the icosahedral phase (I-phase) as a secondary solidification phase in Mg-Zn-Y and Mg-Zn-Al base systems provides useful advantages in designing high performance wrought magnesium alloys. The strengthening in two-phase composites (I-phase + α -Mg) can be explained by dispersion hardening due to the presence of I-phase particles and by the strong bonding property at the I-phase/matrix interface. The presence of an additional secondary solidification phase can further enhance formability and mechanical properties. In Mg-Zn-Y alloys, the co-presence of I and Ca 2 Mg 6 Zn 3 phases by addition of Ca can significantly enhance formability, while in Mg-Zn-Al alloys, the co-presence of the I-phase and Mg 2 Sn phase leads to the enhancement of mechanical properties. Dynamic and static recrystallization are significantly accelerated by addition of Ca in Mg-Zn-Y alloy, resulting in much smaller grain size and more random texture. The high strength of Mg-Zn-Al-Sn alloys is attributed to the presence of finely distributed Mg 2 Sn and I-phase particles embedded in the α -Mg matrix.

Quasicrystal-reinforced Mg alloys

PubMed Central

Kyun Kim, Young; Tae Kim, Won; Hyang Kim, Do

2014-01-01

The formation of the icosahedral phase (I-phase) as a secondary solidification phase in Mg–Zn–Y and Mg–Zn–Al base systems provides useful advantages in designing high performance wrought magnesium alloys. The strengthening in two-phase composites (I-phase + α-Mg) can be explained by dispersion hardening due to the presence of I-phase particles and by the strong bonding property at the I-phase/matrix interface. The presence of an additional secondary solidification phase can further enhance formability and mechanical properties. In Mg–Zn–Y alloys, the co-presence of I and Ca2Mg6Zn3 phases by addition of Ca can significantly enhance formability, while in Mg–Zn–Al alloys, the co-presence of the I-phase and Mg2Sn phase leads to the enhancement of mechanical properties. Dynamic and static recrystallization are significantly accelerated by addition of Ca in Mg–Zn–Y alloy, resulting in much smaller grain size and more random texture. The high strength of Mg–Zn–Al–Sn alloys is attributed to the presence of finely distributed Mg2Sn and I-phase particles embedded in the α-Mg matrix. PMID:27877660

Geometry induced sequence of nanoscale Frank–Kasper and quasicrystal mesophases in giant surfactants

PubMed Central

Yue, Kan; Huang, Mingjun; Marson, Ryan L.; He, Jinlin; Huang, Jiahao; Zhou, Zhe; Wang, Jing; Liu, Chang; Yan, Xuesheng; Wu, Kan; Guo, Zaihong; Liu, Hao; Ni, Peihong; Wesdemiotis, Chrys; Zhang, Wen-Bin; Glotzer, Sharon C.; Cheng, Stephen Z. D.

2016-01-01

Frank–Kasper (F-K) and quasicrystal phases were originally identified in metal alloys and only sporadically reported in soft materials. These unconventional sphere-packing schemes open up possibilities to design materials with different properties. The challenge in soft materials is how to correlate complex phases built from spheres with the tunable parameters of chemical composition and molecular architecture. Here, we report a complete sequence of various highly ordered mesophases by the self-assembly of specifically designed and synthesized giant surfactants, which are conjugates of hydrophilic polyhedral oligomeric silsesquioxane cages tethered with hydrophobic polystyrene tails. We show that the occurrence of these mesophases results from nanophase separation between the heads and tails and thus is critically dependent on molecular geometry. Variations in molecular geometry achieved by changing the number of tails from one to four not only shift compositional phase boundaries but also stabilize F-K and quasicrystal phases in regions where simple phases of spheroidal micelles are typically observed. These complex self-assembled nanostructures have been identified by combining X-ray scattering techniques and real-space electron microscopy images. Brownian dynamics simulations based on a simplified molecular model confirm the architecture-induced sequence of phases. Our results demonstrate the critical role of molecular architecture in dictating the formation of supramolecular crystals with “soft” spheroidal motifs and provide guidelines to the design of unconventional self-assembled nanostructures. PMID:27911786

Diphosphine-protected ultrasmall gold nanoclusters: opened icosahedral Au 13 and heart-shaped Au 8 clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Shan-Shan; Feng, Lei; Senanayake, Ravithree D.

Two ultrasmall gold clusters, Au 13 and Au 8 , were identified as a distorted I h icosahedral Au 13 and edge-shared “core + 4 exo ” structure Au 8 S 2 cores, respectively. They showed interesting luminescence and electrochemical properties.

Diphosphine-protected ultrasmall gold nanoclusters: opened icosahedral Au 13 and heart-shaped Au 8 clusters

DOE PAGES

Zhang, Shan-Shan; Feng, Lei; Senanayake, Ravithree D.; ...

2018-01-01

Two ultrasmall gold clusters, Au 13 and Au 8 , were identified as a distorted I h icosahedral Au 13 and edge-shared “core + 4 exo ” structure Au 8 S 2 cores, respectively. They showed interesting luminescence and electrochemical properties.

Studies of inactivation mechanism of non-enveloped icosahedral virus by a visible ultrashort pulsed laser

PubMed Central

2014-01-01

Background Low-power ultrashort pulsed (USP) lasers operating at wavelengths of 425 nm and near infrared region have been shown to effectively inactivate viruses such as human immunodeficiency virus (HIV), M13 bacteriophage, and murine cytomegalovirus (MCMV). It was shown previously that non-enveloped, helical viruses such as M13 bacteriophage, were inactivated by a USP laser through an impulsive stimulated Raman scattering (ISRS) process. Recently, enveloped virus like MCMV has been shown to be inactivated by a USP laser via protein aggregation induced by an ISRS process. However, the inactivation mechanism for a clinically important class of viruses – non-enveloped, icosahedral viruses remains unknown. Results and discussions We have ruled out the following four possible inactivation mechanisms for non-enveloped, icosahedral viruses, namely, (1) inactivation due to ultraviolet C (UVC) photons produced by non-linear optical process of the intense, fundamental laser beam at 425 nm; (2) inactivation caused by thermal heating generated by the direct laser absorption/heating of the virion; (3) inactivation resulting from a one-photon absorption process via chromophores such as porphyrin molecules, or indicator dyes, potentially producing reactive oxygen or other species; (4) inactivation by the USP lasers in which the extremely intense laser pulse produces shock wave-like vibrations upon impact with the viral particle. We present data which support that the inactivation mechanism for non-enveloped, icosahedral viruses is the impulsive stimulated Raman scattering process. Real-time PCR experiments show that, within the amplicon size of 273 bp tested, there is no damage on the genome of MNV-1 caused by the USP laser irradiation. Conclusion We conclude that our model non-enveloped virus, MNV-1, is inactivated by the ISRS process. These studies provide fundamental knowledge on photon-virus interactions on femtosecond time scales. From the analysis of the transmission

Frustration and thermalization in an artificial magnetic quasicrystal

NASA Astrophysics Data System (ADS)

Shi, Dong; Budrikis, Zoe; Stein, Aaron; Morley, Sophie A.; Olmsted, Peter D.; Burnell, Gavin; Marrows, Christopher H.

2018-03-01

Artificial frustrated systems offer a playground to study the emergent properties of interacting systems. Most work to date has been on spatially periodic systems, known as artificial spin ices when the interacting elements are magnetic. Here we have studied artificial magnetic quasicrystals based on quasiperiodic Penrose tiling patterns of interacting nanomagnets. We construct a low-energy configuration from a step-by-step approach that we propose as a ground state. Topologically induced emergent frustration means that this configuration cannot be constructed from vertices in their ground states. It has two parts, a quasi-one-dimensional `skeleton' that spans the entire pattern and is capable of long-range order, surrounding `flippable' clusters of macrospins that lead to macroscopic degeneracy. Magnetic force microscopy imaging of Penrose tiling arrays revealed superdomains that are larger for more strongly coupled arrays, especially after annealing the array above its blocking temperature.

Photonic band gap spectra in Octonacci metamaterial quasicrystals

NASA Astrophysics Data System (ADS)

Brandão, E. R.; Vasconcelos, M. S.; Albuquerque, E. L.; Fulco, U. L.

2017-02-01

In this work we study theoretically the photonic band gap spectra for a one-dimensional quasicrystal made up of SiO2 (layer A) and a metamaterial (layer B) organized following the Octonacci sequence, where its nth-stage Sn is given by the inflation rule Sn =Sn - 1Sn - 2Sn - 1 for n ≥ 3 , with initial conditions S1 = A and S2 = B . The metamaterial is characterized by a frequency dependent electric permittivity ε(ω) and magnetic permeability μ(ω) . The polariton dispersion relation is obtained analytically by employing a theoretical calculation based on a transfer-matrix approach. A quantitative analysis of the spectra is then discussed, stressing the distribution of the allowed photonic band widths for high generations of the Octonacci structure, which depict a self-similar scaling property behavior, with a power law depending on the common in-plane wavevector kx .

Studies of Inactivation Mechanism of non-enveloped icosahedral viruses by a visible ultrashort pulsed laser

USDA-ARS?s Scientific Manuscript database

The inactivation mechanism of ultrashort pulsed laser irradiation at a wavelength of 425 nm has been studied using two different-sized, non-enveloped icosahedral viruses, murine norovirus-1 (MNV-1) and human papillomavirus-16 (HPV-16) pseudovirions. Our experimental results are consistent with a mo...

Geometry induced sequence of nanoscale Frank–Kasper and quasicrystal mesophases in giant surfactants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yue, Kan; Huang, Mingjun; Marson, Ryan L.

Frank–Kasper (F-K) and quasicrystal phases were originally identified in metal alloys and only sporadically reported in soft materials. These unconventional sphere-packing schemes open up possibilities to design materials with different properties. The challenge in soft materials is how to correlate complex phases built from spheres with the tunable parameters of chemical composition and molecular architecture. Here, we report a complete sequence of various highly ordered mesophases by the self-assembly of specifically designed and synthesized giant surfactants, which are conjugates of hydrophilic polyhedral oligomeric silsesquioxane cages tethered with hydrophobic polystyrene tails. We show that the occurrence of these mesophases results frommore » nanophase separation between the heads and tails and thus is critically dependent on molecular geometry. Variations in molecular geometry achieved by changing the number of tails from one to four not only shift compositional phase boundaries but also stabilize F-K and quasicrystal phases in regions where simple phases of spheroidal micelles are typically observed. These complex self-assembled nanostructures have been identified by combining X-ray scattering techniques and real-space electron microscopy images. Brownian dynamics simulations based on a simplified molecular model confirm the architecture-induced sequence of phases. Our results demonstrate the critical role of molecular architecture in dictating the formation of supramolecular crystals with “soft” spheroidal motifs and provide guidelines to the design of unconventional self-assembled nanostructures.« less

Direct imaging of coexisting ordered and frustrated sublattices in artificial ferromagnetic quasicrystals

DOE PAGES

Farmer, B.; Bhat, V. S.; Balk, A.; ...

2016-04-25

Here, we have used scanning electron microscopy with polarization analysis and photoemission electron microscopy to image the two-dimensional magnetization of permalloy films patterned into Penrose P2 tilings (P2T). The interplay of exchange interactions in asymmetrically coordinated vertices and short-range dipole interactions among connected film segments stabilize magnetically ordered, spatially distinct sublattices that coexist with frustrated sublattices at room temperature. Numerical simulations that include long-range dipole interactions between sublattices agree with images of as-grown P2T samples and predict a magnetically ordered ground state for a two-dimensional quasicrystal lattice of classical Ising spins.

3-dimensional indexation of the icosahedral diffraction pattern using the techniques of electron microscopy

NASA Astrophysics Data System (ADS)

Bourdillon, Antony

2012-11-01

The following facts about icosahedra need wider attention. 1) The golden section τ is as fundamental to the icosahedral structure (length /edge) as π is to the sphere (circumference /diameter). 2) The diffraction series are in restricted Fibonacci order because the ratio of adjacent terms fn/fn-1 does not vary, but is the constant τ. The series is therefore geometric. 3) Because of the tetragonal subgroup in the icosahedral point group symmetry, many axes in the icosahedral structure have identical orientation to axes in the face centered cubic matrix of Al6Mn [1] (e.g. [100] and [111]). On these bases, a three dimensional stereographic projection will be presented. 4) A quasi-Bragg law is derived that correctly represents the diffraction series in powers of τ [2]. Furthermore, by employing the normal conventions of electron microscopy, all diffraction patterns are completely indexed in three dimensions. These are the topic of this presentation. Significant consequences will be presented elsewhere: 1) The diffraction pattern intensities near all main axes are correctly simulated, and all atoms are located on a specimen image. 2) The quasi-Bragg law has a special metric. Atomic locations are consistently calculated for the first time. 3) Whereas the Bragg law transforms a crystal lattice in real space into a reciprocal lattice in diffraction space, the quasi-Bragg law transforms a geometric diffraction pattern into a hierarchic structure. 4) Hyperspatial indexation [3] is superceded. [1] Shechtman, D.; Blech, I.; Gratias, D.; Cahn, J.W., Metallic phase with long-range orientational order and no translational symmetry, Phys. Rev. Lett., 1984, 53, 1951-3. [2] Bourdillon, A. J., Nearly free electron band structures in a logarithmically periodic solid, Sol. State Comm. 2009, 149, 1221-1225. [3] Duneau, M., and Katz, A., Phys Rev Lett 54, 2688-2691

Frustration and thermalization in an artificial magnetic quasicrystal

DOE PAGES

Shi, Dong; Budrikis, Zoe; Stein, Aaron; ...

2017-12-11

Here, artificial frustrated systems offer a playground to study the emergent properties of interacting systems. Most work to date has been on spatially periodic systems, known as artificial spin ices when the interacting elements are magnetic. Here we have studied artificial magnetic quasicrystals based on quasiperiodic Penrose tiling patterns of interacting nanomagnets. We construct a low-energy configuration from a step-by-step approach that we propose as a ground state. Topologically induced emergent frustration means that this configuration cannot be constructed from vertices in their ground states. It has two parts, a quasi-one-dimensional ‘skeleton’ that spans the entire pattern and is capablemore » of long-range order, surrounding ‘flippable’ clusters of macrospins that lead to macroscopic degeneracy. Magnetic force microscopy imaging of Penrose tiling arrays revealed superdomains that are larger for more strongly coupled arrays, especially after annealing the array above its blocking temperature.« less

Dodecagonal photonic quasi-crystal fiber with high birefringence.

PubMed

Cai, Weicheng; Liu, Exian; Feng, Bo; Xiao, Wei; Liu, Hongfei; Wang, Ziming; Wang, Shuo; Liang, Taiyuan; Liu, Jianqiang; Liu, Jianjun

2016-10-01

A photonic quasi-crystal fiber (PQF) with high birefringence is proposed. A dodecagonal Stampfli quasi-periodic lattice of air holes constitutes the cladding of the PQF. The PQF maintains the properties of high birefringence and single-mode operation regime in a wide wavelength range from 1.2 to 2.0 μm by optimizing the size of the air holes around the core of the PQF. A birefringence with 3.86×10^-2 can be obtained at 1.31 and 1.55 μm optical telecommunication windows. The birefringence is of the order of 10^-2, which is two orders of magnitude larger than that of the conventional polarization-maintaining fibers and hardly affected by the incident wavelength. The proposed PQF also maintains a high nonlinear coefficient and low confinement loss. Our structure and simulation results are expected to provide a valuable reference and basic data to relative fabrication and experiments.

Frustration and thermalization in an artificial magnetic quasicrystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Dong; Budrikis, Zoe; Stein, Aaron

Here, artificial frustrated systems offer a playground to study the emergent properties of interacting systems. Most work to date has been on spatially periodic systems, known as artificial spin ices when the interacting elements are magnetic. Here we have studied artificial magnetic quasicrystals based on quasiperiodic Penrose tiling patterns of interacting nanomagnets. We construct a low-energy configuration from a step-by-step approach that we propose as a ground state. Topologically induced emergent frustration means that this configuration cannot be constructed from vertices in their ground states. It has two parts, a quasi-one-dimensional ‘skeleton’ that spans the entire pattern and is capablemore » of long-range order, surrounding ‘flippable’ clusters of macrospins that lead to macroscopic degeneracy. Magnetic force microscopy imaging of Penrose tiling arrays revealed superdomains that are larger for more strongly coupled arrays, especially after annealing the array above its blocking temperature.« less

Dynamic and Kinetic Assembly Studies of an Icosahedral Virus Capsid

NASA Astrophysics Data System (ADS)

Lee, Kelly

2011-03-01

Hepatitis B virus has an icosahedrally symmetrical core particle (capsid), composed of either 90 or 120 copies of a dimeric protein building block. We are using time-resolved, solution small-angle X-ray scattering and single-molecule fluorescence microscopy to probe the core particle assembly reaction at the ensemble and individual assembly levels. Our experiments to date reveal the assembly process to be highly cooperative with minimal population of stable intermediate species. Solution conditions, particularly salt concentration, appears to influence the partitioning of assembly products into the two sizes of shells. Funding from NIH R00-GM080352 and University of Washington.

A narrowband filter based on 2D 8-fold photonic quasicrystal

NASA Astrophysics Data System (ADS)

Ren, Jie; Sun, XiaoHong; Wang, Shuai

2018-04-01

In this paper, a novel structure of narrowband filter based on 2D 8-fold photonic quasicrystal (PQC) is proposed and investigated. The structure size is 8 μm × 8 μm, which promises its applications in optical integrated circuits and communication devices. Finite Element Method (FEM) has been employed to investigate the band gap of the filter. The resonance wavelength, transmission coefficient and 3 dB bandwidth are analyzed by varying the parameters of the structure. By optimizing the parameters of the filter, two design formulas of resonance wavelength are obtained. Also, for its better linearity of the resonance, the structure with line-defect has also seen a large uptake in sensor design.

Allosteric Control of Icosahedral Capsid Assembly

PubMed Central

Lazaro, Guillermo R.

2017-01-01

During the lifecycle of a virus, viral proteins and other components self-assemble to form an ordered protein shell called a capsid. This assembly process is subject to multiple competing constraints, including the need to form a thermostable shell while avoiding kinetic traps. It has been proposed that viral assembly satisfies these constraints through allosteric regulation, including the interconversion of capsid proteins among conformations with different propensities for assembly. In this article we use computational and theoretical modeling to explore how such allostery affects the assembly of icosahedral shells. We simulate assembly under a wide range of protein concentrations, protein binding affinities, and two different mechanisms of allosteric control. We find that, above a threshold strength of allosteric control, assembly becomes robust over a broad range of subunit binding affinities and concentrations, allowing the formation of highly thermostable capsids. Our results suggest that allostery can significantly shift the range of protein binding affinities that lead to successful assembly, and thus should be accounted for in models that are used to estimate interaction parameters from experimental data. PMID:27117092

Structural evolutions and hereditary characteristics of icosahedral nano-clusters formed in Mg70Zn30 alloys during rapid solidification processes

NASA Astrophysics Data System (ADS)

Liang, Yong-Chao; Liu, Rang-Su; Xie, Quan; Tian, Ze-An; Mo, Yun-Fei; Zhang, Hai-Tao; Liu, Hai-Rong; Hou, Zhao-Yang; Zhou, Li-Li; Peng, Ping

2017-02-01

To investigate the structural evolution and hereditary mechanism of icosahedral nano-clusters formed during rapid solidification, a molecular dynamics (MD) simulation study has been performed for a system consisting of 107 atoms of liquid Mg70Zn30 alloy. Adopting Honeycutt-Anderson (HA) bond-type index method and cluster type index method (CTIM-3) to analyse the microstructures in the system it is found that for all the nano-clusters including 2~8 icosahedral clusters in the system, there are 62 kinds of geometrical structures, and those can be classified, by the configurations of the central atoms of basic clusters they contained, into four types: chain-like, triangle-tailed, quadrilateral-tailed and pyramidal-tailed. The evolution of icosahedral nano-clusters can be conducted by perfect heredity and replacement heredity, and the perfect heredity emerges when temperature is slightly less than Tm then increase rapidly and far exceeds the replacement heredity at Tg; while for the replacement heredity, there are three major modes: replaced by triangle (3-atoms), quadrangle (4-atoms) and pentagonal pyramid (6-atoms), rather than by single atom step by step during rapid solidification processes.

Mixed-mode crack tip loading and crack deflection in 1D quasicrystals

NASA Astrophysics Data System (ADS)

Wang, Zhibin; Scheel, Johannes; Ricoeur, Andreas

2016-12-01

Quasicrystals (QC) are a new class of materials besides crystals and amorphous solids and have aroused much attention of researchers since they were discovered. This paper presents a generalized fracture theory including the J-integral and crack closure integrals, relations between J1, J2 and the stress intensity factors as well as the implementation of the near-tip stress and displacement solutions of 1D QC. Different crack deflection criteria, i.e. the J-integral and maximum circumferential stress criteria, are investigated for mixed-mode loading conditions accounting for phonon-phason coupling. One focus is on the influence of phason stress intensity factors on crack deflection angles.

Curating viscoelastic properties of icosahedral viruses, virus-based nanomaterials, and protein cages.

PubMed

Kant, Ravi; Rayaprolu, Vamseedhar; McDonald, Kaitlyn; Bothner, Brian

2018-06-01

The beauty, symmetry, and functionality of icosahedral virus capsids has attracted the attention of biologists, physicists, and mathematicians ever since they were first observed. Viruses and protein cages assemble into functional architectures in a range of sizes, shapes, and symmetries. To fulfill their biological roles, these structures must self-assemble, resist stress, and are often dynamic. The increasing use of icosahedral capsids and cages in materials science has driven the need to quantify them in terms of structural properties such as rigidity, stiffness, and viscoelasticity. In this study, we employed Quartz Crystal Microbalance with Dissipation technology (QCM-D) to characterize and compare the mechanical rigidity of different protein cages and viruses. We attempted to unveil the relationships between rigidity, radius, shell thickness, and triangulation number. We show that the rigidity and triangulation numbers are inversely related to each other and the comparison of rigidity and radius also follows the same trend. Our results suggest that subunit orientation, protein-protein interactions, and protein-nucleic acid interactions are important for the resistance to deformation of these complexes, however, the relationships are complex and need to be explored further. The QCM-D based viscoelastic measurements presented here help us elucidate these relationships and show the future prospect of this technique in the field of physical virology and nano-biotechnology.

Many-molecule encapsulation by an icosahedral shell

PubMed Central

Perlmutter, Jason D; Mohajerani, Farzaneh; Hagan, Michael F

2016-01-01

We computationally study how an icosahedral shell assembles around hundreds of molecules. Such a process occurs during the formation of the carboxysome, a bacterial microcompartment that assembles around many copies of the enzymes ribulose 1,5-bisphosphate carboxylase/ oxygenase and carbonic anhydrase to facilitate carbon fixation in cyanobacteria. Our simulations identify two classes of assembly pathways leading to encapsulation of many-molecule cargoes. In one, shell assembly proceeds concomitantly with cargo condensation. In the other, the cargo first forms a dense globule; then, shell proteins assemble around and bud from the condensed cargo complex. Although the model is simplified, the simulations predict intermediates and closure mechanisms not accessible in experiments, and show how assembly can be tuned between these two pathways by modulating protein interactions. In addition to elucidating assembly pathways and critical control parameters for microcompartment assembly, our results may guide the reengineering of viruses as nanoreactors that self-assemble around their reactants. DOI: http://dx.doi.org/10.7554/eLife.14078.001 PMID:27166515

Insights into plant consciousness from neuroscience, physics and mathematics: A role for quasicrystals?

PubMed Central

2012-01-01

There is considerable debate over whether plants are conscious and this, indeed, is an important question. Here I look at developments in neuroscience, physics and mathematics that may impact on this question. Two major concomitants of consciousness in animals are microtubule function and electrical gamma wave synchrony. Both these factors may also play a role in plant consciousness. I show that plants possess aperiodic quasicrystal structures composed of ribosomes that may enable quantum computing, which has been suggested to lie at the core of animal consciousness. Finally I look at whether a microtubule fractal suggests that electric current plays a part in conventional neurocomputing processes in plants. PMID:22899055

Insights into plant consciousness from neuroscience, physics and mathematics: a role for quasicrystals?

PubMed

Gardiner, John

2012-09-01

There is considerable debate over whether plants are conscious and this, indeed, is an important question. Here I look at developments in neuroscience, physics and mathematics that may impact on this question. Two major concomitants of consciousness in animals are microtubule function and electrical gamma wave synchrony. Both these factors may also play a role in plant consciousness. I show that plants possess aperiodic quasicrystal structures composed of ribosomes that may enable quantum computing, which has been suggested to lie at the core of animal consciousness. Finally I look at whether a microtubule fractal suggests that electric current plays a part in conventional neurocomputing processes in plants.

Au13(8e): A secondary block for describing a special group of liganded gold clusters containing icosahedral Au13 motifs

NASA Astrophysics Data System (ADS)

Xu, Wen Wu; Zeng, Xiao Cheng; Gao, Yi

2017-05-01

A grand unified model (GUM) has been proposed recently to understand structure anatomy and evolution of liganded gold clusters. In this work, besides the two types of elementary blocks (triangular Au3(2e) and tetrahedral Au4(2e)), we introduce a secondary block, namely, the icosahedral Au13 with 8e valence electrons, noted as Au13(8e). Using this secondary block, structural anatomy and evolution of a special group of liganded gold nanoclusters containing icosahedral Au13 motifs can be conveniently analyzed. In addition, a new ligand-protected cluster Au49(PR3)10(SR)15Cl2 is predicted to exhibit high chemical and thermal stability, suggesting likelihood of its synthesis in the laboratory.

Analytical and computational modeling of early penetration of non-enveloped icosahedral viruses into cells.

PubMed

Katzengold, Rona; Zaharov, Evgeniya; Gefen, Amit

2016-07-27

As obligate intracellular parasites, all viruses penetrate target cells to initiate replication and infection. This study introduces two approaches for evaluating the contact loads applied to a cell during early penetration of non-enveloped icosahedral viruses. The first approach is analytical modeling which is based on Hertz's theory for the contact of two elastic bodies; here we model the virus capsid as a triangle and the cell as an order-of-magnitude larger sphere. The second approach is finite element modeling, where we simulate three types of viruses: adeno-, papilloma- and polio- viruses, each interacting with a cell section. We find that the peak contact pressures and forces generated at the initial virus-cell contact depend on the virus geometry - that is both size and shape. With respect to shape, we show that the icosahedral virus shape induces greater peak pressures compared to a spherical virus shape. With respect to size, it is shown that the larger the virus is the greater are the contact loads in the attacked cell. Utilization of our modeling can be substantially useful not only for basic science studies, but also in other, more applied fields, such as in the field of gene therapy, or in `phage' virus studies.

Science Using an Electrostatic Levitation Furnace in the MUCAT Sector at the APS

NASA Technical Reports Server (NTRS)

Goldman, A.; Kelton, K. F.; Rogers, J. R.

2004-01-01

The original motivation for the construction of the BESL prototype was to obtain the first proof of a 50-year-old hypothesis regarding the solidification of liquid metals. Since the 1950s it has been known that under proper conditions liquid metals can be cooled below their melting temperature (undercooled) without crystallizing to the stable solid phase. In 1952 Frank proposed that this was because the atoms in the metallic liquid were arranged with the symmetry of an icosahedron, a Platonic solid consisting of 20 tetrahedra (4-sided pyramid-shaped polyhedra) arranged around a common center. Since this local atomic order is incompatible with the long-range translational periodicity of crystal phases, a barrier is formed to the formation of small regions of the crystal phase, the nucleation barrier. A proof of Frank's hypothesis required a direct correlation between measured icosahedral order in the undercooled liquid and the nucleation barrier. The tendency of sample containers to catalyze nucleation obscured this relation, requiring containerless techniques. Combining containerless processing techniques for electrostatically levitated droplets (ESL) with x-ray synchrotron methods, a team from Washington University, St. Louis, MO, NASA Marshall Space Flight Center, and MUCAT at the APS demonstrated an increasing icosahedral order in TiZrNi liquids with decreasing temperature below the melting temperature. The increased icosahedral order caused the transformation of the liquid to a metastable icosahedral quasicrystal phase, instead of the stable tetrahedrally-coordinated crystal intermetallic, giving the first clear demonstration of the connection between the nucleation barrier and the local structure of the liquid, verifying Frank's hypothesis for this alloy.

Quantum transport through single and multilayer icosahedral fullerenes

NASA Astrophysics Data System (ADS)

Lovey, Daniel A.; Romero, Rodolfo H.

2013-10-01

We use a tight-binding Hamiltonian and Green functions methods to calculate the quantum transmission through single-wall fullerenes and bilayered and trilayered onions of icosahedral symmetry attached to metallic leads. The electronic structure of the onion-like fullerenes takes into account the curvature and finite size of the fullerenes layers as well as the strength of the intershell interactions depending on to the number of interacting atom pairs belonging to adjacent shells. Misalignment of the symmetry axes of the concentric iscosahedral shells produces breaking of the level degeneracies of the individual shells, giving rise some narrow quasi-continuum bands instead of the localized discrete peaks of the individual fullerenes. As a result, the transmission function for non symmetrical onions is rapidly varying functions of the Fermi energy. Furthermore, we found that most of the features of the transmission through the onions are due to the electronic structure of the outer shell with additional Fano-like antiresonances arising from coupling with or between the inner shells.

Isolation and Characterization of Metallosphaera turreted icosahedral virus (MTIV), a founding member of a new family of archaeal viruses.

PubMed

Wagner, Cassia; Reddy, Vijay; Asturias, Francisco; Khoshouei, Maryam; Johnson, John E; Manrique, Pilar; Munson-McGee, Jacob; Baumeister, Wolfgang; Lawrence, C Martin; Young, Mark J

2017-08-02

Our understanding of archaeal virus diversity and structure is just beginning to emerge. Here we describe a new archaeal virus, tentatively named Metallosphaera turreted icosahedral virus (MTIV), that was isolated from an acidic hot spring in Yellowstone National Park, USA. Two strains of the virus were identified and found to replicate in an archaeal host species closely related to Metallosphaera yellowstonensis Each strain encodes for a 9.8-9.9 kb, linear dsDNA genome with large inverted terminal repeats. Each genome encodes for 21 ORFs. Between the strains the ORFs display high homology, but they are quite distinct from other known viral genes. The 70-nm diameter virion is built upon on a T=28 icosahedral lattice. Both single particle cryo-electron microscopy and cryo-tomography reconstructions reveal an unusual structure that has 42 turret-like projections: 12 from each of the 5-fold axes and 30 hexameric units positioned on icosahedral 2-fold axes. Both the virion structural properties and genome content support MTIV as the founding member of a new family of archaeal viruses. Importance: Many archaeal viruses are quite different than viruses infecting bacteria and eukaryotes. Initial characterization of MTIV reveals a virus distinct from other known bacterial, eukaryotic, and archaeal viruses; this finding suggests that viruses infecting Archaea are still an understudied group of viruses. As the first known virus infecting the Metallosphaera , MTIV provides a new system for exploring archaeal virology by examining host-virus interactions and the unique features of MTIV structure-function relationships. These studies will likely expand our understanding of virus ecology and evolution. Copyright © 2017 American Society for Microbiology.

Structure of periodic crystals and quasicrystals in ultrathin films of Ba-Ti-O

DOE PAGES

Cockayne, Eric; Mihalkovič, Marek; Henley, Christopher L.

2016-01-07

Here, we model the remarkable thin-film Ba-Ti-O structures formed by heat treatment of an initial perovskite BaTiO 3 thin film on a Pt(111) surface. All structures contain a rumpled Ti-O network with all Ti threefold coordinated with O, and with Ba occupying the larger. mainly Ti 7O 7, pores. The quasicrystal structue is a simple decoration of three types of tiles: square, triangle and 30° rhombus, with edge lengths 6.85 Å, joined edge-to-edge in a quasicrystalline pattern; observed periodic crystals in ultrathin film Ba-Ti-O are built from these and other tiles. Simulated STM images reproduce the patterns seen experimentally, andmore » identify the bright protrusions as Ba atoms. The models are consistent with all experimental observations.« less

A low threshold nanocavity in a two-dimensional 12-fold photonic quasicrystal

NASA Astrophysics Data System (ADS)

Ren, Jie; Sun, XiaoHong; Wang, Shuai

2018-05-01

In this article, a low threshold nanocavity is built and investigated in a two-dimensional 12-fold holographic photonic quasicrystal (PQC). The cavity is formed by using the method of multi-beam common-path interference. By finely adjusting the structure parameters of the cavity, the Q factor and the mode volume are optimized, which are two keys to low-threshold on the basis of Purcell effect. Finally, an optimal cavity is obtained with Q value of 6023 and mode volume of 1.24 ×10-12cm3 . On the other hand, by Fourier Transformation of the electric field components in the cavity, the in-plane wave vectors are calculated and fitted to evaluate the cavity performance. The performance analysis of the cavity further proves the effectiveness of the optimization process. This has a guiding significance for the research of low threshold nano-laser.

Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral Viruses from Cryo-Electron Micrographs

PubMed Central

Baker, T. S.; Olson, N. H.; Fuller, S. D.

1999-01-01

Viruses are cellular parasites. The linkage between viral and host functions makes the study of a viral life cycle an important key to cellular functions. A deeper understanding of many aspects of viral life cycles has emerged from coordinated molecular and structural studies carried out with a wide range of viral pathogens. Structural studies of viruses by means of cryo-electron microscopy and three-dimensional image reconstruction methods have grown explosively in the last decade. Here we review the use of cryo-electron microscopy for the determination of the structures of a number of icosahedral viruses. These studies span more than 20 virus families. Representative examples illustrate the use of moderate- to low-resolution (7- to 35-Å) structural analyses to illuminate functional aspects of viral life cycles including host recognition, viral attachment, entry, genome release, viral transcription, translation, proassembly, maturation, release, and transmission, as well as mechanisms of host defense. The success of cryo-electron microscopy in combination with three-dimensional image reconstruction for icosahedral viruses provides a firm foundation for future explorations of more-complex viral pathogens, including the vast number that are nonspherical or nonsymmetrical. PMID:10585969

Possible nucleus of the Bergman cluster in the Zn-Mg-Y alloy system

NASA Astrophysics Data System (ADS)

Nakayama, Kei; Nakagawa, Masaya; Koyama, Yasumasa

2018-01-01

To understand the formation of the Bergman cluster in the F-type icosahedral quasicrystal (IQ), crystallographic relations between the quasicrystal and the intermetallic-compound H and Zn23Y6 phases in the Zn-Mg-Y alloy system were investigated mainly by transmission electron microscopy. It was found that, although sample rotations of about 1° were required to obtain simple crystallographic relations, the orientation relationship was established among the cubic-Fm?m Zn23Y6 structure, the hexagonal-P63/mmc H structure and the F-type IQ; that is, [? 1 3]c // the five-fold axis in the IQ // N(2 ? 0)H, and [1 1 0]c // the two-fold axis in the IQ // N(0 5 ? 3)H, where N(h k m l)H means the normal direction of the (h k m l)H plane in the H structure. The correspondences between atomic positions in the Bergman cluster and in the Zn23Y6 structure and between those in the cluster and in the H structure were investigated on the basis of the established relationship. As a result, an assembly of six short-penetrated-decagonal columns was identified as an appropriate nucleus in the formation of the Bergman cluster from these two structures.

Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids.

PubMed

Nguyen, Hung D; Reddy, Vijay S; Brooks, Charles L

2007-02-01

Self-assembly of viral proteins into icosahedral capsids is an interesting yet poorly understood phenomenon of which elucidation may aid the exploration of beneficial applications of capsids in materials science and medicine. Using molecular dynamics simulations of coarse-grained models for capsid proteins, we show that the competition between the formation of full capsids and nonidealized structures is strongly dependent upon the protein concentration and temperature, occurring kinetically as a cascade of elementary reactions in which free monomers are added to the growing oligomers on a downhill free-energy landscape. However, the insertion of the final subunits is the rate-limiting, energetically unfavorable step in viral capsid assembly. A phase diagram has been constructed to show the regions where capsids or nonidealized structures are stable at each concentration and temperature. We anticipate that our findings will provide guidance in identifying suitable conditions required for in vitro viral capsid assembly experiments.

Simultaneous large band gaps and localization of electromagnetic and elastic waves in defect-free quasicrystals.

PubMed

Yu, Tianbao; Wang, Zhong; Liu, Wenxing; Wang, Tongbiao; Liu, Nianhua; Liao, Qinghua

2016-04-18

We report numerically large and complete photonic and phononic band gaps that simultaneously exist in eight-fold phoxonic quasicrystals (PhXQCs). PhXQCs can possess simultaneous photonic and phononic band gaps over a wide range of geometric parameters. Abundant localized modes can be achieved in defect-free PhXQCs for all photonic and phononic polarizations. These defect-free localized modes exhibit multiform spatial distributions and can confine simultaneously electromagnetic and elastic waves in a large area, thereby providing rich selectivity and enlarging the interaction space of optical and elastic waves. The simulated results based on finite element method show that quasiperiodic structures formed of both solid rods in air and holes in solid materials can simultaneously confine and tailor electromagnetic and elastic waves; these structures showed advantages over the periodic counterparts.

Time Crystal Platform: From Quasicrystal Structures in Time to Systems with Exotic Interactions.

PubMed

Giergiel, Krzysztof; Miroszewski, Artur; Sacha, Krzysztof

2018-04-06

Time crystals are quantum many-body systems that, due to interactions between particles, are able to spontaneously self-organize their motion in a periodic way in time by analogy with the formation of crystalline structures in space in condensed matter physics. In solid state physics properties of space crystals are often investigated with the help of external potentials that are spatially periodic and reflect various crystalline structures. A similar approach can be applied for time crystals, as periodically driven systems constitute counterparts of spatially periodic systems, but in the time domain. Here we show that condensed matter problems ranging from single particles in potentials of quasicrystal structure to many-body systems with exotic long-range interactions can be realized in the time domain with an appropriate periodic driving. Moreover, it is possible to create molecules where atoms are bound together due to destructive interference if the atomic scattering length is modulated in time.

Time Crystal Platform: From Quasicrystal Structures in Time to Systems with Exotic Interactions

NASA Astrophysics Data System (ADS)

Giergiel, Krzysztof; Miroszewski, Artur; Sacha, Krzysztof

2018-04-01

Time crystals are quantum many-body systems that, due to interactions between particles, are able to spontaneously self-organize their motion in a periodic way in time by analogy with the formation of crystalline structures in space in condensed matter physics. In solid state physics properties of space crystals are often investigated with the help of external potentials that are spatially periodic and reflect various crystalline structures. A similar approach can be applied for time crystals, as periodically driven systems constitute counterparts of spatially periodic systems, but in the time domain. Here we show that condensed matter problems ranging from single particles in potentials of quasicrystal structure to many-body systems with exotic long-range interactions can be realized in the time domain with an appropriate periodic driving. Moreover, it is possible to create molecules where atoms are bound together due to destructive interference if the atomic scattering length is modulated in time.

Exact solution of two collinear cracks normal to the boundaries of a 1D layered hexagonal piezoelectric quasicrystal

NASA Astrophysics Data System (ADS)

Zhou, Y.-B.; Li, X.-F.

2018-07-01

The electroelastic problem related to two collinear cracks of equal length and normal to the boundaries of a one-dimensional hexagonal piezoelectric quasicrystal layer is analysed. By using the finite Fourier transform, a mixed boundary value problem is solved when antiplane mechanical loading and inplane electric loading are applied. The problem is reduce to triple series equations, which are then transformed to a singular integral equation. For uniform remote loading, an exact solution is obtained in closed form, and explicit expressions for the electroelastic field are determined. The intensity factors of the electroelastic field and the energy release rate at the inner and outer crack tips are given and presented graphically.

Al-centered icosahedral ordering in Cu46Zr46Al8 bulk metallic glass

NASA Astrophysics Data System (ADS)

Fang, H. Z.; Hui, X.; Chen, G. L.; Liu, Z. K.

2009-03-01

Icosahedral short-range order, of which Al atoms are caged in the center of icosahedra with Cu and Zr atoms being the vertices, has been evidenced in the Cu46Zr46Al8 glassy structure by ab initio molecular dynamics simulation. These Al-centered clusters distribute irregularly in the three-dimensional space and form a "backbone" structure of the Cu46Zr46Al8 glass alloy. It is suggested that this kind of local structural feature is attributed to the requirement of efficient dense packing and the chemical affinity between Zr-Zr, Zr-Al, and Cu-Zr atoms. Our calculated results are found to be in good agreement with the experimental data.

Physical properties of i-R-Cd quasicrystals(R = Y, Gd-Tm)

NASA Astrophysics Data System (ADS)

Kong, Tai; Bud'Ko, Sergey L.; Jesche, Anton; Goldman, Alan I.; Kreyssig, Andreas; Dennis, Kevin W.; Ramazanoglu, Mehmet; Canfield, Paul C.; McArthur, John

2014-03-01

Detailed characterization of recently discovered i-R-Cd (R = Y, Gd-Tm) binary quasicrystals by means of room-temperature powder x-ray diffraction, dc and ac magnetization, resistivity and specific heat measurements will be presented. i-Y-Cd is weakly diamagnetic. The dc magnetization of i-R-Cd (R = Gd, Ho-Tm) shows typical spin-glass type splitting between field-cooled (FC) and zero-field-cooled (ZFC) data. i-Tb-Cd and i-Dy-Cd do not show a clear cusp in their ZFC dc magnetization. ac magnetization measured on i-Gd-Cd indicates a clear frequency-dependence and the third-order non-linear magnetization, χ3, is consistent with a spin-glass transition. The resistivity for i-R-Cd is of order 100 μΩ cm and weakly temperature-dependent. No feature that can be associated with long-range magnetic order was observed in any of the measurements. Characteristic freezing temperatures for i-R-Cd (R = Gd-Tm) deviate from ideal de Gennes scaling. This work is supported by the US DOE, Basic Energy Sciences under Contract No. DE-AC02-07CH11358.

Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology

PubMed Central

Legendre, Matthieu; Bartoli, Julia; Shmakova, Lyubov; Jeudy, Sandra; Labadie, Karine; Adrait, Annie; Lescot, Magali; Poirot, Olivier; Bertaux, Lionel; Bruley, Christophe; Couté, Yohann; Rivkina, Elizaveta; Abergel, Chantal; Claverie, Jean-Michel

2014-01-01

The largest known DNA viruses infect Acanthamoeba and belong to two markedly different families. The Megaviridae exhibit pseudo-icosahedral virions up to 0.7 μm in diameter and adenine–thymine (AT)-rich genomes of up to 1.25 Mb encoding a thousand proteins. Like their Mimivirus prototype discovered 10 y ago, they entirely replicate within cytoplasmic virion factories. In contrast, the recently discovered Pandoraviruses exhibit larger amphora-shaped virions 1 μm in length and guanine–cytosine-rich genomes up to 2.8 Mb long encoding up to 2,500 proteins. Their replication involves the host nucleus. Whereas the Megaviridae share some general features with the previously described icosahedral large DNA viruses, the Pandoraviruses appear unrelated to them. Here we report the discovery of a third type of giant virus combining an even larger pandoravirus-like particle 1.5 μm in length with a surprisingly smaller 600 kb AT-rich genome, a gene content more similar to Iridoviruses and Marseillevirus, and a fully cytoplasmic replication reminiscent of the Megaviridae. This suggests that pandoravirus-like particles may be associated with a variety of virus families more diverse than previously envisioned. This giant virus, named Pithovirus sibericum, was isolated from a >30,000-y-old radiocarbon-dated sample when we initiated a survey of the virome of Siberian permafrost. The revival of such an ancestral amoeba-infecting virus used as a safe indicator of the possible presence of pathogenic DNA viruses, suggests that the thawing of permafrost either from global warming or industrial exploitation of circumpolar regions might not be exempt from future threats to human or animal health. PMID:24591590

Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology.

PubMed

Legendre, Matthieu; Bartoli, Julia; Shmakova, Lyubov; Jeudy, Sandra; Labadie, Karine; Adrait, Annie; Lescot, Magali; Poirot, Olivier; Bertaux, Lionel; Bruley, Christophe; Couté, Yohann; Rivkina, Elizaveta; Abergel, Chantal; Claverie, Jean-Michel

2014-03-18

The largest known DNA viruses infect Acanthamoeba and belong to two markedly different families. The Megaviridae exhibit pseudo-icosahedral virions up to 0.7 μm in diameter and adenine-thymine (AT)-rich genomes of up to 1.25 Mb encoding a thousand proteins. Like their Mimivirus prototype discovered 10 y ago, they entirely replicate within cytoplasmic virion factories. In contrast, the recently discovered Pandoraviruses exhibit larger amphora-shaped virions 1 μm in length and guanine-cytosine-rich genomes up to 2.8 Mb long encoding up to 2,500 proteins. Their replication involves the host nucleus. Whereas the Megaviridae share some general features with the previously described icosahedral large DNA viruses, the Pandoraviruses appear unrelated to them. Here we report the discovery of a third type of giant virus combining an even larger pandoravirus-like particle 1.5 μm in length with a surprisingly smaller 600 kb AT-rich genome, a gene content more similar to Iridoviruses and Marseillevirus, and a fully cytoplasmic replication reminiscent of the Megaviridae. This suggests that pandoravirus-like particles may be associated with a variety of virus families more diverse than previously envisioned. This giant virus, named Pithovirus sibericum, was isolated from a >30,000-y-old radiocarbon-dated sample when we initiated a survey of the virome of Siberian permafrost. The revival of such an ancestral amoeba-infecting virus used as a safe indicator of the possible presence of pathogenic DNA viruses, suggests that the thawing of permafrost either from global warming or industrial exploitation of circumpolar regions might not be exempt from future threats to human or animal health.

Semiconducting icosahedral boron arsenide crystal growth for neutron detection

NASA Astrophysics Data System (ADS)

Whiteley, C. E.; Zhang, Y.; Gong, Y.; Bakalova, S.; Mayo, A.; Edgar, J. H.; Kuball, M.

2011-03-01

Semiconducting icosahedral boron arsenide, B12As2, is an excellent candidate for neutron detectors, thermoelectric converters, and radioisotope batteries, for which high quality single crystals are required. Thus, the present study was undertaken to grow B12As2 crystals by precipitation from metal solutions (nickel) saturated with elemental boron (or B12As2 powder) and arsenic in a sealed quartz ampoule. B12As2 crystals of 10-15 mm were produced when a homogeneous mixture of the three elements was held at 1150 °C for 48-72 h and slowly cooled (3.5 °C/h). The crystals varied in color and transparency from black and opaque to clear and transparent. X-ray topography (XRT), and elemental analysis by energy dispersive X-ray spectroscopy (EDS) confirmed that the crystals had the expected rhombohedral structure and chemical stoichiometry. The concentrations of residual impurities (nickel, carbon, etc.) were low, as measured by Raman spectroscopy and secondary ion mass spectrometry (SIMS). Additionally, low etch-pit densities (4.4×107 cm-2) were observed after etching in molten KOH at 500 °C. Thus, the flux growth method is viable for growing large, high-quality B12As2 crystals.

Cooperative Jahn-Teller phase transition of icosahedral molecular units

NASA Astrophysics Data System (ADS)

Nasrollahi, Seyed H.; Vvedensky, Dimitri D.

2017-02-01

Non-linear molecules undergo distortions when the orbital degeneracy of the highest occupied level is lifted by the Jahn-Teller effect. If such molecules or clusters of atoms are coupled to one another, the system may experience a cooperative Jahn-Teller effect (CJTE). In this paper, we describe a model of how the CJTE leads to the crystallization of the disordered phase. The model Hamiltonian is based on a normal mode decomposition of the clusters in order to maintain the symmetry labels. We take account of the electron-strain and the electron-phonon couplings and, by displacing the coordinates of the oscillators, obtain a term that explicitly couples the Jahn-Teller centers, enabling us to perform a mean-field analysis. The calculation of the free energy then becomes straightforward, and obtaining phase diagrams in various regimes follows from the minimization of this free energy. The results show that the character of the phase transition may change from strong to weak first order and even to second-order, depending on the coupling to the vibrational modes. Taken together, these results may serve as a paradigm for crystallization near the transition temperature, where the atoms tend to form clusters of icosahedral symmetry.

Present knowledge of electronic properties and charge transport of icosahedral boron-rich solids

NASA Astrophysics Data System (ADS)

Werheit, Helmut

2009-06-01

B12 icosahedra or related structure elements determine the different modifications of elementary boron and numerous boron-rich compounds from α-rhombohedral boron with 12 to YB66 type with about 1584 atoms per unit cell. Typical are well-defined high density intrinsic defects: Jahn-Teller distorted icosahedra, vacancies, incomplete occupancies, statistical occupancies and antisite defects. The correlation between intrinsic point defects and electron deficiencies solves the discrepancy between theoretically predicted metal and experimentally proved semiconducting character. The electron deficiencies generate split-off valence states, which are decisive for the electronic transport, a superposition of band-type and hopping-type conduction. Their share depends on actual conditions like temperature or pre-excitation. The theoretical model of bipolaron hopping is incompatible with numerous experiments. Technical application of the typically p-type icosahedral boron-rich solids requires suitable n-type counterparts; doping and other possibilities are discussed.

Impact-induced shock and the formation of natural quasicrystals in the early solar system

NASA Astrophysics Data System (ADS)

Hollister, Lincoln S.; Bindi, Luca; Yao, Nan; Poirier, Gerald R.; Andronicos, Christopher L.; MacPherson, Glenn J.; Lin, Chaney; Distler, Vadim V.; Eddy, Michael P.; Kostin, Alexander; Kryachko, Valery; Steinhardt, William M.; Yudovskaya, Marina; Eiler, John M.; Guan, Yunbin; Clarke, Jamil J.; Steinhardt, Paul J.

2014-06-01

The discovery of a natural quasicrystal, icosahedrite (Al63Cu24Fe13), accompanied by khatyrkite (CuAl2) and cupalite (CuAl) in the CV3 carbonaceous chondrite Khatyrka has posed a mystery as to what extraterrestrial processes led to the formation and preservation of these metal alloys. Here we present a range of evidence, including the discovery of high-pressure phases never observed before in a CV3 chondrite, indicating that an impact shock generated a heterogeneous distribution of pressures and temperatures in which some portions reached at least 5 GPa and 1,200 °C. The conditions were sufficient to melt Al-Cu-bearing minerals, which then rapidly solidified into icosahedrite and other Al-Cu metal phases. The meteorite also contains heretofore unobserved phases of iron-nickel and iron sulphide with substantial amounts of Al and Cu. The presence of these phases in Khatyrka provides further proof that the Al-Cu alloys are natural products of unusual processes that occurred in the early solar system.

Crystal electric field excitations in the quasicrystal approximant TbCd 6 studied by inelastic neutron scattering

DOE PAGES

Das, Pinaki; Lory, P. -F.; Flint, R.; ...

2017-02-07

Here, we have performed inelastic neutron scattering measurements on powder samples of the quasicrystal approximant, TbCd 6, grown using isotopically enriched 112Cd. Both quasielastic scattering and distinct inelastic excitations were observed below 3 meV. The intensity of the quasielastic scattering measured in the paramag- netic phase diverges as T N ~ 22 K is approached from above. The inelastic excitations, and their evolution with temperature, are well characterized by the leading term, Bmore » $$0\\atop{2}$$O$$0\\atop{2}$$, of the crystalline electric field (CEF) level scheme for local pentagonal symmetry for the rare-earth ions [1] indicating that the Tb moment is directed primarily along the unique local pseudo-five-fold axis of the Tsai-type clusters. We also find good agreement between the inverse susceptibility determined from magnetization measurements using a magnetically diluted Tb 0.05Y 0.95Cd 6 sample and that calculated using the CEF level scheme determined from the neutron measurements.« less

Crystal electric field excitations in the quasicrystal approximant TbCd6 studied by inelastic neutron scattering

NASA Astrophysics Data System (ADS)

Das, Pinaki; Lory, P.-F.; Flint, R.; Kong, T.; Hiroto, T.; Bud'ko, S. L.; Canfield, P. C.; de Boissieu, M.; Kreyssig, A.; Goldman, A. I.

2017-02-01

We have performed inelastic neutron scattering measurements on powder samples of the quasicrystal approximant, TbCd6, grown using isotopically enriched 112Cd. Both quasielastic scattering and distinct inelastic excitations were observed below 3 meV. The intensity of the quasielastic scattering measured in the paramagnetic phase diverges as TN˜22 K is approached from above. The inelastic excitations, and their evolution with temperature, are well characterized by the leading term, B20O20 , of the crystal electric field (CEF) level scheme for local pentagonal symmetry for the rare-earth ions [S. Jazbec et al., Phys. Rev. B 93, 054208 (2016), 10.1103/PhysRevB.93.054208] indicating that the Tb moment is directed primarily along the unique local pseudofivefold axis of the Tsai-type clusters. We also find good agreement between the inverse susceptibility determined from magnetization measurements using a magnetically diluted Tb0.05Y0.95Cd6 sample and that calculated using the CEF level scheme determined from the neutron measurements.

Proteomic Analysis of Sulfolobus solfataricus During Sulfolobus Turreted Icosahedral Virus Infection

PubMed Central

Maaty, Walid S.; Selvig, Kyla; Ryder, Stephanie; Tarlykov, Pavel; Hilmer, Jonathan K.; Heinemann, Joshua; Steffens, Joseph; Snyder, Jamie C.; Ortmann, Alice C.; Movahed, Navid; Spicka, Kevin; Chetia, Lakshindra; Grieco, Paul A.; Dratz, Edward A.; Douglas, Trevor; Young, Mark J.; Bothner, Brian

2012-01-01

Where there is life, there are viruses. The impact of viruses on evolution, global nutrient cycling, and disease has driven research on their cellular and molecular biology. Knowledge exists for a wide range of viruses, however, a major exception are viruses with archaeal hosts. Archaeal virus-host systems are of great interest because they have similarities to both eukaryotic and bacterial systems and often live in extreme environments. Here we report the first proteomics-based experiments on archaeal host response to viral infection. Sulfolobus Turreted Icosahedral Virus (STIV) infection of Sulfolobus solfataricus P2 was studied using 1D and 2D differential gel electrophoresis (DIGE) to measure abundance and redox changes. Cysteine reactivity was measured using novel fluorescent zwitterionic chemical probes that, together with abundance changes, suggest that virus and host are both vying for control of redox status in the cells. Proteins from nearly 50% of the predicted viral open reading frames were found along with a new STIV protein with a homolog in STIV2. This study provides insight to features of viral replication novel to the archaea, makes strong connections to well described mechanisms used by eukaryotic viruses such as ESCRT-III mediated transport, and emphasizes the complementary nature of different omics approaches. PMID:22217245

Development of a genetic system for the archaeal virus Sulfolobus turreted icosahedral virus (STIV).

PubMed

Wirth, Jennifer Fulton; Snyder, Jamie C; Hochstein, Rebecca A; Ortmann, Alice C; Willits, Deborah A; Douglas, Trevor; Young, Mark J

2011-06-20

Our understanding of archaeal viruses has been limited by the lack of genetic systems for examining viral function. We describe the construction of an infectious clone for the archaeal virus Sulfolobus turreted icosahedral virus (STIV). STIV was isolated from a high temperature (82°C) acidic (pH 2.2) hot spring in Yellowstone National Park and replicates in the archaeal model organism Sulfolobus solfataricus (Rice et al., 2004). While STIV is one of most studied archaeal viruses, little is known about its replication cycle. The development of an STIV infectious clone allows for directed gene disruptions and detailed genetic analysis of the virus. The utility of the STIV infectious clone was demonstrated by gene disruption of STIV open reading frame (ORF) B116 which resulted in crippled virus replication, while disruption of ORFs A197, C381 and B345 was lethal for virus replication. Copyright © 2011. Published by Elsevier Inc.

Sulfolobus turreted icosahedral virus c92 protein responsible for the formation of pyramid-like cellular lysis structures.

PubMed

Snyder, Jamie C; Brumfield, Susan K; Peng, Nan; She, Qunxin; Young, Mark J

2011-07-01

Host cells infected by Sulfolobus turreted icosahedral virus (STIV) have been shown to produce unusual pyramid-like structures on the cell surface. These structures represent a virus-induced lysis mechanism that is present in Archaea and appears to be distinct from the holin/endolysin system described for DNA bacteriophages. This study investigated the STIV gene products required for pyramid formation in its host Sulfolobus solfataricus. Overexpression of STIV open reading frame (ORF) c92 in S. solfataricus alone is sufficient to produce the pyramid-like lysis structures in cells. Gene disruption of c92 within STIV demonstrates that c92 is an essential protein for virus replication. Immunolocalization of c92 shows that the protein is localized to the cellular membranes forming the pyramid-like structures.

Wavelet data compression for archiving high-resolution icosahedral model data

NASA Astrophysics Data System (ADS)

Wang, N.; Bao, J.; Lee, J.

2011-12-01

With the increase of the resolution of global circulation models, it becomes ever more important to develop highly effective solutions to archive the huge datasets produced by those models. While lossless data compression guarantees the accuracy of the restored data, it can only achieve limited reduction of data size. Wavelet transform based data compression offers significant potentials in data size reduction, and it has been shown very effective in transmitting data for remote visualizations. However, for data archive purposes, a detailed study has to be conducted to evaluate its impact to the datasets that will be used in further numerical computations. In this study, we carried out two sets of experiments for both summer and winter seasons. An icosahedral grid weather model and a highly efficient wavelet data compression software were used for this study. Initial conditions were compressed and input to the model to run to 10 days. The forecast results were then compared to those forecast results from the model run with the original uncompressed initial conditions. Several visual comparisons, as well as the statistics of numerical comparisons are presented. These results indicate that with specified minimum accuracy losses, wavelet data compression achieves significant data size reduction, and at the same time, it maintains minimum numerical impacts to the datasets. In addition, some issues are discussed to increase the archive efficiency while retaining a complete set of meta data for each archived file.

Tailoring microstructure of Mg–Zn–Y alloys with quasicrystal and related phases for high mechanical strength

PubMed Central

Singh, Alok

2014-01-01

The occurrence of a stable icosahedral (i-) phase, which is quasicrystalline with an icosahedral (fivefold) symmetry, on the equilibrium phase diagram of Mg–Zn–RE (RE = Y, Gd, Tb, Dy, Ho or Er) alloys opened up an interesting possibility of developing a new series of magnesium alloys for structural applications. Alloys based on the i-phase have been studied for the past 14 years. Ultra-high strengths combined with good ductility have been shown. Here we show two strategies for tailoring microstructures for very high strengths in Mg–Zn–Y alloys. One of them involves strengthening by a fine distribution of rod-like precipitates, where the matrix grain size is not critical. The alloy is solutionized at a high temperature of 480 °C to dissolve a large part of the i-phase, followed by a high temperature extrusion (∼430 °C) and a low temperature ageing to reprecipitate phases with fine size distribution. At first, phase transformations involved in this procedure are described. The closeness of the structure of the precipitates to the i-phase is brought out. By this procedure, tensile yield strengths of over 370 MPa are obtained in grain sizes of 20 μm. In another strategy, the alloys are chill cast and then extruded at low temperatures of about 250 °C. Ultra-fine grains are produced by enhanced recrystallization due to presence of the i-phase. At the same time nano-sized precipitates are precipitated dynamically during extrusion from the supersaturated matrix. Ultra-high tensile strengths of up to 400 MPa are obtained in combination with ductility of 12 to 16%. Analysis of the microstructure shows that strengthening by the i-phase occurs by enhanced recrystallization during extrusion. It produces ultra-fine grain sizes to give very high strengths, and moderate texture for good ductility. Fine distribution of the i-phase and precipitates contribute to strengthening and provide microstructre stability. Ultra-high strength over a very wide range of grain sizes

Highly-nonlinear polarization-maintaining As2Se3-based photonic quasi-crystal fiber for supercontinuum generation

NASA Astrophysics Data System (ADS)

Zhao, Tongtong; Lian, Zhenggang; Benson, Trevor; Wang, Xin; Zhang, Wan; Lou, Shuqin

2017-11-01

We propose an As2Se3-based photonic quasi-crystal fiber (PQF) with high nonlinearity and birefringence. By optimizing the structure parameters, a nonlinear coefficient up to 2079 W-1km-1 can be achieved at the wavelength of 2 μm; the birefringence reaches up to the order of 10-2 due to the introduction of large circular air holes in the cladding. Using an optical pulse with a peak power of 6 kW, a pulse width of 150 fs, and a central wavelength of 2.94 μm as the pump pulse, a mid-infrared polarized supercontinuum is obtained by using a 15 mm long PQF. The spectral width for x- and y-polarizations covers 1 μm-10.2 μm and 1 μm-12.5 μm, respectively. The polarization state can be well maintained when the incident angle of the input pulse changes within ±2°. The proposed PQF, with high nonlinear coefficient and birefringence, has potential applications in mid-infrared polarization-maintaining supercontinuum generation.

Imaging and Quantitation of a Succession of Transient Intermediates Reveal the Reversible Self-Assembly Pathway of a Simple Icosahedral Virus Capsid.

PubMed

Medrano, María; Fuertes, Miguel Ángel; Valbuena, Alejandro; Carrillo, Pablo J P; Rodríguez-Huete, Alicia; Mateu, Mauricio G

2016-11-30

Understanding the fundamental principles underlying supramolecular self-assembly may facilitate many developments, from novel antivirals to self-organized nanodevices. Icosahedral virus particles constitute paradigms to study self-assembly using a combination of theory and experiment. Unfortunately, assembly pathways of the structurally simplest virus capsids, those more accessible to detailed theoretical studies, have been difficult to study experimentally. We have enabled the in vitro self-assembly under close to physiological conditions of one of the simplest virus particles known, the minute virus of mice (MVM) capsid, and experimentally analyzed its pathways of assembly and disassembly. A combination of electron microscopy and high-resolution atomic force microscopy was used to structurally characterize and quantify a succession of transient assembly and disassembly intermediates. The results provided an experiment-based model for the reversible self-assembly pathway of a most simple (T = 1) icosahedral protein shell. During assembly, trimeric capsid building blocks are sequentially added to the growing capsid, with pentamers of building blocks and incomplete capsids missing one building block as conspicuous intermediates. This study provided experimental verification of many features of self-assembly of a simple T = 1 capsid predicted by molecular dynamics simulations. It also demonstrated atomic force microscopy imaging and automated analysis, in combination with electron microscopy, as a powerful single-particle approach to characterize at high resolution and quantify transient intermediates during supramolecular self-assembly/disassembly reactions. Finally, the efficient in vitro self-assembly achieved for the oncotropic, cell nucleus-targeted MVM capsid may facilitate its development as a drug-encapsidating nanoparticle for anticancer targeted drug delivery.

Photonic band gap properties of one-dimensional Thue-Morse all-dielectric photonic quasicrystal

NASA Astrophysics Data System (ADS)

Yue, Chenxi; Tan, Wei; Liu, Jianjun

2018-05-01

In this paper, the photonic band gap (PBG) properties of one-dimensional (1D) Thue-Morse photonic quasicrystal (PQC) S4 structure are theoretically investigated by using transfer matrix method in Bragg condition. The effects of the center wavelength, relative permittivity and incident angle on PBG properties are elaborately analyzed. Numerical results reveal that, in the case of normal incidence, the symmetry and periodicity properties of the photonic band structure are presented. As the center wavelength increases, the PBG center frequency and PBG width decrease while the photonic band structure is always symmetrical about the central frequency and the photonic band structure repeats periodically in the expanding observation frequency range. With the decrease of relative permittivity contrast, the PBG width and the relative PBG width gradually decreases until PBG disappears while the symmetry of the photonic band structure always exists. In the case of oblique incidence, as the incident angle increases, multiple narrow PBGs gradually merge into a wide PBG for the TE mode while for the TM mode, the number of PBG continuously decreases and eventually disappears, i.e., multiple narrow PBGs become a wide passband for the TM mode. The research results will provide a reference for the choice of the material, the incident angle for the PBG properties and its applications of 1D Thue-Morse PQC.

Magnetic Resonance Characterization of Defects in Icosahedral and Cubic Boron Arsenide Bulk Crystals

NASA Astrophysics Data System (ADS)

Glaser, E. R.; Freitas, J. A., Jr.; Cress, C. D.; Perkins, F. K.; Prokes, S. M.; Ruppalt, L. B.; Culbertson, J. C.; Whiteley, C.; Edgar, J. H.; Tian, F.; Ren, Z.; Kim, J.; Shi, L.; Naval Research Lab Team; Kansas State U. Team; U. Houston Team; U. Texas Team

Low-temperature electron spin resonance (ESR) at 9.5 GHz and optically-detected magnetic resonance (ODMR) at 24 GHz were employed to investigate point defects in icosahedral and cubic Boron Arsenide bulk crystals. These semiconductors are of interest for use in high radiation and/or high temperature environments. ESR of the (001) B12As2 (Eg = 3.47 eV) mm-size platelets revealed two distinct features of unknown origin. The first signal is characterized by Zeeman splitting g-values of g|| = 2.017, g⊥ = 2.0183 while the second with g|| = 2.0182, g⊥ = 1.9997. Most notably, the second signal was also observed from ODMR on the broad 2.4 eV ``yellow/green'' photoluminescence band previously reported for these crystals and suggests its direct involvement in this likely defect-related radiative recombination process. Preliminary ESR obtained for the 100-300 micron-size cubic BAs crystals revealed a signal with g-value of 2.018 (very similar to that found for the B12As2 crystals) and broad FWHM value of 182 G. Possible origins of these defects will be discussed.

Nanothermodynamics of iron clusters: Small clusters, icosahedral and fcc-cuboctahedral structures

NASA Astrophysics Data System (ADS)

Angelié, C.; Soudan, J.-M.

2017-05-01

The study of the thermodynamics and structures of iron clusters has been carried on, focusing on small clusters and initial icosahedral and fcc-cuboctahedral structures. Two combined tools are used. First, energy intervals are explored by the Monte Carlo algorithm, called σ-mapping, detailed in the work of Soudan et al. [J. Chem. Phys. 135, 144109 (2011), Paper I]. In its flat histogram version, it provides the classical density of states, gp(Ep), in terms of the potential energy of the system. Second, the iron system is described by a potential which is called "corrected EAM" (cEAM), explained in the work of Basire et al. [J. Chem. Phys. 141, 104304 (2014), Paper II]. Small clusters from 3 to 12 atoms in their ground state have been compared first with published Density Functional Theory (DFT) calculations, giving a complete agreement of geometries. The series of 13, 55, 147, and 309 atom icosahedrons is shown to be the most stable form for the cEAM potential. However, the 147 atom cluster has a special behaviour, since decreasing the energy from the liquid zone leads to the irreversible trapping of the cluster in a reproducible amorphous state, 7.38 eV higher in energy than the icosahedron. This behaviour is not observed at the higher size of 309 atoms. The heat capacity of the 55, 147, and 309 atom clusters revealed a pronounced peak in the solid zone, related to a solid-solid transition, prior to the melting peak. The corresponding series of 13, 55, and 147 atom cuboctahedrons has been compared, underscoring the unstability towards the icosahedral structure. This unstability occurs clearly in several steps for the 147 atom cluster, with a sudden transformation at a transition state. This illustrates the concerted icosahedron-cuboctahedron transformation of Buckminster Fuller-Mackay, which is calculated for the cEAM potential. Two other clusters of initial fcc structures with 24 and 38 atoms have been studied, as well as a 302 atom cluster. Each one relaxes

Structure-based engineering of an icosahedral virus for nanomedicine and nanotechnology.

PubMed

Steinmetz, N F; Lin, T; Lomonossoff, G P; Johnson, J E

2009-01-01

A quintessential tenet of nanotechnology is the self-assembly of nanometer-sized components into devices. Biological macromolecular systems such as viral particles were found to be suitable building blocks for nanotechnology for several reasons: viral capsids are extremely robust and can be produced in large quantities with ease, the particles self-assemble into monodisperse particles with a high degree of symmetry and polyvalency, they have the propensity to form arrays, and they offer programmability through genetic and chemical engineering. Here, we review the recent advances in engineering the icosahedral plant virus Cowpea mosaic virus (CPMV) for applications in nano-medicine and -technology. In the first part, we will discuss how the combined knowledge of the structure of CPMV at atomic resolution and the use of chimeric virus technology led to the generation of CPMV particles with short antigenic peptides for potential use as vaccine candidates. The second part focuses on the chemical addressability of CPMV. Strategies to chemically attach functional molecules at designed positions on the exterior surface of the viral particle are described. Biochemical conjugation methods led to the fabrication of electronically conducting CPMV particles and networks. In addition, functional proteins for targeted delivery to mammalian cells were successfully attached to CPMV. In the third part, we focus on the utilization of CPMV as a building block for the generation of 2D and 3D arrays. Overall, the potential applications of viral nanobuilding blocks are manifold and range from nanoelectronics to biomedical applications.

Polarization filtering in the visible wavelength range using surface plasmon resonance and a sunflower-type photonic quasi-crystal fiber

NASA Astrophysics Data System (ADS)

Yan, Bei; Wang, Anran; Liu, Exian; Tan, Wei; Xie, Jianlan; Ge, Rui; Liu, Jianjun

2018-04-01

A novel polarization filter based on a sunflower-type photonic quasi-crystal fiber (PQF) is proposed in this paper. We also discuss different methods to tune the filter wavelength. The proposed filter can efficiently produce polarized light with visible wavelengths by using the resonance between the second-order surface plasmon polariton mode and the core mode of the PQF. The filtered wavelength can be tuned between 0.55 µm and 0.68 µm by adjusting the thickness of the gold film. When the thickness of the gold film is 25.3 nm, the resonance loss in the y-polarized direction reaches 11707 dB m‑1 for a wavelength of 0.6326 µm, and the full width at half maximum is only 5 nm. Due to the flexible design and absence of both polarization coupling and polarization dispersion, this polarization filter can be used in devices that require narrow-band filtering.

Dynamics of Transformation from Platinum Icosahedral Nanoparticles to Larger FCC Crystal at Millisecond Time Resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Wenpei; Wu, Jianbo; Yoon, Aram

Atomic motion at grain boundaries is essential to microstructure development, growth and stability of catalysts and other nanostructured materials. However, boundary atomic motion is often too fast to observe in a conventional transmission electron microscope (TEM) and too slow for ultrafast electron microscopy. We report on the entire transformation process of strained Pt icosahedral nanoparticles (ICNPs) into larger FCC crystals, captured at 2.5 ms time resolution using a fast electron camera. Results show slow diffusive dislocation motion at nm/s inside ICNPs and fast surface transformation at μm/s. By characterizing nanoparticle strain, we show that the fast transformation is driven bymore » inhomogeneous surface stress. And interaction with pre-existing defects led to the slowdown of the transformation front inside the nanoparticles. Particle coalescence, assisted by oxygen-induced surface migration at T ≥ 300°C, also played a critical role. Thus by studying transformation in the Pt ICNPs at high time and spatial resolution, we obtain critical insights into the transformation mechanisms in strained Pt nanoparticles.« less

Atomic structure solution of the complex quasicrystal approximant Al77Rh15Ru8 from electron diffraction data.

PubMed

Samuha, Shmuel; Mugnaioli, Enrico; Grushko, Benjamin; Kolb, Ute; Meshi, Louisa

2014-12-01

The crystal structure of the novel Al77Rh15Ru8 phase (which is an approximant of decagonal quasicrystals) was determined using modern direct methods (MDM) applied to automated electron diffraction tomography (ADT) data. The Al77Rh15Ru8 E-phase is orthorhombic [Pbma, a = 23.40 (5), b = 16.20 (4) and c = 20.00 (5) Å] and has one of the most complicated intermetallic structures solved solely by electron diffraction methods. Its structural model consists of 78 unique atomic positions in the unit cell (19 Rh/Ru and 59 Al). Precession electron diffraction (PED) patterns and high-resolution electron microscopy (HRTEM) images were used for the validation of the proposed atomic model. The structure of the E-phase is described using hierarchical packing of polyhedra and a single type of tiling in the form of a parallelogram. Based on this description, the structure of the E-phase is compared with that of the ε6-phase formed in Al-Rh-Ru at close compositions.

Na8Au9.8(4)Ga7.2 and Na17Au5.87(2)Ga46.63: The diversity of pseudo 5-fold symmetries in the Na-Au-Ga system

NASA Astrophysics Data System (ADS)

Smetana, Volodymyr; Corbett, John D.; Miller, Gordon J.

2013-11-01

The Na-rich part (~30% Na) of the Na-Au-Ga system between NaAu2, NaGa4, and Na22Ga39 has been found to contain the ternary phases Na8Au9.8(4)Ga7.2 (I) and Na17Au5.87(2)Ga46.63 (II), according to the results of single crystal X-ray diffraction measurements. I is orthorhombic, Cmcm, a=5.3040(1), b=24.519(5), c=14.573(3) Å, and contains a network of clusters with local 5-fold symmetry along the a-axis. Such clusters are frequent building units in decagonal quasicrystals and their approximants. II is rhombohedral, R3¯m, a=16.325(2), c=35.242(7) Å, and contains building blocks that are structurally identical to the Bergman-type clusters as well as fused icosahedral units known with active metals, triels and late transition elements. II also contains a polycationic network with elements of the clathrate V type structure. Tight-binding electronic structure calculations using linear muffin-tin-orbital (LMTO) methods on idealized models of I and II indicate that both compounds are metallic with evident pseudogaps at the corresponding Fermi levels. The overall Hamilton bond populations are generally dominated by Au-Ga and Au-Au bonds in I and by Ga-Ga bonds in II; moreover, the Na-Au and Na-Ga contributions in I are unexpectedly large, ~20% of the total. A similar involvement of sodium in covalent bonding has also been found in the electron-richer i-Na13Au12Ga15 quasicrystal approximant.

Atomistic modeling of the low-frequency mechanical modes and Raman spectra of icosahedral virus capsids

NASA Astrophysics Data System (ADS)

Dykeman, Eric C.; Sankey, Otto F.

2010-02-01

We describe a technique for calculating the low-frequency mechanical modes and frequencies of a large symmetric biological molecule where the eigenvectors of the Hessian matrix are determined with full atomic detail. The method, which follows order N methods used in electronic structure theory, determines the subset of lowest-frequency modes while using group theory to reduce the complexity of the problem. We apply the method to three icosahedral viruses of various T numbers and sizes; the human viruses polio and hepatitis B, and the cowpea chlorotic mottle virus, a plant virus. From the normal-mode eigenvectors, we use a bond polarizability model to predict a low-frequency Raman scattering profile for the viruses. The full atomic detail in the displacement patterns combined with an empirical potential-energy model allows a comparison of the fully atomic normal modes with elastic network models and normal-mode analysis with only dihedral degrees of freedom. We find that coarse-graining normal-mode analysis (particularly the elastic network model) can predict the displacement patterns for the first few (˜10) low-frequency modes that are global and cooperative.

Deformation Behavior and Structure of i-Al-Cu-Fe Quasicrystalline Alloy in Vicinity of Nanoindenter Indentation

NASA Astrophysics Data System (ADS)

Shalaeva, E. V.; Selyanin, I. O.; Smirnova, E. O.; Smirnov, S. V.; Novachek, D. D.

2018-02-01

The nanoindentation tests have been carried out for the quasicrystalline polygrain Al62.4Cu25.3Fe12.3 alloy with the icosahedral structure i; the load P-displacement h diagrams have been used to estimate the contributions of plastic deformation (monotonic and intermittent), and the structures of the transverse microscopic sections have been studied in the vicinity of indentations by electron microscopy. It is shown that several systems of deformation bands are formed in the elasto-plastic zone in the vicinity of the indentations along the close-packed planes of the i lattice with the five-fold and two-fold symmetry axes; the bands often begin from cracks and manifest the signs of the dislocation structure. The traces of the phase transformation with the formation of the β-phase areas are observed only in a thin layer under an indenter. The effects of intermittent deformation are up to 50% of the total inelastic deformation and are related to the plastic behavior of the quasicrystal-activation and passage of deformation bands and also the formation of undersurface micro- and nanosized cracks.

Tropical cyclones over the North Indian Ocean: experiments with the high-resolution global icosahedral grid point model GME

NASA Astrophysics Data System (ADS)

Kumkar, Yogesh V.; Sen, P. N.; Chaudhari, Hemankumar S.; Oh, Jai-Ho

2018-02-01

In this paper, an attempt has been made to conduct a numerical experiment with the high-resolution global model GME to predict the tropical storms in the North Indian Ocean during the year 2007. Numerical integrations using the icosahedral hexagonal grid point global model GME were performed to study the evolution of tropical cyclones, viz., Akash, Gonu, Yemyin and Sidr over North Indian Ocean during 2007. It has been seen that the GME model forecast underestimates cyclone's intensity, but the model can capture the evolution of cyclone's intensity especially its weakening during landfall, which is primarily due to the cutoff of the water vapor supply in the boundary layer as cyclones approach the coastal region. A series of numerical simulation of tropical cyclones have been performed with GME to examine model capability in prediction of intensity and track of the cyclones. The model performance is evaluated by calculating the root mean square errors as cyclone track errors.

Molecular Structure of a 9-MDa Icosahedral Pyruvate Dehydrogenase Subcomplex Containing the E2 and E3 Enzymes Using Cryoelectron Microscopy*

PubMed Central

Milne, Jacqueline L. S.; Wu, Xiongwu; Borgnia, Mario J.; Lengyel, Jeffrey S.; Brooks, Bernard R.; Shi, Dan; Perham, Richard N.; Subramaniam, Sriram

2006-01-01

The pyruvate dehydrogenase multienzyme complexes are among the largest multifunctional catalytic machines in cells, catalyzing the production of acetyl CoA from pyruvate. We have previously reported the molecular architecture of an 11-MDa subcomplex comprising the 60-mer icosahedral dihydrolipoyl acetyltransferase (E2) decorated with 60 copies of the heterotetrameric (α2β2) 153-kDa pyruvate decarboxylase (E1) from Bacillus stearothermophilus (Milne, J. L. S., Shi, D., Rosenthal, P. B., Sunshine, J. S., Domingo, G. J., Wu, X., Brooks, B. R., Perham, R. N., Henderson, R., and Subramaniam, S. (2002) EMBO J. 21, 5587–5598). An annular gap of ~90 Å separates the acetyltransferase catalytic domains of the E2 from an outer shell formed of E1 tetramers. Using cryoelectron microscopy, we present here a three-dimensional reconstruction of the E2 core decorated with 60 copies of the homodimeric 100-kDa dihydrolipoyl dehydrogenase (E3). The E2E3 complex has a similar annular gap of ~75 Å between the inner icosahedral assembly of acetyltransferase domains and the outer shell of E3 homodimers. Automated fitting of the E3 coordinates into the map suggests excellent correspondence between the density of the outer shell map and the positions of the two best fitting orientations of E3. As in the case of E1 in the E1E2 complex, the central 2-fold axis of the E3 homodimer is roughly oriented along the periphery of the shell, making the active sites of the enzyme accessible from the annular gap between the E2 core and the outer shell. The similarities in architecture of the E1E2 and E2E3 complexes indicate fundamental similarities in the mechanism of active site coupling involved in the two key stages requiring motion of the swinging lipoyl domain across the annular gap, namely the synthesis of acetyl CoA and regeneration of the dithiolane ring of the lipoyl domain. PMID:16308322

The icosahedral RNA virus as a grotto: organizing the genome into stalagmites and stalactites.

PubMed

Harvey, Stephen C; Zeng, Yingying; Heitsch, Christine E

2013-03-01

There are two important problems in the assembly of small, icosahedral RNA viruses. First, how does the capsid protein select the viral RNA for packaging, when there are so many other candidate RNA molecules available? Second, what is the mechanism of assembly? With regard to the first question, there are a number of cases where a particular RNA sequence or structure--often one or more stem-loops--either promotes assembly or is required for assembly, but there are others where specific packaging signals are apparently not required. With regard to the assembly pathway, in those cases where stem-loops are involved, the first step is generally believed to be binding of the capsid proteins to these "fingers" of the RNA secondary structure. In the mature virus, the core of the RNA would then occupy the center of the viral particle, and the stem-loops would reach outward, towards the capsid, like stalagmites reaching up from the floor of a grotto towards the ceiling. Those viruses whose assembly does not depend on protein binding to stem-loops could have a different structure, with the core of the RNA lying just under the capsid, and the fingers reaching down into the interior of the virus, like stalactites. We review the literature on these alternative structures, focusing on RNA selectivity and the assembly mechanism, and we propose experiments aimed at determining, in a given virus, which of the two structures actually occurs.

Sigma-phase packing of icosahedral clusters in 780-atom tetragonal crystals of Cr5Ni3Si2 and V15Ni10Si that by twinning achieve 8-fold rotational point-group symmetry

PubMed Central

Pauling, Linus

1988-01-01

A 780-atom primitive tetragonal unit with edges 27.3, 27.3, and 12.6 Å is assigned to rapidly solidified Cu5Ni3Si2 and V15Ni10Si by analysis of electron diffraction photographs with the assumption that the crystals contain icosahedral clusters. There are thirty 26-atom clusters at the sigma-phase positions. Apparent 8-fold symmetry results from 45° twinning on the basal plane. PMID:16593915

Sigma-phase packing of icosahedral clusters in 780-atom tetragonal crystals of Cr(5)Ni(3)Si(2) and V(15)Ni(10)Si that by twinning achieve 8-fold rotational point-group symmetry.

PubMed

Pauling, L

1988-04-01

A 780-atom primitive tetragonal unit with edges 27.3, 27.3, and 12.6 A is assigned to rapidly solidified Cu(5)Ni(3)Si(2) and V(15)Ni(10)Si by analysis of electron diffraction photographs with the assumption that the crystals contain icosahedral clusters. There are thirty 26-atom clusters at the sigma-phase positions. Apparent 8-fold symmetry results from 45 degrees twinning on the basal plane.

Probing of the pseudogap via thermoelectric properties in the Au-Al-Gd quasicrystal approximant

NASA Astrophysics Data System (ADS)

Ishikawa, Asuka; Takagiwa, Yoshiki; Kimura, Kaoru; Tamura, Ryuji

2017-03-01

The pseudogap of the recently discovered Au-Al-Gd quasicrystal approximant crystal (AC) is investigated over a wide electron-per-atom (e /a ) ratio of ˜0.5 using thermoelectric properties as an experimental probe. This Au-Al-Gd AC provides an ideal platform for fine probing of the pseudogap among a number of known ACs because the Au-Al-Gd AC possesses an extraordinarily wide single-phase region with respect to the variation in the electron concentration [A. Ishikawa, T. Hiroto, K. Tokiwa, T. Fujii, and R. Tamura, Phys. Rev. B 93, 024416 (2016), 10.1103/PhysRevB.93.024416], in striking contrast to, for instance, binary stoichiometric C d6R ACs. As a result, a salient peak structure is observed in the Seebeck coefficient, S , with the composition as well as that of the power factor S2σ , in addition to a gradual variation in the conductivity, σ , and S . These two features are directly associated with rapid and slow variations, respectively, of spectral conductivity σ (E ) , and hence the fine structure inside the pseudogap, in the vicinity of the Fermi level EF. Based on the observed continuous variation of the Fermi wave vector reported in the previous experimental work, fine tuning of EF toward an optimal position was attempted, which led to the successful observation of a sharp peak in S2σ with a value of ˜270 μ W /m .K2 at 873 K. This is the highest value ever reported among both Tsai-type and Bergman-type compounds. The dimensionless figure of merit was determined as 0.026 at 873 K, which is also the highest reported among both Tsai-type and Bergman-type compounds.

Use of frit-disc crucibles for routine and exploratory solution growth of single crystalline samples

DOE PAGES

Canfield, Paul C.; Kong, Tai; Kaluarachchi, Udhara S.; ...

2016-01-05

Solution growth of single crystals from high temperature solutions often involves the separation of residual solution from the grown crystals. For many growths of intermetallic compounds, this separation has historically been achieved with the use of plugs of silica wool. Whereas this is generally efficient in a mechanical sense, it leads to a significant contamination of the decanted liquid with silica fibres. In this paper, we present a simple design for frit-disc alumina crucible sets that has made their use in the growth single crystals from high temperature solutions both simple and affordable. An alumina frit-disc allows for the cleanmore » separation of the residual liquid from the solid phase. This allows for the reuse of the decanted liquid, either for further growth of the same phase, or for subsequent growth of other, related phases. In this article, we provide examples of the growth of isotopically substituted TbCd 6 and icosahedral i-RCd quasicrystals, as well as the separation of (i) the closely related Bi 2Rh 3S 2 and Bi 2Rh 3.5S 2 phases and (ii) and PrZn 11 and PrZn 17.« less

Improvement of aerosol optical properties modeling over Eastern Asia with MODIS AOD assimilation in a global non-hydrostatic icosahedral aerosol transport model.

PubMed

Dai, Tie; Schutgens, Nick A J; Goto, Daisuke; Shi, Guangyu; Nakajima, Teruyuki

2014-12-01

A new global aerosol assimilation system adopting a more complex icosahedral grid configuration is developed. Sensitivity tests for the assimilation system are performed utilizing satellite retrieved aerosol optical depth (AOD) from the Moderate Resolution Imaging Spectroradiometer (MODIS), and the results over Eastern Asia are analyzed. The assimilated results are validated through independent Aerosol Robotic Network (AERONET) observations. Our results reveal that the ensemble and local patch sizes have little effect on the assimilation performance, whereas the ensemble perturbation method has the largest effect. Assimilation leads to significantly positive effect on the simulated AOD field, improving agreement with all of the 12 AERONET sites over the Eastern Asia based on both the correlation coefficient and the root mean square difference (assimilation efficiency). Meanwhile, better agreement of the Ångström Exponent (AE) field is achieved for 8 of the 12 sites due to the assimilation of AOD only. Copyright © 2014 Elsevier Ltd. All rights reserved.

Enhancement of light output power of GaN-based light-emitting diodes with photonic quasi-crystal patterned on p-GaN surface and n-side sidewall roughing.

PubMed

Lai, Fang-I; Yang, Jui-Fu

2013-05-17

In this paper, GaN-based light-emitting diodes (LEDs) with photonic quasi-crystal (PQC) structure on p-GaN surface and n-side roughing by nano-imprint lithography are fabricated and investigated. At an injection current of 20 mA, the LED with PQC structure on p-GaN surface and n-side roughing increased the light output power of the InGaN/GaN multiple quantum well LEDs by a factor of 1.42, and the wall-plug efficiency is 26% higher than the conventional GaN-based LED type. After 500-h life test (55°C/50 mA), it was found that the normalized output power of GaN-based LED with PQC structure on p-GaN surface and n-side roughing only decreased by 6%. These results offer promising potential to enhance the light output powers of commercial light-emitting devices using the technique of nano-imprint lithography.

Enhancement of light output power of GaN-based light-emitting diodes with photonic quasi-crystal patterned on p-GaN surface and n-side sidewall roughing

PubMed Central

2013-01-01

In this paper, GaN-based light-emitting diodes (LEDs) with photonic quasi-crystal (PQC) structure on p-GaN surface and n-side roughing by nano-imprint lithography are fabricated and investigated. At an injection current of 20 mA, the LED with PQC structure on p-GaN surface and n-side roughing increased the light output power of the InGaN/GaN multiple quantum well LEDs by a factor of 1.42, and the wall-plug efficiency is 26% higher than the conventional GaN-based LED type. After 500-h life test (55°C/50 mA), it was found that the normalized output power of GaN-based LED with PQC structure on p-GaN surface and n-side roughing only decreased by 6%. These results offer promising potential to enhance the light output powers of commercial light-emitting devices using the technique of nano-imprint lithography. PMID:23683526

Highly specific salt bridges govern bacteriophage P22 icosahedral capsid assembly: identification of the site in coat protein responsible for interaction with scaffolding protein.

PubMed

Cortines, Juliana R; Motwani, Tina; Vyas, Aashay A; Teschke, Carolyn M

2014-05-01

Icosahedral virus assembly requires a series of concerted and highly specific protein-protein interactions to produce a proper capsid. In bacteriophage P22, only coat protein (gp5) and scaffolding protein (gp8) are needed to assemble a procapsid-like particle, both in vivo and in vitro. In scaffolding protein's coat binding domain, residue R293 is required for procapsid assembly, while residue K296 is important but not essential. Here, we investigate the interaction of scaffolding protein with acidic residues in the N-arm of coat protein, since this interaction has been shown to be electrostatic. Through site-directed mutagenesis of genes 5 and 8, we show that changing coat protein N-arm residue 14 from aspartic acid to alanine causes a lethal phenotype. Coat protein residue D14 is shown by cross-linking to interact with scaffolding protein residue R293 and, thus, is intimately involved in proper procapsid assembly. To a lesser extent, coat protein N-arm residue E18 is also implicated in the interaction with scaffolding protein and is involved in capsid size determination, since a cysteine mutation at this site generated petite capsids. The final acidic residue in the N-arm that was tested, E15, is shown to only weakly interact with scaffolding protein's coat binding domain. This work supports growing evidence that surface charge density may be the driving force of virus capsid protein interactions. Bacteriophage P22 infects Salmonella enterica serovar Typhimurium and is a model for icosahedral viral capsid assembly. In this system, coat protein interacts with an internal scaffolding protein, triggering the assembly of an intermediate called a procapsid. Previously, we determined that there is a single amino acid in scaffolding protein required for P22 procapsid assembly, although others modulate affinity. Here, we identify partners in coat protein. We show experimentally that relatively weak interactions between coat and scaffolding proteins are capable of driving

Studies of Nucleation and Growth, Specific Heat and Viscosity of Undercooled Melts of Quasicrystal and Polytetrahedral-Phase Forming Alloys

NASA Technical Reports Server (NTRS)

Kelton, K. F.; Gangopadhyay, Anup K.; Lee, G. W.; Hyers, Robert W.; Rathz, T. J.; Robinson, Michael B.; Rogers, Jan R.

2003-01-01

From extensive ground based work on the phase diagram and undercooling studies of Ti-Zr-Ni alloys, have clearly identified the composition of three different phases with progressively increasing polytetrahedral order such as, (Ti/Zr), the C14 Laves phase, and the i-phase, that nucleate directly from the undercooled liquid. The reduced undercooling decreases progressively with increasing polytetrahedral order in the solid, supporting Frank s hypothesis. A new facility for direct measurements of the structures and phase transitions in undercooled liquids (BESL) was developed and has provided direct proof of the primary nucleation of a metastable icosahedral phase in some Ti-Zr-Ni alloys. The first measurements of specific heat and viscosity in the undercooled liquid of this alloy system have been completed. Other than the importance of thermo-physical properties for modeling nucleation and growth processes in these materials, these studies have also revealed some interesting new results (such as a maximum of C(sup q, sub p) in the undercooled state). These ground-based results have clearly established the necessary background and the need for conducting benchmark nucleation experiments at the ISS on this alloy system.

Assembly/disassembly of a complex icosahedral virus to incorporate heterologous nucleic acids

NASA Astrophysics Data System (ADS)

Pascual, Elena; Mata, Carlos P.; Carrascosa, José L.; Castón, José R.

2017-12-01

Hollow protein containers are widespread in nature, and include virus capsids as well as eukaryotic and bacterial complexes. Protein cages are studied extensively for applications in nanotechnology, nanomedicine and materials science. Their inner and outer surfaces can be modified chemically or genetically, and the internal cavity can be used to template, store and/or arrange molecular cargos. Virus capsids and virus-like particles (VLP, noninfectious particles) provide versatile platforms for nanoscale bioengineering. Study of capsid protein self-assembly into monodispersed particles, and of VLP structure and biophysics is necessary not only to understand natural processes, but also to infer how these platforms can be redesigned to furnish novel functional VLP. Here we address the assembly dynamics of infectious bursal disease virus (IBDV), a complex icosahedral virus. IBDV has a ~70 nm-diameter T  =  13 capsid with VP2 trimers as the only structural subunits. During capsid assembly, VP2 is synthesized as a precursor (pVP2) whose C terminus is cleaved. The pVP2 C terminus has an amphipathic helix that controls VP2 polymorphism. In the absence of the VP3 scaffolding protein, necessary for control of assembly, 466/456-residue pVP2 intermediates bearing this helix assemble into VLP only when expressed with an N-terminal His6 tag (the HT-VP2-466 protein). HT-VP2-466 capsids are optimal for genetic insertion of proteins (cargo space ~78 000 nm3). We established an in vitro assembly/disassembly system of HT-VP2-466-based VLP for heterologous nucleic acid packaging and/or encapsulation of drugs and other molecules. HT-VP2-466 (empty) capsids were disassembled and reassembled by dialysis against low-salt/basic pH and high-salt/acid pH buffers, respectively, thus illustrating the reversibility in vitro of IBDV capsid assembly. HT-VP2-466 VLP also packed heterologous DNA by non-specific confinement during assembly. These and previous results establish the bases

A mimetic, semi-implicit, forward-in-time, finite volume shallow water model: comparison of hexagonal-icosahedral and cubed sphere grids

NASA Astrophysics Data System (ADS)

Thuburn, J.; Cotter, C. J.; Dubos, T.

2013-12-01

A new algorithm is presented for the solution of the shallow water equations on quasi-uniform spherical grids. It combines a mimetic finite volume spatial discretization with a Crank-Nicolson time discretization of fast waves and an accurate and conservative forward-in-time advection scheme for mass and potential vorticity (PV). The algorithm is implemented and tested on two families of grids: hexagonal-icosahedral Voronoi grids, and modified equiangular cubed-sphere grids. Results of a variety of tests are presented, including convergence of the discrete scalar Laplacian and Coriolis operators, advection, solid body rotation, flow over an isolated mountain, and a barotropically unstable jet. The results confirm a number of desirable properties for which the scheme was designed: exact mass conservation, very good available energy and potential enstrophy conservation, consistent mass, PV and tracer transport, and good preservation of balance including vanishing ∇ × ∇, steady geostrophic modes, and accurate PV advection. The scheme is stable for large wave Courant numbers and advective Courant numbers up to about 1. In the most idealized tests the overall accuracy of the scheme appears to be limited by the accuracy of the Coriolis and other mimetic spatial operators, particularly on the cubed sphere grid. On the hexagonal grid there is no evidence for damaging effects of computational Rossby modes, despite attempts to force them explicitly.

A mimetic, semi-implicit, forward-in-time, finite volume shallow water model: comparison of hexagonal-icosahedral and cubed-sphere grids

NASA Astrophysics Data System (ADS)

Thuburn, J.; Cotter, C. J.; Dubos, T.

2014-05-01

A new algorithm is presented for the solution of the shallow water equations on quasi-uniform spherical grids. It combines a mimetic finite volume spatial discretization with a Crank-Nicolson time discretization of fast waves and an accurate and conservative forward-in-time advection scheme for mass and potential vorticity (PV). The algorithm is implemented and tested on two families of grids: hexagonal-icosahedral Voronoi grids, and modified equiangular cubed-sphere grids. Results of a variety of tests are presented, including convergence of the discrete scalar Laplacian and Coriolis operators, advection, solid body rotation, flow over an isolated mountain, and a barotropically unstable jet. The results confirm a number of desirable properties for which the scheme was designed: exact mass conservation, very good available energy and potential enstrophy conservation, consistent mass, PV and tracer transport, and good preservation of balance including vanishing ∇ × ∇, steady geostrophic modes, and accurate PV advection. The scheme is stable for large wave Courant numbers and advective Courant numbers up to about 1. In the most idealized tests the overall accuracy of the scheme appears to be limited by the accuracy of the Coriolis and other mimetic spatial operators, particularly on the cubed-sphere grid. On the hexagonal grid there is no evidence for damaging effects of computational Rossby modes, despite attempts to force them explicitly.

Extending High-Order Flux Operators on Spherical Icosahedral Grids and Their Applications in the Framework of a Shallow Water Model

NASA Astrophysics Data System (ADS)

Zhang, Yi

2018-01-01

This study extends a set of unstructured third/fourth-order flux operators on spherical icosahedral grids from two perspectives. First, the fifth-order and sixth-order flux operators of this kind are further extended, and the nominally second-order to sixth-order operators are then compared based on the solid body rotation and deformational flow tests. Results show that increasing the nominal order generally leads to smaller absolute errors. Overall, the standard fifth-order scheme generates the smallest errors in limited and unlimited tests, although it does not enhance the convergence rate. Even-order operators show higher limiter sensitivity than the odd-order operators. Second, a triangular version of these high-order operators is repurposed for transporting the potential vorticity in a space-time-split shallow water framework. Results show that a class of nominally third-order upwind-biased operators generates better results than second-order and fourth-order counterparts. The increase of the potential enstrophy over time is suppressed owing to the damping effect. The grid-scale noise in the vorticity is largely alleviated, and the total energy remains conserved. Moreover, models using high-order operators show smaller numerical errors in the vorticity field because of a more accurate representation of the nonlinear Coriolis term. This improvement is especially evident in the Rossby-Haurwitz wave test, in which the fluid is highly rotating. Overall, high-order flux operators with higher damping coefficients, which essentially behave like the Anticipated Potential Vorticity Method, present better results.

Understanding the interface of six-shell cuboctahedral and icosahedral palladium clusters on reduced graphene oxide: experimental and theoretical study.

PubMed

Gracia-Espino, Eduardo; Hu, Guangzhi; Shchukarev, Andrey; Wågberg, Thomas

2014-05-07

Studies on noble-metal-decorated carbon nanostructures are reported almost on a daily basis, but detailed studies on the nanoscale interactions for well-defined systems are very rare. Here we report a study of reduced graphene oxide (rGOx) homogeneously decorated with palladium (Pd) nanoclusters with well-defined shape and size (2.3 ± 0.3 nm). The rGOx was modified with benzyl mercaptan (BnSH) to improve the interaction with Pd clusters, and N,N-dimethylformamide was used as solvent and capping agent during the decoration process. The resulting Pd nanoparticles anchored to the rGOx-surface exhibit high crystallinity and are fully consistent with six-shell cuboctahedral and icosahedral clusters containing ~600 Pd atoms, where 45% of these are located at the surface. According to X-ray photoelectron spectroscopy analysis, the Pd clusters exhibit an oxidized surface forming a PdO(x) shell. Given the well-defined experimental system, as verified by electron microscopy data and theoretical simulations, we performed ab initio simulations using 10 functionalized graphenes (with vacancies or pyridine, amine, hydroxyl, carboxyl, or epoxy groups) to understand the adsorption process of BnSH, their further role in the Pd cluster formation, and the electronic properties of the graphene-nanoparticle hybrid system. Both the experimental and theoretical results suggest that Pd clusters interact with functionalized graphene by a sulfur bridge while the remaining Pd surface is oxidized. Our study is of significant importance for all work related to anchoring of nanoparticles on nanocarbon-based supports, which are used in a variety of applications.

q-Derivatives, quantization methods and q-algebras

DOE Office of Scientific and Technical Information (OSTI.GOV)

Twarock, Reidun

1998-12-15

Using the example of Borel quantization on S{sup 1}, we discuss the relation between quantization methods and q-algebras. In particular, it is shown that a q-deformation of the Witt algebra with generators labeled by Z is realized by q-difference operators. This leads to a discrete quantum mechanics. Because of Z, the discretization is equidistant. As an approach to a non-equidistant discretization of quantum mechanics one can change the Witt algebra using not the number field Z as labels but a quadratic extension of Z characterized by an irrational number {tau}. This extension is denoted as quasi-crystal Lie algebra, because thismore » is a relation to one-dimensional quasicrystals. The q-deformation of this quasicrystal Lie algebra is discussed. It is pointed out that quasicrystal Lie algebras can be considered also as a 'deformed' Witt algebra with a 'deformation' of the labeling number field. Their application to the theory is discussed.« less

Formation pathways of mesoporous silica nanoparticles with dodecagonal tiling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Yao; Ma, Kai; Kao, Teresa

Considerable progress in the fabrication of quasicrystals demonstrates that they can be realized in a broad range of materials. However, the development of chemistries enabling direct experimental observation of early quasicrystal growth pathways remains challenging. Here, we report the synthesis of four surfactant-directed mesoporous silica nanoparticle structures, including dodecagonal quasicrystalline nanoparticles, as a function of micelle pore expander concentration or stirring rate. We demonstrate that the early formation stages of dodecagonal quasicrystalline mesoporous silica nanoparticles can be preserved, where precise control of mesoporous silica nanoparticle size down to <30 nm facilitates comparison between mesoporous silica nanoparticles and simulated single-particle growthmore » trajectories beginning with a single tiling unit. Our results reveal details of the building block size distributions during early growth and how they promote quasicrystal formation. This work identifies simple synthetic parameters, such as stirring rate, that may be exploited to design other quasicrystal-forming self-assembly chemistries and processes.« less

Formation pathways of mesoporous silica nanoparticles with dodecagonal tiling

DOE PAGES

Sun, Yao; Ma, Kai; Kao, Teresa; ...

2017-08-15

Considerable progress in the fabrication of quasicrystals demonstrates that they can be realized in a broad range of materials. However, the development of chemistries enabling direct experimental observation of early quasicrystal growth pathways remains challenging. Here, we report the synthesis of four surfactant-directed mesoporous silica nanoparticle structures, including dodecagonal quasicrystalline nanoparticles, as a function of micelle pore expander concentration or stirring rate. We demonstrate that the early formation stages of dodecagonal quasicrystalline mesoporous silica nanoparticles can be preserved, where precise control of mesoporous silica nanoparticle size down to <30 nm facilitates comparison between mesoporous silica nanoparticles and simulated single-particle growthmore » trajectories beginning with a single tiling unit. Our results reveal details of the building block size distributions during early growth and how they promote quasicrystal formation. This work identifies simple synthetic parameters, such as stirring rate, that may be exploited to design other quasicrystal-forming self-assembly chemistries and processes.« less

Thermodynamic consideration and ground-state search of icosahedral boron subselenide B12(B1-xSex) 2 from a first-principles cluster expansion

NASA Astrophysics Data System (ADS)

Ektarawong, A.

2018-05-01

The phase stability of icosahedral boron subselenide B12(B1-xSex) 2 , where 0.5 ≤x ≤1 , is explored using a first-principles cluster expansion. The results shows that, instead of a continuous solid solution, B12(B1-xSex) 2 is thermodynamically stable as an individual line compound at the composition of B9.5Se . The ground-state configuration of B9.5Se is represented by a mixture of B12(Se-Se), B12(B-Se), and B12(Se-B) with a ratio of 1:1:1, where they form a periodic A B C A B C ⋯ stacking sequence of B12(Se-Se), B12(B-Se), and B12(Se-B) layers along the c axis of the hexagonal conventional unit cell. The structural and electronic properties of the ground-state B9.5Se are also derived and discussed. By comparing the derived ground-state properties of B9.5Se to the existing experimental data of boron subselenide B˜13Se , I proposed that the as-synthesized boron subselenide B˜13Se , as reported in the literature, has the actual composition of B9.5Se .

Innovative Techniques for Studying New Materials and New Developments in Solid State Physics

DTIC Science & Technology

1992-09-14

acoustic resonators to study superfluid-filled silica aerogel , high Tc superconductors, and quasicrystals", to be published in J. Low Temp. Phys. 4. J. D...McKenna, and J. D. Maynard, "Using acoustic resonators to study superfluid-filled silica aerogel , high Tc superconductors, and quasicrystals", Symposium

Dirac Sea and its Evolution

NASA Astrophysics Data System (ADS)

Volfson, Boris

2013-09-01

The hypothesis of transition from a chaotic Dirac Sea, via highly unstable positronium, into a Simhony Model of stable face-centered cubic lattice structure of electrons and positrons securely bound in vacuum space, is considered. 13.75 Billion years ago, the new lattice, which, unlike a Dirac Sea, is permeable by photons and phonons, made the Universe detectable. Many electrons and positrons ended up annihilating each other producing energy quanta and neutrino-antineutrino pairs. The weak force of the electron-positron crystal lattice, bombarded by the chirality-changing neutrinos, may have started capturing these neutrinos thus transforming from cubic crystals into a quasicrystal lattice. Unlike cubic crystal lattice, clusters of quasicrystals are "slippery" allowing the formation of centers of local torsion, where gravity condenses matter into galaxies, stars and planets. In the presence of quanta, in a quasicrystal lattice, the Majorana neutrinos' rotation flips to the opposite direction causing natural transformations in a category comprised of three components; two others being positron and electron. In other words, each particle-antiparticle pair "e-" and "e+", in an individual crystal unit, could become either a quasi- component "e- ve e+", or a quasi- component "e+ - ve e-". Five-to-six six billion years ago, a continuous stimulation of the quasicrystal aetherial lattice by the same, similar, or different, astronomical events, could have triggered Hebbian and anti-Hebbian learning processes. The Universe may have started writing script into its own aether in a code most appropriate for the quasicrystal aether "hardware": Eight three-dimensional "alphabet" characters, each corresponding to the individual quasi-crystal unit shape. They could be expressed as quantum Turing machine qubits, or, alternatively, in a binary code. The code numerals could contain terminal and nonterminal symbols of the Chomsky's hierarchy, wherein, the showers of quanta, forming the

Model Parameter Estimation Using Ensemble Data Assimilation: A Case with the Nonhydrostatic Icosahedral Atmospheric Model NICAM and the Global Satellite Mapping of Precipitation Data

NASA Astrophysics Data System (ADS)

Kotsuki, Shunji; Terasaki, Koji; Yashiro, Hasashi; Tomita, Hirofumi; Satoh, Masaki; Miyoshi, Takemasa

2017-04-01

This study aims to improve precipitation forecasts from numerical weather prediction (NWP) models through effective use of satellite-derived precipitation data. Kotsuki et al. (2016, JGR-A) successfully improved the precipitation forecasts by assimilating the Japan Aerospace eXploration Agency (JAXA)'s Global Satellite Mapping of Precipitation (GSMaP) data into the Nonhydrostatic Icosahedral Atmospheric Model (NICAM) at 112-km horizontal resolution. Kotsuki et al. mitigated the non-Gaussianity of the precipitation variables by the Gaussian transform method for observed and forecasted precipitation using the previous 30-day precipitation data. This study extends the previous study by Kotsuki et al. and explores an online estimation of model parameters using ensemble data assimilation. We choose two globally-uniform parameters, one is the cloud-to-rain auto-conversion parameter of the Berry's scheme for large scale condensation and the other is the relative humidity threshold of the Arakawa-Schubert cumulus parameterization scheme. We perform the online-estimation of the two model parameters with an ensemble transform Kalman filter by assimilating the GSMaP precipitation data. The estimated parameters improve the analyzed and forecasted mixing ratio in the lower troposphere. Therefore, the parameter estimation would be a useful technique to improve the NWP models and their forecasts. This presentation will include the most recent progress up to the time of the symposium.

Theoretical and Numerical Modeling of faceted Ionic crystalline vesicles

NASA Astrophysics Data System (ADS)

Olvera de La Cruz, Monica

2007-03-01

Icosahedral shape is found in several natural structures including large viruses, large fullerenes and cationic-anionic vesicles. Faceting into icosahedral shape can occur in large crystalline membranes via elasticity theory. Icosahedral symmetry is found in small systems of particles with short-range interactions on a sphere. Dr G. Vernizzi and I show a novel electrostatic-driven mechanism of ionic crystalline shells faceting into icosahedral shapes even for systems with a small number of particles. Icosahedral shape is possible in cationic and anionic molecules adsorbed onto spherical interfaces, such as emulsions or other immiscible liquid droplets because the large concentration of charges at the interface can lead to ionic crystals on the curved interface. Such self-organized ionic structures favors the formation of flat surfaces. We find that these ionic crystalline shells can have lower energy when faceted into icosahedra along particular directions. Indeed, the ``ionic'' buckling is driven by preferred bending directions of the planar ionic structure, along which is more likely for the icosahedral shape to develop an edge. Since only certain orientations are allowed, rotational symmetry is broken. One can hope to exploit this mechanism to generate functional materials where, for instance, proteins with specific charge groups can orient at specific directions along an icosahedral cationic-anionic vesicle.

Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus

NASA Astrophysics Data System (ADS)

Jiang, Wen; Chang, Juan; Jakana, Joanita; Weigele, Peter; King, Jonathan; Chiu, Wah

2006-02-01

The critical viral components for packaging DNA, recognizing and binding to host cells, and injecting the condensed DNA into the host are organized at a single vertex of many icosahedral viruses. These component structures do not share icosahedral symmetry and cannot be resolved using a conventional icosahedral averaging method. Here we report the structure of the entire infectious Salmonella bacteriophage epsilon15 (ref. 1) determined from single-particle cryo-electron microscopy, without icosahedral averaging. This structure displays not only the icosahedral shell of 60 hexamers and 11 pentamers, but also the non-icosahedral components at one pentameric vertex. The densities at this vertex can be identified as the 12-subunit portal complex sandwiched between an internal cylindrical core and an external tail hub connecting to six projecting trimeric tailspikes. The viral genome is packed as coaxial coils in at least three outer layers with ~90 terminal nucleotides extending through the protein core and the portal complex and poised for injection. The shell protein from icosahedral reconstruction at higher resolution exhibits a similar fold to that of other double-stranded DNA viruses including herpesvirus, suggesting a common ancestor among these diverse viruses. The image reconstruction approach should be applicable to studying other biological nanomachines with components of mixed symmetries.

Interpenetration of a 3D Icosahedral M@Ni12 (M=Al, Ga) Framework with Porphyrin-Reminiscent Boron Layers in MNi9 B8.

PubMed

Zheng, Qiang; Wagner, Frank R; Ormeci, Alim; Prots, Yurii; Burkhardt, Ulrich; Schmidt, Marcus; Schnelle, Walter; Grin, Yuri; Leithe-Jasper, Andreas

2015-11-09

Two ternary borides MNi9 B8 (M=Al, Ga) were synthesized by thermal treatment of mixtures of the elements. Single-crystal X-ray diffraction data reveal AlNi9 B8 and GaNi9 B8 crystallizing in a new type of structure within the space group Cmcm and the lattice parameters a=7.0896(3) Å, b=8.1181(3) Å, c=10.6497(4) Å and a=7.0897(5) Å, b=8.1579(4) Å, c=10.6648(7) Å, respectively. The boron atoms build up two-dimensional layers, which consist of puckered [B16 ] rings with two tailing B atoms, whereas the M atoms reside in distorted vertices-condensed [Ni12 ] icosahedra, which form a three-dimensional framework interpenetrated by boron porphyrin-reminiscent layers. An unusual local arrangement resembling a giant metallo-porphyrin entity is formed by the [B16 ] rings, which, due to their large annular size of approximately 8 Å, chelate four of the twelve icosahedral Ni atoms. An analysis of the chemical bonding by means of the electron localizability approach reveals strong covalent B-B interactions and weak Ni-Ni interactions. Multi-center dative B-Ni interaction occurs between the Al-Ni framework and the boron layers. In agreement with the chemical bonding analysis and band structure calculations, AlNi9 B8 is a Pauli-paramagnetic metal. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Decagonal quasicrystal and related crystalline phases in Mn-Ga alloys with 52 to 63 a/o Ga

NASA Astrophysics Data System (ADS)

Wu, J. S.; Kuo, K. H.

1997-03-01

A decagonal quasicrystal (DQC) and six related intermetallic phases with large unit cells have been found in binary Mn-Ga alloys with 52 to 63 at. pct Ga by means of transmission electron microscopy (TEM). As does the Al-Mn DQC, the Ga-Mn DQC also has a periodicity of 1.25 nm along its tenfold axis. However, its Mn content, determined by electron microprobe X-ray analysis (about 45 to 50 at. pct Mn), is much higher than that of the Al-Mn DQC (about 20 to 30 at. pct Mn). The compositions of the intermetallic phases are about 53, 56, 58, and 62 at. pct Ga, corresponding respectively to the unknown structures of MnGa (50.7 to 53.4 at. pct Ga), Mn5Ga6 (55 at pct Ga), Mn5Ga7 (57.9 at. pct Ga), and Mn3Ga5 (62.9 at. pct Ga) given in the binary Mn-Ga phase diagram ( Metals Hand-book, T.B. Massalski, J.L. Murray, L.H. Benneft, and H. Baker, eds., ASM, Metals Park, OH, 1986, vol. 2, p. 1144). Their lattice types have been determined by selected area electron diffraction. The ferromagnetic Mn3Ga5 is tetragonal, a=1.25 nm and c=2.50 nm; Mn5Ga7 is orthorhombic, a=4.57 nm, b=1.25 nm, and c=1.44 nm; Mn5Ga6 has two different but closely related orthorhombic unit cells, a=1.26 nm, b=1.25 nm, and c=1.48 nm as well as a=0.77 nm, b=1.25 nm, and c=2.36 nm; MnGa also has two different and related unit cells, one orthorhombic with a=2.04 nm, b=1.25 nm, and c=1.48 nm and the other monoclinic with a=2.59 nm, b=1.25 nm, c=1.15 nm, and β≈=110 deg. All these orthorhombic phases have b=1.25 nm, being the same as the periodicity along the tenfold axis of the Ga-Mn and Al-Mn DQCs. Moreover, all these six intermetallic phases give electron diffraction patterns displaying a pseudo-tenfold distribution of strong diffraction spots and are considered to be crystalline approximants of the Ga-Mn DQC.

Extending high-order flux operators on spherical icosahedral grids and their application in a Shallow Water Model for transporting the Potential Vorticity

NASA Astrophysics Data System (ADS)

Zhang, Y.

2017-12-01

The unstructured formulation of the third/fourth-order flux operators used by the Advanced Research WRF is extended twofold on spherical icosahedral grids. First, the fifth- and sixth-order flux operators of WRF are further extended, and the nominally second- to sixth-order operators are then compared based on the solid body rotation and deformational flow tests. Results show that increasing the nominal order generally leads to smaller absolute errors. Overall, the fifth-order scheme generates the smallest errors in limited and unlimited tests, although it does not enhance the convergence rate. The fifth-order scheme also exhibits smaller sensitivity to the damping coefficient than the third-order scheme. Overall, the even-order schemes have higher limiter sensitivity than the odd-order schemes. Second, a triangular version of these high-order operators is repurposed for transporting the potential vorticity in a space-time-split shallow water framework. Results show that a class of nominally third-order upwind-biased operators generates better results than second- and fourth-order counterparts. The increase of the potential enstrophy over time is suppressed owing to the damping effect. The grid-scale noise in the vorticity is largely alleviated, and the total energy remains conserved. Moreover, models using high-order operators show smaller numerical errors in the vorticity field because of a more accurate representation of the nonlinear Coriolis term. This improvement is especially evident in the Rossby-Haurwitz wave test, in which the fluid is highly rotating. Overall, flux operators with higher damping coefficients, which essentially behaves like the Anticipated Potential Vorticity Method, present optimal results.

A diagnostic interface for the ICOsahedral Non-hydrostatic (ICON) modelling framework based on the Modular Earth Submodel System (MESSy v2.50)

NASA Astrophysics Data System (ADS)

Kern, Bastian; Jöckel, Patrick

2016-10-01

Numerical climate and weather models have advanced to finer scales, accompanied by large amounts of output data. The model systems hit the input and output (I/O) bottleneck of modern high-performance computing (HPC) systems. We aim to apply diagnostic methods online during the model simulation instead of applying them as a post-processing step to written output data, to reduce the amount of I/O. To include diagnostic tools into the model system, we implemented a standardised, easy-to-use interface based on the Modular Earth Submodel System (MESSy) into the ICOsahedral Non-hydrostatic (ICON) modelling framework. The integration of the diagnostic interface into the model system is briefly described. Furthermore, we present a prototype implementation of an advanced online diagnostic tool for the aggregation of model data onto a user-defined regular coarse grid. This diagnostic tool will be used to reduce the amount of model output in future simulations. Performance tests of the interface and of two different diagnostic tools show, that the interface itself introduces no overhead in form of additional runtime to the model system. The diagnostic tools, however, have significant impact on the model system's runtime. This overhead strongly depends on the characteristics and implementation of the diagnostic tool. A diagnostic tool with high inter-process communication introduces large overhead, whereas the additional runtime of a diagnostic tool without inter-process communication is low. We briefly describe our efforts to reduce the additional runtime from the diagnostic tools, and present a brief analysis of memory consumption. Future work will focus on optimisation of the memory footprint and the I/O operations of the diagnostic interface.

Nanosized (mu12-Pt)Pd164-xPtx(CO)72(PPh3)20 (x approximately 7) containing Pt-centered four-shell 165-atom Pd-Pt core with unprecedented intershell bridging carbonyl ligands: comparative analysis of icosahedral shell-growth patterns with geometrically related Pd145(CO)x(PEt3)30 (x approximately 60) containing capped three-shell Pd145 core.

PubMed

Mednikov, Evgueni G; Jewell, Matthew C; Dahl, Lawrence F

2007-09-19

Presented herein are the preparation and crystallographic/microanalytical/magnetic/spectroscopic characterization of the Pt-centered four-shell 165-atom Pd-Pt cluster, (mu(12)-Pt)Pd(164-x)Pt(x)(CO)(72)(PPh(3))(20) (x approximately 7), 1, that replaces the geometrically related capped three-shell icosahedral Pd(145) cluster, Pd(145)(CO)(x)(PEt(3))(30) (x approximately 60), 2, as the largest crystallographically determined discrete transition metal cluster with direct metal-metal bonding. A detailed comparison of their shell-growth patterns gives rise to important stereochemical implications concerning completely unexpected structural dissimilarities as well as similarities and provides new insight concerning possible synthetic approaches for generation of multi-shell metal clusters. 1 was reproducibly prepared in small yields (<10%) from the reaction of Pd(10)(CO)(12)(PPh(3))(6) with Pt(CO)(2)(PPh(3))(2). Its 165-atom metal-core geometry and 20 PPh(3) and 72 CO ligands were established from a low-temperature (100 K) CCD X-ray diffraction study. The well-determined crystal structure is attributed largely to 1 possessing cubic T(h) (2/m3) site symmetry, which is the highest crystallographic subgroup of the noncrystallographic pseudo-icosahedral I(h) (2/m35) symmetry. The "full" four-shell Pd-Pt anatomy of 1 consists of: (a) shell 1 with the centered (mu(12)-Pt) atom encapsulated by the 12-atom icosahedral Pt(x)Pd(12-x) cage, x = 1.2(3); (b) shell 2 with the 42-atom nu(2) icosahedral Pt(x)Pd(42-x) cage, x = 3.5(5); (c) shell 3 with the anti-Mackay 60-atom semi-regular rhombicosidodecahedral Pt(x)Pd(60-x) cage, x = 2.2(6); (d) shell 4 with the 50-atom nu(2) pentagonal dodecahedral Pd(50) cage. The total number of crystallographically estimated Pt atoms, 8 +/- 3, which was obtained from least-squares (Pt(x)/Pd(1-x))-occupancy analysis of the X-ray data that conclusively revealed the central atom to be pure Pt (occupancy factor, x = 1.00(3)), is fortuitously in agreement

In-situ neutron diffraction of a quasicrystal-containing Mg alloy interpreted using a new polycrystal plasticity model of hardening due to {10.2} tensile twinning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agnew, S. R.; Singh, A.; Calhoun, C. A.

Due to the excellent balance of strength and ductility exhibited by some Mg-Zn-RE (Y subgroup rare earth element) alloys, which contain icosahedral quasicrystalline precipitates, it is of interest to examine their deformation mechanisms. Furthermore, the internal strain evolution Mg-3at%Zn-0.5 at%Y with 4 vol% i-phase was measured using in-situ neutron diffraction. The extruded samples exhibit an initially weak <10.0> || extrusion direction “rod texture,” distinct from the normally strong texture of extruded Mg alloys, but the grain size is unexceptional (16.7 ± 2.1 μm). The initially weak texture contributes to a nearly symmetric yielding response between tension and compression. The hardeningmore » responses are asymmetric, however, since {10.2} extension twinning is significantly more active during compressive straining, despite the initially weak texture. In-situ neutron diffraction tension and compression experiments parallel to the extrusion direction, together with elasto-plastic self-consistent (EPSC) crystal plasticity modeling, reveal the strength and hardening behavior of individual slip and twinning modes. A model that was previously published about twinning-detwinning (TDT) is implemented within the EPSC framework, and it is proven effective for describing the observed, mild tension-compression asymmetry. This is not possible with previous EPSC-based models of twinning. Finally, the description of hardening within the TDT model is modified, in order to accurately describe the evolution of internal strains within the twins.« less

In-situ neutron diffraction of a quasicrystal-containing Mg alloy interpreted using a new polycrystal plasticity model of hardening due to {10.2} tensile twinning

DOE PAGES

Agnew, S. R.; Singh, A.; Calhoun, C. A.; ...

2018-09-17

Due to the excellent balance of strength and ductility exhibited by some Mg-Zn-RE (Y subgroup rare earth element) alloys, which contain icosahedral quasicrystalline precipitates, it is of interest to examine their deformation mechanisms. Furthermore, the internal strain evolution Mg-3at%Zn-0.5 at%Y with 4 vol% i-phase was measured using in-situ neutron diffraction. The extruded samples exhibit an initially weak <10.0> || extrusion direction “rod texture,” distinct from the normally strong texture of extruded Mg alloys, but the grain size is unexceptional (16.7 ± 2.1 μm). The initially weak texture contributes to a nearly symmetric yielding response between tension and compression. The hardeningmore » responses are asymmetric, however, since {10.2} extension twinning is significantly more active during compressive straining, despite the initially weak texture. In-situ neutron diffraction tension and compression experiments parallel to the extrusion direction, together with elasto-plastic self-consistent (EPSC) crystal plasticity modeling, reveal the strength and hardening behavior of individual slip and twinning modes. A model that was previously published about twinning-detwinning (TDT) is implemented within the EPSC framework, and it is proven effective for describing the observed, mild tension-compression asymmetry. This is not possible with previous EPSC-based models of twinning. Finally, the description of hardening within the TDT model is modified, in order to accurately describe the evolution of internal strains within the twins.« less

A Novel Liquid-Liquid Transition in Undercooled Ti-Zr-Ni Liquids

NASA Technical Reports Server (NTRS)

Lee, G. W.; Gangopadhyay, A. K.; Kelton, K. F.; Bradshaw, R. C.; Hyers, R. W.; Rathz, T. J.; Rogers, J. R.

2004-01-01

If crystallization can be avoided, liquids enter a metastable (undercooled) state below their equilibrium liquidus temperatures, T(sub l), finally 'freezing' into a glass below a characteristic temperature called the glass transition temperature, T(sub g). In rare cases, the undercooled liquid may undergo a liquid-liquid phase transition (liquid polymorphism) before entering the glassy state. This has been suggested from experimental studies of H2O and Si. Such phase transitions have been predicted in some stable liquids, ie. above T(sub l) at atmospheric pressure, for SiO2 and BeF2, but these have not been verified experimentally. They have been observed in liquids of P, Si and C, but only under high pressure. In this letter we present the first experimental evidence for a phase transition in a low viscosity metallic liquid that is driven by an approach to a constant entropy configuration state and correlated with a growing icosahedral order in the liquid. A maximum in the specific heat at constant pressure, similar to what is normally observed near T(sub g), is reported for undercooled liquids of quasicrystal-forming Ti-Zr-Ni alloys. A two-state excitation model that includes cooperativity by incorporating a temperature-dependent excitation energy, fits the specific heat data well, signaling a phase transition. An inflection in the liquid density with decreasing temperature instead of a discontinuity indicates that this is not a typical first order phase transition; it could be a weakly first order or higher order transition. While showing many similarities to a glass transition, this liquid-liquid phase transition occurs in a mobile liquid, making it novel.

A model for a transition from a quasicrystalline to a microcrystalline state

NASA Astrophysics Data System (ADS)

Coddens, G.; Launois, P.

1991-07-01

We propose a monoatomic model for a quasicrystal transition as observed recently in systems with icosahedral [3] and decagonal [5] symmetry. It is developed here for the case of decagonal symmetry and is inspired by the experimental results on the system Al-Cu-Co-Si [5,6]. The model goes beyond the purely geometrical description by an important physical aspect: the transition mediates through a single atomic jump distance such that only one unique double-well potential has to be invoked to describe it; in conformity with the symmetry there are 10 jump vectors. In the framework of the model, the microcrystalline state is energetically more favourable than a monocrystalline approximant phase. Nous proposons un modèle mono-atomique pour une transition quasicristal-microcristal du type de celles observées récemment dans des systèmes à symétrie icosaédrique [3] et décagonale [5]. Il est développé ici pour la symétrie décagonale et est inspiré par des résultats expérimentaux concernant l'alliage Al-Cu-Co-Si [5,6]. Le modèle va au-delà d'une description purement géometrique par un aspect physique important : la transition se fait via une seule distance de saut inter-atomique de telle sorte q'un seul double-puits de potentiel doit être pris en compte ; conformément à la symétrie, il y a 10 directions de saut. Dans le cadre du modèle, la phase microcristalline est énergétiquement favorisée par rapport à une phase approximante monocristalline.

Structure-Based Mutagenesis of Sulfolobus Turreted Icosahedral Virus B204 Reveals Essential Residues in the Virion-Associated DNA-Packaging ATPase.

PubMed

Dellas, Nikki; Snyder, Jamie C; Dills, Michael; Nicolay, Sheena J; Kerchner, Keshia M; Brumfield, Susan K; Lawrence, C Martin; Young, Mark J

2015-12-23

Sulfolobus turreted icosahedral virus (STIV), an archaeal virus that infects the hyperthermoacidophile Sulfolobus solfataricus, is one of the most well-studied viruses of the domain Archaea. STIV shares structural, morphological, and sequence similarities with viruses from other domains of life, all of which are thought to belong to the same viral lineage. Several of these common features include a conserved coat protein fold, an internal lipid membrane, and a DNA-packaging ATPase. B204 is the ATPase encoded by STIV and is thought to drive packaging of viral DNA during the replication process. Here, we report the crystal structure of B204 along with the biochemical analysis of B204 mutants chosen based on structural information and sequence conservation patterns observed among members of the same viral lineage and the larger FtsK/HerA superfamily to which B204 belongs. Both in vitro ATPase activity assays and transfection assays with mutant forms of B204 confirmed the essentiality of conserved and nonconserved positions. We also have identified two distinct particle morphologies during an STIV infection that differ in the presence or absence of the B204 protein. The biochemical and structural data presented here are not only informative for the STIV replication process but also can be useful in deciphering DNA-packaging mechanisms for other viruses belonging to this lineage. STIV is a virus that infects a host from the domain Archaea that replicates in high-temperature, acidic environments. While STIV has many unique features, there exist several striking similarities between this virus and others that replicate in different environments and infect a broad range of hosts from Bacteria and Eukarya. Aside from structural features shared by viruses from this lineage, there exists a significant level of sequence similarity between the ATPase genes carried by these different viruses; this gene encodes an enzyme thought to provide energy that drives DNA packaging into

Analysis of boron carbides' electronic structure

NASA Technical Reports Server (NTRS)

Howard, Iris A.; Beckel, Charles L.

1986-01-01

The electronic properties of boron-rich icosahedral clusters were studied as a means of understanding the electronic structure of the icosahedral borides such as boron carbide. A lower bound was estimated on bipolaron formation energies in B12 and B11C icosahedra, and the associated distortions. While the magnitude of the distortion associated with bipolaron formation is similar in both cases, the calculated formation energies differ greatly, formation being much more favorable on B11C icosahedra. The stable positions of a divalent atom relative to an icosahedral borane was also investigated, with the result that a stable energy minimum was found when the atom is at the center of the borane, internal to the B12 cage. If incorporation of dopant atoms into B12 cages in icosahedral boride solids is feasible, novel materials might result. In addition, the normal modes of a B12H12 cluster, of the C2B10 cage in para-carborane, and of a B12 icosahedron of reduced (D sub 3d) symmetry, such as is found in the icosahedral borides, were calculated. The nature of these vibrational modes will be important in determining, for instance, the character of the electron-lattice coupling in the borides, and in analyzing the lattice contribution to the thermal conductivity.

Evidence from x-ray and neutron powder diffraction patterns that the so-called icosahedral and decagonal quasicrystals of MnAl(6) and other alloys are twinned cubic crystals.

PubMed

Pauling, L

1987-06-01

It is shown that the x-ray powder diffraction patterns of rapidly quenched MnAl(6) and Mg(32)(Al,Zn)(49) and the neutron powder diffraction pattern of MnAl(6) are compatible with the proposed 820-atom primitive cubic structure [Pauling, L. (1987) Phys. Rev. Lett. 58, 365-368]. The values found for the edge of the unit cube are 23.365 A (x-ray) and 23.416 A (neutron) for MnAl(6) and 24.313 A (x-ray) for Mg(32)(Al,Zn)(49).

Evidence from x-ray and neutron powder diffraction patterns that the so-called icosahedral and decagonal quasicrystals of MnAl6 and other alloys are twinned cubic crystals

PubMed Central

Pauling, Linus

1987-01-01

It is shown that the x-ray powder diffraction patterns of rapidly quenched MnAl6 and Mg32(Al,Zn)49 and the neutron powder diffraction pattern of MnAl6 are compatible with the proposed 820-atom primitive cubic structure [Pauling, L. (1987) Phys. Rev. Lett. 58, 365-368]. The values found for the edge of the unit cube are 23.365 Å (x-ray) and 23.416 Å (neutron) for MnAl6 and 24.313 Å (x-ray) for Mg32(Al,Zn)49. PMID:16593841

Role of Hf on Phase Formation in Ti45Zr(38-x)Hf(x)Ni17 Liquids and Solids

NASA Technical Reports Server (NTRS)

Wessels, V.; Sahu, K. K.; Gangopadhyay, A. K.; Huett, V. T.; Canepari, S.; Goldman, A. I.; Hyers, R. W.; Kramer, M. J.; Rogers, J. R.; Kelton, K. F.;

Crystallographic features of the approximant H (Mn7Si2V) phase in the Mn-Si-V alloy system

NASA Astrophysics Data System (ADS)

Nakayama, Kei; Komatsuzaki, Takumi; Koyama, Yasumasa

2018-07-01

The intermetallic compound H (Mn7Si2V) phase in the Mn-Si-V alloy system can be regarded as an approximant phase of the dodecagonal quasicrystal as one of the two-dimensional quasicrystals. To understand the features of the approximant H phase, in this study, the crystallographic features of both the H phase and the (σ → H) reaction in Mn-Si-V alloy samples were investigated, mainly by transmission electron microscopy. It was found that, in the H phase, there were characteristic structural disorders with respect to an array of a dodecagonal structural unit consisting of 19 dodecagonal atomic columns. Concretely, penetrated structural units consisting of two dodecagonal structural units were presumed to be typical of such disorders. An interesting feature of the (σ → H) reaction was that regions with a rectangular arrangement of penetrated structural units (RAPU) first appeared in the σ matrix as the initial state, and H regions were then nucleated in contact with RAPU regions. The subsequent conversion of RAPU regions into H regions eventually resulted in the formation of the approximant H state as the final state. Furthermore, atomic positions in both the H structure and the dodecagonal quasicrystal were examined using a simple plane-wave model with 12 plane waves.

Distinct DNA exit and packaging portals in the virus Acanthamoeba polyphaga mimivirus.

PubMed

Zauberman, Nathan; Mutsafi, Yael; Halevy, Daniel Ben; Shimoni, Eyal; Klein, Eugenia; Xiao, Chuan; Sun, Siyang; Minsky, Abraham

2008-05-13

Icosahedral double-stranded DNA viruses use a single portal for genome delivery and packaging. The extensive structural similarity revealed by such portals in diverse viruses, as well as their invariable positioning at a unique icosahedral vertex, led to the consensus that a particular, highly conserved vertex-portal architecture is essential for viral DNA translocations. Here we present an exception to this paradigm by demonstrating that genome delivery and packaging in the virus Acanthamoeba polyphaga mimivirus occur through two distinct portals. By using high-resolution techniques, including electron tomography and cryo-scanning electron microscopy, we show that Mimivirus genome delivery entails a large-scale conformational change of the capsid, whereby five icosahedral faces open up. This opening, which occurs at a unique vertex of the capsid that we coined the "stargate", allows for the formation of a massive membrane conduit through which the viral DNA is released. A transient aperture centered at an icosahedral face distal to the DNA delivery site acts as a non-vertex DNA packaging portal. In conjunction with comparative genomic studies, our observations imply a viral packaging pathway akin to bacterial DNA segregation, which might be shared by diverse internal membrane-containing viruses.

Distinct DNA Exit and Packaging Portals in the Virus Acanthamoeba polyphaga mimivirus

PubMed Central

Zauberman, Nathan; Mutsafi, Yael; Halevy, Daniel Ben; Shimoni, Eyal; Klein, Eugenia; Xiao, Chuan; Sun, Siyang; Minsky, Abraham

2008-01-01

Icosahedral double-stranded DNA viruses use a single portal for genome delivery and packaging. The extensive structural similarity revealed by such portals in diverse viruses, as well as their invariable positioning at a unique icosahedral vertex, led to the consensus that a particular, highly conserved vertex-portal architecture is essential for viral DNA translocations. Here we present an exception to this paradigm by demonstrating that genome delivery and packaging in the virus Acanthamoeba polyphaga mimivirus occur through two distinct portals. By using high-resolution techniques, including electron tomography and cryo-scanning electron microscopy, we show that Mimivirus genome delivery entails a large-scale conformational change of the capsid, whereby five icosahedral faces open up. This opening, which occurs at a unique vertex of the capsid that we coined the “stargate”, allows for the formation of a massive membrane conduit through which the viral DNA is released. A transient aperture centered at an icosahedral face distal to the DNA delivery site acts as a non-vertex DNA packaging portal. In conjunction with comparative genomic studies, our observations imply a viral packaging pathway akin to bacterial DNA segregation, which might be shared by diverse internal membrane–containing viruses. PMID:18479185

Unlocking Internal Prestress from Protein Nanoshells

NASA Astrophysics Data System (ADS)

Klug, W. S.; Roos, W. H.; Wuite, G. J. L.

2012-10-01

The capsids of icosahedral viruses are closed shells assembled from a hexagonal lattice of proteins with fivefold angular defects located at the icosahedral vertices. Elasticity theory predicts that these disclinations are subject to an internal compressive prestress, which provides an explanation for the link between size and shape of capsids. Using a combination of experiment and elasticity theory we investigate the question of whether macromolecular assemblies are subject to residual prestress, due to basic geometric incompatibility of the subunits. Here we report the first direct experimental test of the theory: by controlled removal of protein pentamers from the icosahedral vertices, we measure the mechanical response of so-called “whiffle ball” capsids of herpes simplex virus, and demonstrate the signature of internal prestress locked into wild-type capsids during assembly.

Why Are Buckyonions Round?

NASA Technical Reports Server (NTRS)

Bates, Kevin R.; Scuseria, Gustavo E.

1997-01-01

Multi-layered round carbon particles (onions) containing tens to hundreds of thousands of atoms form during electron irradiation of graphite carbon. However, theoretical models of large icosahedral fullerenes predict highly faceted shapes for molecules with more than a few hundred atoms. This discrepancy in shape may be explained by the presence of defects during the formation of carbon onions. Here, we use the semi-empirical tight-binding method for carbon to simulate the incorporation of pentagon-heptagon defects on to the surface of large icosahedral fullerenes. We show a simple mechanism that results in energetically competitive derivative structures and a global change in molecular shape from faceted to round. Our results provide a plausible explanation of the apparent discrepancy between experimental observations of round buckyonions and theoretical predictions of faceted icosahedral fullerenes.

Why are Buckyonions Round?

NASA Technical Reports Server (NTRS)

Bates, Kevin R.; Scuseria, Gustavo E.

1998-01-01

Multi-layered round carbon particles (onions) containing tens to hundreds of thousands of atoms form during electron irradiation of graphite. However. theoretical models or large icosahedral fullerenes predict highly faceted shapes for molecules with more than a few hundred atoms. This discrepancy in shape may be explained by the presence of defects during the formation of carbon onions. Here, we use the semi-empirical tight-binding method for carbon to simulate the incorporation of pentagon-heptagon defects on to the surface of large icosahedral fullerenes. We show a simple mechanism that results in energetically competitive derivative structures and a global change in molecular shape from faceted to round. Our results provide a plausible explanation of the apparent discrepancy between experimental observations or round buckyonions and theoretical predictions of faceted icosahedral fullerenes.

Daniel Shechtman and Quasicrystals

Science.gov Websites

toolbox that included transmission electron microscopy, X-ray diffraction and neutron diffraction. The searchQuery x Find DOE R&D Acccomplishments Navigation dropdown arrow The Basics dropdown arrow Home About Letters, Vol. 53, Issue 20: 1951-1953; November 12, 1984 Nuclear γ-ray resonance observations in an

Containerless Measurement of Thermophysical Properties of Ti-Zr-Ni Alloys

NASA Technical Reports Server (NTRS)

Hyers, Robert; Bradshaw, Richard C.; Rogers, Jan C.; Rathz, Thomas J.; Lee, Geun W.; Gangopadhyay, Anup K.; Kelton, Kenneth F.

2004-01-01

The surface tension, viscosity, density, and thermal expansion of Ti-Zr-Ni alloys were measured for a number of compositions by electrostatic levitation methods. Containerless methods greatly reduce heterogeneous nucleation, increasing access to the undercooled liquid regime at finite cooling rates. The density and thermal expansion are measured optically, while the surface tension and viscosity are measured by the oscillating drop method. The measured alloys include compositions which form a metastable quasicrystal phase from the undercooled liquid, and alloys close to the composition of several multi-component bulk metallic glass-forming alloys. Measurements of surface tension show behavior typical of transition metals at high temperature, but a sudden decrease in the deeply undercooled liquid for alloys near the quasicrystal-forming composition range, but not for compositions which form the solid-solution phase first.

Formation of fivefold axes in the FCC-metal nanoclusters

NASA Astrophysics Data System (ADS)

Myasnichenko, Vladimir S.; Starostenkov, Mikhail D.

2012-11-01

Formation of atomistic structures of metallic Cu, Au, Ag clusters and bimetallic Cu-Au clusters was studied with the help of molecular dynamics using the many-body tight-binding interatomic potential. The simulation of the crystallization process of clusters with the number of atoms ranging from 300 to 1092 was carried out. The most stable configurations of atoms in the system, corresponding to the minimum of potential energy, was found during super-fast cooling from 1000 K. Atoms corresponding to fcc, hcp, and Ih phases were identified by the method of common neighbor analysis. Incomplete icosahedral core can be discovered at the intersection of one of the Ih axes with the surface of monometallic cluster. The decahedron-shaped structure of bimetallic Cu-Au cluster with seven completed icosahedral cores was obtained. The principles of the construction of small bimetallic clusters with icosahedral symmetry and increased fractal dimensionality were offered.

New Icosahedral Boron Carbide Semiconductors

NASA Astrophysics Data System (ADS)

Echeverria Mora, Elena Maria

Novel semiconductor boron carbide films and boron carbide films doped with aromatic compounds have been investigated and characterized. Most of these semiconductors were formed by plasma enhanced chemical vapor deposition. The aromatic compound additives used, in this thesis, were pyridine (Py), aniline, and diaminobenzene (DAB). As one of the key parameters for semiconducting device functionality is the metal contact and, therefore, the chemical interactions or band bending that may occur at the metal/semiconductor interface, X-ray photoemission spectroscopy has been used to investigate the interaction of gold (Au) with these novel boron carbide-based semiconductors. Both n- and p-type films have been tested and pure boron carbide devices are compared to those containing aromatic compounds. The results show that boron carbide seems to behave differently from other semiconductors, opening a way for new analysis and approaches in device's functionality. By studying the electrical and optical properties of these films, it has been found that samples containing the aromatic compound exhibit an improvement in the electron-hole separation and charge extraction, as well as a decrease in the band gap. The hole carrier lifetimes for each sample were extracted from the capacitance-voltage, C(V), and current-voltage, I(V), curves. Additionally, devices, with boron carbide with the addition of pyridine, exhibited better collection of neutron capture generated pulses at ZERO applied bias, compared to the pure boron carbide samples. This is consistent with the longer carrier lifetimes estimated for these films. The I-V curves, as a function of external magnetic field, of the pure boron carbide films and films containing DAB demonstrate that significant room temperature negative magneto-resistance (> 100% for pure samples, and > 50% for samples containing DAB) is possible in the resulting dielectric thin films. Inclusion of DAB is not essential for significant negative magneto-resistance, however, these results suggest practical device applications, especially as such effects are manifested in nanoscale films with facile fabrication. Overall, the greater negative magneto-resistance, when undoped with an aromatic, suggests a material with more defects and is consistent with a shorter carrier lifetime.

Theory of morphological transformation of viral capsid shell during the maturation process in the HK97 bacteriophage and similar viruses

NASA Astrophysics Data System (ADS)

Konevtsova, O. V.; Lorman, V. L.; Rochal, S. B.

2016-05-01

We consider the symmetry and physical origin of collective displacement modes playing a crucial role in the morphological transformation during the maturation of the HK97 bacteriophage and similar viruses. It is shown that the experimentally observed hexamer deformation and pentamer twist in the HK97 procapsid correspond to the simplest irreducible shear strain mode of a spherical shell. We also show that the icosahedral faceting of the bacteriophage capsid shell is driven by the simplest irreducible radial displacement field. The shear field has the rotational icosahedral symmetry group I while the radial field has the full icosahedral symmetry Ih. This difference makes their actions independent. The radial field sign discriminates between the icosahedral and the dodecahedral shapes of the faceted capsid shell, thus making the approach relevant not only for the HK97-like viruses but also for the parvovirus family. In the frame of the Landau-Ginzburg formalism we propose a simple phenomenological model valid for the first reversible step of the HK97 maturation process. The calculated phase diagram illustrates the discontinuous character of the virus shape transformation. The characteristics of the virus shell faceting and expansion obtained in the in vitro and in vivo experiments are related to the decrease in the capsid shell thickness and to the increase of the internal capsid pressure.

Impact of a nonuniform charge distribution on virus assembly

NASA Astrophysics Data System (ADS)

Li, Siyu; Erdemci-Tandogan, Gonca; Wagner, Jef; van der Schoot, Paul; Zandi, Roya

2017-08-01

Many spherical viruses encapsulate their genomes in protein shells with icosahedral symmetry. This process is spontaneous and driven by electrostatic interactions between positive domains on the virus coat proteins and the negative genomes. We model the effect of the nonuniform icosahedral charge distribution from the protein shell instead using a mean-field theory. We find that this nonuniform charge distribution strongly affects the optimal genome length and that it can explain the experimentally observed phenomenon of overcharging of virus and viruslike particles.

Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus

NASA Astrophysics Data System (ADS)

Hespenheide, B. M.; Jacobs, D. J.; Thorpe, M. F.

2004-11-01

The cowpea chlorotic mottle virus (CCMV) has a protein cage, or capsid, which encloses its genetic material. The structure of the capsid consists of 180 copies of a single protein that self-assemble inside a cell to form a complete capsid with icosahedral symmetry. The icosahedral surface can be naturally divided into pentagonal and hexagonal faces, and the formation of either of these faces has been proposed to be the first step in the capsid assembly process. We have used the software FIRST to analyse the rigidity of pentameric and hexameric substructures of the complete capsid to explore the viability of certain capsid assembly pathways. FIRST uses the 3D pebble game to determine structural rigidity, and a brief description of this algorithm, as applied to body-bar networks, is given here. We find that the pentameric substructure, which corresponds to a pentagonal face on the icosahedral surface, provides the best structural properties for nucleating the capsid assembly process, consistent with experimental observations.

Morphological evidence for phages in Xylella fastidiosa

PubMed Central

Chen, Jianchi; Civerolo, Edwin L

2008-01-01

Presumptive phage particles associated with Xylella fastidiosa strain Temecula-1 grown in PW broth were observed by transmission electron microscopy (TEM) in ultrathin sections of bacterial cell-containing low speed centrifugation pellets and in partially purified preparations from CsCl equilibrium centrifugation density gradients. Ultrathin-sectioned cell pellets contained icosahedral particles of about 45 nm in diameter. Samples collected from CsCl density gradients revealed mostly non-tailed icosahedral but also tailed particles. The icosahedral particles could be divided into two types: a large type (about 45 nm) and a small type (about 30 nm). Filamentous phage-like particles (17 × 120 to 6,300 nm) were also observed. The presence of different types of phage-like particles resembling to those in several bacteriophage families provides new physical evidence, in addition to X. fastidiosa genomic information, that X. fastidiosa possesses active phages. This is the first report of phage particles released in X. fastidiosa cultures. PMID:18538030

Cooling rate dependence and local structure in aluminum monatomic metallic glass

NASA Astrophysics Data System (ADS)

Kbirou, M.; Trady, S.; Hasnaoui, A.; Mazroui, M.

2017-10-01

The local atomic structure in aluminium monatomic metallic glass is studied using molecular dynamics simulations combined with the embedded atom method (EAM). We have used a variety of analytical methods to characterise the atomic configurations of our system: the Pair Distribution Function (PDF), the Common Neighbour Analysis (CNA) and the Voronoi Tessellation Analysis. CNA was used to investigate the order change from liquid to amorphous phases, recognising that the amount of icosahedral clusters increases with the decrease of temperature. The Voronoi analysis revealed that the icosahedral-like polyhedral are the predominant ones. It has been observed that the PDF function shows a splitting in the second peak, which cannot be attributed to the only ideal icosahedral polyhedron 〈0, 0, 12, 0〉, but also to the formation of other Voronoi polyhedra 〈0, 1, 10, 2〉 . Further, the PDFs were then integrated giving the cumulative coordination number in order to compute the fractal dimension (df).

Fourth class of convex equilateral polyhedron with polyhedral symmetry related to fullerenes and viruses.

PubMed

Schein, Stan; Gayed, James Maurice

2014-02-25

The three known classes of convex polyhedron with equal edge lengths and polyhedral symmetry--tetrahedral, octahedral, and icosahedral--are the 5 Platonic polyhedra, the 13 Archimedean polyhedra--including the truncated icosahedron or soccer ball--and the 2 rhombic polyhedra reported by Johannes Kepler in 1611. (Some carbon fullerenes, inorganic cages, icosahedral viruses, geodesic structures, and protein complexes resemble these fundamental shapes.) Here we add a fourth class, "Goldberg polyhedra," which are also convex and equilateral. We begin by decorating each of the triangular facets of a tetrahedron, an octahedron, or an icosahedron with the T vertices and connecting edges of a "Goldberg triangle." We obtain the unique set of internal angles in each planar face of each polyhedron by solving a system of n equations and n variables, where the equations set the dihedral angle discrepancy about different types of edge to zero, and the variables are a subset of the internal angles in 6gons. Like the faces in Kepler's rhombic polyhedra, the 6gon faces in Goldberg polyhedra are equilateral and planar but not equiangular. We show that there is just a single tetrahedral Goldberg polyhedron, a single octahedral one, and a systematic, countable infinity of icosahedral ones, one for each Goldberg triangle. Unlike carbon fullerenes and faceted viruses, the icosahedral Goldberg polyhedra are nearly spherical. The reasoning and techniques presented here will enable discovery of still more classes of convex equilateral polyhedra with polyhedral symmetry.

Design of a hyperstable 60-subunit protein icosahedron

NASA Astrophysics Data System (ADS)

Hsia, Yang; Bale, Jacob B.; Gonen, Shane; Shi, Dan; Sheffler, William; Fong, Kimberly K.; Nattermann, Una; Xu, Chunfu; Huang, Po-Ssu; Ravichandran, Rashmi; Yi, Sue; Davis, Trisha N.; Gonen, Tamir; King, Neil P.; Baker, David

2016-07-01

The icosahedron is the largest of the Platonic solids, and icosahedral protein structures are widely used in biological systems for packaging and transport. There has been considerable interest in repurposing such structures for applications ranging from targeted delivery to multivalent immunogen presentation. The ability to design proteins that self-assemble into precisely specified, highly ordered icosahedral structures would open the door to a new generation of protein containers with properties custom-tailored to specific applications. Here we describe the computational design of a 25-nanometre icosahedral nanocage that self-assembles from trimeric protein building blocks. The designed protein was produced in Escherichia coli, and found by electron microscopy to assemble into a homogenous population of icosahedral particles nearly identical to the design model. The particles are stable in 6.7 molar guanidine hydrochloride at up to 80 degrees Celsius, and undergo extremely abrupt, but reversible, disassembly between 2 molar and 2.25 molar guanidinium thiocyanate. The icosahedron is robust to genetic fusions: one or two copies of green fluorescent protein (GFP) can be fused to each of the 60 subunits to create highly fluorescent ‘standard candles’ for use in light microscopy, and a designed protein pentamer can be placed in the centre of each of the 20 pentameric faces to modulate the size of the entrance/exit channels of the cage. Such robust and customizable nanocages should have considerable utility in targeted drug delivery, vaccine design and synthetic biology.

Effect of cooling rate and Mg addition on the structural evaluation of rapidly solidified Al-20wt%Cu-12wt%Fe alloy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karaköse, Ercan, E-mail: ekarakose@karatekin.edu.t

2016-11-15

The present work examines the effect of Mg contents and cooling rate on the morphology and mechanical properties of Al{sub 20}Cu{sub 12}Fe quasicrystalline alloy. The microstructure of the alloys was analyzed by scanning electron microscopy and the phase composition was identified by X-ray diffractometry. The melting characteristics were studied by differential thermal analysis under an Ar atmosphere. The mechanical features of the melt-spun and conventionally solidified alloys were tested by tensile-strength test and Vickers micro-hardness test. It was found that the final microstructure of the Al{sub 20}Cu{sub 12}Fe samples mainly depends on the cooling rate and Mg contents, which suggestsmore » that different cooling rates and Mg contents produce different microstructures and properties. The average grain sizes of the melt spun samples were about 100–300 nm at 35 m/s. The nanosize, dispersed, different shaped quasicrystal particles possessed a remarkable effect to the mechanical characteristics of the rapidly solidified ribbons. The microhardness values of the melt spun samples were approximately 18% higher than those of the conventionally counterparts. - Highlights: •Quasicrystal-creating materials have high potential for applications. •Different shaped nanosize quasicrystal particles were observed. •The addition of Mg has an important impact on the mechanical properties. •H{sub V} values of the MS0, MS3 and MS5 samples at 35 m/s were 8.56, 8.66 and 8.80 GPa. •The volume fraction of IQC increases with increasing cooling rates.« less

Reduction of variance in spectral estimates for correction of ultrasonic aberration.

PubMed

Astheimer, Jeffrey P; Pilkington, Wayne C; Waag, Robert C

2006-01-01

A variance reduction factor is defined to describe the rate of convergence and accuracy of spectra estimated from overlapping ultrasonic scattering volumes when the scattering is from a spatially uncorrelated medium. Assuming that the individual volumes are localized by a spherically symmetric Gaussian window and that centers of the volumes are located on orbits of an icosahedral rotation group, the factor is minimized by adjusting the weight and radius of each orbit. Conditions necessary for the application of the variance reduction method, particularly for statistical estimation of aberration, are examined. The smallest possible value of the factor is found by allowing an unlimited number of centers constrained only to be within a ball rather than on icosahedral orbits. Computations using orbits formed by icosahedral vertices, face centers, and edge midpoints with a constraint radius limited to a small multiple of the Gaussian width show that a significant reduction of variance can be achieved from a small number of centers in the confined volume and that this reduction is nearly the maximum obtainable from an unlimited number of centers in the same volume.

PREFACE: 6th International Conference on Aperiodic Crystals (APERIODIC'09)

NASA Astrophysics Data System (ADS)

Grimm, Uwe; McGrath, Rónán; Degtyareva, Olga; Sharma, Hem Raj

2010-04-01

on quasicrystals (Eiji Abe), complex metal alloys (Alessandra Beni) and incommensurately modulated structures (Gervais Chapuis). While these were mainly aimed at younger researchers in the field, the lectures were very well attended and appreciated by the participants. The main programme ran from Monday morning until Friday lunchtime. It comprised 13 invited and 40 contributed plenary talks, and more than 40 posters, which were presented at two afternoon/evening poster sessions. The topics covered in the programme range from mathematical foundations, mathematical models, new materials, sample preparation, structure determination, physical properties and surface properties to industrial applications. Every presenter was invited to submit an article for this proceedings volume, and the 36 peer-reviewed papers in this volume present a cross-section of the range of presentations at the conference. They have been arranged into four categories, (i) quasicrystals, (ii) modulated structures, (iii) mathematical and theoretical aspects of aperiodic order, and (iv) approximants and complex phases. Prizes for best student presentations were awarded to Heinrich Orsini-Rosenberg (ETH Zurich) for his poster Tailor-made sevenfold approximants: ab-initio investigations on formation and stability and to Holger Euchner (Universität Stuttgart) for his contributed talk on Lattice dynamics in complex metallic alloys - vibrational properties of Zn11Mg2. In addition to a cash prize, Heinrich Orsini-Rosenberg received an icosahedral teapot, which was manufactured and donated by David Warrington, and Holger Euchner received a book prize. The meeting started with a welcome reception in the University's recently refurbished Victoria Gallery and Museum. A public lecture Simple sets of shapes that tile the plane but cannot ever repeat by Professor Sir Roger Penrose FRS attracted a wide audience and gave a fascinating insight into the discovery of the Penrose tiling, which is still the paradigm

Synthesis of boron suboxide from boron and boric acid under mild pressure and temperature conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiao, Xiaopeng; Jin, Hua; Ding, Zhanhui

2011-05-15

Graphical abstract: Well-crystallized and icosahedral B{sub 6}O crystals were prepared by reacting boron and boric acid at milder reaction conditions (1 GPa and 1300 {sup o}C for 2 h) as compared to previous work.. Research highlights: {yields} Well-crystallized icosahedral B{sub 6}O was synthesized by reacting boric acid and boron. {yields} The synthesis conditions (1 GPa and 1300 {sup o}C for 2 h) are milder in comparison with previous work. {yields} The more practical synthesis method may make B{sub 6}O as a potential substitute for diamond in industry. -- Abstract: Boron suboxide (B{sub 6}O) was synthesized by reacting boron and boricmore » acid (H{sub 3}BO{sub 3}) at pressures between 1 and 10 GPa, and at temperatures between 1300 and 1400 {sup o}C. The B{sub 6}O samples prepared were icosahedral with diameters ranging from 20 to 300 nm. Well-crystallized and icosahedral crystals with an average size of {approx}100 nm can be obtained at milder reaction conditions (1 GPa and 1300 {sup o}C for 2 h) as compared to previous work. The bulk B{sub 6}O sample was stable in air at 600 {sup o}C and then slowly oxidized up to 1000 {sup o}C. The relatively mild synthetic conditions developed in this study provide a more practical synthesis of B{sub 6}O, which may potentially be used as a substitute for diamond in industry as a new superhard material.« less

JPRS Report, Science & Technology, Japan, Structure, Properties of Al Amorphous Alloys

DTIC Science & Technology

1990-12-04

present report, and to the members of the staff, particularly Masaji Nomura, Tetsuya Ishikawa , and Atsushi Koyama, of the High Energy Physics Laboratory...Aichi Educational University, and the research on Al-based quasicrystals was with Shin Takeuchi, and Kaoru Kimura, both of Tokyo University, and Takeshi

Abrasion resistant coating and method of making the same

DOEpatents

Sordelet, Daniel J.; Besser, Matthew F.

2001-06-05

An abrasion resistant coating is created by adding a ductile phase to a brittle matrix phase during spray coating where an Al--Cu--Fe quasicrystalline phase (brittle matrix) and an FeAl intermetallic (ductile phase) are combined. This composite coating produces a coating mostly of quasicrystal phase and an inter-splat layer of the FeAl phase to help reduce porosity and cracking within the coating. Coatings are prepared by plasma spraying unblended and blended quasicrystal and intermetallic powders. The blended powders contain 1, 5, 10 and 20 volume percent of the intermetallic powders. The unblended powders are either 100 volume percent quasicrystalline or 100 volume percent intermetallic; these unblended powders were studied for comparison to the others. Sufficient ductile phase should be added to the brittle matrix to transform abrasive wear mode from brittle fracture to plastic deformation, while at the same time the hardness of the composite should not be reduced below that of the original brittle phase material.

Imaging quasiperiodic electronic states in a synthetic Penrose tiling

NASA Astrophysics Data System (ADS)

Collins, Laura C.; Witte, Thomas G.; Silverman, Rochelle; Green, David B.; Gomes, Kenjiro K.

2017-06-01

Quasicrystals possess long-range order but lack the translational symmetry of crystalline solids. In solid state physics, periodicity is one of the fundamental properties that prescribes the electronic band structure in crystals. In the absence of periodicity and the presence of quasicrystalline order, the ways that electronic states change remain a mystery. Scanning tunnelling microscopy and atomic manipulation can be used to assemble a two-dimensional quasicrystalline structure mapped upon the Penrose tiling. Here, carbon monoxide molecules are arranged on the surface of Cu(111) one at a time to form the potential landscape that mimics the ionic potential of atoms in natural materials by constraining the electrons in the two-dimensional surface state of Cu(111). The real-space images reveal the presence of the quasiperiodic order in the electronic wave functions and the Fourier analysis of our results links the energy of the resonant states to the local vertex structure of the quasicrystal.

Imaging quasiperiodic electronic states in a synthetic Penrose tiling.

PubMed

Collins, Laura C; Witte, Thomas G; Silverman, Rochelle; Green, David B; Gomes, Kenjiro K

2017-06-22

Quasicrystals possess long-range order but lack the translational symmetry of crystalline solids. In solid state physics, periodicity is one of the fundamental properties that prescribes the electronic band structure in crystals. In the absence of periodicity and the presence of quasicrystalline order, the ways that electronic states change remain a mystery. Scanning tunnelling microscopy and atomic manipulation can be used to assemble a two-dimensional quasicrystalline structure mapped upon the Penrose tiling. Here, carbon monoxide molecules are arranged on the surface of Cu(111) one at a time to form the potential landscape that mimics the ionic potential of atoms in natural materials by constraining the electrons in the two-dimensional surface state of Cu(111). The real-space images reveal the presence of the quasiperiodic order in the electronic wave functions and the Fourier analysis of our results links the energy of the resonant states to the local vertex structure of the quasicrystal.

A characterization of linearly repetitive cut and project sets

NASA Astrophysics Data System (ADS)

Haynes, Alan; Koivusalo, Henna; Walton, James

2018-02-01

For the development of a mathematical theory which can be used to rigorously investigate physical properties of quasicrystals, it is necessary to understand regularity of patterns in special classes of aperiodic point sets in Euclidean space. In one dimension, prototypical mathematical models for quasicrystals are provided by Sturmian sequences and by point sets generated by substitution rules. Regularity properties of such sets are well understood, thanks mostly to well known results by Morse and Hedlund, and physicists have used this understanding to study one dimensional random Schrödinger operators and lattice gas models. A key fact which plays an important role in these problems is the existence of a subadditive ergodic theorem, which is guaranteed when the corresponding point set is linearly repetitive. In this paper we extend the one-dimensional model to cut and project sets, which generalize Sturmian sequences in higher dimensions, and which are frequently used in mathematical and physical literature as models for higher dimensional quasicrystals. By using a combination of algebraic, geometric, and dynamical techniques, together with input from higher dimensional Diophantine approximation, we give a complete characterization of all linearly repetitive cut and project sets with cubical windows. We also prove that these are precisely the collection of such sets which satisfy subadditive ergodic theorems. The results are explicit enough to allow us to apply them to known classical models, and to construct linearly repetitive cut and project sets in all pairs of dimensions and codimensions in which they exist. Research supported by EPSRC grants EP/L001462, EP/J00149X, EP/M023540. HK also gratefully acknowledges the support of the Osk. Huttunen foundation.

The 3.2 Angstrom Resolution Structure of the Polymorphic Cowpea Chlorotic Mottle Virus Ribonucleoprotein Particle

NASA Astrophysics Data System (ADS)

Speir, Jeffrey Alan

Structural studies of the polymorphic cowpea chlorotic mottle virus have resulted in high resolution structures for two distinct icosahedral ribonucleoprotein particle conformations dependent upon whether acidic or basic pH conditions prevail. CCMV is stable below pH 6.5, however metal-free particles maintain a 10% increase in hydrodynamic volume at pH >=q 7.5. Identification of this swollen' form of CCMV, which can easily be disrupted with 1M NaCl, led to the first reassembly of an icosahedral virus in vitro from purified viral protein and RNA to form infectious particles, and its assembly has been the subject of biochemical and biophysical investigations for over twenty-five years. Under well defined conditions of pH, ionic strength and divalent metal ion concentration, CCMV capsid protein or capsid protein and RNA will reassemble to form icosahedral particles of various sizes, sheets, tubes, rosettes, and a variety of laminar structures which resemble virion structures from non-related virus families. Analysis of native particles at 3.2A resolution and swollen particles at 28A resolution has suggested that the chemical basis for the formation of polymorphic icosahedral and anisometric structures is: (i) hexamers formed of beta-barrel subunits stabilized by an unusual hexameric parallel beta structure made up of their N-termini, (ii) the location of protein-RNA interactions, (iii) divalent metal cation binding sites that regulate quasi-symmetrical subunit associations, (iv) charge repulsion across the same interfaces when lacking divalent metal ions at basic pH, which induces the formation of sixty 20A diameter portals for RNA release, and (v) a novel, C-terminal-based, subunit dimer assembly unit. The use of C- and N-terminal arms in CCMV has not been observed in other icosahedral RNA virus structures determined at near atomic resolution, however, their detailed interactions and roles in stabilizing the quaternary organization of CCMV are related to that found

The Crystallographic Structure of Panicum Mosaic Virus (PMV)

PubMed Central

Makino, Debora L.; Larson, Steven B.; McPherson, Alexander

2012-01-01

The structure of Panicum Mosaic Virus (PMV) was determined by X-ray diffraction analysis to 2.9 Å resolution. The crystals were of pseudo symmetry F23; the true crystallographic unit cell was of space group P21 with a=411.7 Å, b=403.9 Å and c=412.5 Å, with β=89.7°. The asymmetric unit was two entire T=3 virus particles, or 360 protein subunits. The structure was solved by conventional molecular replacement from two distant homologues, Cocksfoot Mottle Virus (CfMV) and Tobacco Necrosis Virus (TNV), of ~20% sequence identity followed by phase extension. The model was initially refined with exact icosahedral constraints and then with icosahedral restraints. The virus has Ca++ ions octahedrally coordinated by six aspartic acid residues on quasi threefold axes, which is completely different than for either CfMV or TNV. Amino terminal residues 1–53, 1–49 and 1-21 of the A, B and C subunits, respectively, and the four C-terminal residues (239-242) are not visible in electron density maps. The additional ordered residues of the C chain form a prominent “arm” that intertwines with symmetry equivalent “arms” at icosahedral threefold axes, as was seen in both CfMV and TNV. A 17 nucleotide hairpin segment of genomic RNA is icosahedrally ordered and bound at 60 equivalent sites at quasi twofold A–B subunit interfaces at the interior surface of the capsid. This segment of RNA may serve as a conformational switch for coat protein subunits, as has been proposed for similar RNA segments in other viruses. PMID:23123270

Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data.

PubMed

Xu, Nan; Veesler, David; Doerschuk, Peter C; Johnson, John E

2018-05-01

The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways. First, instead of imposing icosahedral symmetry on every particle in the data set during the variance analysis, we only assume that the data set as a whole has icosahedral symmetry. This change removes artifacts of high variance along icosahedral symmetry axes, but retains all of the features previously reported in the HK97 data set. Second we present a covariance analysis that reveals correlations in structural dynamics (variance) between the interior of the HK97 procapsid with the protease and regions of the exterior (not seen in the absence of the protease). The latter analysis corresponds well with hydrogen deuterium exchange studies previously published that reveal the same correlation. Copyright © 2018 Elsevier Inc. All rights reserved.

Atomic Scale Investigation of Structural Properties and Glass Forming Ability of Ti100-x Al x Metallic Glasses

NASA Astrophysics Data System (ADS)

Tahiri, M.; Hasnaoui, A.; Sbiaai, K.

2018-03-01

In this work, we employed molecular dynamics (MD) simulations to study Ti-Al metallic glasses (MGs) using the embedded atom method (EAM) potential to model the atomic interaction with different compositions. The results showed evidence of the metallic glass formation induced by the split occurring in the second peak of the radial distribution function (RDF) curves implying both Ti and Al atoms. The common neighbor analysis (CNA) method confirmed the presence of the icosahedral clusters with a maximum amount observed for an alloy with 75 pct of Al. Analysis of coordination numbers (CNs) indicated that the total CNs are nearly unchanged in these systems. Finally, Voronoi tessellation analyses (VTA) showed a higher value of the number of icosahedral units at Ti25Al75 composition. This specific composition represents a nearby peritectic point localized at a low melting point in the Ti-Al binary phase diagram. The glass forming ability (GFA) becomes important when the fraction of Al increases by forming and connecting "icosahedral-like" clusters (12-coordinated <0, 0, 12, 0> and 13-coordinated <0, 1, 10, 2>) and by playing a main role in the structure stability of the Ti-Al MGs.

Atomic Scale Investigation of Structural Properties and Glass Forming Ability of Ti100- x Al x Metallic Glasses

NASA Astrophysics Data System (ADS)

Tahiri, M.; Hasnaoui, A.; Sbiaai, K.

2018-06-01

In this work, we employed molecular dynamics (MD) simulations to study Ti-Al metallic glasses (MGs) using the embedded atom method (EAM) potential to model the atomic interaction with different compositions. The results showed evidence of the metallic glass formation induced by the split occurring in the second peak of the radial distribution function (RDF) curves implying both Ti and Al atoms. The common neighbor analysis (CNA) method confirmed the presence of the icosahedral clusters with a maximum amount observed for an alloy with 75 pct of Al. Analysis of coordination numbers (CNs) indicated that the total CNs are nearly unchanged in these systems. Finally, Voronoi tessellation analyses (VTA) showed a higher value of the number of icosahedral units at Ti25Al75 composition. This specific composition represents a nearby peritectic point localized at a low melting point in the Ti-Al binary phase diagram. The glass forming ability (GFA) becomes important when the fraction of Al increases by forming and connecting "icosahedral-like" clusters (12-coordinated <0, 0, 12, 0> and 13-coordinated <0, 1, 10, 2>) and by playing a main role in the structure stability of the Ti-Al MGs.

Spanning the scales of mechanical metamaterials using time domain simulations in transformed crystals, graphene flakes and structured soils

NASA Astrophysics Data System (ADS)

Aznavourian, Ronald; Puvirajesinghe, Tania M.; Brûlé, Stéphane; Enoch, Stefan; Guenneau, Sébastien

2017-11-01

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 the 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

The structure factor of primes

NASA Astrophysics Data System (ADS)

Zhang, G.; Martelli, F.; Torquato, S.

2018-03-01

Although the prime numbers are deterministic, they can be viewed, by some measures, as pseudo-random numbers. In this article, we numerically study the pair statistics of the primes using statistical-mechanical methods, particularly the structure factor S(k) in an interval M ≤slant p ≤slant M + L with M large, and L/M smaller than unity. We show that the structure factor of the prime-number configurations in such intervals exhibits well-defined Bragg-like peaks along with a small ‘diffuse’ contribution. This indicates that primes are appreciably more correlated and ordered than previously thought. Our numerical results definitively suggest an explicit formula for the locations and heights of the peaks. This formula predicts infinitely many peaks in any non-zero interval, similar to the behavior of quasicrystals. However, primes differ from quasicrystals in that the ratio between the location of any two predicted peaks is rational. We also show numerically that the diffuse part decays slowly as M and L increases. This suggests that the diffuse part vanishes in an appropriate infinite-system-size limit.

First-principles study of configurational disorder in B4C using a superatom-special quasirandom structure method

NASA Astrophysics Data System (ADS)

Ektarawong, A.; Simak, S. I.; Hultman, L.; Birch, J.; Alling, B.

2014-07-01

Configurationally disordered crystalline boron carbide, with the composition B4C, is studied using first-principles calculations. We investigate both dilute and high concentrations of carbon-boron substitutional defects. For the latter purpose, we suggest a superatom's picture of the complex structure and combine it with a special quasirandom structure approach for disorder. In this way, we model a random distribution of high concentrations of the identified low-energy defects: (1) bipolar defects and (2) rotation of icosahedral carbon among the three polar-up sites. Additionally, the substitutional disorder of the icosahedral carbon at all six polar sites, as previously discussed in the literature, is also considered. Two configurational phase transitions from the ordered to the disordered configurations are predicted to take place upon an increase in temperature using a mean-field approximation for the entropy. The first transition, at 870 K, induces substitutional disorder of the icosahedral carbon atoms among the three polar-up sites; meanwhile the second transition, at 2325 K, reveals the random substitution of the icosahedral carbon atoms at all six polar sites coexisting with bipolar defects. Already the first transition removes the monoclinic distortion existing in the ordered ground-state configuration and restore the rhombohedral system (R3m). The restoration of inversion symmetry yielding the full rhombohedral symmetry (R3¯m ) on average, corresponding to what is reported in the literature, is achieved after the second transition. Investigating the effects of high pressure on the configurational stability of the disordered B4C phases reveals a tendency to stabilize the ordered ground-state configuration as the configurationally ordering/disordering transition temperature increases with pressure exerted on B4C. The electronic density of states, obtained from the disordered phases, indicates a sensitivity of the band gap to the degree of configurational

Cryo-Electron Microscopy of Viruses Infecting Bacterium

NASA Astrophysics Data System (ADS)

Chiu, Wah

2010-03-01

Single particle cryo-EM can yield structures of infectious bacterial viruses with and without imposed icosahedral symmetry at subnanometer resolution. Reconstructions of infectious and empty phage particles show substantial differences in the portal vertex protein complex at one of the 12 pentameric vertices in the icosahedral virus particle through which the viral genomes are packaged or released. In addition, electron cryo-tomography of viruses during infecting its bacterial host cell displayed multiple conformations of the tail fiber of the virus. Our structural observations by single particle and tomographic reconstructions suggest a mechanism whereby the viral tail fibers, upon binding to the host cell, induce a cascade of structural alterations of the portal vertex protein complex that triggers DNA release.

Colloidal diffusion over a quasicrystalline-patterned substrate

NASA Astrophysics Data System (ADS)

Su, Yun; Lai, Pik-Yin; Ackerson, Bruce; Tong, Penger

We report a systematic study of colloidal diffusion over a quasicrystalline-patterned substrate. The sample substrate is made of a flat thin layer of photoresist and contains identical cylindrical holes of diameter dh, which are arranged on a quasicrystal lattice. A monolayer of silica spheres of diameter comparable to dh diffuse over the rugged quasicrystalline-patterned substrate and experience a gravitational potential U (x , y) . With optical microscopy and the particle tracking method, we measure U (x , y) and particle's diffusion trajectories, which are found to undergo two distinct states: a trapped state when the particles are inside the holes and a free diffusion state when they are over the flat portion of the substrate. The dynamic properties of the diffusing particle, such as its mean dwell time, mean square displacement, and long-time diffusion coefficient DL are obtained from the particle trajectories. The measured DL is found to be in good agreement with the prediction of two theoretical models proposed for diffusion over a quasicrystal lattice. The experiment demonstrates the applications of this newly constructed colloidal potential landscape. This work was supported by the Research Grants Council of Hong Kong SAR.

Convection in containerless processing.

PubMed

Hyers, Robert W; Matson, Douglas M; Kelton, Kenneth F; Rogers, Jan R

2004-11-01

Different containerless processing techniques have different strengths and weaknesses. Applying more than one technique allows various parts of a problem to be solved separately. For two research projects, one on phase selection in steels and the other on nucleation and growth of quasicrystals, a combination of experiments using electrostatic levitation (ESL) and electromagnetic levitation (EML) is appropriate. In both experiments, convection is an important variable. The convective conditions achievable with each method are compared for two very different materials: a low-viscosity, high-temperature stainless steel, and a high-viscosity, low-temperature quasicrystal-forming alloy. It is clear that the techniques are complementary when convection is a parameter to be explored in the experiments. For a number of reasons, including the sample size, temperature, and reactivity, direct measurement of the convective velocity is not feasible. Therefore, we must rely on computation techniques to estimate convection in these experiments. These models are an essential part of almost any microgravity investigation. The methods employed and results obtained for the projects levitation observation of dendrite evolution in steel ternary alloy rapid solidification (LODESTARS) and quasicrystalline undercooled alloys for space investigation (QUASI) are explained.

Effects of Al addition on atomic structure of Cu-Zr metallic glass

NASA Astrophysics Data System (ADS)

Li, Feng; Zhang, Huajian; Liu, Xiongjun; Dong, Yuecheng; Yu, Chunyan; Lu, Zhaoping

2018-02-01

The atomic structures of Cu52Zr48 and Cu45Zr48Al7 metallic glasses (MGs) have been studied by molecular dynamic simulations. The results reveal that the molar volume of the Cu45Zr48Al7 MG is smaller than that of the Cu52Zr48 MG, although the size of the Al atom is larger than that of the Cu atom, implying an enhanced atomic packing density achieved by introducing Al into the ternary MG. Bond shortening in unlike atomic pairs Zr-Al and Cu-Al is observed in the Cu45Zr48Al7 MG, which is attributed to strong interactions between Al and (Zr, Cu) atoms. Meanwhile, the atomic packing efficiency is enhanced by the minor addition of Al. Compared with the Cu52Zr48 binary MG, the potential energy of the ternary MG decreases and the glass transition temperature increases. Structural analyses indicate that more Cu- and Al-centered full icosahedral clusters emerge in the Cu45Zr48Al7 MG as some Cu atoms are substituted by Al. Furthermore, the addition of Al leads to more icosahedral medium-range orders in the ternary MG. The increase of full icosahedral clusters and the enhancement of the packing density are responsible for the improved glass-forming ability of Cu45Zr48Al7.

JPRS Report, Science & Technology, Japan

DTIC Science & Technology

1990-08-08

gap is created. Many research accomplishments concerning such syn- Based on these requirements, the concept of totally new thesis technologies have...the targets have shifted to active functions, such as Although the theory on characteristics of quasicrystals the conversion of solar ray to electric...organisms, such as humans, there are intel- committee chairman for the report compilation, to dis- ligent materials, including the nerve cells (neurons

Ab initio molecular dynamics simulation of binary Cu64Zr36 bulk metallic glass: Validation of the cluster-plus-glue-atom model

NASA Astrophysics Data System (ADS)

Tian, Hua; Zhang, Chong; Wang, Lu; Zhao, JiJun; Dong, Chuang; Wen, Bin; Wang, Qing

2011-06-01

We have performed ab initio molecular dynamics simulation of Cu64Zr36 alloy at descending temperatures (from 2000 K to 400 K) and discussed the evolution of short-range order with temperature. The pair-correlation functions, coordination numbers, and chemical compositions of the most abundant local clusters have been analyzed. We found that icosahedral short-range order exists in the liquid, undercooled, and glass states, and it becomes dominant in the glass states. Moreover, we demonstrated the existence of Cu-centered Cu8Zr5 icosahedral clusters as the major local structural unit in the Cu64Zr36 amorphous alloy. This finding agrees well with our previous cluster model of Cu-Zr-based BMG as well as experimental evidences from synchrotron x ray and neutron diffraction measurements.

Shellwise Mackay transformation in iron nanoclusters.

PubMed

Rollmann, Georg; Gruner, Markus E; Hucht, Alfred; Meyer, Ralf; Entel, Peter; Tiago, Murilo L; Chelikowsky, James R

2007-08-24

Structure and magnetism of iron clusters with up to 641 atoms have been investigated by means of density functional theory calculations including full geometric optimizations. Body-centered cubic (bcc) isomers are found to be lowest in energy when the clusters contain more than about 100 atoms. In addition, another stable conformation has been identified for magic-number clusters, which lies well within the range of thermal energies as compared to the bcc isomers. Its structure is characterized by a close-packed particle core and an icosahedral surface, while intermediate shells are partially transformed along the Mackay path between icosahedral and cuboctahedral geometry. The gradual transformation results in a favorable bcc environment for the subsurface atoms. For Fe55, the shellwise Mackay-transformed morphology is a promising candidate for the ground state.

Assembly of viral capsids, buckling, and the Asaro-Grinfeld-Tiller instability

NASA Astrophysics Data System (ADS)

Morozov, Alexander Yu.; Bruinsma, Robijn F.

2010-04-01

Icosahedral viral shells are characterized by intrinsic elastic stress focused on the 12 structurally required pentamers. We show that, according to thin-shell theory, assembling icosahedral viral shells should be subject to the Asaro-Grinfeld-Tiller instability (AGTI). AGTIs are encountered in growing epitaxial films exposed to extrinsic elastic stress. For viral shells, the AGTI relieves intrinsic elastic stresses by generating corrugation along the perimeter of the assembling shell. The buckling transition of Lidmar, Mirny, and Nelson provides an alternative mechanism for stress release, which in principle would allow for avoidance of AGTIs. For system parameters appropriate for viral shells however, the AGTI appears to be unavoidable. The azimuthal stress condensation produced by the AGTI might actually assist assembly by providing a guiding mechanism for the insertion of pentamers during viral assembly.

Monitoring Physiological Changes in Haloarchaeal Cell during Virus Release

PubMed Central

Svirskaitė, Julija; Oksanen, Hanna M.; Daugelavičius, Rimantas; Bamford, Dennis H.

2016-01-01

The slow rate of adsorption and non-synchronous release of some archaeal viruses have hindered more thorough analyses of the mechanisms of archaeal virus release. To address this deficit, we utilized four viruses that infect Haloarcula hispanica that represent the four virion morphotypes currently known for halophilic euryarchaeal viruses: (1) icosahedral internal membrane-containing SH1; (2) icosahedral tailed HHTV-1; (3) spindle-shaped His1; and (4) pleomorphic His2. To discern the events occurring as the progeny viruses exit, we monitored culture turbidity, as well as viable cell and progeny virus counts of infected and uninfected cultures. In addition to these traditional metrics, we measured three parameters associated with membrane integrity: the binding of the lipophilic anion phenyldicarbaundecaborane, oxygen consumption, and both intra- and extra-cellular ATP levels. PMID:26927156

The Hölder continuity of spectral measures of an extended CMV matrix

NASA Astrophysics Data System (ADS)

Munger, Paul E.; Ong, Darren C.

2014-09-01

We prove results about the Hölder continuity of the spectral measures of the extended CMV matrix, given power law bounds of the solution of the eigenvalue equation. We thus arrive at a unitary analogue of the results of Damanik, Killip, and Lenz ["Uniform spectral properties of one-dimensional quasicrystals, III. α-continuity," Commun. Math. Phys. 212, 191-204 (2000)] about the spectral measure of the discrete Schrödinger operator.

The Hölder continuity of spectral measures of an extended CMV matrix.

PubMed

Munger, Paul E; Ong, Darren C

2014-09-01

We prove results about the Hölder continuity of the spectral measures of the extended CMV matrix, given power law bounds of the solution of the eigenvalue equation. We thus arrive at a unitary analogue of the results of Damanik, Killip, and Lenz ["Uniform spectral properties of one-dimensional quasicrystals, III. α-continuity," Commun. Math. Phys.55, 191-204 (2000)] about the spectral measure of the discrete Schrödinger operator.

Structure and tribological properties of composite materials based on Al-Cu-Fe formed at high pressure

NASA Astrophysics Data System (ADS)

Golovkova, E. A.; Ekimov, E. A.; Ivanov, A. S.; Kruglov, V. S.; Pal', A. F.; Ryabinkin, A. N.; Serov, A. O.; Starostin, A. N.; Tsetlin, M. B.

2017-11-01

The use of high pressure ( 8 GPa) in the formation of composite quasi-crystalline materials from powders made it possible to create practically poreless samples with a density close to the maximum known for this type of quasi-crystals. For samples with a nickel binder, sintered at a temperature of 550°C, a very low coefficient of friction was obtained, which retain its value during the testing.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cameron, Maria K., E-mail: cameron@math.umd.edu

We develop computational tools for spectral analysis of stochastic networks representing energy landscapes of atomic and molecular clusters. Physical meaning and some properties of eigenvalues, left and right eigenvectors, and eigencurrents are discussed. We propose an approach to compute a collection of eigenpairs and corresponding eigencurrents describing the most important relaxation processes taking place in the system on its way to the equilibrium. It is suitable for large and complex stochastic networks where pairwise transition rates, given by the Arrhenius law, vary by orders of magnitude. The proposed methodology is applied to the network representing the Lennard-Jones-38 cluster created bymore » Wales's group. Its energy landscape has a double funnel structure with a deep and narrow face-centered cubic funnel and a shallower and wider icosahedral funnel. However, the complete spectrum of the generator matrix of the Lennard-Jones-38 network has no appreciable spectral gap separating the eigenvalue corresponding to the escape from the icosahedral funnel. We provide a detailed description of the escape process from the icosahedral funnel using the eigencurrent and demonstrate a superexponential growth of the corresponding eigenvalue. The proposed spectral approach is compared to the methodology of the Transition Path Theory. Finally, we discuss whether the Lennard-Jones-38 cluster is metastable from the points of view of a mathematician and a chemical physicist, and make a connection with experimental works.« less

Next generation of the self-consistent and environment-dependent Hamiltonian: Applications to various boron allotropes from zero- to three-dimensional structures

NASA Astrophysics Data System (ADS)

Tandy, P.; Yu, Ming; Leahy, C.; Jayanthi, C. S.; Wu, S. Y.

2015-03-01

An upgrade of the previous self-consistent and environment-dependent linear combination of atomic orbitals Hamiltonian (referred as SCED-LCAO) has been developed. This improved version of the semi-empirical SCED-LCAO Hamiltonian, in addition to the inclusion of self-consistent determination of charge redistribution, multi-center interactions, and modeling of electron-electron correlation, has taken into account the effect excited on the orbitals due to the atomic aggregation. This important upgrade has been subjected to a stringent test, the construction of the SCED-LCAO Hamiltonian for boron. It was shown that the Hamiltonian for boron has successfully characterized the electron deficiency of boron and captured the complex chemical bonding in various boron allotropes, including the planar and quasi-planar, the convex, the ring, the icosahedral, and the fullerene-like clusters, the two-dimensional monolayer sheets, and the bulk alpha boron, demonstrating its transferability, robustness, reliability, and predictive power. The molecular dynamics simulation scheme based on the Hamiltonian has been applied to explore the existence and the energetics of ˜230 compact boron clusters BN with N in the range from ˜100 to 768, including the random, the rhombohedral, and the spherical icosahedral structures. It was found that, energetically, clusters containing whole icosahedral B12 units are more stable for boron clusters of larger size (N > 200). The ease with which the simulations both at 0 K and finite temperatures were completed is a demonstration of the efficiency of the SCED-LCAO Hamiltonian.

Single-particle cryo-electron microscopy of Rift Valley fever virus

PubMed Central

Sherman, Michael B.; Freiberg, Alexander N.; Holbrook, Michael R.; Watowich, Stanley J.

2009-01-01

Rift Valley fever virus (RVFV; Bunyaviridae; Phlebovirus) is an emerging human veterinary pathogen causing acute hepatitis in ruminants and has the potential to Single-particle cryo-EM reconstruction of RVFV MP-12 hemorrhagic fever in humans. We report a three-dimensional reconstruction of RVFV vaccine strain MP-12 (RVFV MP-12) by cryo-electron microcopy using icosahedral symmetry of individual virions. Although the genomic core of RVFV MP-12 is apparently poorly ordered, the glycoproteins on the virus surface are highly symmetric and arranged on a T=12 icosahedral lattice. Our RVFV MP-12 structure allowed clear identification of inter-capsomer contacts and definition of possible glycoprotein arrangements within capsomers. This structure provides a detailed model for phleboviruses, opens new avenues for high-resolution structural studies of the bunyavirus family, and aids the design of antiviral diagnostics and effective subunit-vaccines. PMID:19304307

Single-particle cryo-electron microscopy of Rift Valley fever virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sherman, Michael B.; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555; Freiberg, Alexander N.

2009-04-25

Rift Valley fever virus (RVFV; Bunyaviridae; Phlebovirus) is an emerging human and veterinary pathogen causing acute hepatitis in ruminants and has the potential to cause hemorrhagic fever in humans. We report a three-dimensional reconstruction of RVFV vaccine strain MP-12 (RVFV MP-12) by cryo-electron microcopy using icosahedral symmetry of individual virions. Although the genomic core of RVFV MP-12 is apparently poorly ordered, the glycoproteins on the virus surface are highly symmetric and arranged on a T = 12 icosahedral lattice. Our RVFV MP-12 structure allowed clear identification of inter-capsomer contacts and definition of possible glycoprotein arrangements within capsomers. This structure providesmore » a detailed model for phleboviruses, opens new avenues for high-resolution structural studies of the bunyavirus family, and aids the design of antiviral diagnostics and effective subunit vaccines.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krumeich, F., E-mail: krumeich@inorg.chem.ethz.ch; Mueller, E.; Wepf, R.A.

While HRTEM is the well-established method to characterize the structure of dodecagonal tantalum (vanadium) telluride quasicrystals and their periodic approximants, phase-contrast imaging performed on an aberration-corrected scanning transmission electron microscope (STEM) represents a favorable alternative. The (Ta,V){sub 151}Te{sub 74} clusters, the basic structural unit in all these phases, can be visualized with high resolution. A dependence of the image contrast on defocus and specimen thickness has been observed. In thin areas, the projected crystal potential is basically imaged with either dark or bright contrast at two defocus values close to Scherzer defocus as confirmed by image simulations utilizing the principlemore » of reciprocity. Models for square-triangle tilings describing the arrangement of the basic clusters can be derived from such images. - Graphical abstract: PC-STEM image of a (Ta,V){sub 151}Te{sub 74} cluster. Highlights: Black-Right-Pointing-Pointer C{sub s}-corrected STEM is applied for the characterization of dodecagonal quasicrystals. Black-Right-Pointing-Pointer The projected potential of the structure is mirrored in the images. Black-Right-Pointing-Pointer Phase-contrast STEM imaging depends on defocus and thickness. Black-Right-Pointing-Pointer For simulations of phase-contrast STEM images, the reciprocity theorem is applicable.« less

Extraordinary Effects in Quasi-Periodic Gold Nanocavities: Enhanced Transmission and Polarization Control of Cavity Modes.

PubMed

Dhama, Rakesh; Caligiuri, Vincenzo; Petti, Lucia; Rashed, Alireza R; Rippa, Massimo; Lento, Raffaella; Termine, Roberto; Caglayan, Humeyra; De Luca, Antonio

2018-01-23

Plasmonic quasi-periodic structures are well-known to exhibit several surprising phenomena with respect to their periodic counterparts, due to their long-range order and higher rotational symmetry. Thanks to their specific geometrical arrangement, plasmonic quasi-crystals offer unique possibilities in tailoring the coupling and propagation of surface plasmons through their lattice, a scenario in which a plethora of fascinating phenomena can take place. In this paper we investigate the extraordinary transmission phenomenon occurring in specifically patterned Thue-Morse nanocavities, demonstrating noticeable enhanced transmission, directly revealed by near-field optical experiments, performed by means of a scanning near-field optical microscope (SNOM). SNOM further provides an intuitive picture of confined plasmon modes inside the nanocavities and confirms that localization of plasmon modes is based on size and depth of nanocavities, while cross talk between close cavities via propagating plasmons holds the polarization response of patterned quasi-crystals. Our performed numerical simulations are in good agreement with the experimental results. Thus, the control on cavity size and incident polarization can be used to alter the intensity and spatial properties of confined cavity modes in such structures, which can be exploited in order to design a plasmonic device with customized optical properties and desired functionalities, to be used for several applications in quantum plasmonics.

Presence of Two Virus-Like Particles in Penicillium citrinum

PubMed Central

Volterra, L.; Cassone, A.; Tonolo, A.; Bruzzone, M. L.

1975-01-01

Two icosahedral virus-like particles (28 and 19 nm in diameter, respectively) have been detected in sporogenic and asporogenic segregants of a strain of Penicillium citrinum. The distribution of the two particles differed among the two segregants. Images PMID:50049

Characterization of a Nepovirus causing a leaf mottling disease in Petunia hybrida

USDA-ARS?s Scientific Manuscript database

This report describes the complete genome sequence and characterization of a new virus infecting petunia. Icosahedral virus-like particles were isolated from Petunia hybrida cuttings with interveinal chlorotic mottling. The virus was transmitted by mechanical inoculation from infected to healthy P. ...

The diversity of the orthoreoviruses: molecular taxonomy and phylogentic divides.

USDA-ARS?s Scientific Manuscript database

The family Reoviridae is a diverse group of viruses with double-stranded ribonucleic acid (RNA) genomes contained within icosahedral, layered protein capsids. Within the Reoviridae, the Orthoreovirus genus includes viruses that infect reptiles, birds and mammals (including humans). Recent sequencing...

Aperiodic crystals and beyond.

PubMed

Grimm, Uwe

2015-06-01

Crystals are paradigms of ordered structures. While order was once seen as synonymous with lattice periodic arrangements, the discoveries of incommensurate crystals and quasicrystals led to a more general perception of crystalline order, encompassing both periodic and aperiodic crystals. The current definition of crystals rests on their essentially point-like diffraction. Considering a number of recently investigated toy systems, with particular emphasis on non-crystalline ordered structures, the limits of the current definition are explored.

First-principles prediction of stabilities and instabilities of compounds and alloys in the ternary B-As-P system

NASA Astrophysics Data System (ADS)

Ektarawong, A.; Simak, S. I.; Alling, B.

2017-07-01

We examine the thermodynamic stability of compounds and alloys in the ternary B-As-P system theoretically using first-principles calculations. We demonstrate that the icosahedral B12As2 is the only stable compound in the binary B-As system, while the zinc-blende BAs is thermodynamically unstable with respect to B12As2 and the pure arsenic phase at 0 K, and increasingly so at higher temperature, suggesting that BAs may merely exist as a metastable phase. On the contrary, in the binary B-P system, both zinc-blende BP and icosahedral B12P2 are predicted to be stable. As for the binary As-P system, As1 -xPx disordered alloys are predicted at elevated temperature—for example, a disordered solid solution of up to ˜75 at.% As in black phosphorus as well as a small solubility of ˜1 at.% P in gray arsenic at T =750 K, together with the presence of miscibility gaps. The calculated large solubility of As in black phosphorus explains the experimental syntheses of black-phosphorus-type As1 -xPx alloys with tunable compositions, recently reported in the literature. We investigate the phase stabilities in the ternary B-As-P system and demonstrate a high tendency for a formation of alloys in the icosahedral B12(As1 -xPx )2 structure by intermixing of As and P atoms at the diatomic chain sites. The phase diagram displays noticeable mutual solubility of the icosahedral subpnictides in each other even at room temperature as well as a closure of a pseudobinary miscibility gap around 900 K. As for pseudobinary BAs1 -xPx alloys, only a tiny amount of BAs is predicted to be able to dissolve in BP to form the BAs1 -xPx disordered alloys at elevated temperature. For example, less than 5% of BAs can dissolve in BP at T =1000 K. The small solubility limit of BAs in BP is attributed to the thermodynamic instability of BAs with respect to B12As2 and As.

Correlation of Mechanical Properties in Bulk Metallic Glasses with 27Al NMR Characteristics

DTIC Science & Technology

2011-12-01

recycle delay of 300 ms. Magnetization measurements were conducted at room temperature using a Quantum Design SQUID magne- tometer. The magnetization of...Gangopadhyay A K, et al. First X-ray scattering studies on electrostatically levitated metallic liquids: Demonstrated influence of local icosahedral

New ligand platforms featuring boron-rich clusters as organomimetic substituents*,**

PubMed Central

Spokoyny, Alexander M.

2013-01-01

200 years of research with carbon-rich molecules have shaped the development of modern chemistry. Research pertaining to the chemistry of boron-rich species has historically trailed behind its more distinguished neighbor (carbon) in the periodic table. Notably, a potentially rich and, in many cases, unmatched field of coordination chemistry using boronrich clusters remains fundamentally underdeveloped. Our work has been devoted to examining several basic concepts related to the functionalization of icosahedral boron-rich clusters and their use as ligands, aimed at designing fundamentally new hybrid molecular motifs and materials. Particularly interesting are icosahedral carboranes, which can be regarded as 3D analogs of benzene. These species comprise a class of boron-rich clusters that were discovered in the 1950s during the “space race” while researchers were developing energetic materials for rocket fuels. Ultimately, the unique chemical and physical properties of carborane species, such as rigidity, indefinite stability to air and moisture, and 3D aromaticity, may allow one to access a set of properties not normally available in carbon-based chemistry. While technically these species are considered as inorganic clusters, the chemical properties they possess make these boron-rich species suitable for replacing and/or altering structural and functional features of the organic and organometallic molecules—a phenomenon best described as “organomimetic”. Aside from purely fundamental features associated with the organomimetic chemistry of icosahedral carboranes, their use can also provide new avenues in the development of systems relevant to solving current problems associated with energy production, storage, and conversion. PMID:24311823

How faceted liquid droplets grow tails: from surface topology to active motion

NASA Astrophysics Data System (ADS)

Sloutskin, Eli

Among all possible shapes of a volume V, a sphere has the smallest surface area A. Therefore, liquid droplets are spherical, minimizing their interfacial energy γA for a given interfacial tension γ > 0 . This talk will demonstrate that liquid oil (alkane) droplets in water, stabilized by a common surfactant can be temperature-tuned to adopt icosahedral and other faceted shapes, above the bulk melting temperature of the oil. Although emulsions have been studied for centuries no faceted liquid droplets have ever been reported. The formation of an icosahedral shape is attributed to the interplay between γ and the elastic properties of the interfacial monomolecular layer, which crystallizes here 10-15K above bulk melting, leaving the droplet's bulk liquid. The icosahedral symmetry is dictated by twelve five-fold topological defects, forming within the hexagonally-packed interfacial crystalline monolayer. Moreover, we demonstrate that upon further cooling this `interfacial freezing' effect makes γ transiently switch its sign, leading to a spontaneous splitting of droplets and an active growth of their surface area, reminiscent of the classical spontaneous emulsification, yet driven by completely different physics. The observed phenomena allow deeper insights to be gained into the fundamentals of molecular elasticity and open new vitas for a wide range of novel nanotechnological applications, from self-assembly of complex shapes to new delivery strategies in bio-medicine. Acknowledgment is made to the Donors of the American Chemical Society Petroleum Research Fund for support of this research and to the Kahn Foundation for the purchase of equipment.

Changes in the stability and biomechanics of P22 bacteriophage capsid during maturation.

PubMed

Kant, Ravi; Llauró, Aida; Rayaprolu, Vamseedhar; Qazi, Shefah; de Pablo, Pedro J; Douglas, Trevor; Bothner, Brian

2018-03-15

The capsid of P22 bacteriophage undergoes a series of structural transitions during maturation that guide it from spherical to icosahedral morphology. The transitions include the release of scaffold proteins and capsid expansion. Although P22 maturation has been investigated for decades, a unified model that incorporates thermodynamic and biophysical analyses is not available. A general and specific model of icosahedral capsid maturation is of significant interest to theoreticians searching for fundamental principles as well as virologists and material scientists seeking to alter maturation to their advantage. To address this challenge, we have combined the results from orthogonal biophysical techniques including differential scanning fluorimetry, atomic force microscopy, circular dichroism, and hydrogen-deuterium exchange mass spectrometry. By integrating these results from single particle and population measurements, an energy landscape of P22 maturation from procapsid through expanded shell to wiffle ball emerged, highlighting the role of metastable structures and the thermodynamics guiding maturation. The propagation of weak quaternary interactions across symmetric elements of the capsid is a key component for stability in P22. A surprising finding is that the progression to wiffle ball, which lacks pentamers, shows that chemical and thermal stability can be uncoupled from mechanical rigidity, elegantly demonstrating the complexity inherent in capsid protein interactions and the emergent properties that can arise from icosahedral symmetry. On a broader scale, this work demonstrates the power of applying orthogonal biophysical techniques to elucidate assembly mechanisms for supramolecular complexes and provides a framework within which other viral systems can be compared. Copyright © 2018 Elsevier B.V. All rights reserved.

Nanometer scale atomic structure of zirconium based bulk metallic glass

NASA Astrophysics Data System (ADS)

Hwang, Jinwoo

We have studied the nanometer scale structure of bulk metallic glass (BMG) using fluctuation electron microscopy (FEM). The nanometer scale medium range order (MRO) in BMG is of significant interest because of its possible relationship to the properties, but the experimental study of the MRO is difficult because conventional diffraction techniques are not sensitive to the MRO scale. FEM is a quantitative transmission electron microscopy technique which measures the nanoscale structural fluctuation associated with MRO in amorphous materials, and provides information about the size, distribution, and internal structure of MRO. In this work, we developed an improved method for FEM using energy-filtered STEM nanodiffraction with highly coherent probes with size up to 11nm in a state-of-the-art Cs- corrected STEM. We also developed an effective way to eliminate the effect of sample thickness variation to the FEM data by using Z-contrast images as references. To study the detailed structure of MRO, we developed a hybrid reverse Monte Carlo (H-RMC) simulation which combines an empirical atomic potential and the FEM data. H-RMC generated model structures that match the experimental data at short and medium range. In addition, the subtle rotational symmetries in the FEM nanodiffraction patterns were analyzed by angular correlation function to reveal more details of the internal structure of MRO. Our experiments and simulations show that Zr-based BMG contains pseudo-planar, crystal-like MRO as well as icosahedral clusters in its nanoscale structure. We found that some icosahedral clusters may be connected, and that structural relaxation by annealing increases the population of icosahedral clusters.

Fourth class of convex equilateral polyhedron with polyhedral symmetry related to fullerenes and viruses

PubMed Central

Schein, Stan; Gayed, James Maurice

2014-01-01

The three known classes of convex polyhedron with equal edge lengths and polyhedral symmetry––tetrahedral, octahedral, and icosahedral––are the 5 Platonic polyhedra, the 13 Archimedean polyhedra––including the truncated icosahedron or soccer ball––and the 2 rhombic polyhedra reported by Johannes Kepler in 1611. (Some carbon fullerenes, inorganic cages, icosahedral viruses, geodesic structures, and protein complexes resemble these fundamental shapes.) Here we add a fourth class, “Goldberg polyhedra,” which are also convex and equilateral. We begin by decorating each of the triangular facets of a tetrahedron, an octahedron, or an icosahedron with the T vertices and connecting edges of a “Goldberg triangle.” We obtain the unique set of internal angles in each planar face of each polyhedron by solving a system of n equations and n variables, where the equations set the dihedral angle discrepancy about different types of edge to zero, and the variables are a subset of the internal angles in 6gons. Like the faces in Kepler’s rhombic polyhedra, the 6gon faces in Goldberg polyhedra are equilateral and planar but not equiangular. We show that there is just a single tetrahedral Goldberg polyhedron, a single octahedral one, and a systematic, countable infinity of icosahedral ones, one for each Goldberg triangle. Unlike carbon fullerenes and faceted viruses, the icosahedral Goldberg polyhedra are nearly spherical. The reasoning and techniques presented here will enable discovery of still more classes of convex equilateral polyhedra with polyhedral symmetry. PMID:24516137

Next generation of the self-consistent and environment-dependent Hamiltonian: Applications to various boron allotropes from zero- to three-dimensional structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tandy, P.; Yu, Ming; Leahy, C.

2015-03-28

An upgrade of the previous self-consistent and environment-dependent linear combination of atomic orbitals Hamiltonian (referred as SCED-LCAO) has been developed. This improved version of the semi-empirical SCED-LCAO Hamiltonian, in addition to the inclusion of self-consistent determination of charge redistribution, multi-center interactions, and modeling of electron-electron correlation, has taken into account the effect excited on the orbitals due to the atomic aggregation. This important upgrade has been subjected to a stringent test, the construction of the SCED-LCAO Hamiltonian for boron. It was shown that the Hamiltonian for boron has successfully characterized the electron deficiency of boron and captured the complex chemicalmore » bonding in various boron allotropes, including the planar and quasi-planar, the convex, the ring, the icosahedral, and the fullerene-like clusters, the two-dimensional monolayer sheets, and the bulk alpha boron, demonstrating its transferability, robustness, reliability, and predictive power. The molecular dynamics simulation scheme based on the Hamiltonian has been applied to explore the existence and the energetics of ∼230 compact boron clusters B{sub N} with N in the range from ∼100 to 768, including the random, the rhombohedral, and the spherical icosahedral structures. It was found that, energetically, clusters containing whole icosahedral B{sub 12} units are more stable for boron clusters of larger size (N > 200). The ease with which the simulations both at 0 K and finite temperatures were completed is a demonstration of the efficiency of the SCED-LCAO Hamiltonian.« less

Quantum and spectral properties of the Labyrinth model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Takahashi, Yuki, E-mail: takahasy@math.uci.edu

2016-06-15

We consider the Labyrinth model, which is a two-dimensional quasicrystal model. We show that the spectrum of this model, which is known to be a product of two Cantor sets, is an interval for small values of the coupling constant. We also consider the density of states measure of the Labyrinth model and show that it is absolutely continuous with respect to Lebesgue measure for almost all values of coupling constants in the small coupling regime.

Vertical Wave Coupling associated with Stratospheric Sudden Warming Events analyzed in an Isentropic-Coordinate NWP Model.

NASA Astrophysics Data System (ADS)

Bleck, R.; Sun, S.; Benjamin, S.; Brown, J. M.

2017-12-01

Two- to four-week predictions of stratospheric sudden warming events during the winter seasons of 1999-2014, carried out with a high-resolution icosahedral NWP model using potential temperature as vertical coordinate, are inspected for commonalities in the evolution of both minor and major warmings. Emphasis is on the evolution of the potential vorticity field at different levels in the stratosphere, as well as on the sign and magnitude of the vertical component of the Eliassen-Palm flux vector suggestive of wave forcing in either direction. Material is presented shedding light on the skill of the model (FIM, developed at NOAA/ESRL) in predicting stratospheric warmings generally 2 weeks in advance. With an icosahedral grid ideally suited for studying polar processes, and a vertical coordinate faithfully reproducing details in the evolution of the potential vorticity and EP flux vector fields, FIM is found to be a good tool for investigating the SSW mechanism.

Mechanisms of Size Control and Polymorphism in Viral Capsid Assembly

PubMed Central

Elrad, Oren M.; Hagan, Michael F.

2009-01-01

We simulate the assembly dynamics of icosahedral capsids from subunits that interconvert between different conformations (or quasi-equivalent states). The simulations identify mechanisms by which subunits form empty capsids with only one morphology, but adaptively assemble into different icosahedral morphologies around nanoparticle cargoes with varying sizes, as seen in recent experiments with brome mosaic virus (BMV) capsid proteins. Adaptive cargo encapsidation requires moderate cargo-subunit interaction strengths; stronger interactions frustrate assembly by stabilizing intermediates with incommensurate curvature. We compare simulation results to experiments with cowpea chlorotic mottle virus empty capsids and BMV capsids assembled on functionalized nanoparticles, and suggest new cargo encapsidation experiments. Finally, we find that both empty and templated capsids maintain the precise spatial ordering of subunit conformations seen in the crystal structure even if interactions that preserve this arrangement are favored by as little as the thermal energy, consistent with experimental observations that different subunit conformations are highly similar. PMID:18950240

Chain-like structure elements in Ni40Ta60 metallic glasses observed by scanning tunneling microscopy

PubMed Central

Pawlak, Rémy; Marot, Laurent; Sadeghi, Ali; Kawai, Shigeki; Glatzel, Thilo; Reimann, Peter; Goedecker, Stefan; Güntherodt, Hans-Joachim; Meyer, Ernst

2015-01-01

The structure of metallic glasses is a long-standing question because the lack of long-range order makes diffraction based techniques difficult to be applied. Here, we used scanning tunneling microscopy with large tunneling resistance of 6 GΩ at low temperature in order to minimize forces between probe and sample and reduce thermal fluctuations of metastable structures. Under these extremely gentle conditions, atomic structures of Ni40Ta60 metallic glasses are revealed with unprecedented lateral resolution. In agreement with previous models and experiments, icosahedral-like clusters are observed. The clusters show a high degree of mobility, which explains the need of low temperatures for stable imaging. In addition to icosahedrons, chain-like structures are resolved and comparative density functional theory (DFT) calculations confirm that these structures are meta-stable. The co-existence of icosahedral and chain-like structures might be an key ingredient for the understanding of the mechanical properties of metallic glasses. PMID:26268430

All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits

PubMed Central

Perilla, Juan R; Schlicksup, Christopher John; Venkatakrishnan, Balasubramanian; Zlotnick, Adam; Schulten, Klaus

2018-01-01

The hepatitis B virus capsid represents a promising therapeutic target. Experiments suggest the capsid must be flexible to function; however, capsid structure and dynamics have not been thoroughly characterized in the absence of icosahedral symmetry constraints. Here, all-atom molecular dynamics simulations are leveraged to investigate the capsid without symmetry bias, enabling study of capsid flexibility and its implications for biological function and cryo-EM resolution limits. Simulation results confirm flexibility and reveal a propensity for asymmetric distortion. The capsid’s influence on ionic species suggests a mechanism for modulating the display of cellular signals and implicates the capsid’s triangular pores as the location of signal exposure. A theoretical image reconstruction performed using simulated conformations indicates how capsid flexibility may limit the resolution of cryo-EM. Overall, the present work provides functional insight beyond what is accessible to experimental methods and raises important considerations regarding asymmetry in structural studies of icosahedral virus capsids. PMID:29708495

Structural properties of medium-range order in CuNiZr alloy

NASA Astrophysics Data System (ADS)

Gao, Tinghong; Hu, Xuechen; Xie, Quan; Li, Yidan; Ren, Lei

2017-10-01

The evolution characteristics of icosahedral clusters during the rapid solidification of Cu50Ni10Zr40 alloy at cooling rate of 1011 K s-1 are investigated based on molecular dynamics simulations. The structural properties of the short-range order and medium-range order of Cu50Ni10Zr40 alloy are analyzed by several structural characterization methods. The results reveal that the icosahedral clusters are the dominant short-range order structure, and that they assemble themselves into medium-range order by interpenetrating connections. The different morphologies of medium-range order are found in the system and include chain, triangle, tetrahedral, and their combination structures. The tetrahedral morphologies of medium-range order have excellent structural stability with decreasing temperature. The Zr atoms are favorable to form longer chains, while the Cu atoms are favorable to form shorter chains in the system. Those chains interlocked with each other to improve the structural stability.

Evidence of cross-cutting and redox reaction in Khatyrka meteorite reveals metallic-Al minerals formed in outer space.

PubMed

Lin, Chaney; Hollister, Lincoln S; MacPherson, Glenn J; Bindi, Luca; Ma, Chi; Andronicos, Christopher L; Steinhardt, Paul J

2017-05-09

We report on a fragment of the quasicrystal-bearing CV3 carbonaceous chondrite Khatyrka recovered from fine-grained, clay-rich sediments in the Koryak Mountains, Chukotka (Russia). We show higher melting-point silicate glass cross-cutting lower melting-point Al-Cu-Fe alloys, as well as unambiguous evidence of a reduction-oxidation reaction history between Al-Cu-Fe alloys and silicate melt. The redox reactions involve reduction of FeO and SiO 2 to Fe and Fe-Si metal, and oxidation of metallic Al to Al 2 O 3 , occurring where silicate melt was in contact with Al-Cu-Fe alloys. In the reaction zone, there are metallic Fe and Fe-Si beads, aluminous spinel rinds on the Al-Cu-Fe alloys, and Al 2 O 3 enrichment in the silicate melt surrounding the alloys. From this and other evidence, we demonstrate that Khatyrka must have experienced at least two distinct events: first, an event as early as 4.564 Ga in which the first Al-Cu-Fe alloys formed; and, second, a more recent impact-induced shock in space that led to transformations of and reactions between the alloys and the meteorite matrix. The new evidence firmly establishes that the Al-Cu-Fe alloys (including quasicrystals) formed in outer space in a complex, multi-stage process.

Shape transformation of viral capsids and HIV

NASA Astrophysics Data System (ADS)

Nguyen, Toan

2005-03-01

We present a continuum description of the shape transformation of viral capsids. The cone-like HIV virus is shown to be an thermodynamic stable shape, intermediate between icosahedral and sphero-cylinder capsid shapes. A generalized Caspar-Klug classification is introduced to describe spherical, conical and cylinderical shapes of virus.

ICTV Virus taxonomy profile: Asfarviridae

USDA-ARS?s Scientific Manuscript database

The family Asfarviridae includes the single species African swine fever virus, isolates of which have linear dsDNA genomes of 170-194 kbp. Virons have an internal core, an internal lipid membrane, an icosahedral capsid and an outer lipid envelope. Infection of domestic pigs and wild boar results i...

The FIM-iHYCOM Model in SubX: Evaluation of Subseasonal Errors and Variability

NASA Astrophysics Data System (ADS)

Green, B.; Sun, S.; Benjamin, S.; Grell, G. A.; Bleck, R.

2017-12-01

NOAA/ESRL/GSD has produced both real-time and retrospective forecasts for the Subseasonal Experiment (SubX) using the FIM-iHYCOM model. FIM-iHYCOM couples the atmospheric Flow-following finite volume Icosahedral Model (FIM) to an icosahedral-grid version of the Hybrid Coordinate Ocean Model (HYCOM). This coupled model is unique in terms of its grid structure: in the horizontal, the icosahedral meshes are perfectly matched for FIM and iHYCOM, eliminating the need for a flux interpolator; in the vertical, both models use adaptive arbitrary Lagrangian-Eulerian hybrid coordinates. For SubX, FIM-iHYCOM initializes four time-lagged ensemble members around each Wednesday, which are integrated forward to provide 32-day forecasts. While it has already been shown that this model has similar predictive skill as NOAA's operational CFSv2 in terms of the RMM index, FIM-iHYCOM is still fairly new and thus its overall performance needs to be thoroughly evaluated. To that end, this study examines model errors as a function of forecast lead week (1-4) - i.e., model drift - for key variables including 2-m temperature, precipitation, and SST. Errors are evaluated against two reanalysis products: CFSR, from which FIM-iHYCOM initial conditions are derived, and the quasi-independent ERA-Interim. The week 4 error magnitudes are similar between FIM-iHYCOM and CFSv2, albeit with different spatial distributions. Also, intraseasonal variability as simulated in these two models will be compared with reanalyses. The impact of hindcast frequency (4 times per week, once per week, or once per day) on the model climatology is also examined to determine the implications for systematic error correction in FIM-iHYCOM.

An Externalized Polypeptide Partitions between Two Distinct Sites on Genome-Released Poliovirus Particles ▿

PubMed Central

Lin, Jun; Cheng, Naiqian; Chow, Marie; Filman, David J.; Steven, Alasdair C.; Hogle, James M.; Belnap, David M.

2011-01-01

During cell entry, native poliovirus (160S) converts to a cell-entry intermediate (135S) particle, resulting in the externalization of capsid proteins VP4 and the amino terminus of VP1 (residues 1 to 53). Externalization of these entities is followed by release of the RNA genome (uncoating), leaving an empty (80S) particle. The antigen-binding fragment (Fab) of a monospecific peptide 1 (P1) antibody, which was raised against a peptide corresponding to amino-terminal residues 24 to 40 of VP1, was utilized to track the location of the amino terminus of VP1 in the 135S and 80S states of poliovirus particles via cryogenic electron microscopy (cryo-EM) and three-dimensional image reconstruction. On 135S, P1 Fabs bind to a prominent feature on the external surface known as the “propeller tip.” In contrast, our initial 80S-P1 reconstruction showed P1 Fabs also binding to a second site, at least 50 Å distant, at the icosahedral 2-fold axes. Further analysis showed that the overall population of 80S-P1 particles consisted of three kinds of capsids: those with P1 Fabs bound only at the propeller tips, P1 Fabs bound only at the 2-fold axes, or P1 Fabs simultaneously bound at both positions. Our results indicate that, in 80S particles, a significant fraction of VP1 can deviate from icosahedral symmetry. Hence, this portion of VP1 does not change conformation synchronously when switching from the 135S state. These conclusions are compatible with previous observations of multiple conformations of the 80S state and suggest that movement of the amino terminus of VP1 has a role in uncoating. Similar deviations from icosahedral symmetry may be biologically significant during other viral transitions. PMID:21775460

Local order and crystallization of dense polydisperse hard spheres

NASA Astrophysics Data System (ADS)

Coslovich, Daniele; Ozawa, Misaki; Berthier, Ludovic

2018-04-01

Computer simulations give precious insight into the microscopic behavior of supercooled liquids and glasses, but their typical time scales are orders of magnitude shorter than the experimentally relevant ones. We recently closed this gap for a class of models of size polydisperse fluids, which we successfully equilibrate beyond laboratory time scales by means of the swap Monte Carlo algorithm. In this contribution, we study the interplay between compositional and geometric local orders in a model of polydisperse hard spheres equilibrated with this algorithm. Local compositional order has a weak state dependence, while local geometric order associated to icosahedral arrangements grows more markedly but only at very high density. We quantify the correlation lengths and the degree of sphericity associated to icosahedral structures and compare these results to those for the Wahnström Lennard-Jones mixture. Finally, we analyze the structure of very dense samples that partially crystallized following a pattern incompatible with conventional fractionation scenarios. The crystal structure has the symmetry of aluminum diboride and involves a subset of small and large particles with size ratio approximately equal to 0.5.

Melting phenomena: effect of composition for 55-atom Ag-Pd bimetallic clusters.

PubMed

Cheng, Daojian; Wang, Wenchuan; Huang, Shiping

2008-05-14

Understanding the composition effect on the melting processes of bimetallic clusters is important for their applications. Here, we report the relationship between the melting point and the metal composition for the 55-atom icosahedral Ag-Pd bimetallic clusters by canonical Monte Carlo simulations, using the second-moment approximation of the tight-binding potentials (TB-SMA) for the metal-metal interactions. Abnormal melting phenomena for the systems of interest are found. Our simulation results reveal that the dependence of the melting point on the composition is not a monotonic change, but experiences three different stages. The melting temperatures of the Ag-Pd bimetallic clusters increase monotonically with the concentration of the Ag atoms first. Then, they reach a plateau presenting almost a constant value. Finally, they decrease sharply at a specific composition. The main reason for this change can be explained in terms of the relative stability of the Ag-Pd bimetallic clusters at different compositions. The results suggest that the more stable the cluster, the higher the melting point for the 55-atom icosahedral Ag-Pd bimetallic clusters at different compositions.

Sequence and structural characterization of great salt lake bacteriophage CW02, a member of the T7-like supergroup.

PubMed

Shen, Peter S; Domek, Matthew J; Sanz-García, Eduardo; Makaju, Aman; Taylor, Ryan M; Hoggan, Ryan; Culumber, Michele D; Oberg, Craig J; Breakwell, Donald P; Prince, John T; Belnap, David M

2012-08-01

Halophage CW02 infects a Salinivibrio costicola-like bacterium, SA50, isolated from the Great Salt Lake. Following isolation, cultivation, and purification, CW02 was characterized by DNA sequencing, mass spectrometry, and electron microscopy. A conserved module of structural genes places CW02 in the T7 supergroup, members of which are found in diverse aquatic environments, including marine and freshwater ecosystems. CW02 has morphological similarities to viruses of the Podoviridae family. The structure of CW02, solved by cryogenic electron microscopy and three-dimensional reconstruction, enabled the fitting of a portion of the bacteriophage HK97 capsid protein into CW02 capsid density, thereby providing additional evidence that capsid proteins of tailed double-stranded DNA phages have a conserved fold. The CW02 capsid consists of bacteriophage lambda gpD-like densities that likely contribute to particle stability. Turret-like densities were found on icosahedral vertices and may represent a unique adaptation similar to what has been seen in other extremophilic viruses that infect archaea, such as Sulfolobus turreted icosahedral virus and halophage SH1.

The microviridae: Diversity, assembly, and experimental evolution.

PubMed

Doore, Sarah M; Fane, Bentley A

2016-04-01

The Microviridae, comprised of ssDNA, icosahedral bacteriophages, are a model system for studying morphogenesis and the evolution of assembly. Historically limited to the φX174-like viruses, recent results demonstrate that this richly diverse family is broadly divided into two groups. The defining feature appears to be whether one or two scaffolding proteins are required for assembly. The single-scaffolding systems contain an internal scaffolding protein, similar to many dsDNA viruses, and have a more complex coat protein fold. The two-scaffolding protein systems (φX174-like) encode an internal and external species, as well as an additional structural protein: a spike on the icosahedral vertices. Here, we discuss recent in silico and in vivo evolutionary analyses conducted with chimeric viruses and/or chimeric proteins. The results suggest 1) how double scaffolding systems can evolve into single and triple scaffolding systems; and 2) how assembly is the critical factor governing adaptation and the maintenance of species boundaries. Copyright © 2016 Elsevier Inc. All rights reserved.

Medium-range structure and glass forming ability in Zr–Cu–Al bulk metallic glasses

DOE PAGES

Zhang, Pei; Maldonis, Jason J.; Besser, M. F.; ...

2016-03-05

Fluctuation electron microscopy experiments combined with hybrid reverse Monte Carlo modeling show a correlation between medium-range structure at the nanometer scale and glass forming ability in two Zr–Cu–Al bulk metallic glass (BMG) alloys. Both Zr 50Cu 35Al 15 and Zr 50Cu 45Al 5 exhibit two nanoscale structure types, one icosahedral and the other more crystal-like. In Zr 50Cu 35Al 15, the poorer glass former, the crystal-like structure is more stable under annealing below the glass transition temperature, T g, than in Zr 50Cu 45Al 5. Variable resolution fluctuation microscopy of the MRO clusters show that in Zr 50Cu 35Al 15more » on sub-Tg annealing, the crystal-like clusters shrink even as they grow more ordered, while icosahedral-like clusters grow. Furthermore, the results suggest that achieving better glass forming ability in this alloy system may depend more on destabilizing crystal-like structures than enhancing non-crystalline structures.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Pei; Maldonis, Jason J.; Besser, M. F.

Fluctuation electron microscopy experiments combined with hybrid reverse Monte Carlo modeling show a correlation between medium-range structure at the nanometer scale and glass forming ability in two Zr–Cu–Al bulk metallic glass (BMG) alloys. Both Zr 50Cu 35Al 15 and Zr 50Cu 45Al 5 exhibit two nanoscale structure types, one icosahedral and the other more crystal-like. In Zr 50Cu 35Al 15, the poorer glass former, the crystal-like structure is more stable under annealing below the glass transition temperature, T g, than in Zr 50Cu 45Al 5. Variable resolution fluctuation microscopy of the MRO clusters show that in Zr 50Cu 35Al 15more » on sub-Tg annealing, the crystal-like clusters shrink even as they grow more ordered, while icosahedral-like clusters grow. Furthermore, the results suggest that achieving better glass forming ability in this alloy system may depend more on destabilizing crystal-like structures than enhancing non-crystalline structures.« less

Shape-dependent surface magnetism of Co-Pt and Fe-Pt nanoparticles from first principles

NASA Astrophysics Data System (ADS)

Liu, Zhenyu; Wang, Guofeng

2017-12-01

In this paper, we have performed the first-principles density functional theory calculations to predict the magnetic properties of the CoPt and FePt nanoparticles in cuboctahedral, decahedral, and icosahedral shapes. The modeled alloy nanoparticles have a diameter of 1.1 nm and consist of 31 5 d Pt atoms and 24 3 d Co (or Fe) atoms. For both CoPt and FePt, we found that the decahedral nanoparticles had appreciably lower surface magnetic moments than the cuboctahedral and icosahedral nanoparticles. Our analysis indicated that this reduction in the surface magnetism was related to a large contraction of atomic spacing and high local Co (or Fe) concentration in the surface of the decahedral nanoparticles. More interestingly, we predicted that the CoPt and FePt cuboctahedral nanoparticles exhibited dramatically different surface spin structures when noncollinear magnetism was taken into account. Our calculation results revealed that surface anisotropy energy decided the fashion of surface spin canting in the CoPt and FePt nanoparticles, confirming previous predictions from atomistic Monte Carlo simulations.

The quantum structure of anionic hydrogen clusters

NASA Astrophysics Data System (ADS)

Calvo, F.; Yurtsever, E.

2018-03-01

A flexible and polarizable interatomic potential has been developed to model hydrogen clusters interacting with one hydrogen anion, (H2)nH-, in a broad range of sizes n = 1-54 and parametrized against coupled cluster quantum chemical calculations. Using path-integral molecular dynamics simulations at 1 K initiated from the putative classical global minima, the equilibrium structures are found to generally rely on icosahedral shells with the hydrogen molecules pointing toward the anion, producing geometric magic numbers at sizes n = 12, 32, and 44 that are in agreement with recent mass spectrometry measurements. The energetic stability of the clusters is also connected with the extent of vibrational delocalization, measured here by the fluctuations among inherent structures hidden in the vibrational wave function. As the clusters grow, the outer molecules become increasingly free to rotate, and strong finite size effects are also found between magic numbers, associated with more prominent vibrational delocalization. The effective icosahedral structure of the 44-molecule cluster is found to originate from quantum nuclear effects as well, the classical structure showing no particular symmetry.

Photonic Choke-Joints for Dual-Polarization Waveguides

NASA Technical Reports Server (NTRS)

Wollack, Edward J.; U-yen, Kongpop; Chuss, David T.

2010-01-01

Photonic choke joint (PCJ) structures for dual-polarization waveguides have been investigated for use in device and component packaging. This interface enables the realization of a high performance non-contacting waveguide joint without degrading the in-band signal propagation properties. The choke properties of two tiling approaches, symmetric square Cartesian and octagonal quasi-crystal lattices of metallic posts, are explored and optimal PCJ design parameters are presented. For each of these schemes, the experimental results for structures with finite tilings demonstrate near ideal transmission and reflection performance over a full waveguide band.

The Mpemba Effect, Shechtman's Quasicrystals and Student Exploration Activities

ERIC Educational Resources Information Center

Balazovic, Marek; Tomasik, Boris

2012-01-01

In the 1960s, Tanzanian student Erasto Mpemba and his teacher published a paper with the title "Cool?" in this journal (Mpemba and Osborne 1969 "Phys. Educ." 4 172-5). They claimed that hot water freezes more quickly than cold water. The paper not only led to a wave of discussion, and more publications about this topic, but also to a whole series…

Conformational Asymmetry and Quasicrystal Approximants in Linear Diblock Copolymers

NASA Astrophysics Data System (ADS)

Schulze, Morgan W.; Lewis, Ronald M.; Lettow, James H.; Hickey, Robert J.; Gillard, Timothy M.; Hillmyer, Marc A.; Bates, Frank S.

2017-05-01

Small angle x-ray scattering experiments on three model low molar mass diblock copolymer systems containing minority polylactide and majority hydrocarbon blocks demonstrate that conformational asymmetry stabilizes the Frank-Kasper σ phase. Differences in block flexibility compete with space filling at constant density inducing the formation of polyhedral shaped particles that assemble into this low symmetry ordered state with local tetrahedral coordination. These results confirm predictions from self-consistent field theory that establish the origins of symmetry breaking in the ordering of block polymer melts subjected to compositional and conformational asymmetry.

Electrically tunable graphene plasmonic quasicrystal metasurfaces for transformation optics

PubMed Central

Zeng, Chao; Liu, Xueming; Wang, Guoxi

2014-01-01

The past few years have witnessed tremendous achievements of transformation optics applied to metallic plasmonic systems. Due to the poor tunability of metals, however, the ultimate control over surface plasmons remains a challenge. Here we propose a new type of graphene plasmonic (GP) metasurfaces by shaping the dielectrics underneath monolayer graphene into specific photonic crystals. The radial and axial gradient-index (GRIN) lenses are implemented to demonstrate the feasibility and versatility of the proposal. It is found that the designed GP-GRIN lenses work perfectly well for focusing, collimating, and guiding the GP waves. Especially, they exhibit excellent performances in the THz regime as diverse as ultra-small focusing spot (λ0/60) and broadband electrical tunability. The proposed method offers potential opportunities in exploiting active transformational plasmonic elements operating at THz frequencies. PMID:25042132

Surface decorated platinum carbonyl clusters

NASA Astrophysics Data System (ADS)

Ciabatti, Iacopo; Femoni, Cristina; Iapalucci, Maria Carmela; Longoni, Giuliano; Zacchini, Stefano; Zarra, Salvatore

2012-06-01

Four molecular Pt-carbonyl clusters decorated by Cd-Br fragments, i.e., [Pt13(CO)12{Cd5(μ-Br)5Br2(dmf)3}2]2- (1), [Pt19(CO)17{Cd5(μ-Br)5Br3(Me2CO)2}{Cd5(μ-Br)5Br(Me2CO)4}]2- (2), [H2Pt26(CO)20(CdBr)12]8- (3) and [H4Pt26(CO)20(CdBr)12(PtBr)x]6- (4) (x = 0-2), have been obtained from the reactions between [Pt3n(CO)6n]2- (n = 2-6) and CdBr2.H2O in dmf at 120 °C. The structures of these molecular clusters with diameters of 1.5-2 nm have been determined by X-ray crystallography. Both 1 and 2 are composed of icosahedral or bis-icosahedral Pt-CO cores decorated on the surface by Cd-Br motifs, whereas 3 and 4 display a cubic close packed Pt26Cd12 metal frame decorated by CO and Br ligands. An oversimplified and unifying approach to interpret the electron count of these surface decorated platinum carbonyl clusters is suggested, and extended to other low-valent organometallic clusters and Au-thiolate nanoclusters.Four molecular Pt-carbonyl clusters decorated by Cd-Br fragments, i.e., [Pt13(CO)12{Cd5(μ-Br)5Br2(dmf)3}2]2- (1), [Pt19(CO)17{Cd5(μ-Br)5Br3(Me2CO)2}{Cd5(μ-Br)5Br(Me2CO)4}]2- (2), [H2Pt26(CO)20(CdBr)12]8- (3) and [H4Pt26(CO)20(CdBr)12(PtBr)x]6- (4) (x = 0-2), have been obtained from the reactions between [Pt3n(CO)6n]2- (n = 2-6) and CdBr2.H2O in dmf at 120 °C. The structures of these molecular clusters with diameters of 1.5-2 nm have been determined by X-ray crystallography. Both 1 and 2 are composed of icosahedral or bis-icosahedral Pt-CO cores decorated on the surface by Cd-Br motifs, whereas 3 and 4 display a cubic close packed Pt26Cd12 metal frame decorated by CO and Br ligands. An oversimplified and unifying approach to interpret the electron count of these surface decorated platinum carbonyl clusters is suggested, and extended to other low-valent organometallic clusters and Au-thiolate nanoclusters. CCDC 867747 and 867748. For crystallographic data in CIF or other electronic format see DOI: 10.1039/c2nr30400g

Boundary modes in quasiperiodic elastic structures

NASA Astrophysics Data System (ADS)

Rosa, Matheus I. N.; Pal, Raj K.; Arruda, José R. F.; Ruzzene, Massimo

2018-03-01

Topological metamaterials are a new class of materials that support topological modes such as edge modes and interface modes, which are commonly immune to scattering and imperfections. This novelty has been the subject of extensive research in many branches of physics such as electronics, photonics, phononics, and acoustics. The nontrivial topological properties related to the presence of topological modes are tipically found in periodic media. However, it was recently demonstrated that structures called quasicrystals may also exhibit nontrivial topological behavior attributed to dimensions higher than that of the quasicrystal. While quasiperiodicity has received a lot of attention in the fields of crystallography and photonics, research into quasiperiodic elastic structures has been scarce. In this paper, we show how the concepts of quasiperiodicity may be applied to the design of topological mechanical metamaterials. We start by investigating the boundary modes present in quasiperiodic 1D phononic lattices. These modes have the interesting property of being localized at either one of the two different boundaries depending on the value of an additional parameter, which is remnant of the higher dimension. A smooth variation of this parameter in either time or a spatial dimension can lead to a robust transfer of energy between two sites of the structure. We present an idealized mechanical system composed by an array of coupled rods that may be used as a platform for realizing this kind of robust transfer of energy. These are preliminary investigations into a entirely new class of structures which may lead to novel engineering applications.

The characterisation of atomic structure and glass-forming ability of the Zr-Cu-Co metallic glasses studied by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Celtek, M.; Sengul, S.

2018-03-01

In the present work, the glass formation process and structural properties of Zr50Cu50-xCox (0 ≤ x ≤ 50) bulk metallic glasses were investigated by a molecular dynamics simulation with the many body tight-binding potentials. The evolution of structure and glass formation process with temperature were discussed using the coordination number, the radial distribution functions, the volume-temperature curve, icosahedral short-range order, glass transition temperature, Voronoi analysis, Honeycutt-Andersen pair analysis technique and the distribution of bond-angles. Results indicate that adding Co causes similar responses on the nature of the Zr50Cu50-xCox (0 ≤ x ≤ 50) alloys except for higher glass transition temperature and ideal icosahedral type ordered local atomic environment. Also, the differences of the atomic radii play the key role in influencing the atomic structure of these alloys. Both Cu and Co atoms play a significant role in deciding the chemical and topological short-range orders of the Zr50Cu50-xCox ternary liquids and amorphous alloys. The glass-forming ability of these alloys is supported by the experimental observations reported in the literature up to now.

Pd surface and Pt subsurface segregation in Pt1-c Pd c nanoalloys

NASA Astrophysics Data System (ADS)

De Clercq, A.; Giorgio, S.; Mottet, C.

2016-02-01

The structure and chemical arrangement of Pt1-c Pd c nanoalloys with the icosahedral and face centered cubic symmetry are studied using Monte Carlo simulations with a tight binding interatomic potential fitted to density-functional theory calculations. Pd surface segregation from the lowest to the highest coordinated sites is predicted by the theory together with a Pt enrichment at the subsurface, whatever the structure and the size of the nanoparticles, and which subsists when increasing the temperature. The onion-shell chemical configuration is found for both symmetries and is initiated from the Pd surface segregation. It is amplified in the icosahedral symmetry and small sizes but when considering larger sizes, the oscillating segregation profile occurs near the surface on about three to four shells whatever the structure. Pd segregation results from the significant lower cohesive energy of Pd as compared to Pt and the weak ordering tendency leads to the Pt subsurface segregation. The very weak size mismatch does not prevent the bigger atoms (Pt) from occupying subsurface sites which are in compression whereas the smaller ones (Pd) occupy the central site of the icosahedra where the compression is an order of magnitude higher.

Problems in understanding the structure and assembly of viruses

DOE Office of Scientific and Technical Information (OSTI.GOV)

King, J.

1997-12-01

Though viruses infect the cells of all groups of animals, plants, and microorganisms, their structures follow a limited number of general themes; spherical or cylindrical shells built of hundreds of repeated protein subunits enclosing a nucleic acid - DNA or RNA - genome. Since the 1960s it has been known that the protein shells of spherical viruses in fact conform to icosahedral symmetry or to subtle deviations from icosahedral symmetry. The construction of the shell lattices and the transformations they go through in the different stages of the viral life cycle are not fully understood. The shells contain the nucleicmore » in a highly condensed state, of unknown coiling/organization. Features of the well studied bacterial viruses will be reviewed, with examples from adenoviruses, herpesviruses, poliovirus, and HIV. The emergence of new viral disease has led to increased interest in the development of agents which interfere with virus reproduction at the level of the assembly or function of the organized particle. Recently computational approaches to the problem of virus assembly have made important contributions to clarifying shell assembly processes. 1 ref.« less

Components of Adenovirus Genome Packaging

PubMed Central

Ahi, Yadvinder S.; Mittal, Suresh K.

2016-01-01

Adenoviruses (AdVs) are icosahedral viruses with double-stranded DNA (dsDNA) genomes. Genome packaging in AdV is thought to be similar to that seen in dsDNA containing icosahedral bacteriophages and herpesviruses. Specific recognition of the AdV genome is mediated by a packaging domain located close to the left end of the viral genome and is mediated by the viral packaging machinery. Our understanding of the role of various components of the viral packaging machinery in AdV genome packaging has greatly advanced in recent years. Characterization of empty capsids assembled in the absence of one or more components involved in packaging, identification of the unique vertex, and demonstration of the role of IVa2, the putative packaging ATPase, in genome packaging have provided compelling evidence that AdVs follow a sequential assembly pathway. This review provides a detailed discussion on the functions of the various viral and cellular factors involved in AdV genome packaging. We conclude by briefly discussing the roles of the empty capsids, assembly intermediates, scaffolding proteins, portal vertex and DNA encapsidating enzymes in AdV assembly and packaging. PMID:27721809

Structure of Sputnik, a virophage, at 3.5-Å resolution

PubMed Central

Zhang, Xinzheng; Sun, Siyang; Xiang, Ye; Wong, Jimson; Klose, Thomas; Raoult, Didier; Rossmann, Michael G.

2012-01-01

“Sputnik” is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. We have used cryo-EM to produce an electron density map of the icosahedral Sputnik virus at 3.5-Å resolution, sufficient to verify the identity of most amino acids in the capsid proteins and to establish the identity of the pentameric protein forming the fivefold vertices. It was also shown that the virus lacks an internal membrane. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double “jelly-roll” major capsid proteins creating pseudohexameric capsomer symmetry. The pentameric capsomers consist of five single jelly-roll proteins. The release of the genome by displacing one or more of the pentameric capsomers may be the result of a low-pH environment. These results suggest a mechanism of Sputnik DNA ejection that probably also occurs in other big icosahedral double jelly-roll viruses such as Adenovirus. In this study, the near-atomic resolution structure of a virus has been established where crystallization for X-ray crystallography was not feasible. PMID:23091035

Structure of Sputnik, a virophage, at 3.5-Å resolution.

PubMed

Zhang, Xinzheng; Sun, Siyang; Xiang, Ye; Wong, Jimson; Klose, Thomas; Raoult, Didier; Rossmann, Michael G

2012-11-06

"Sputnik" is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. We have used cryo-EM to produce an electron density map of the icosahedral Sputnik virus at 3.5-Å resolution, sufficient to verify the identity of most amino acids in the capsid proteins and to establish the identity of the pentameric protein forming the fivefold vertices. It was also shown that the virus lacks an internal membrane. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double "jelly-roll" major capsid proteins creating pseudohexameric capsomer symmetry. The pentameric capsomers consist of five single jelly-roll proteins. The release of the genome by displacing one or more of the pentameric capsomers may be the result of a low-pH environment. These results suggest a mechanism of Sputnik DNA ejection that probably also occurs in other big icosahedral double jelly-roll viruses such as Adenovirus. In this study, the near-atomic resolution structure of a virus has been established where crystallization for X-ray crystallography was not feasible.

Unparalleled lithium and sodium superionic conduction in solid electrolytes with large monovalent cage-like anions

DOE PAGES

Tang, Wan Si; Unemoto, Atsushi; Zhou, Wei; ...

2015-10-08

Solid electrolytes with sufficiently high conductivities and stabilities are the elusive answer to the inherent shortcomings of organic liquid electrolytes prevalent in today's rechargeable batteries. We recently revealed a novel fast-ion-conducting sodium salt, Na 2B 12H 12, which contains large, icosahedral, divalent B 12H 12 2– anions that enable impressive superionic conductivity, albeit only above its 529 K phase transition. Its lithium congener, Li 2B 12H 12, possesses an even more technologically prohibitive transition temperature above 600 K. Here we show that the chemically related LiCB 11H 12 and NaCB 11H 12 salts, which contain icosahedral, monovalent CB 11H 12–more » anions, both exhibit much lower transition temperatures near 400 K and 380 K, respectively, and truly stellar ionic conductivities (>0.1 S cm –1) unmatched by any other known polycrystalline materials at these temperatures. Furthermore with proper modifications, we are confident that room-temperature-stabilized superionic salts incorporating such large polyhedral anion building blocks are attainable, thus enhancing their future prospects as practical electrolyte materials in next-generation, all-solid-state batteries.« less

Dynamical, structural and chemical heterogeneities in a binary metallic glass-forming liquid

NASA Astrophysics Data System (ADS)

Puosi, F.; Jakse, N.; Pasturel, A.

2018-04-01

As it approaches the glass transition, particle motion in liquids becomes highly heterogeneous and regions with virtually no mobility coexist with liquid-like domains. This complex dynamic is believed to be responsible for different phenomena including non-exponential relaxation and the breakdown of the Stokes-Einstein relation. Understanding the relationships between dynamical heterogeneities and local structure in metallic liquids and glasses is a major scientific challenge. Here we use classical molecular dynamics simulations to study the atomic dynamics and microscopic structure of Cu50Zr50 alloy in the supercooling regime. Dynamical heterogeneities are identified via an isoconfigurational analysis. We demonstrate the transition from isolated to clustering low mobility with decreasing temperature. These slow clusters, whose sizes grow upon cooling, are also associated with concentration fluctuations, characterized by a Zr-enriched phase, with a composition CuZr2 . In addition, a structural analysis of slow clusters based on Voronoi tessellation evidences an increase with respect of the bulk system of the fraction of Cu atoms having a local icosahedral order. These results are in agreement with the consolidated scenario of the relevant role played by icosahedral order in the dynamic slowing-down in supercooled metal alloys.

Potential Applications of Quasicrystalline Materials

NASA Astrophysics Data System (ADS)

Dubois, Jean-Marie; Brunet, Pierre; Belin-FerrÉ, Esther

Since their first public report by the end of 1984, quasicrystailine materials were dreamt of for a variety of possible technological applications. These may be categorized in two broad families: coatings, already secured in a patent in 1988, and composites, appeared more recently. A few examples of products derived from such materials are now on the market. The aim of this chapter is to give insight into a few central questions that arise along with the technological prospects of quasicrystals, namely alloy design, thin films, industrial processing of thick coatings, surface preparation and properties, and new potential applications.

Generalized Kubo formulas for the transport properties of incommensurate 2D atomic heterostructures

NASA Astrophysics Data System (ADS)

Cancès, Eric; Cazeaux, Paul; Luskin, Mitchell

2017-06-01

We give an exact formulation for the transport coefficients of incommensurate two-dimensional atomic multilayer systems in the tight-binding approximation. This formulation is based upon the C* algebra framework introduced by Bellissard and collaborators [Coherent and Dissipative Transport in Aperiodic Solids, Lecture Notes in Physics (Springer, 2003), Vol. 597, pp. 413-486 and J. Math. Phys. 35(10), 5373-5451 (1994)] to study aperiodic solids (disordered crystals, quasicrystals, and amorphous materials), notably in the presence of magnetic fields (quantum Hall effect). We also present numerical approximations and test our methods on a one-dimensional incommensurate bilayer system.

Thermal Emission Control via Bandgap Engineering in Aperiodically Designed Nanophotonic Devices.

PubMed

Maciá, Enrique

2015-05-20

Aperiodic photonic crystals can open up novel routes for more efficient photon management due to increased degrees of freedom in their design along with the unique properties brought about by the long-range aperiodic order as compared to their periodic counterparts. In this work we first describe the fundamental notions underlying the idea of thermal emission/absorption control on the basis of the systematic use of aperiodic multilayer designs in photonic quasicrystals. Then, we illustrate the potential applications of this approach in order to enhance the performance of daytime radiative coolers and solar thermoelectric energy generators.

Thermal Emission Control via Bandgap Engineering in Aperiodically Designed Nanophotonic Devices

PubMed Central

Maciá, Enrique

2015-01-01

Aperiodic photonic crystals can open up novel routes for more efficient photon management due to increased degrees of freedom in their design along with the unique properties brought about by the long-range aperiodic order as compared to their periodic counterparts. In this work we first describe the fundamental notions underlying the idea of thermal emission/absorption control on the basis of the systematic use of aperiodic multilayer designs in photonic quasicrystals. Then, we illustrate the potential applications of this approach in order to enhance the performance of daytime radiative coolers and solar thermoelectric energy generators. PMID:28347037

Holographic fabrication of 3D photonic crystals through interference of multi-beams with 4 + 1, 5 + 1 and 6 + 1 configurations.

PubMed

George, D; Lutkenhaus, J; Lowell, D; Moazzezi, M; Adewole, M; Philipose, U; Zhang, H; Poole, Z L; Chen, K P; Lin, Y

2014-09-22

In this paper, we are able to fabricate 3D photonic crystals or quasi-crystals through single beam and single optical element based holographic lithography. The reflective optical elements are used to generate multiple side beams with s-polarization and one central beam with circular polarization which in turn are used for interference based holographic lithography without the need of any other bulk optics. These optical elements have been used to fabricate 3D photonic crystals with 4, 5 or 6-fold symmetry. A good agreement has been observed between fabricated holographic structures and simulated interference patterns.

Measures with locally finite support and spectrum.

PubMed

Meyer, Yves F

2016-03-22

The goal of this paper is the construction of measures μ on R(n)enjoying three conflicting but fortunately compatible properties: (i) μ is a sum of weighted Dirac masses on a locally finite set, (ii) the Fourier transform μ f μ is also a sum of weighted Dirac masses on a locally finite set, and (iii) μ is not a generalized Dirac comb. We give surprisingly simple examples of such measures. These unexpected patterns strongly differ from quasicrystals, they provide us with unusual Poisson's formulas, and they might give us an unconventional insight into aperiodic order.

Measures with locally finite support and spectrum

PubMed Central

Meyer, Yves F.

2016-01-01

The goal of this paper is the construction of measures μ on Rn enjoying three conflicting but fortunately compatible properties: (i) μ is a sum of weighted Dirac masses on a locally finite set, (ii) the Fourier transform μ^ of μ is also a sum of weighted Dirac masses on a locally finite set, and (iii) μ is not a generalized Dirac comb. We give surprisingly simple examples of such measures. These unexpected patterns strongly differ from quasicrystals, they provide us with unusual Poisson's formulas, and they might give us an unconventional insight into aperiodic order. PMID:26929358

On the spectra of Pisot-cyclotomic numbers

NASA Astrophysics Data System (ADS)

Hare, Kevin G.; Masáková, Zuzana; Vávra, Tomáš

2018-07-01

We investigate the complex spectra X^A(β )= \\sum _{j=0}^na_jβ ^j : n\\in N, a_j\\in A where β is a quadratic or cubic Pisot-cyclotomic number and the alphabet A is given by 0 along with a finite collection of roots of unity. Such spectra are discrete aperiodic structures with crystallographically forbidden symmetries. We discuss in general terms under which conditions they possess the Delone property required for point sets modeling quasicrystals. We study the corresponding Voronoi tilings and we relate these structures to quasilattices arising from the cut-and-project method.

Reconstruction of viruses from solution x-ray scattering data

NASA Astrophysics Data System (ADS)

Zheng, Yibin; Doerschuk, Peter C.; Johnson, John E.

1995-08-01

A model-based method for reconstructing the 3D structure of icosahedrally-symmetric viruses from solution x-ray scattering is presented. An example of the reconstruction, for data from cowpea mosaic virus, is described. The major opportunity provided by solution x-ray scattering is the ability to study the dynamics of virus particles in solution, information that is not accessible to crystal x-ray diffraction experiments.

Use of ion-mobility mass spectrometry (IMS-MS) to map polyoxometalate Keplerate clusters and their supramolecular assemblies.

PubMed

Robbins, Philip J; Surman, Andrew J; Thiel, Johannes; Long, De-Liang; Cronin, Leroy

2013-03-07

We present the high-resolution (HRES-MS) and ion-mobility (IMS-MS) mass spectrometry studies of icosahedral nanoscale polyoxometalate-based {L(30)}{(Mo)Mo(5)} Keplerate clusters, and demonstrate the use of IMS-MS to resolve and map intact nanoclusters, and its potential for the discovery of new structures, in this case the first gas phase observation of 'proto-clustering' of higher order Keplerate supramolecular aggregates.

Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification.

PubMed

Sinclair, Robert M; Ravantti, Janne J; Bamford, Dennis H

2017-04-15

Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between individual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification. We reinvestigate whether the structure-based classification for viral coat proteins making icosahedral virus capsids is in fact supported by previously undetected sequence similarity. Since codon choices can influence nascent protein folding cotranslationally, we searched for both amino acid and nucleotide sequence similarity. To demonstrate the sensitivity of the approach, we identify a candidate gene for the pandoravirus capsid protein. We show that the structure-based classification is strongly supported by amino acid and also nucleotide sequence similarities, suggesting that the similarities are due to common descent. The correspondence between structure-based and sequence-based analyses of the same proteins shown here allow them to be used in future analyses of the relationship between linear sequence information and macromolecular function, as well as between linear sequence and protein folds. IMPORTANCE Viral capsids protect nucleic acid genomes, which in turn encode capsid proteins. This tight coupling of protein shell and nucleic acids, together with strong functional constraints on capsid protein folding and architecture, leads to the hypothesis that capsid protein-coding nucleotide sequences may retain signatures of ancient viral evolution. We have been able to show that this is indeed the case, using the major capsid proteins of viruses forming icosahedral capsids. Importantly

Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification

PubMed Central

Sinclair, Robert M.; Ravantti, Janne J.

2017-01-01

ABSTRACT Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between individual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification. We reinvestigate whether the structure-based classification for viral coat proteins making icosahedral virus capsids is in fact supported by previously undetected sequence similarity. Since codon choices can influence nascent protein folding cotranslationally, we searched for both amino acid and nucleotide sequence similarity. To demonstrate the sensitivity of the approach, we identify a candidate gene for the pandoravirus capsid protein. We show that the structure-based classification is strongly supported by amino acid and also nucleotide sequence similarities, suggesting that the similarities are due to common descent. The correspondence between structure-based and sequence-based analyses of the same proteins shown here allow them to be used in future analyses of the relationship between linear sequence information and macromolecular function, as well as between linear sequence and protein folds. IMPORTANCE Viral capsids protect nucleic acid genomes, which in turn encode capsid proteins. This tight coupling of protein shell and nucleic acids, together with strong functional constraints on capsid protein folding and architecture, leads to the hypothesis that capsid protein-coding nucleotide sequences may retain signatures of ancient viral evolution. We have been able to show that this is indeed the case, using the major capsid proteins of viruses forming icosahedral capsids

A Molecular Dynamics Study of the Structure-Dynamics Relationships of Supercooled Liquids and Glasses

NASA Astrophysics Data System (ADS)

Soklaski, Ryan

Central to the field of condensed matter physics is a decades old outstanding problem in the study of glasses -- namely explaining the extreme slowing of dynamics in a liquid as it is supercooled towards the so-called glass transition. Efforts to universally describe the stretched relaxation processes and heterogeneous dynamics that characteristically develop in supercooled liquids remain divided in both their approaches and successes. Towards this end, a consensus on the role that atomic and molecular structures play in the liquid is even more tenuous. However, mounting material science research efforts have culminated to reveal that the vast diversity of metallic glass species and their properties are rooted in an equally-broad set of structural archetypes. Herein lies the motivation of this dissertation: the detailed information available regarding the structure-property relationships of metallic glasses provides a new context in which one can study the evolution of a supercooled liquid by utilizing a structural motif that is known to dominate the glass. Cu64Zr36 is a binary alloy whose good glass-forming ability and simple composition makes it a canonical material to both empirical and numerical studies. Here, we perform classical molecular dynamics simulations and conduct a comprehensive analysis of the dynamical regimes of liquid Cu64Zr36, while focusing on the roles played by atomic icosahedral ordering -- a structural motif which ultimately percolates the glass' structure. Large data analysis techniques are leveraged to obtain uniquely detailed structural and dynamical information in this context. In doing so, we develop the first account of the origin of icosahedral order in this alloy, revealing deep connections between this incipient structural ordering, frustration-limited domain theory, and recent important empirical findings that are relevant to the nature of metallic liquids at large. Furthermore, important dynamical landmarks such as the breakdown

Spin wave propagation spectra in Octonacci one-dimensional magnonic quasicrystals

NASA Astrophysics Data System (ADS)

Valeriano, Analine P.; Costa, Carlos H.; Bezerra, Claudionor G.

2018-06-01

In this paper, we study spin wave propagation in quasiperiodic magnonic superlattices that follow the so-called Octonacci quasiperiodic sequence, where the N-th stage can be obtained through the recurrence rule SN =SN-1SN-2SN-1 , for N ⩾ 3 , and starting with S1 = A and S2 = B . The multilayered magnonic nanostructure is composed of two simple cubic ferromagnetic materials, labeled A and B, which interact through bilinear and biquadratic exchange couplings at their interfaces. The ferromagnetic materials are described by the Heisenberg model, and a transfer matrix treatment is employed, with the calculations performed for the exchange-dominated regime, taking the random phase approximation (RPA) into account. The obtained numerical results show the effects of both (i) the Octonacci quasiperiodic sequence and (ii) the biquadratic exchange coupling on the band structure and transmission spectra of spin waves. Comparisons are also performed with the spectra found in other periodic and quasiperiodic structures.

Method of making quasicrystal alloy powder, protective coatings and articles

DOEpatents

Shield, J.E.; Goldman, A.I.; Anderson, I.E.; Ellis, T.W.; McCallum, R.W.; Sordelet, D.J.

1995-07-18

A method of making quasicrystalline alloy particulates is disclosed wherein an alloy is superheated and the melt is atomized to form generally spherical alloy particulates free of mechanical fracture and exhibiting a predominantly quasicrystalline in the atomized condition structure. The particulates can be plasma sprayed to form a coating or consolidated to form an article of manufacture. 3 figs.

Method of making quasicrystal alloy powder, protective coatings and articles

DOEpatents

Shield, Jeffrey E.; Goldman, Alan I.; Anderson, Iver E.; Ellis, Timothy W.; McCallum, R. William; Sordelet, Daniel J.

1995-07-18

A method of making quasicrystalline alloy particulates wherein an alloy is superheated and the melt is atomized to form generally spherical alloy particulates free of mechanical fracture and exhibiting a predominantly quasicrystalline in the atomized condition structure. The particulates can be plasma sprayed to form a coating or consolidated to form an article of manufacture.

Necrotizing hepatitis in a domestic pigeon (Columba livia).

PubMed

Himmel, L; O'Connor, M; Premanandan, C

2014-11-01

An adult male domestic pigeon (Columba livia) was presented for necropsy following natural death after a period of chronic weight loss and severe intestinal ascariasis. Histopathologic examination of the liver found moderate to marked, multifocal necrotizing hepatitis with large, basophilic intranuclear inclusion bodies. Transmission electron microscopy of affected hepatocytes demonstrated numerous intra- and perinuclear icosahedral virions arranged in a lattice structure, consistent with adenoviral infection. © The Author(s) 2014.

Detection of Intermediates And Kinetic Control During Assembly of Bacteriophage P22 Procapsid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuma, R.; Tsuruta, H.; French, K.H.

2009-05-26

Bacteriophage P22 serves as a model for the assembly and maturation of other icosahedral double-stranded DNA viruses. P22 coat and scaffolding proteins assemble in vitro into an icosahedral procapsid, which then expands during DNA packaging (maturation). Efficient in vitro assembly makes this system suitable for design and production of monodisperse spherical nanoparticles (diameter {approx} 50 nm). In this work, we explore the possibility of controlling the outcome of assembly by scaffolding protein engineering. The scaffolding protein exists in monomer-dimer-tetramer equilibrium. We address the role of monomers and dimers in assembly by using three different scaffolding proteins with altered monomer-dimer equilibriummore » (weak dimer, covalent dimer, monomer). The progress and outcome of assembly was monitored by time-resolved X-ray scattering, which allowed us to distinguish between closed shells and incomplete assembly intermediates. Binding of scaffolding monomer activates the coat protein for assembly. Excess dimeric scaffolding protein resulted in rapid nucleation and kinetic trapping yielding incomplete shells. Addition of monomeric wild-type scaffold with excess coat protein completed these metastable shells. Thus, the monomeric scaffolding protein plays an essential role in the elongation phase by activating the coat and effectively lowering its critical concentration for assembly.« less

Archaeal Viruses Multiply: Temporal Screening in a Solar Saltern

PubMed Central

Atanasova, Nina S.; Demina, Tatiana A.; Buivydas, Andrius; Bamford, Dennis H.; Oksanen, Hanna M.

2015-01-01

Hypersaline environments around the world are dominated by archaea and their viruses. To date, very little is known about these viruses and their interaction with the host strains when compared to bacterial and eukaryotic viruses. We performed the first culture-dependent temporal screening of haloarchaeal viruses and their hosts in the saltern of Samut Sakhon, Thailand, during two subsequent years (2009, 2010). Altogether we obtained 36 haloarchaeal virus isolates and 36 archaeal strains, significantly increasing the number of known archaeal virus isolates. Interestingly, the morphological distribution of our temporal isolates (head-tailed, pleomorphic, and icosahedral membrane-containing viruses) was similar to the outcome of our previous spatial survey supporting the observations of a global resemblance of halophilic microorganisms and their viruses. Myoviruses represented the most abundant virus morphotype with strikingly broad host ranges. The other viral morphotypes (siphoviruses, as well as pleomorphic and icosahedral internal membrane-containing viruses) were more host-specific. We also identified a group of Halorubrum strains highly susceptible to numerous different viruses (up to 26). This high virus sensitivity, the abundance of broad host range viruses, and the maintenance of infectivity over a period of one year suggest constant interplay of halophilic microorganisms and their viruses within an extreme environment. PMID:25866903

Membrane Remodeling by the Double-Barrel Scaffolding Protein of Poxvirus

PubMed Central

Hijnen, Marcel; Schult, Philipp; Pettikiriarachchi, Anne; Mitra, Alok K.; Coulibaly, Fasséli

2011-01-01

In contrast to most enveloped viruses, poxviruses produce infectious particles that do not acquire their internal lipid membrane by budding through cellular compartments. Instead, poxvirus immature particles are generated from atypical crescent-shaped precursors whose architecture and composition remain contentious. Here we describe the 2.6 Å crystal structure of vaccinia virus D13, a key structural component of the outer scaffold of viral crescents. D13 folds into two jellyrolls decorated by a head domain of novel fold. It assembles into trimers that are homologous to the double-barrel capsid proteins of adenovirus and lipid-containing icosahedral viruses. We show that, when tethered onto artificial membranes, D13 forms a honeycomb lattice and assembly products structurally similar to the viral crescents and immature particles. The architecture of the D13 honeycomb lattice and the lipid-remodeling abilities of D13 support a model of assembly that exhibits similarities with the giant mimivirus. Overall, these findings establish that the first committed step of poxvirus morphogenesis utilizes an ancestral lipid-remodeling strategy common to icosahedral DNA viruses infecting all kingdoms of life. Furthermore, D13 is the target of rifampicin and its structure will aid the development of poxvirus assembly inhibitors. PMID:21931553

Archaeal viruses multiply: temporal screening in a solar saltern.

PubMed

Atanasova, Nina S; Demina, Tatiana A; Buivydas, Andrius; Bamford, Dennis H; Oksanen, Hanna M

2015-04-10

Hypersaline environments around the world are dominated by archaea and their viruses. To date, very little is known about these viruses and their interaction with the host strains when compared to bacterial and eukaryotic viruses. We performed the first culture-dependent temporal screening of haloarchaeal viruses and their hosts in the saltern of Samut Sakhon, Thailand, during two subsequent years (2009, 2010). Altogether we obtained 36 haloarchaeal virus isolates and 36 archaeal strains, significantly increasing the number of known archaeal virus isolates. Interestingly, the morphological distribution of our temporal isolates (head-tailed, pleomorphic, and icosahedral membrane-containing viruses) was similar to the outcome of our previous spatial survey supporting the observations of a global resemblance of halophilic microorganisms and their viruses. Myoviruses represented the most abundant virus morphotype with strikingly broad host ranges. The other viral morphotypes (siphoviruses, as well as pleomorphic and icosahedral internal membrane-containing viruses) were more host-specific. We also identified a group of Halorubrum strains highly susceptible to numerous different viruses (up to 26). This high virus sensitivity, the abundance of broad host range viruses, and the maintenance of infectivity over a period of one year suggest constant interplay of halophilic microorganisms and their viruses within an extreme environment.

Formation mechanism of atomic cluster structures in Al-Mg alloy during rapid solidification processes

NASA Astrophysics Data System (ADS)

Liu, Feng-xiang; Liu, Rang-su; Hou, Zhao-yang; Liu, Hai-Rong; Tian, Ze-an; Zhou, Li-li

2009-02-01

The rapid solidification processes of Al 50Mg 50 liquid alloy consisting of 50,000 atoms have been simulated by using molecular dynamics method based on the effective pair potential derived from the pseudopotential theory. The formation mechanisms of atomic clusters during the rapid solidification processes have been investigated adopting a new cluster description method—cluster-type index method (CTIM). The simulated partial structure factors are in good agreement with the experimental results. And Al-Mg amorphous structure characterized with Al-centered icosahedral topological short-range order (SRO) is found to form during the rapid solidification processes. The icosahedral cluster plays a key role in the microstructure transition. Besides, it is also found that the size distribution of various clusters in the system presents a magic number sequence of 13, 19, 23, 25, 29, 31, 33, 37, …. The magic clusters are more stable and mainly correspond to the incompact arrangements of linked icosahedra in the form of rings, chains or dendrites. And each magic number point stands correspondingly for one certain combining form of icosahedra. This magic number sequence is different from that generated in the solidification structure of liquid Al and those obtained by methods of gaseous deposition and ionic spray, etc.

Molecular characterization of birnaviruses isolated from wild marine fishes at the Flemish Cap (Newfoundland)

USGS Publications Warehouse

Romero-Brey, I.; Batts, W.N.; Bandin, I.; Winton, J.R.; Dopazo, C.P.

2004-01-01

Several isolates of aquatic birnaviruses were recovered from different species of wild fish caught in the Flemish Cap, a Newfoundland fishery close to the Atlantic coast of Canada. The nucleotide sequence of a region of the NS gene was identical among the isolates and was most similar to the Dry Mills and West Buxton reference strains of infectious pancreatic necrosis virus (IPNV). Phylogenetic analysis of the sequence of a region of the VP2 gene demonstrated that the isolates were most closely aligned with the American strains of IPNV serotype Al. Electron microscopy of virus structures clarified and concentrated from cultures of infected chinook salmon embryo (CHSE-214) cells revealed a majority of typical IPNV-like icosahedral particles, as well as a low proportion of type I tubules having a diameter of approximately 55 nm and a variable length of up to 2 ??m. The tubules could be propagated in cell cultures, but always in the presence of low proportions of icosahedral particles. Cloning of selected isolates by serial dilution yielded preparations with a high proportion of the tubular structures with a density in CsCl gradients of approximately 1.30 g cm-3. Polyacrylamide gel electrophoresis revealed the material in the band was composed of the IPNV pVP2 and VP2 proteins.

A first-principles core-level XPS study on the boron impurities in germanium crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamauchi, Jun; Yoshimoto, Yoshihide; Suwa, Yuji

2013-12-04

We systematically investigated the x-ray photoelectron spectroscopy (XPS) core-level shifts and formation energies of boron defects in germanium crystals and compared the results to those in silicon crystals. Both for XPS core-level shifts and formation energies, relationship between defects in Si and Ge is roughly linear. From the similarity in the formation energy, it is expected that the exotic clusters like icosahedral B12 exist in Ge as well as in Si.

Correlation of nonorthogonality of best hybrid bond orbitals with bond strength of orthogonal orbitals.

PubMed

Pauling, L

1976-02-01

An expression is derived for the bond length of two spd orbitals with maximum values in two directions forming a given bond angle by consideration of the nonorthogonality integral of two best orbitals in these directions. This equation is equivalent to the expression derived by formulating the pair of orthogonal orbitals. Similar expressions are derived for spdf orbitals. Applications are made to icosahedral and cuboctahedral bonds and to the packing of nucleons in atomic nuclei.

Development of a High Throughput Assay for Indirectly Measuring Phage Growth Using the OmniLog (trademark) System

DTIC Science & Technology

2012-09-01

and phage Giraffe exhibits a similar morphology (Fig. 1A). Phage BA39 (Fig. 1E) appears to belong to the Myoviridae family (icosahedral head and...see later) but this assignment is tentative. Monitoring the kinetics of bacterial growth using OmniLogTM system upon infection with Giraffe phage...spores with and without infection by Giraffe phage are shown in Figure 2A and B respectively. The growth of 7702 without phage infection followed a

Smooth Scaling of Valence Electronic Properties in Fullerenes: From One Carbon Atom, to C60, to Graphene

DTIC Science & Technology

2012-09-18

Smooth scaling of valence electronic properties in fullerenes: from one carbon atom , to C60, to graphene Greyson R. Lewis,1 William E. Bunting,1...pacitance scaling lines of the fullerenes. Lastly, it is found that points representing the carbon atom and the graphene limit lie on scaling lines for...icosahedral fullerenes, so their quantum capacitances and their detachment energies scale smoothly from one C atom , through C60, to graphene. I

Correlation of nonorthogonality of best hybrid bond orbitals with bond strength of orthogonal orbitals

PubMed Central

Pauling, Linus

1976-01-01

An expression is derived for the bond length of two spd orbitals with maximum values in two directions forming a given bond angle by consideration of the nonorthogonality integral of two best orbitals in these directions. This equation is equivalent to the expression derived by formulating the pair of orthogonal orbitals. Similar expressions are derived for spdf orbitals. Applications are made to icosahedral and cuboctahedral bonds and to the packing of nucleons in atomic nuclei. PMID:16578736

Structure of the orthorhombic form of Mn(2)Al(7), Fe(2)Al(7), and (Mn(0.7)Fe(0.3))(2)Al(7) that by twinning produces grains with decagonal point-group symmetry.

PubMed

Pauling, L

1988-04-01

Analysis of electron diffraction photographs of grains of Mn(2)Al(7), Fe(2)Al(7), and (Mn(0.7)Fe(0.3))(2)Al(7) leads to the conclusion that they are 5-fold twins of a 1664-atom orthorhombic crystal with a = 32.86 A, b = 31.23 A, and c = 24.80 A and with 16 icosahedral clusters of 104 atoms in positions shifted by small amounts from those of the cubic beta-tungsten structure.

Pairing Heterocyclic Cations with closo-dodecafluorododecaborate (2-) Synthesis of Binary Heterocyclium (1+) Salts and a Ag4(heterocycle)8(4+) Salt of B12F12(2-)

DTIC Science & Technology

2011-01-01

10989). 13. SUPPLEMENTARY NOTES Journal article published in the Journal of Fluorine Chemistry, Vol. 132, Nov 2011. PA Case Number: 10989...TELEPHONE NUMBER (include area code) N/A Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std. 239.18 Journal of Fluorine Chemistry 132 (2011... Fluorine Chemistry jo ur n al h o mep ag e: www .e lsev ier . c om / loc ate / f luo r1. Introduction Eight new binary salts that pair the icosahedral

Optical fabrication of large area photonic microstructures by spliced lens

NASA Astrophysics Data System (ADS)

Jin, Wentao; Song, Meng; Zhang, Xuehua; Yin, Li; Li, Hong; Li, Lin

2018-05-01

We experimentally demonstrate a convenient approach to fabricate large area photorefractive photonic microstructures by a spliced lens device. Large area two-dimensional photonic microstructures are optically induced inside an iron-doped lithium niobate crystal. The experimental setups of our method are relatively compact and stable without complex alignment devices. It can be operated in almost any optical laboratories. We analyze the induced triangular lattice microstructures by plane wave guiding, far-field diffraction pattern imaging and Brillouin-zone spectroscopy. By designing the spliced lens appropriately, the method can be easily extended to fabricate other complex large area photonic microstructures, such as quasicrystal microstructures. Induced photonic microstructures can be fixed or erased and re-recorded in the photorefractive crystal.

High extraction efficiency GaN-based light-emitting diodes on embedded SiO2 nanorod array and nanoscale patterned sapphire substrate

NASA Astrophysics Data System (ADS)

Huang, Hung-Wen; Huang, Jhi-Kai; Kuo, Shou-Yi; Lee, Kang-Yuan; Kuo, Hao-Chung

2010-06-01

In this paper, GaN-based LEDs with a nanoscale patterned sapphire substrate (NPSS) and a SiO2 photonic quasicrystal (PQC) structure on an n-GaN layer using nanoimprint lithography are fabricated and investigated. The light output power of LED with a NPSS and a SiO2 PQC structure on an n-GaN layer was 48% greater than that of conventional LED. Strong enhancement in output power is attributed to better epitaxial quality and higher reflectance resulted from NPSS and PQC structures. Transmission electron microscopy images reveal that threading dislocations are blocked or bended in the vicinities of NPSS layer. These results provide promising potential to increase output power for commercial light emitting devices.

Broadband multiple responses of surface modes in quasicrystalline plasmonic structure

PubMed Central

Yuan, Haiming; Jiang, Xiangqian; Huang, Feng; Sun, Xiudong

2016-01-01

We numerically study the multiple excitation of surface modes in 2D photonic quasicrystal/metal/substrate structure. An improved rigorous coupled wave analysis method that can handle the quasicrystalline structure is presented. The quasicrystalline lattice, which refers to Penrose tiling in this paper, is generated by the cut-and-project method. The normal incidence spectrum presents a broadband multiple responses property. We find that the phase matching condition determines the excitation frequency for a given incident angle, while the depth of the reflection valley depends on the incident polarization. The modes will split into several sub-modes at oblique incidence, which give rise to the appearance of more responses on the spectrum. PMID:27492782

The Efficiency of Delone Coverings of the Canonical Tilings T^*(A4) and T^*(D6)

NASA Astrophysics Data System (ADS)

Papadopolos, Zorka; Kasner, Gerald

This chapter is devoted to the coverings of the two quasiperiodic canonical tilings T^*(A4) and T^*(D6) T^*(2F), obtained by projection from the root lattices A4 and D6, respectively. In the first major part of this chapter, in Sect. 5.2, we shall introduce a Delone covering C^sT^*(A4) of the 2-dimensional decagonal tiling T^*(A4). In the second major part of this chapter, Sect. 5.3, we summarize the results related to the Delone covering of the icosahedral tiling T^*(D6), CT^*(D6) and determine the zero-, single-, and double- deckings and the resulting thickness of the covering. In the conclusions section, we give some suggestions as to how the definition of the Delone covering might be changed in order to reach some real (full) covering of the icosahedral tiling T^*(D6). In Section 5.2 the definition of the Delone covering is also changed in order to avoid an unnecessary large thickness of the covering.

Cryo-Electron Tomography of Rubella Virus

PubMed Central

Battisti, Anthony J.; Yoder, Joshua D.; Plevka, Pavel; Winkler, Dennis C.; Mangala Prasad, Vidya; Kuhn, Richard J.; Frey, Teryl K.; Steven, Alasdair C.

2012-01-01

Rubella virus is the only member of the Rubivirus genus within the Togaviridae family and is the causative agent of the childhood disease known as rubella or German measles. Here, we report the use of cryo-electron tomography to examine the three-dimensional structure of rubella virions and compare their structure to that of Ross River virus, a togavirus belonging the genus Alphavirus. The ectodomains of the rubella virus glycoproteins, E1 and E2, are shown to be organized into extended rows of density, separated by 9 nm on the viral surface. We also show that the rubella virus nucleocapsid structure often forms a roughly spherical shell which lacks high density at its center. While many rubella virions are approximately spherical and have dimensions similar to that of the icosahedral Ross River virus, the present results indicate that rubella exhibits a large degree of pleomorphy. In addition, we used rotation function calculations and other analyses to show that approximately spherical rubella virions lack the icosahedral organization which characterizes Ross River and other alphaviruses. The present results indicate that the assembly mechanism of rubella virus, which has previously been shown to differ from that of the alphavirus assembly pathway, leads to an organization of the rubella virus structural proteins that is different from that of alphaviruses. PMID:22855483

Ab initio molecular dynamics simulations of short-range order in Zr50Cu45Al5 and Cu50Zr45Al5 metallic glasses

NASA Astrophysics Data System (ADS)

Huang, Yuxiang; Huang, Li; Wang, C. Z.; Kramer, M. J.; Ho, K. M.

2016-03-01

Comparative analysis between Zr-rich Zr50Cu45Al5 and Cu-rich Cu50Zr45Al5 metallic glasses (MGs) is extensively performed to locate the key structural motifs accounting for their difference of glass forming ability. Here we adopt ab initio molecular dynamics simulations to investigate the local atomic structures of Zr50Cu45Al5 and Cu50Zr45Al5 MGs. A high content of icosahedral-related (full and distorted) orders was found in both samples, while in the Zr-rich MG full icosahedrons < 0,0,12,0> is dominant, and in the Cu-rich one the distorted icosahedral orders, especially < 0,2,8,2> and < 0,2,8,1> , are prominent. And the < 0,2,8,2> polyhedra in Cu50Zr45Al5 MG mainly originate from Al-centered clusters, while the < 0,0,12,0> in Zr50Cu45Al5 derives from both Cu-centered clusters and Al-centered clusters. These difference may be ascribed to the atomic size difference and chemical property between Cu and Zr atoms. The relatively large size of Zr and large negative heat of mixing between Zr and Al atoms, enhancing the packing density and stability of metallic glass system, may be responsible for the higher glass forming ability of Zr50Cu45Al5.

Ultrafast Relaxation Dynamics of Au 38 (SC 2 H 4 Ph) 24 Nanoclusters and Effects of Structural Isomerism

DOE PAGES

Zhou, Meng; Tian, Shubo; Zeng, Chenjie; ...

2016-12-22

Structural isomerism in nanoparticles has recently emerged as a new topic and stimulated research interest because the atomic structures of ultrasmall nanoparticles may have great impact on their fundamental properties and applications. We report the correlation between ultrafast relaxation dynamics and atomic structures of two isomers of thiolate-protected Au 38(SC 2H 4Ph) 24. The bi-icosahedral Au 38 (denoted as Au 38Q) with a Au 23 inner core in its atomic structure shows rapid decay (1.5 ps) followed by nanosecond relaxation to the ground state, whereas its structural isomer (Au 38T) exhibits similar relaxation processes, but the rapid decay is acceleratedmore » by ~50% (1.0 ps). The picosecond relaxations in both cases can be assigned to core–shell charge transfer or electronic rearrangement within the metal core. The acceleration of the fast decay in Au38T is ascribed to its unique core structure, which is made up of a mono-icosahedral Au 13 capped by a Au 12 tri-tetrahedron by sharing two atoms. Interestingly, coherent phonon emissions (25 cm –1 for Au 38Q, 27 and 60 cm –1 for Au 38T) are observed in both isomers with pumping in the NIR region. These results illustrate for the first time the importance of atomic structures in the photophysics of same sized gold nanoclusters.« less

Electrical Characterization of Irradiated Semiconducting Amorphous Hydrogenated Boron Carbide

NASA Astrophysics Data System (ADS)

Peterson, George Glenn

Semiconducting amorphous partially dehydrogenated boron carbide has been explored as a neutron voltaic for operation in radiation harsh environments, such as on deep space satellites/probes. A neutron voltaic device could also be used as a solid state neutron radiation detector to provide immediate alerts for radiation workers/students, as opposed to the passive dosimetry badges utilized today. Understanding how the irradiation environment effects the electrical properties of semiconducting amorphous partially dehydrogenated boron carbide is important to predicting the stability of these devices in operation. p-n heterojunction diodes were formed from the synthesis of semiconducting amorphous partially dehydrogenated boron carbide on silicon substrates through the use of plasma enhanced chemical vapor deposition (PECVD). Many forms of structural and electrical measurements and analysis have been performed on the p-n heterojunction devices as a function of both He+ ion and neutron irradiation including: transmission electron microscopy (TEM), selected area electron diffraction (SAED), current versus voltage I(V), capacitance versus voltage C(V), conductance versus frequency G(f), and charge carrier lifetime (tau). In stark contrast to nearly all other electronic devices, the electrical performance of these p-n heterojunction diodes improved with irradiation. This is most likely the result of bond defect passivation and resolution of degraded icosahedral based carborane structures (icosahedral molecules missing a B, C, or H atom(s)).

Ultrafast Relaxation Dynamics of Au 38 (SC 2 H 4 Ph) 24 Nanoclusters and Effects of Structural Isomerism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Meng; Tian, Shubo; Zeng, Chenjie

Structural isomerism in nanoparticles has recently emerged as a new topic and stimulated research interest because the atomic structures of ultrasmall nanoparticles may have great impact on their fundamental properties and applications. We report the correlation between ultrafast relaxation dynamics and atomic structures of two isomers of thiolate-protected Au 38(SC 2H 4Ph) 24. The bi-icosahedral Au 38 (denoted as Au 38Q) with a Au 23 inner core in its atomic structure shows rapid decay (1.5 ps) followed by nanosecond relaxation to the ground state, whereas its structural isomer (Au 38T) exhibits similar relaxation processes, but the rapid decay is acceleratedmore » by ~50% (1.0 ps). The picosecond relaxations in both cases can be assigned to core–shell charge transfer or electronic rearrangement within the metal core. The acceleration of the fast decay in Au38T is ascribed to its unique core structure, which is made up of a mono-icosahedral Au 13 capped by a Au 12 tri-tetrahedron by sharing two atoms. Interestingly, coherent phonon emissions (25 cm –1 for Au 38Q, 27 and 60 cm –1 for Au 38T) are observed in both isomers with pumping in the NIR region. These results illustrate for the first time the importance of atomic structures in the photophysics of same sized gold nanoclusters.« less

Structure, function and dynamics in adenovirus maturation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mangel, Walter F.; San Martín, Carmen

2014-11-21

Here we review the current knowledge on maturation of adenovirus, a non-enveloped icosahedral eukaryotic virus. The adenovirus dsDNA genome fills the capsid in complex with a large amount of histone-like viral proteins, forming the core. Maturation involves proteolytic cleavage of several capsid and core precursor proteins by the viral protease (AVP). AVP uses a peptide cleaved from one of its targets as a “molecular sled” to slide on the viral genome and reach its substrates, in a remarkable example of one-dimensional chemistry. Immature adenovirus containing the precursor proteins lacks infectivity because of its inability to uncoat. The immature core ismore » more compact and stable than the mature one, due to the condensing action of unprocessed core polypeptides; shell precursors underpin the vertex region and the connections between capsid and core. Maturation makes the virion metastable, priming it for stepwise uncoating by facilitating vertex release and loosening the condensed genome and its attachment to the icosahedral shell. The packaging scaffold protein L1 52/55k is also a substrate for AVP. Proteolytic processing of L1 52/55k disrupts its interactions with other virion components, providing a mechanism for its removal during maturation. In conclusion, possible roles for maturation of the terminal protein are discussed.« less

Cryo-electron tomography of rubella virus.

PubMed

Battisti, Anthony J; Yoder, Joshua D; Plevka, Pavel; Winkler, Dennis C; Prasad, Vidya Mangala; Kuhn, Richard J; Frey, Teryl K; Steven, Alasdair C; Rossmann, Michael G

2012-10-01

Rubella virus is the only member of the Rubivirus genus within the Togaviridae family and is the causative agent of the childhood disease known as rubella or German measles. Here, we report the use of cryo-electron tomography to examine the three-dimensional structure of rubella virions and compare their structure to that of Ross River virus, a togavirus belonging the genus Alphavirus. The ectodomains of the rubella virus glycoproteins, E1 and E2, are shown to be organized into extended rows of density, separated by 9 nm on the viral surface. We also show that the rubella virus nucleocapsid structure often forms a roughly spherical shell which lacks high density at its center. While many rubella virions are approximately spherical and have dimensions similar to that of the icosahedral Ross River virus, the present results indicate that rubella exhibits a large degree of pleomorphy. In addition, we used rotation function calculations and other analyses to show that approximately spherical rubella virions lack the icosahedral organization which characterizes Ross River and other alphaviruses. The present results indicate that the assembly mechanism of rubella virus, which has previously been shown to differ from that of the alphavirus assembly pathway, leads to an organization of the rubella virus structural proteins that is different from that of alphaviruses.

Electronic shell structure in Ga12 icosahedra and the relation to the bulk forms of gallium.

PubMed

Schebarchov, D; Gaston, N

2012-07-28

The electronic structure of known cluster compounds with a cage-like icosahedral Ga(12) centre is studied by first-principles theoretical methods, based on density functional theory. We consider these hollow metalloid nanostructures in the context of the polymorphism of the bulk, and identify a close relation to the α phase of gallium. This previously unrecognised connection is established using the electron localisation function, which reveals the ubiquitous presence of radially-pointing covalent bonds around the Ga(12) centre--analogous to the covalent bonds between buckled deltahedral planes in α-Ga. Furthermore, we find prominent superatom shell structure in these clusters, despite their hollow icosahedral motif and the presence of covalent bonds. The exact nature of the electronic shell structure is contrasted with simple electron shell models based on jellium, and we demonstrate how the interplay between gallium dimerisation, ligand- and crystal-field effects can alter the splitting of the partially filled 1F shell. Finally, in the unique compound where the Ga(12) centre is bridged by six phosphorus ligands, the electronic structure most closely resembles that of δ-Ga and there are no well-defined superatom orbitals. The results of this comprehensive study bring new insights into the nature of chemical bonding in metalloid gallium compounds and the relation to bulk gallium metal, and they may also guide the development of more general models for ligand-protected clusters.

Nano-jewellery: C5Au12--a gold-plated diamond at molecular level.

PubMed

Naumkin, F

2006-06-07

A mixed carbon-metal cluster is designed by combining the tetrahedral C(5) radical (with a central atom-the skeleton of the C(5)H(12) molecule) and the spherical Au(12) layer (the external atomic shell of the Au(13) cluster). The C(5)Au(12) cluster and its negative and positive ionic derivatives, C(5)Au(12)(+/-), are investigated ab initio (DFT) in terms of optimized structures and relative energies of a few spin-states, for the icosahedral-like and octahedral-like isomers. The cluster is predicted to be generally more stable in its octahedral shape (similar to C(5)H(12)) which prevails for the negative ion and may compete with the icosahedral shape for the neutral system and positive ion. Adiabatic ionization energies (AIE) and electron affinities (AEA) of C(5)Au(12), vertical electron-detachment (VDE) energies of C(5)Au(12)(-), and vertical ionization and electron-attachment energies (VIE, VEA) of C(5)Au(12) are calculated as well, and compared with those for the corresponding isomers of the Au(13) cluster. The AIE and VIE values are found to be close for the two systems, while the AEA and VDE values are significantly reduced for the radical-based species. A simple fragment-based model is proposed for the decomposition of the total interaction into carbon-gold and gold-gold components.

Ultrastructural morphogenesis of a virus associated with lymphocystis-like lesions in parore Girella tricuspidata (Kyphosidae: Perciformes).

PubMed

Hine, P M; Wakefield, St J; Mackereth, G; Morrison, R

2016-09-26

The morphogenesis of large icosahedral viruses associated with lymphocystis-like lesions in the skin of parore Girella tricuspidata is described. The electron-lucent perinuclear viromatrix comprised putative DNA with open capsids at the periphery, very large arrays of smooth endoplasmic reticulum (sER), much of it with a reticulated appearance (rsER) or occurring as rows of vesicles. Lysosomes, degenerating mitochondria and virions in various stages of assembly, and paracrystalline arrays were also present. Long electron-dense inclusions (EDIs) with 15 nm repeating units split terminally and curled to form tubular structures internalising the 15 nm repeating structures. These tubular structures appeared to form the virion capsids. Large parallel arrays of sER sometimes alternated with aligned arrays of crinkled cisternae along which passed a uniformly wide (20 nm) thread-like structure. Strings of small vesicles near open capsids may also have been involved in formation of an inner lipid layer. Granules with a fine fibrillar appearance also occurred in the viromatrix, and from the presence of a halo around mature virions it appeared that the fibrils may form a layer around the capsid. The general features of virogenesis of large icosahedral dsDNA viruses, the large amount of ER, particularly rsER and the EDIs, are features of nucleo-cytoplasmic large DNA viruses, rather than features of 1 genus or family.

Average crystal structure(s) of the embedded meta stable η‧-phase in the Al-Mg-Zn system

NASA Astrophysics Data System (ADS)

Bøvik Larsen, Helge; Thorkildsen, Gunnar; Natland, Sølvi; Pattison, Philip

2014-05-01

Meta stable embedded nano-sized ?-particles within a single grain extracted from an alloy having the nominal composition ? have been examined with X-ray diffraction. By applying the orientational and metric relationships that exist between the hexagonal unit cell of the ?-particles and the cubic unit cell of the Al-matrix, it has been proven possible to directly collect diffracted intensity data from the ?-particle ensemble. This has been done using synchrotron radiation and a ?-diffractometer having a scintillator point detector setup. The approach has resulted in improved data quality compared to previous experiments. The interpretation of the data set, based on a combination of Patterson syntheses, direct methods and geometrical restraints, yielded two possible average structural representations: one Al-rich with the approximate stoichiometric composition ? and one Al-depleted with approximate stoichiometric composition ?. Both structures are realized in the same space group, ?, and are most probably superimposed in the crystalline system examined. The geometries are discussed within the atomic environment approach where icosahedral or near-icosahedral configurations are encountered. Comparison with previous published models and the equilibrium structure reveals a main difference related to the distribution of the Zn-sites in the unit cell. A possible transformation path is also suggested. Various aspects and challenges regarding data collection, data reduction and data quality are specifically addressed.

Simulating Self-Assembly with Simple Models

NASA Astrophysics Data System (ADS)

Rapaport, D. C.

Results from recent molecular dynamics simulations of virus capsid self-assembly are described. The model is based on rigid trapezoidal particles designed to form polyhedral shells of size 60, together with an atomistic solvent. The underlying bonding process is fully reversible. More extensive computations are required than in previous work on icosahedral shells built from triangular particles, but the outcome is a high yield of closed shells. Intermediate clusters have a variety of forms, and bond counts provide a useful classification scheme

Structure of the orthorhombic form of Mn2Al7, Fe2Al7, and (Mn0.7Fe0.3)2Al7 that by twinning produces grains with decagonal point-group symmetry

PubMed Central

Pauling, Linus

1988-01-01

Analysis of electron diffraction photographs of grains of Mn2Al7, Fe2Al7, and (Mn0.7Fe0.3)2Al7 leads to the conclusion that they are 5-fold twins of a 1664-atom orthorhombic crystal with a = 32.86 Å, b = 31.23 Å, and c = 24.80 Å and with 16 icosahedral clusters of 104 atoms in positions shifted by small amounts from those of the cubic β-tungsten structure. PMID:16593921

Estimating contrast transfer function and associated parameters by constrained non-linear optimization.

PubMed

Yang, C; Jiang, W; Chen, D-H; Adiga, U; Ng, E G; Chiu, W

2009-03-01

The three-dimensional reconstruction of macromolecules from two-dimensional single-particle electron images requires determination and correction of the contrast transfer function (CTF) and envelope function. A computational algorithm based on constrained non-linear optimization is developed to estimate the essential parameters in the CTF and envelope function model simultaneously and automatically. The application of this estimation method is demonstrated with focal series images of amorphous carbon film as well as images of ice-embedded icosahedral virus particles suspended across holes.

Draft genome sequence of the Coccolithovirus Emiliania huxleyi virus 203.

PubMed

Nissimov, Jozef I; Worthy, Charlotte A; Rooks, Paul; Napier, Johnathan A; Kimmance, Susan A; Henn, Matthew R; Ogata, Hiroyuki; Allen, Michael J

2011-12-01

The Coccolithoviridae are a recently discovered group of viruses that infect the marine coccolithophorid Emiliania huxleyi. Emiliania huxleyi virus 203 (EhV-203) has a 160- to 180-nm-diameter icosahedral structure and a genome of approximately 400 kbp, consisting of 464 coding sequences (CDSs). Here we describe the genomic features of EhV-203 together with a draft genome sequence and its annotation, highlighting the homology and heterogeneity of this genome in comparison with the EhV-86 reference genome.

Electronic Transport Behaviors due to Charge Density Waves in Ni-Nb-Zr-H Glassy Alloys

NASA Astrophysics Data System (ADS)

Fukuhara, Mikio; Umemori, Yoshimasa

2013-11-01

The amorphous Ni-Nb-Zr-H glassy alloy containing subnanometer-sized icosahedral Zr5 Nb5Ni3 clusters exhibited four types of electronic phenomena: a metal/insulator transition, an electric current-induced voltage oscillation (Coulomb oscillation), giant capacitor behavior and an electron avalanche with superior resistivity. These findings could be excluded by charge density waves that the low-dimensional component of clusters, in which the atoms are lined up in chains along the [130] direction, plays important roles in various electron transport phenomena.

Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 202.

PubMed

Nissimov, Jozef I; Worthy, Charlotte A; Rooks, Paul; Napier, Johnathan A; Kimmance, Susan A; Henn, Matthew R; Ogata, Hiroyuki; Allen, Michael J

2012-02-01

Emiliania huxleyi virus 202 (EhV-202) is a member of the Coccolithoviridae, a group of viruses that infect the marine coccolithophorid Emiliania huxleyi. EhV-202 has a 160- to 180-nm-diameter icosahedral structure and a genome of approximately 407 kbp, consisting of 485 coding sequences (CDSs). Here we describe the genomic features of EhV-202, together with a draft genome sequence and its annotation, highlighting the homology and heterogeneity of this genome in comparison with the EhV-86 reference genome.

Innovative acoustic technique for studying new materials and new developments in solid state physics

NASA Astrophysics Data System (ADS)

Maynard, Julian D.

1993-10-01

The goals of this project involve the use of innovative acoustic techniques to study new materials and new developments in solid state physics, such as effects in mesoscopic electronic systems. Major accomplishments include (1) the preparation and publication of a number of major papers and chapters in books, (2) the comparison of the anisotropy of an aluminum alloy quasicrystal with that of its cubic approximant, (3) the measurement of the elastic constants of a diamond substitute material, TiB2, (4) the measurement of an extremely low (possibly the lowest) infrared optical-absorption coefficient, (5) the measurement of the effects of disorder on the propagation of a nonlinear pulse, and (6) the acquisition of initial data in an experiment on the onset of fracture.

Cooling rate dependence of simulated Cu{sub 64.5}Zr{sub 35.5} metallic glass structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryltsev, R. E.; Ural Federal University, 19 Mira Str., 620002 Ekaterinburg; L.D. Landau Institute for Theoretical Physics, Russian Academy of Sciences, 2 Kosygina Str., 119334 Moscow

Using molecular dynamics simulations with embedded atom model potential, we study structural evolution of Cu{sub 64.5}Zr{sub 35.5} alloy during the cooling in a wide range of cooling rates γ ∈ (1.5 ⋅ 10{sup 9}, 10{sup 13}) K/s. Investigating short- and medium-range orders, we show that the structure of Cu{sub 64.5}Zr{sub 35.5} metallic glass essentially depends on cooling rate. In particular, a decrease of the cooling rate leads to an increase of abundances of both the icosahedral-like clusters and Frank-Kasper Z16 polyhedra. The amounts of these clusters in the glassy state drastically increase at the γ{sub min} = 1.5 ⋅ 10{supmore » 9} K/s. Analysing the structure of the glass at γ{sub min}, we observe the formation of nano-sized crystalline grain of Cu{sub 2}Zr intermetallic compound with the structure of Cu{sub 2}Mg Laves phase. The structure of this compound is isomorphous with that for Cu{sub 5}Zr intermetallic compound. Both crystal lattices consist of two types of clusters: Cu-centered 13-atom icosahedral-like cluster and Zr-centered 17-atom Frank-Kasper polyhedron Z16. That suggests the same structural motifs for the metallic glass and intermetallic compounds of Cu–Zr system and explains the drastic increase of the abundances of these clusters observed at γ{sub min}.« less

Ab initio molecular dynamics simulations of short-range order in Zr 50Cu 45Al 5 and Cu 50Zr 45Al 5 metallic glasses

DOE PAGES

Huang, Yuxiang; Huang, Li; Wang, C. Z.; ...

2016-02-01

Comparative analysis between Zr-rich Zr 50Cu 45Al 5 and Cu-rich Cu 50Zr 45Al 5 metallic glasses (MGs) is extensively performed to locate the key structural motifs accounting for their difference of glass forming ability. Here we adopt ab initio molecular dynamics simulations to investigate the local atomic structures of Zr 50Cu 45Al 5 and Cu 50Zr 45Al 5 MGs. A high content of icosahedral-related (full and distorted) orders was found in both samples, while in the Zr-rich MG full icosahedrons < 0,0,12,0 > is dominant, and in the Cu-rich one the distorted icosahedral orders, especially < 0,2,8,2 > and , are prominent. And the < 0,2,8,2 > polyhedra in Cu 50Zr 45Al 5 MG mainly originate from Al-centered clusters, while the < 0,0,12,0 > in Zr 50Cu 45Al 5 derives from both Cu-centered clusters and Al-centered clusters. These difference may be ascribed to the atomic size difference and chemical property between Cu and Zr atoms. Lastly, the relatively large size of Zr and large negative heat of mixing between Zr and Al atoms, enhancing the packing density and stability of metallic glass system, may be responsible for the higher glass forming ability of Zr 50Cu 45Al 5.« less

Viral Uncoating Is Directional: Exit of the Genomic RNA in a Common Cold Virus Starts with the Poly-(A) Tail at the 3′-End

PubMed Central

Sedivy, Arthur; Subirats, Xavier; Kowalski, Heinrich; Köhler, Gottfried; Blaas, Dieter

2013-01-01

Upon infection, many RNA viruses reorganize their capsid for release of the genome into the host cell cytosol for replication. Often, this process is triggered by receptor binding and/or by the acidic environment in endosomes. In the genus Enterovirus, which includes more than 150 human rhinovirus (HRV) serotypes causing the common cold, there is persuasive evidence that the viral RNA exits single-stranded through channels formed in the protein shell. We have determined the time-dependent emergence of the RNA ends from HRV2 on incubation of virions at 56°C using hybridization with specific oligonucleotides and detection by fluorescence correlation spectroscopy. We report that psoralen UV crosslinking prevents complete RNA release, allowing for identification of the sequences remaining inside the capsid. We also present the structure of uncoating intermediates in which parts of the RNA are condensed and take the form of a rod that is directed roughly towards a two-fold icosahedral axis, the presumed RNA exit point. Taken together, in contrast to schemes frequently depicted in textbooks and reviews, our findings demonstrate that exit of the RNA starts from the 3′-end. This suggests that packaging also occurs in an ordered manner resulting in the 3′-poly-(A) tail becoming located close to a position of pore formation during conversion of the virion into a subviral particle. This directional genome release may be common to many icosahedral non-enveloped single-stranded RNA viruses. PMID:23592991

Hepatitis Virus Capsid Polymorphs Respond Differently to Changes in Encapsulated Cargo Size

PubMed Central

He, Li; Porterfield, J. Zachary; van der Schoot, Paul; Zlotnick, Adam; Dragnea, Bogdan

2017-01-01

A templated assembly approach for Hepatitis B virus-like particles was employed to determine how the T = 3 and T = 4 polymorphs of the Hepatitis B virus (HBV) icosahedral cores respond to a systematic, gradual change in the encapsulated cargo size. It was found that assembly into complete virus-like particles occurs cooperatively around a variety of core diameters, albeit the degree of cooperativity varies. Among these virus-like particles, it was found that those of an outer diameter similar to T = 4 are able to accommodate the widest range of cargo sizes. PMID:24010404

Presence of Panulirus argus virus 1 (PaV1) in juvenile spiny lobsters Panulirus argus from the Caribbean coast of Mexico.

PubMed

Huchin-Mian, Juan Pablo; Rodríguez-Canul, Rossanna; Arias-Bañuelos, Efrain; Simá-Alvarez, Raúl; Pérez-Vega, Juan A; Briones-Fourzán, Patricia; Lozano-Alvarez, Enrique

2008-04-01

Macroscopic evidence, histological sections, transmission electron microscopy (TEM) evaluation, and PCR analyses of 25 apparently diseased juvenile spiny lobsters Panulirus argus from the reef lagoon of Puerto Morelos, Mexico, showed the presence of Panulirus argus Virus 1 (PaV1). Cowdry Type A intranuclear viral inclusions were observed in histological analyses, icosahedral viral particles were observed by TEM, and PCR using specific primers for PaV1 amplified a fragment of 499 bp. This is the first report of PaV1 infecting P. argus outside the Florida Keys, USA.

Organizational Forms of Matter: An Inorganic Super Fullerene and Keplerate Based on Molybdenum Oxide.

PubMed

Müller, Achim; Krickemeyer, Erich; Bögge, Hartmut; Schmidtmann, Marc; Peters, Frank

1998-12-31

Plato and Kepler would have been pleased. Despite the large number of atoms present the cluster anion 1 resembles an icosahedral-type structure. This represents definitively an unprecedented event in chemistry! The structure is made up of 12 {Mo 11 } fragments such that the fivefold symmetry axes are retained in the resulting spherical object. As an inscribed icosahedron can be recognized in the spherical shell of 1 (see picture), similarities with Kepler's famous shell model of the cosmos can be seen. © 1998 WILEY-VCH Verlag GmbH, Weinheim, Fed. Rep. of Germany.

Structure of large dsDNA viruses

PubMed Central

Klose, Thomas; Rossmann, Michael G.

2015-01-01

Nucleocytoplasmic large dsDNA viruses (NCLDVs) encompass an ever-increasing group of large eukaryotic viruses, infecting a wide variety of organisms. The set of core genes shared by all these viruses includes a major capsid protein with a double jelly-roll fold forming an icosahedral capsid, which surrounds a double layer membrane that contains the viral genome. Furthermore, some of these viruses, such as the members of the Mimiviridae and Phycodnaviridae have a unique vertex that is used during infection to transport DNA into the host. PMID:25003382

Ti12Xe: A twelve-coordinated Xe-containing molecule

NASA Astrophysics Data System (ADS)

Miao, Junjian; Xu, Wenwu; Zhu, Beien; Gao, Yi

2017-08-01

A twelve-coordinated Xe-containing molecule Ti12Xe has been predicted by DFT calculations with quasi-icosahedral symmetry. Structural and NBO analyses show the chemical bonding exists between the central Xe atom and peripheral Ti atoms, which leads to the high stability of the molecule to a considerable degree. First principle molecular dynamics simulations further reveal the particularly high thermal stability of Ti12Xe up to 1500 K. This unique species may disclose new physics and chemistry of xenon element and stir interest in the Xe-transition metal cluster physics and chemistry.

Simultaneous localization of photons and phonons in defect-free dodecagonal phoxonic quasicrystals

NASA Astrophysics Data System (ADS)

Xu, Bihang; Wang, Zhong; Tan, Yixiang; Yu, Tianbao

2018-03-01

In dodecagonal phoxonic quasicrytals (PhXQCs) with a very high rotational symmetry, we demonstrate numerically large phoxonic band gaps (PhXBGs, the coexistence of photonic and phononic band gaps). By computing the existence and dependence of PhXBGs on the choice of radius of holes, we find that PhXQCs can possess simultaneous photonic and phononic band gaps over a rather wide range of geometric parameters. Furthermore, localized modes of THz photons and tens of MHz phonons may exist inside and outside band gaps in defect-free PhXQCs. The electromagnetic and elastic field can be confined simultaneously around the quasicrytals center and decay in a length scale of several basic cells. As a kind of quasiperiodic structures, 12-fold PhXQCs provide a good candidate for simultaneously tailoring electromagnetic and elastic waves. Moreover, these structures exhibit some interesting characteristics due to the very high symmetry.

Syntheses of super-hard boron-rich solids in the B-C-N-O system

NASA Astrophysics Data System (ADS)

Hubert, Herve Pierre

Alpha-rhombohedral (alpha-rh.) B-rich materials belonging to the B-C-N-O system were prepared using high-pressure, high-temperature techniques. The samples were synthesized using a multianvil device and characterized by powder X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and parallel electron energy-loss spectroscopy (PEELS). In the B-O system, the formation of BsbxO materials produced from mixtures of B and Bsb2Osb3 between 1 to 10 GPa and 1000 to 1800sp°C was investigated. Graphitic and diamond-like Bsb2O, reported in previous studies, were not detected. The refractory boron suboxide, nominally Bsb6O, which has the alpha-rh. B structure, is the dominant suboxide in the P and T range of our investigation. High-pressure techniques were used successfully to synthesize boron suboxide of improved purity and crystallinity, and less oxygen-deficient (i.e., closer to the nominal Bsb6O composition) in comparison to room-pressure syntheses. Quantitative analyses indicate compositions of Bsb6Osb{0.95} and Bsb6Osb{0.77} for high-pressure and room-pressure samples, respectively. The first preparation, between 4 to 5.5 GPa, of Bsb6O in which the preferred form of the material is as macroscopic near-perfect regular icosahedra (to 30 mum in diameter) is reported. The Bsb6O icosahedra are similar to the multiply-twinned particles observed in some cubic materials. However, a major difference is that Bsb6O has a rhombohedral structure that closely fits the geometrical requirements for obtaining icosahedral twins. The Bsb6O grains are neither 3D-periodic nor quasicrystalline. Their formation can be described as a Mackay packing of icosahedral Bsb{12} units and provides an alternative to crystal formation by propagation of translational symmetry. Icosahedral twins ranging from 20 nm to 30 mum in diameter, as well as micron-sized euhedral crystals (to 40 mum) were prepared. The structural similarity of compounds with the alpha

Discovery of a Frank-Kasper [sigma] Phase in Sphere-Forming Block Copolymer Melts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Sangwoo; Bluemle, Michael J.; Bates, Frank S.

Sphere-forming block copolymers are known to self-assemble into body-centered cubic crystals near the order-disorder transition temperature. Small-angle x-ray scattering and transmission electron microscopy experiments on diblock and tetrablock copolymer melts have revealed an equilibrium phase characterized by a large tetragonal unit cell containing 30 microphase-separated spheres. This structure, referred to as the sigma ({sigma}) phase by Frank and Kasper more than 50 years ago, nucleates and grows from the body-centered cubic phase similar to its occurrence in metal alloys and is a crystal approximant to dodecagonal quasicrystals. Formation of the {sigma} phase in undiluted linear block copolymers (and certain branchedmore » dendrimers) appears to be mediated by macromolecular packing frustration, an entropic contribution to the interparticle interactions that control the sphere-packing geometry.« less

Close packing in curved space by simulated annealing

NASA Astrophysics Data System (ADS)

Wille, L. T.

1987-12-01

The problem of packing spheres of a maximum radius on the surface of a four-dimensional hypersphere is considered. It is shown how near-optimal solutions can be obtained by packing soft spheres, modelled as classical particles interacting under an inverse power potential, followed by a subsequent hardening of the interaction. In order to avoid trapping in high-lying local minima, the simulated annealing method is used to optimise the soft-sphere packing. Several improvements over other work (based on local optimisation of random initial configurations of hard spheres) have been found. The freezing behaviour of this system is discussed as a function of particle number, softness of the potential and cooling rate. Apart from their geometric interest, these results are useful in the study of topological frustration, metallic glasses and quasicrystals.

Direct imaging of isofrequency contours in photonic structures

DOE PAGES

Regan, E. C.; Igarashi, Y.; Zhen, B.; ...

2016-11-25

The isofrequency contours of a photonic crystal are important for predicting and understanding exotic optical phenomena that are not apparent from high-symmetry band structure visualizations. We demonstrate a method to directly visualize the isofrequency contours of high-quality photonic crystal slabs that show quantitatively good agreement with numerical results throughout the visible spectrum. Our technique relies on resonance-enhanced photon scattering from generic fabrication disorder and surface roughness, so it can be applied to general photonic and plasmonic crystals or even quasi-crystals. We also present an analytical model of the scattering process, which explains the observation of isofrequency contours in our technique.more » Furthermore, the isofrequency contours provide information about the characteristics of the disorder and therefore serve as a feedback tool to improve fabrication processes.« less

Innovative acoustic techniques for studying new materials and new developments in solid state physics

NASA Astrophysics Data System (ADS)

Maynard, Julian D.

1994-06-01

The goals of this project involve the use of innovative acoustic techniques to study new materials and new developments in solid state physics. Major accomplishments include (a) the preparation and publication of a number of papers and book chapters, (b) the measurement and new analysis of more samples of aluminum quasicrystal and its cubic approximant to eliminate the possibility of sample artifacts, (c) the use of resonant ultrasound to measure acoustic attenuation and determine the effects of heat treatment on ceramics, (d) the extension of our technique for measuring even lower (possibly the lowest) infrared optical absorption coefficient, and (e) the measurement of the effects of disorder on the propagation of a nonlinear pulse, and (f) the observation of statistical effects in measurements of individual bond breaking events in fracture.

Octonacci photonic crystals with negative refraction index materials

NASA Astrophysics Data System (ADS)

Brandão, E. R.; Vasconcelos, M. S.; Anselmo, D. H. A. L.

2016-12-01

We investigate the optical transmission spectra for s-polarized (TE) and p-polarized (TM) waves in one-dimensional photonic quasicrystals on a quasiperiodic multilayer structure made up by alternate layers of SiO2 and metamaterials, organized by following the Octonacci sequence. Maxwell's equations and the transfer-matrix technique are used to derive the transmission spectra for the propagation of normally and obliquely incident optical fields. We assume Drude-Lorentz-type dispersive response for the dielectric permittivity and magnetic permeability of the metamaterials. For normally incident waves, we observe that the spectra does not have self-similar behavior or mirror symmetry and it also features the absence of optical band gap. Also for normally incident waves, we show regions of full transmittance when the incident angle θC = 0° in a particular frequency range.

Structural Comparison of Different Antibodies Interacting with Parvovirus Capsids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hafenstein, Susan; Bowman, Valorie D.; Sun, Tao

2009-05-13

The structures of canine parvovirus (CPV) and feline parvovirus (FPV) complexed with antibody fragments from eight different neutralizing monoclonal antibodies were determined by cryo-electron microscopy (cryoEM) reconstruction to resolutions varying from 8.5 to 18 {angstrom}. The crystal structure of one of the Fab molecules and the sequence of the variable domain for each of the Fab molecules have been determined. The structures of Fab fragments not determined crystallographically were predicted by homology modeling according to the amino acid sequence. Fitting of the Fab and virus structures into the cryoEM densities identified the footprints of each antibody on the viral surface.more » As anticipated from earlier analyses, the Fab binding sites are directed to two epitopes, A and B. The A site is on an exposed part of the surface near an icosahedral threefold axis, whereas the B site is about equidistant from the surrounding five-, three-, and twofold axes. One antibody directed to the A site binds CPV but not FPV. Two of the antibodies directed to the B site neutralize the virus as Fab fragments. The differences in antibody properties have been linked to the amino acids within the antibody footprints, the position of the binding site relative to the icosahedral symmetry elements, and the orientation of the Fab structure relative to the surface of the virus. Most of the exposed surface area was antigenic, although each of the antibodies had a common area of overlap that coincided with the positions of the previously mapped escape mutations.« less

Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes.

PubMed

Faulkner, Matthew; Rodriguez-Ramos, Jorge; Dykes, Gregory F; Owen, Siân V; Casella, Selene; Simpson, Deborah M; Beynon, Robert J; Liu, Lu-Ning

2017-08-03

Carboxysomes are proteinaceous organelles that play essential roles in enhancing carbon fixation in cyanobacteria and some proteobacteria. These self-assembling organelles encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase using a protein shell structurally resembling an icosahedral viral capsid. The protein shell serves as a physical barrier to protect enzymes from the cytosol and a selectively permeable membrane to mediate transport of enzyme substrates and products. The structural and mechanical nature of native carboxysomes remain unclear. Here, we isolate functional β-carboxysomes from the cyanobacterium Synechococcus elongatus PCC7942 and perform the first characterization of the macromolecular architecture and inherent physical mechanics of single β-carboxysomes using electron microscopy, atomic force microscopy (AFM) and proteomics. Our results illustrate that the intact β-carboxysome comprises three structural domains, a single-layered icosahedral shell, an inner layer and paracrystalline arrays of interior Rubisco. We also observe the protein organization of the shell and partial β-carboxysomes that likely serve as the β-carboxysome assembly intermediates. Furthermore, the topography and intrinsic mechanics of functional β-carboxysomes are determined in native conditions using AFM and AFM-based nanoindentation, revealing the flexible organization and soft mechanical properties of β-carboxysomes compared to rigid viruses. Our study provides new insights into the natural characteristics of β-carboxysome organization and nanomechanics, which can be extended to diverse bacterial microcompartments and are important considerations for the design and engineering of functional carboxysomes in other organisms to supercharge photosynthesis. It offers an approach for inspecting the structural and mechanical features of synthetic metabolic organelles and protein scaffolds in bioengineering.

Microstructure and mechanical properties of aluminium matrix composites reinforced by Al{sub 62}Cu{sub 25.5}Fe{sub 12.5} melt spun ribbon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lityńska-Dobrzyńska, Lidia, E-mail: l.litynska@imim.pl; Mitka, Mikołaj; Góral, Anna

Aluminium matrix composites containing 15, 30 and 50 vol.% of pulverized Al{sub 62}Cu{sub 25.5}Fe{sub 12.5} (in at.%) melt spun ribbons have been prepared by a vacuum hot pressing (T = 673 K, P = 600 MPa). The microstructure of the initial ribbon and the composites was investigated using X-ray, scanning and transmission electron microscopy. In the as-spun ribbon the quasicrystalline icosahedral phase (i-phase) coexisted with the cubic copper rich β-Al(Cu, Fe) intermetallic compound. The phase composition of Al-Cu-Fe particles changed after consolidation process and the i-phase transformed partially to the ω-Al{sub 70}Cu{sub 20}Fe{sub 10} phase. Additionally, the Θ-Al{sub 2}Cu phasemore » formed at the α(Al)/Al-Cu-Fe particle interfaces. With an increase in volume fraction of the reinforcement the hardness of the composites increased up to HV = 180 for the highest amount of added particles. The ultimate compression strength of the same sample reached the value of 545 MPa. - Highlights: • Al and 15, 30, 50% of pulverized Al{sub 62}Cu{sub 25.5}Fe{sub 12.5} melt spun ribbon were consolidated. • The initial ribbon consisted of the icosahedral i-phase and copper rich β-Al(Cu, Fe). • The i-phase partially transforms to ω-Al{sub 7}Cu{sub 2}Fe phase in all composites. • Increase of microhardness and compressive strength with content of reinforcement • Ultimate compression strength 545 MPa for 50% of added particles.« less

Tropical Cyclone Formation in 30-day Simulation Using Cloud-System-Resolving Global Nonhydrostatic Model (NICAM)

NASA Astrophysics Data System (ADS)

Yanase, W.; Satoh, M.; Iga, S.; Tomita, H.

2007-12-01

We are developing an icosahedral-grid non-hydrostatic AGCM, which can explicitly represent cumulus or meso-scale convection over the entire globe. We named the model NICAM (Nonhydrostatic ICosahedral Atmospheric Model). On 2005, we have performed a simulations with horizontal grid intervals of 14, 7 and 3.5 km using realistic topography and sea surface temperature in April 2004 (Miura et al., 2007; GRL). It simulated a typhoon Sudal that actually developed over the Northwestern Pacific in 2004. In the present study, the NICAM model with the horizontal grid interval of 14 km was used for perpetual July experiment with 30 forecasting days. In this simulation, several tropical cyclones formed over the wesetern and eastern North Pacific, althought the formation over the western North Pacific occured a little further north to the actually observed region. The mature tropical cyclones with intense wind speed had a structure of a cloud-free eye and eye wall. We have found that the enviromental parameters associated with the tropical cyclone genesis explain well the simulated region of tropical cyclone generation. Over the North Atlantic and eastern North Pacific, westward-moving disturbances like African wave are simulated, which seems to be related to the cyclone formation over the eastern North Pacific. On the other hand, the simulated tropical cyclones over the western North Pacifis seem to form by different factors as has been suggested by the previous studies based on observation. Although the model still has some problems and is under continuous improvement, we can discuss what dynamics is to be represented using a global high-resolution model.

DYNAMICO, an atmospheric dynamical core for high-performance climate modeling

NASA Astrophysics Data System (ADS)

Dubos, Thomas; Meurdesoif, Yann; Spiga, Aymeric; Millour, Ehouarn; Fita, Lluis; Hourdin, Frédéric; Kageyama, Masa; Traore, Abdoul-Khadre; Guerlet, Sandrine; Polcher, Jan

2017-04-01

Institut Pierre Simon Laplace has developed a very scalable atmospheric dynamical core, DYNAMICO, based on energy-conserving finite-difference/finite volume numerics on a quasi-uniform icosahedral-hexagonal mesh. Scalability is achieved by combining hybrid MPI/OpenMP parallelism to asynchronous I/O. This dynamical core has been coupled to radiative transfer physics tailored to the atmosphere of Saturn, allowing unprecedented simulations of the climate of this giant planet. For terrestrial climate studies DYNAMICO is being integrated into the IPSL Earth System Model IPSL-CM. Preliminary aquaplanet and AMIP-style simulations yield reasonable results when compared to outputs from IPSL-CM5. The observed performance suggests that an order of magnitude may be gained with respect to IPSL-CM CMIP5 simulations either on the duration of simulations or on their resolution. Longer simulations would be of interest for the study of paleoclimate, while higher resolution could improve certain aspects of the modeled climate such as extreme events, as will be explored in the HighResMIP project. Following IPSL's strategic vision of building a unified global-regional modelling system, a fully-compressible, non-hydrostatic prototype of DYNAMICO has been developed, enabling future convection-resolving simulations. Work supported by ANR project "HEAT", grant number CE23_2014_HEAT Dubos, T., Dubey, S., Tort, M., Mittal, R., Meurdesoif, Y., and Hourdin, F.: DYNAMICO-1.0, an icosahedral hydrostatic dynamical core designed for consistency and versatility, Geosci. Model Dev., 8, 3131-3150, doi:10.5194/gmd-8-3131-2015, 2015.

Influence of the shell thickness and charge distribution on the effective interaction between two like-charged hollow spheres.

PubMed

Angelescu, Daniel G; Caragheorgheopol, Dan

2015-10-14

The mean-force and the potential of the mean force between two like-charged spherical shells were investigated in the salt-free limit using the primitive model and Monte Carlo simulations. Apart from an angular homogeneous distribution, a discrete charge distribution where point charges localized on the shell outer surface followed an icosahedral arrangement was considered. The electrostatic coupling of the model system was altered by the presence of mono-, trivalent counterions or small dendrimers, each one bearing a net charge of 9 e. We analyzed in detail how the shell thickness and the radial and angular distribution of the shell charges influenced the effective interaction between the shells. We found a sequence of the potential of the mean force similar to the like-charged filled spheres, ranging from long-range purely repulsive to short-range purely attractive as the electrostatic coupling increased. Both types of potentials were attenuated and an attractive-to-repulsive transition occurred in the presence of trivalent counterions as a result of (i) thinning the shell or (ii) shifting the shell charge from the outer towards the inner surface. The potential of the mean force became more attractive with the icosahedrally symmetric charge model, and additionally, at least one shell tended to line up with 5-fold symmetry axis along the longest axis of the simulation box at the maximum attraction. The results provided a basic framework of understanding the non-specific electrostatic origin of the agglomeration and long-range assembly of the viral nanoparticles.

African Swine Fever Virus Undergoes Outer Envelope Disruption, Capsid Disassembly and Inner Envelope Fusion before Core Release from Multivesicular Endosomes

PubMed Central

Hernáez, Bruno; Guerra, Milagros; Salas, María L.

2016-01-01

African swine fever virus (ASFV) is a nucleocytoplasmic large DNA virus (NCLDV) that causes a highly lethal disease in domestic pigs. As other NCLDVs, the extracellular form of ASFV possesses a multilayered structure consisting of a genome-containing nucleoid successively wrapped by a thick protein core shell, an inner lipid membrane, an icosahedral protein capsid and an outer lipid envelope. This structural complexity suggests an intricate mechanism of internalization in order to deliver the virus genome into the cytoplasm. By using flow cytometry in combination with pharmacological entry inhibitors, as well as fluorescence and electron microscopy approaches, we have dissected the entry and uncoating pathway used by ASFV to infect the macrophage, its natural host cell. We found that purified extracellular ASFV is internalized by both constitutive macropinocytosis and clathrin-mediated endocytosis. Once inside the cell, ASFV particles move from early endosomes or macropinosomes to late, multivesicular endosomes where they become uncoated. Virus uncoating requires acidic pH and involves the disruption of the outer membrane as well as of the protein capsid. As a consequence, the inner viral membrane becomes exposed and fuses with the limiting endosomal membrane to release the viral core into the cytosol. Interestingly, virus fusion is dependent on virus protein pE248R, a transmembrane polypeptide of the inner envelope that shares sequence similarity with some members of the poxviral entry/fusion complex. Collective evidence supports an entry model for ASFV that might also explain the uncoating of other multienveloped icosahedral NCLDVs. PMID:27110717

Structural and Kinetic Properties of Lumazine Synthase Isoenzymes in the Order Rhizobiales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klinke,S.; Zylberman, V.; Bonomi, H.

6, 7-Dimethyl-8-ribityllumazine synthase (lumazine synthase; LS) catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. This protein is known to exhibit different quaternary assemblies between species, existing as free pentamers, decamers (dimers of pentamers) and icosahedrally arranged dodecamers of pentamers. A phylogenetic analysis on eubacterial, fungal and plant LSs allowed us to classify them into two categories: Type I LSs (pentameric or icosahedral) and Type II LSs (decameric). The Rhizobiales represent an order of ?-proteobacteria that includes, among others, the genera Mesorhizobium, Agrobacterium and Brucella. Here, we present structural and kinetic studies on several LSs frommore » Rhizobiales. Interestingly, Mesorhizobium and Brucella encode both a Type-I LS and a Type-II LS called RibH1 and RibH2, respectively. We show that Type II LSs appear to be almost inactive, whereas Type I LSs present a highly variable catalytic activity according to the genus. Additionally, we have solved four RibH1/RibH2 crystallographic structures from the genera Mesorhizobium and Brucella. The relationship between the active-site architecture and catalytic properties in these isoenzymes is discussed, and a model that describes the enzymatic behavior is proposed. Furthermore, sequence alignment studies allowed us to extend our results to the genus Agrobacterium. Our results suggest that the selective pressure controlling the riboflavin pathway favored the evolution of catalysts with low reaction rates, since the excess of flavins in the intracellular pool in Rhizobiales could act as a negative factor when these bacteria are exposed to oxidative or nitrosative stress.« less

Crystallization and preliminary X-ray diffraction analysis of red clover necrotic mosaic virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin, Stanton L.; Guenther, Richard H.; Sit, Tim L.

2010-11-12

Red clover necrotic mosaic virus (RCNMV) is a species that belongs to the Tombusviridae family of plant viruses with a T = 3 icosahedral capsid. RCNMV virions were purified and were crystallized for X-ray analysis using the hanging-drop vapor-diffusion method. Self-rotation functions and systematic absences identified the space group as I23, with two virions in the unit cell. The crystals diffracted to better than 4 {angstrom} resolution but were very radiation-sensitive, causing rapid decay of the high-resolution reflections. The data were processed to 6 {angstrom} in the analysis presented here.

Structural Insights into the Coupling of Virion Assembly and Rotavirus Replication

PubMed Central

Trask, Shane D.; McDonald, Sarah M.; Patton, John T.

2013-01-01

Preface Viral replication is rapid and robust, but it is far from a chaotic process. Instead, successful production of infectious progeny requires that events occur in the correct place and at the correct time. Rotavirus, a segmented double-stranded RNA virus of the Reoviridae family, seems to govern its replication through ordered disassembly and assembly of a triple-layered icosahedral capsid. In recent years, high-resolution structural data have provided unprecedented insight into these events. In this Review, we explore the current understanding of rotavirus replication and how it compares to other Reoviridae family members. PMID:22266782

Quasiperiodic oscillation and possible Second Law violation in a nanosystem

NASA Astrophysics Data System (ADS)

Quick, R.; Singharoy, A.; Ortoleva, P.

2013-05-01

Simulation of a virus-like particle reveals persistent oscillation about a free-energy minimizing structure. For an icosahedral structure of 12 human papillomavirus (HPV) L1 protein pentamers, the period is about 70 picoseconds and has amplitude of about 4 Å at 300 K and pH 7. The pentamers move radially and out-of-phase with their neighbors. As temperature increases the amplitude and period decrease. Since the dynamics are shown to be friction-dominated and free-energy driven, the oscillations are noninertial. These anomalous oscillations are an apparent violation of the Second Law mediated by fluctuations accompanying nanosystem behavior.

The effect of size and composition on structural transitions in monometallic nanoparticles

NASA Astrophysics Data System (ADS)

Rossi, Kevin; Pavan, Luca; Soon, YeeYeen; Baletto, Francesca

2018-02-01

Predicting the morphological stability of nanoparticles is an essential step towards the accurate modelling of their chemophysical properties. Here we investigate solid-solid transitions in monometallic clusters of 0.5-2.0 nm diameter at finite temperatures and we report the complex dependence of the rearrangement mechanism on the nanoparticle's composition and size. The concerted Lipscomb's Diamond-Square-Diamond mechanisms which connects the decahedral or the cuboctahedral to the icosahedral basins, take place only below a material dependent critical size above which surface diffusion prevails and leads to low-symmetry and defected shapes still belonging to the initial basin.

Calculation of spherical harmonics and Wigner d functions by FFT. Applications to fast rotational matching in molecular replacement and implementation into AMoRe.

PubMed

Trapani, Stefano; Navaza, Jorge

2006-07-01

The FFT calculation of spherical harmonics, Wigner D matrices and rotation function has been extended to all angular variables in the AMoRe molecular replacement software. The resulting code avoids singularity issues arising from recursive formulas, performs faster and produces results with at least the same accuracy as the original code. The new code aims at permitting accurate and more rapid computations at high angular resolution of the rotation function of large particles. Test calculations on the icosahedral IBDV VP2 subviral particle showed that the new code performs on the average 1.5 times faster than the original code.

Fourier-space TEM reconstructions with symmetry adapted functions for all rotational point groups.

PubMed

Trapani, Stefano; Navaza, Jorge

2013-05-01

A general-purpose and simple expression for the coefficients of symmetry adapted functions referred to conveniently oriented symmetry axes is given for all rotational point groups. The expression involves the computation of reduced Wigner-matrix elements corresponding to an angle specific to each group and has the computational advantage of leading to Fourier-space TEM (transmission electron microscopy) reconstruction procedures involving only real valued unknowns. Using this expression, a protocol for ab initio view and center assignment and reconstruction so far used for icosahedral particles has been tested with experimental data in other point groups. Copyright © 2013 Elsevier Inc. All rights reserved.

Wave computation on the Poincaré dodecahedral space

NASA Astrophysics Data System (ADS)

Bachelot-Motet, Agnès

2013-12-01

We compute the waves propagating on a compact 3-manifold of constant positive curvature with a non-trivial topology: the Poincaré dodecahedral space that is a plausible model of multi-connected universe. We transform the Cauchy problem to a mixed problem posed on a fundamental domain determined by the quaternionic calculus. We adopt a variational approach using a space of finite elements that is invariant under the action of the binary icosahedral group. The computation of the transient waves is validated with their spectral analysis by computing a lot of eigenvalues of the Laplace-Beltrami operator.

Comparison of Conjugate Gradient Density Matrix Search and Chebyshev Expansion Methods for Avoiding Diagonalization in Large-Scale Electronic Structure Calculations

NASA Technical Reports Server (NTRS)

Bates, Kevin R.; Daniels, Andrew D.; Scuseria, Gustavo E.

1998-01-01

We report a comparison of two linear-scaling methods which avoid the diagonalization bottleneck of traditional electronic structure algorithms. The Chebyshev expansion method (CEM) is implemented for carbon tight-binding calculations of large systems and its memory and timing requirements compared to those of our previously implemented conjugate gradient density matrix search (CG-DMS). Benchmark calculations are carried out on icosahedral fullerenes from C60 to C8640 and the linear scaling memory and CPU requirements of the CEM demonstrated. We show that the CPU requisites of the CEM and CG-DMS are similar for calculations with comparable accuracy.

African Swine Fever Virus Gets Undressed: New Insights on the Entry Pathway.

PubMed

Andrés, Germán

2017-02-15

African swine fever virus (ASFV) is a large, multienveloped DNA virus composed of a genome-containing core successively wrapped by an inner lipid envelope, an icosahedral protein capsid, and an outer lipid envelope. In keeping with this structural complexity, recent studies have revealed an intricate entry program. This Gem highlights how ASFV uses two alternative pathways, macropinocytosis and clathrin-mediated endocytosis, to enter into the host macrophage and how the endocytosed particles undergo a stepwise, low pH-driven disassembly leading to inner envelope fusion and core delivery in the cytoplasm. Copyright © 2017 American Society for Microbiology.

Draft genome sequence of four coccolithoviruses: Emiliania huxleyi virus EhV-88, EhV-201, EhV-207, and EhV-208.

PubMed

Nissimov, Jozef I; Worthy, Charlotte A; Rooks, Paul; Napier, Johnathan A; Kimmance, Susan A; Henn, Matthew R; Ogata, Hiroyuki; Allen, Michael J

2012-03-01

The Coccolithoviridae are a group of viruses which infect the marine coccolithophorid microalga Emiliania huxleyi. The Emiliania huxleyi viruses (known as EhVs) described herein have 160- to 180-nm diameter icosahedral structures, have genomes of approximately 400 kbp, and consist of more than 450 predicted coding sequences (CDSs). Here, we describe the genomic features of four newly sequenced coccolithoviruses (EhV-88, EhV-201, EhV-207, and EhV-208) together with their draft genome sequences and their annotations, highlighting the homology and heterogeneity of these genomes to the EhV-86 model reference genome.

IV INTERNATIONAL CONFERENCE ON ATOM AND MOLECULAR PULSED LASERS (AMPL'99): Spectral properties of optical anisotropy induced by laser radiation in dye solutions

NASA Astrophysics Data System (ADS)

Pikulik, L. G.; Chernyavskii, V. A.; Grib, A. F.

2000-06-01

Spectral studies of induced quasi-crystal properties (which can be quantitatively characterised by the difference in the refractive indices of ordinary and extraordinary waves, Δn=no—ne) in Rhodamine 6G and Rhodamine 4C solutions in glycerine excited in the visible and UV ranges of the absorption spectrum are presented. It is demonstrated that the observed spectral dependences of Δn of these dye solutions excited in the visible (long-wavelength) and UV (short-wavelength) ranges of the absorption spectrum can be interpreted in terms of an oscillator model of a molecule. The proposed method for the analysis of induced optical anisotropy in solutions of organic compounds allows the relative orientation of oscillators in a molecule and, thus, the relative orientation of electronic transitions in a molecule to be determined in a reliable way.

Modeling the structural, dynamical, and magnetic properties of liquid Al1-xMnx ( x=0.14 , 0.2, and 0.4): A first-principles investigation

NASA Astrophysics Data System (ADS)

Jakse, N.; Pasturel, A.

2007-07-01

We report the results of first-principles molecular dynamics simulations of liquid Al1-xMnx alloys at three different compositions. The local structure as defined by the Bhatia-Thornton partial structure factors is found to display significant changes at x=0.4 . In addition, a structural analysis using three-dimensional pair-analysis techniques evidences a fivefold symmetry around x=0.14 , in agreement with the experimental quasicrystal-forming range, and an increasing complexity of the Frank-Kasper polytetrahedral symmetry around Mn atoms at x=0.4 . We also examine the time evolution of the configurations at the three compositions in terms of the mean-square displacements and self-diffusion coefficients. Finally, we show a strong interplay between the structural changes and the evolution of the magnetic properties of the Mn atoms as a function of composition.

High-resolution electron microscopy and its applications.

PubMed

Li, F H

1987-12-01

A review of research on high-resolution electron microscopy (HREM) carried out at the Institute of Physics, the Chinese Academy of Sciences, is presented. Apart from the direct observation of crystal and quasicrystal defects for some alloys, oxides, minerals, etc., and the structure determination for some minute crystals, an approximate image-contrast theory named pseudo-weak-phase object approximation (PWPOA), which shows the image contrast change with crystal thickness, is described. Within the framework of PWPOA, the image contrast of lithium ions in the crystal of R-Li2Ti3O7 has been observed. The usefulness of diffraction analysis techniques such as the direct method and Patterson method in HREM is discussed. Image deconvolution and resolution enhancement for weak-phase objects by use of the direct method are illustrated. In addition, preliminary results of image restoration for thick crystals are given.

Pressure-Induced Phase Transitions in the Cd-Yb Periodic Approximant to a Quasicrystal

NASA Astrophysics Data System (ADS)

Watanuki, Tetsu; Machida, Akihiko; Ikeda, Tomohiro; Aoki, Katsutoshi; Kaneko, Hiroshi; Shobu, Takahisa; Sato, Taku J.; Tsai, An Pang

2006-03-01

The phase study of a Cd-Yb 1/1 approximant crystal over a wide pressure and temperature range is crucial for the comparison study between periodic and quasiperiodic crystals. The Cd4 tetrahedra, the most inner part of the atomic clusters, exhibited various structural ordering in the orientation sensitive to pressure and temperature. Five ordered phases appeared in a P-T span up to 5.2 GPa and down to 10 K. The propagation direction of ordering alternated from [110] to ⟨111⟩ at about 1.0 GPa and again to [110] at 3.5 4.3 GPa. The primarily ordered phases that appeared by cooling to 210 250 K between 1.0 5.2 GPa further transformed to finely ordered ones at 120 155 K. Besides the original short-range type interaction, a long-range type interaction was likely developed under pressure to lead to the primary ordering of Cd4 tetrahedra. Coexistence of these interactions is responsible for the complicated phase behavior.

A Sodium-Containing Quasicrystal: Using Gold To Enhance Sodium's Covalency in Intermetallic Compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smetana, Volodymyr; Lin, Qisheng; Pratt, Daniel K.

2013-09-26

Gold macht stabil: Na 13Au 12Ga 15, ein natriumhaltiges thermodynamisch stabiles quasikristallines Material, wurde bei einer systematischen Studie des polaren Na-Au-Ga-Intermetallsystems entdeckt. Sein Elektron/Atom-Verhältnis von 1.75 ist für Bergman-Ikosaederphasen extrem klein, doch der substanzielle Au-Anteil sorgt für eine Hume-Rothery-Stabilisierung und neuartige polar-kovalente Na-Au-Wechselwirkungen.

Acoustic Studies of New Materials: Quasicrystals, Low-Loss Glasses, and High Tc Superconductors

DTIC Science & Technology

1991-12-18

Progress Report, 1989 2. Tania Slawecki, M.S. Thesis Measuring fourth sound in silica aerogel 3. Chang Yu, Ph.D. Thesis A high Q resonant photoacoustic...Pennsylvania State University The Graduate School Department of Physics Measuring Fourth Sound in Silica Aerogel A Thesis in Physics by Tania Maria...Slawecki Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Science December 1989 Abstract Measuring Fourth Sound in Silica

Acoustic Studies of New Materials: Quasicrystals, Low-Loss Glasses, and High Tc Superconductors

DTIC Science & Technology

1990-08-01

REFEREED JOURNALS TECHNICAL REPORTS PUBLISHED 1. NSF Final Progress Report 2. Tania Slawecki M.S. Thesis "Measuring fourth sound in silica aerogel " 3...Pennsylvania State University The Graduate School Department of Physics Measuring Fourth Sound in Silica Aerogel A Thesis in Physics by Tania Maria...Slawecki Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Science December 1989 Abstract Measuring Fourth Sound in Silica

Recovery of Infectious Pariacoto Virus from cDNA Clones and Identification of Susceptible Cell Lines

PubMed Central

Johnson, Karyn N.; Ball, L. Andrew

2001-01-01

Pariacoto virus (PaV) is a nodavirus that was recently isolated in Peru from the Southern armyworm, Spodoptera eridania. Virus particles are non enveloped and about 30 nm in diameter and have T=3 icosahedral symmetry. The 3.0-Å crystal structure shows that about 35% of the genomic RNA is icosahedrally ordered, with the RNA forming a dodecahedral cage of 25-nucleotide (nt) duplexes that underlie the inner surface of the capsid. The PaV genome comprises two single-stranded, positive-sense RNAs: RNA1 (3,011 nt), which encodes the 108-kDa catalytic subunit of the RNA-dependent RNA polymerase, and RNA2 (1,311 nt), which encodes the 43-kDa capsid protein precursor α. In order to apply molecular genetics to the structure and assembly of PaV, we identified susceptible cell lines and developed a reverse genetic system for this virus. Cell lines that were susceptible to infection by PaV included those from Spodoptera exigua, Helicoverpa zea and Aedes albopictus, whereas cells from Drosophila melanogaster and Spodoptera frugiperda were refractory to infection. To recover virus from molecular clones, full-length cDNAs of PaV RNAs 1 and 2 were cotranscribed by T7 RNA polymerase in baby hamster kidney cells that expressed T7 RNA polymerase. Lysates of these cells were infectious both for cultured cells from Helicoverpa zea (corn earworm) and for larvae of Galleria mellonella (greater wax moth). The combination of infectious cDNA clones, cell culture infectivity, and the ability to produce milligram amounts of virus allows the application of DNA-based genetic methods to the study of PaV structure and assembly. PMID:11711613

Recovery of infectious pariacoto virus from cDNA clones and identification of susceptible cell lines.

PubMed

Johnson, K N; Ball, L A

2001-12-01

Pariacoto virus (PaV) is a nodavirus that was recently isolated in Peru from the Southern armyworm, Spodoptera eridania. Virus particles are non enveloped and about 30 nm in diameter and have T=3 icosahedral symmetry. The 3.0-A crystal structure shows that about 35% of the genomic RNA is icosahedrally ordered, with the RNA forming a dodecahedral cage of 25-nucleotide (nt) duplexes that underlie the inner surface of the capsid. The PaV genome comprises two single-stranded, positive-sense RNAs: RNA1 (3,011 nt), which encodes the 108-kDa catalytic subunit of the RNA-dependent RNA polymerase, and RNA2 (1,311 nt), which encodes the 43-kDa capsid protein precursor alpha. In order to apply molecular genetics to the structure and assembly of PaV, we identified susceptible cell lines and developed a reverse genetic system for this virus. Cell lines that were susceptible to infection by PaV included those from Spodoptera exigua, Helicoverpa zea and Aedes albopictus, whereas cells from Drosophila melanogaster and Spodoptera frugiperda were refractory to infection. To recover virus from molecular clones, full-length cDNAs of PaV RNAs 1 and 2 were cotranscribed by T7 RNA polymerase in baby hamster kidney cells that expressed T7 RNA polymerase. Lysates of these cells were infectious both for cultured cells from Helicoverpa zea (corn earworm) and for larvae of Galleria mellonella (greater wax moth). The combination of infectious cDNA clones, cell culture infectivity, and the ability to produce milligram amounts of virus allows the application of DNA-based genetic methods to the study of PaV structure and assembly.

Visualization of the herpes simplex virus portal in situ by cryo-electron tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cardone, Giovanni; Winkler, Dennis C.; Trus, Benes L.

2007-05-10

Herpes simplex virus type 1 (HSV-1), the prototypical herpesvirus, has an icosahedral nucleocapsid surrounded by a proteinaceous tegument and a lipoprotein envelope. As in tailed bacteriophages, the icosahedral symmetry of the capsid is broken at one of the 12 vertices, which is occupied by a dodecameric ring of portal protein, UL6, instead of a pentamer of the capsid protein, UL19. The portal ring serves as a conduit for DNA entering and exiting the capsid. From a cryo-EM reconstruction of capsids immuno-gold-labeled with anti-UL6 antibodies, we confirmed that UL6 resides at a vertex. To visualize the portal in the context ofmore » the assembled capsid, we used cryo-electron tomography to determine the three-dimensional structures of individual A-capsids (empty, mature capsids). The similarity in size and overall shape of the portal and a UL19 pentamer - both are cylinders of {approx} 800 kDa - combined with residual noise in the tomograms, prevented us from identifying the portal vertices directly; however, this was accomplished by a computational classification procedure. Averaging the portal-containing subtomograms produced a structure that tallies with the isolated portal, as previously reconstructed by cryo-EM. The portal is mounted on the outer surface of the capsid floor layer, with its narrow end pointing outwards. This disposition differs from that of known phage portals in that the bulk of its mass lies outside, not inside, the floor. This distinction may be indicative of divergence at the level of portal-related functions other than its role as a DNA channel.« less

In silico analysis of surface structure variation of PCV2 capsid resulting from loop mutations of its capsid protein (Cap)

PubMed Central

Wang, Aibing; Zhang, Lijie; Khayat, Reza

2016-01-01

Outbreaks of porcine circovirus (PCV) type 2 (PCV2)-associated diseases have caused substantial economic losses worldwide in the last 20 years. The PCV capsid protein (Cap) is the sole structural protein and main antigenic determinant of this virus. In this study, not only were phylogenetic trees reconstructed, but variations of surface structure of the PCV capsid were analysed in the course of evolution. Unique surface patterns of the icosahedral fivefold axes of the PCV2 capsid were identified and characterized, all of which were absent in PCV type 1 (PCV1). Icosahedral fivefold axes, decorated with Loops BC, HI and DE, were distinctly different between PCV2 and PCV1. Loops BC, determining the outermost surface around the fivefold axes of PCV capsids, had limited homology between Caps of PCV1 and PCV2. A conserved tyrosine phosphorylation motif in Loop HI that might be recognized by non-receptor tyrosine kinase(s) in vivo was present only in PCV2. Particularly, the concurrent presence of 60 pairs of the conserved tyrosine and a canonical PXXP motif on the PCV2 capsid surface could be a mechanism for PXXP motif binding to and activation of an SH3-domain-containing tyrosine kinase in host cells. Additionally, a conserved cysteine in Loop DE of the PCV2 Cap was substituted by an arginine in PCV1, indicating potentially distinct assembly mechanisms of the capsid in vitro between PCV1 and PCV2. Therefore, these unique patterns on the PCV2 capsid surface, absent in PCV1 isolates, might be related to cell entry, virus function and pathogenesis. PMID:27902320

In silico analysis of surface structure variation of PCV2 capsid resulting from loop mutations of its capsid protein (Cap).

PubMed

Wang, Naidong; Zhan, Yang; Wang, Aibing; Zhang, Lijie; Khayat, Reza; Yang, Yi

2016-12-01

Outbreaks of porcine circovirus (PCV) type 2 (PCV2)-associated diseases have caused substantial economic losses worldwide in the last 20 years. The PCV capsid protein (Cap) is the sole structural protein and main antigenic determinant of this virus. In this study, not only were phylogenetic trees reconstructed, but variations of surface structure of the PCV capsid were analysed in the course of evolution. Unique surface patterns of the icosahedral fivefold axes of the PCV2 capsid were identified and characterized, all of which were absent in PCV type 1 (PCV1). Icosahedral fivefold axes, decorated with Loops BC, HI and DE, were distinctly different between PCV2 and PCV1. Loops BC, determining the outermost surface around the fivefold axes of PCV capsids, had limited homology between Caps of PCV1 and PCV2. A conserved tyrosine phosphorylation motif in Loop HI that might be recognized by non-receptor tyrosine kinase(s) in vivo was present only in PCV2. Particularly, the concurrent presence of 60 pairs of the conserved tyrosine and a canonical PXXP motif on the PCV2 capsid surface could be a mechanism for PXXP motif binding to and activation of an SH3-domain-containing tyrosine kinase in host cells. Additionally, a conserved cysteine in Loop DE of the PCV2 Cap was substituted by an arginine in PCV1, indicating potentially distinct assembly mechanisms of the capsid in vitro between PCV1 and PCV2. Therefore, these unique patterns on the PCV2 capsid surface, absent in PCV1 isolates, might be related to cell entry, virus function and pathogenesis.

Atomic Force Microscopy in Imaging of Viruses and Virus-Infected Cells

PubMed Central

Kuznetsov, Yurii G.; McPherson, Alexander

2011-01-01

Summary: Atomic force microscopy (AFM) can visualize almost everything pertinent to structural virology and at resolutions that approach those for electron microscopy (EM). Membranes have been identified, RNA and DNA have been visualized, and large protein assemblies have been resolved into component substructures. Capsids of icosahedral viruses and the icosahedral capsids of enveloped viruses have been seen at high resolution, in some cases sufficiently high to deduce the arrangement of proteins in the capsomeres as well as the triangulation number (T). Viruses have been recorded budding from infected cells and suffering the consequences of a variety of stresses. Mutant viruses have been examined and phenotypes described. Unusual structural features have appeared, and the unexpectedly great amount of structural nonconformity within populations of particles has been documented. Samples may be imaged in air or in fluids (including culture medium or buffer), in situ on cell surfaces, or after histological procedures. AFM is nonintrusive and nondestructive, and it can be applied to soft biological samples, particularly when the tapping mode is employed. In principle, only a single cell or virion need be imaged to learn of its structure, though normally images of as many as is practical are collected. While lateral resolution, limited by the width of the cantilever tip, is a few nanometers, height resolution is exceptional, at approximately 0.5 nm. AFM produces three-dimensional, topological images that accurately depict the surface features of the virus or cell under study. The images resemble common light photographic images and require little interpretation. The structures of viruses observed by AFM are consistent with models derived by X-ray crystallography and cryo-EM. PMID:21646429

Prevalence of virus-like particles within a staghorn scleractinian coral ( Acropora muricata) from the Great Barrier Reef

NASA Astrophysics Data System (ADS)

Patten, N. L.; Harrison, P. L.; Mitchell, J. G.

2008-09-01

Transmission electron microscopy (TEM) was used to determine whether Acropora muricata coral colonies from the Great Barrier Reef (GBR), Australia, harboured virus-like particles (VLPs). VLPs were present in all coral colonies sampled at Heron Island (southern GBR) and in tagged coral colonies sampled in at least two of the three sampling periods at Lizard Island (northern GBR). VLPs were observed within gastrodermal and epidermal tissues, and on rarer occasions, within the mesoglea. These VLPs had similar morphologies to known prokaryotic and eukaryotic viruses in other systems. Icosahedral VLPs were observed most frequently, however, filamentous VLPs (FVLPs) and phage were also noted. There were no clear differences in VLP size, morphology or location within the tissues with respect to sample date, coral health status or site. The most common VLP morphotype exhibited icosahedral symmetry, 120-150 nm in diameter, with an electron-dense core and an electronlucent membrane. Larger VLPs of similar morphology were also common. VLPs occurred as single entities, in groups, or in dense clusters, either as free particles within coral tissues, or within membrane-bound vacuoles. VLPs were commonly observed within the perinuclear region, with mitochondria, golgi apparatus and crescent-shaped particles frequently observed within close proximity. The host(s) of these observed VLPs was not clear; however, the different sizes and morphologies of VLPs observed within A. muricata tissues suggest that viruses are infecting either the coral animal, zooxanthellae, intracellular bacteria and/or other coral-associated microbiota, or that the one host is susceptible to infection from more than one type of virus. These results add to the limited but emerging body of evidence that viruses represent another potentially important component of the coral holobiont.

The Effects of Stoichiometry on the Mechanical Properties of Icosahedral Boron Carbide Under Loading

DTIC Science & Technology

2012-11-19

ranging from 10% to 20% C using glancing incidence x - ray diffraction and similar experimental studies of structure as a function of stoichiometry were...blue) positions. it has been suggested that x - ray diffraction analysis of a series of boron-rich materials indicates a distinct change in the c lattice...Angstroms, angles in degrees, volume in cubic Angstroms). Structure Formula % C a b c α β γ Volume Experiment37 B5.6C 15.2 5.19 5.19 5.19 65.18 65.18

Computing methods for icosahedral and symmetry-mismatch reconstruction of viruses by cryo-electron microscopy

NASA Astrophysics Data System (ADS)

Zhu, Bin; Cheng, Lingpeng; Liu, Hongrong

2018-05-01

Not Available Project supported by the National Key R&D Program of China (Grant No. 2016YFA0501100), the National Natural Science Foundation of China (Grant Nos. 91530321, 31570742, and 31570727), and Science and Technology Planning Project of Hunan Province, China (Grant No. 2017RS3033).

Water-soluble Au13 clusters protected by binary thiolates: Structural accommodation and the use for chemosensing

NASA Astrophysics Data System (ADS)

Ding, Weihua; Huang, Chuanqi; Guan, Lingmei; Liu, Xianhu; Luo, Zhixun; Li, Weixue

2017-05-01

Here we report a successful synthesis of water-soluble 13-atoms gold clusters under the monolayer protection of binary thiolates, glutathione and penicillamine, under a molecular formula of Au13(SG)5(PA)7. This monolayer-protected cluster (MPC) finds decent stability and is demonstrated to possess an icosahedral geometry pertaining to structural accommodation in contrast to a planar bare Au13 of local minima energy. Natural bond orbital (NBO) analysis depicts the interaction patterns between gold and the ligands, enlightening to understand the origin of enhanced stability of the Au13 MPCs. Further, the water-soluble Au13 MPCs are found to be a decent candidate for chemosensing and bioimaging.

Thermodynamics at the nanoscale: phase diagrams of nickel-carbon nanoclusters and equilibrium constants for phase transitions

NASA Astrophysics Data System (ADS)

Engelmann, Yannick; Bogaerts, Annemie; Neyts, Erik C.

2014-09-01

Using reactive molecular dynamics simulations, the melting behavior of nickel-carbon nanoclusters is examined. The phase diagrams of icosahedral and Wulff polyhedron clusters are determined using both the Lindemann index and the potential energy. Formulae are derived for calculating the equilibrium constants and the solid and liquid fractions during a phase transition, allowing more rational determination of the melting temperature with respect to the arbitrary Lindemann value. These results give more insight into the properties of nickel-carbon nanoclusters in general and can specifically be very useful for a better understanding of the synthesis of carbon nanotubes using the catalytic chemical vapor deposition method.

Serial femtosecond X-ray diffraction of enveloped virus microcrystals

DOE PAGES

Lawrence, Robert M.; Conrad, Chelsie E.; Zatsepin, Nadia A.; ...

2015-08-20

Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has produced high-resolution, room temperature, time-resolved protein structures. We report preliminary SFX of Sindbis virus, an enveloped icosahedral RNA virus with ~700 Å diameter. Microcrystals delivered in viscous agarose medium diffracted to ~40 Å resolution. Small-angle diffuse X-ray scattering overlaid Bragg peaks and analysis suggests this results from molecular transforms of individual particles. Viral proteins undergo structural changes during entry and infection, which could, in principle, be studied with SFX. This is a pertinent step toward determining room temperature structures from virus microcrystals that may enable time-resolved studies of enveloped viruses.

The effect of hydrogen content on ballistic transport behaviors in the Ni-Nb-Zr-H glassy alloys.

PubMed

Fukuhara, Mikio; Umemori, Yoshimasa

2012-01-01

The electronic transport behaviors of (Ni(0.39)Nb(0.25)Zr(0.35))(100-) (x)H(x) (0 ≤ x < 23.5) glassy alloys with subnanostructural icosahedral Zr(5)Nb(5)Ni(3) clusters have been studied as a function of hydrogen content. These alloys show semiconducting, electric current-induced voltage (Coulomb) oscillation and ballistic transport behaviors. Coulomb oscillation and ballistic transport occur at hydrogen contents between 6.7 and 13.5 at% and between 13.5 and 21.2 at%, respectively. These results suggest that the localization effect of hydrogen in the clusters plays an important role in various electron transport phenomena.

Fate of a giant {Mo72Fe30}-type polyoxometalate cluster in an aqueous solution at higher temperature: understanding related Keplerate chemistry, from molecule to material.

PubMed

Mekala, Raju; Supriya, Sabbani; Das, Samar K

2013-09-03

When the giant icosahedral {Mo72Fe30} cluster containing compound [Mo72Fe30O252(CH3COO)12{Mo2O7(H2O)}2{H2Mo2O8(H2O)}(H2O)91]·150H2O (1) is refluxed in water for 36 h, it results in the formation of nanoiron molybdate, Fe2(MoO4)3, in the form of a yellow precipitate; this simple approach not only generates nanoferric molybdate at a moderate temperature but also helps to understand the stability of {Mo72Fe30} in terms of the linker-pentagon complementary relationship.

Electrodynamical forbiddance of a strong quadrupole interaction in surface enhanced optical processes. Experimental confirmation of the existence in fullerene C{sub 60}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polubotko, A. M., E-mail: alex.marina@mail.ioffe.ru; Chelibanov, V. P., E-mail: Chelibanov@gmail.com

2017-02-15

It is demonstrated that in the SERS and SEIRA spectra of the fullerene C{sub 60}, the lines, which are forbidden in usual Raman and IR spectra and allowed in SERS and SEIRA, are absent. In addition the enhancement SERS coefficient in a single molecule detection regime is ~10{sup 8} instead of the value 10{sup 14}–10{sup 15}, characteristic for this phenomenon. These results are explained by the existence of so-called electrodynamical forbiddance of a strong quadrupole light-molecule interaction, which arises because of belonging of C{sup 60} to the icosahedral symmetry group and due to the electrodynamical law divE = 0.

The Effect of Hydrogen Content on Ballistic Transport Behaviors in the Ni-Nb-Zr-H Glassy Alloys

PubMed Central

Fukuhara, Mikio; Umemori, Yoshimasa

2012-01-01

The electronic transport behaviors of (Ni0.39Nb0.25Zr0.35)100−xHx (0 ≤ x < 23.5) glassy alloys with subnanostructural icosahedral Zr5Nb5Ni3 clusters have been studied as a function of hydrogen content. These alloys show semiconducting, electric current-induced voltage (Coulomb) oscillation and ballistic transport behaviors. Coulomb oscillation and ballistic transport occur at hydrogen contents between 6.7 and 13.5 at% and between 13.5 and 21.2 at%, respectively. These results suggest that the localization effect of hydrogen in the clusters plays an important role in various electron transport phenomena. PMID:22312246

Aperiodic Volume Optics

NASA Astrophysics Data System (ADS)

Gerke, Tim D.

Presented in this thesis is an investigation into aperiodic volume optical devices. The three main topics of research and discussion are the aperiodic volume optical devices that we call computer-generated volume holograms (CGVH), defects within periodic 3D photonic crystals, and non-periodic, but ordered 3D quasicrystals. The first of these devices, CGVHs, are designed and investigated numerically and experimentally. We study the performance of multi-layered amplitude computer-generated volume holograms in terms of efficiency and angular/frequency selectivity. Simulation results show that such aperiodic devices can increase diffraction efficiency relative to periodic amplitude volume holograms while maintaining angular and wavelength selectivity. CGVHs are also designed as voxelated volumes using a new projection optimization algorithm. They are investigated using a volumetric diffraction simulation and a standard 3D beam propagation technique as well as experimentally. Both simulation and experiment verify that the structures function according to their design. These represent the first diffractive structures that have the capacity for generating arbitrary transmission and reflection wave fronts and that provide the ability for multiplexing arbitrary functionality given different illumination conditions. Also investigated and discussed in this thesis are 3D photonic crystals and quasicrystals. We demonstrate that these devices can be fabricated using a femtosecond laser direct writing system that is particularly appropriate for fabrication of such arbitrary 3D structures. We also show that these devices can provide 3D partial bandgaps which could become complete bandgaps if fabricated using high index materials or by coating lower index materials with high index metals. Our fabrication method is particularly suited to the fabrication of engineered defects within the periodic or quasi-periodic systems. We demonstrate the potential for fabricating defects within

Solidification studies of nanocrystalline and quasicrystalline materials from the undercooled state

NASA Astrophysics Data System (ADS)

Croat, Thomas Kevin

2001-07-01

Nanocrystallization occurring during metallic glass devitrification is studied in Zr-Al-Ni-Cu bulk metallic glasses (BMGs) and Al-RE-TM (RE = rare-earth, TM = transition metal) metallic glasses. The importance of transient nucleation in BMG devitrification was established by a direct transmission electron microscopy (TEM) measurement of the grain density in two-stage annealed samples. TEM examination of low temperature annealed BMGs also suggest that amorphous phase separation is occurring prior to crystallization. Nanocrystallization of rapidly quenched Al-RE-Ni glasses was preceded by the compositional segregation of the initially homogeneous glass into Al-rich and solute-rich regions (mainly nickel-enriched) on a ≈50--100 nm length scale, suggesting amorphous phase separation. This pre-existing compositional modulation on a nanometer scale leads naturally to the development of nanocrystals. The average rare earth radius (rRE) in Al-RE-Ni alloys was altered by co-substitution of chemically similar rare earth elements. In glasses with smaller r RE, nucleation of alpha-Al occurred preferentially near the boundaries of the phase-separated regions. However, phase separation did not universally lead to alpha-Al nanocrystallization; glasses with larger rRE crystallized to metastable intermetallic phases with a 50--100 nm grain size. Kinetic analysis of the alpha-Al crystallization was performed using isothermal DSC, yielding abnormally low Avrami exponents (n = 1.0--1.5); these values were found to be consistent with the observed transformation using a model that considers the overlapping diffusion fields of the alpha-Al grains during growth within the phase separated region. Containerless solidification experiments on Ti-based quasicrystal-forming alloys have been performed using various techniques, including drop-tube solidification, electromagnetic levitation (EML) and electrostatic levitation (ESL). In Ti-Fe-Si-O, the alpha-1/1 quasicrystal approximant phase is

Structure and effective interactions in three-component hard sphere liquids.

PubMed

König, A; Ashcroft, N W

2001-04-01

Complete and simple analytical expressions for the partial structure factors of the ternary hard sphere mixture are obtained within the Percus-Yevick approximation and presented as functions of relative packing fractions and relative hard sphere diameters. These solutions follow from the Laplace transform method as applied to multicomponent systems by Lebowitz [Phys. Rev. 133, A895 (1964)]. As an important application, we examine effective interactions in hard sphere liquid mixtures using the microscopic information contained in their partial structure factors. Thus the ensuring pair potential for an effective one-component system is obtained from the correlation functions by using an approximate inversion, and examples of effective potentials for three-component hard sphere mixtures are given. These mixtures may be of particular interest for the study of the packing aspects of melts that form glasses or quasicrystals, since noncrystalline solids often emerge from melts with at least three atomic constituents.

Improved Spectral Calculations for Discrete Schrődinger Operators

NASA Astrophysics Data System (ADS)

Puelz, Charles

This work details an O(n2) algorithm for computing spectra of discrete Schrődinger operators with periodic potentials. Spectra of these objects enhance our understanding of fundamental aperiodic physical systems and contain rich theoretical structure of interest to the mathematical community. Previous work on the Harper model led to an O(n2) algorithm relying on properties not satisfied by other aperiodic operators. Physicists working with the Fibonacci Hamiltonian, a popular quasicrystal model, have instead used a problematic dynamical map approach or a sluggish O(n3) procedure for their calculations. The algorithm presented in this work, a blend of well-established eigenvalue/vector algorithms, provides researchers with a more robust computational tool of general utility. Application to the Fibonacci Hamiltonian in the sparsely studied intermediate coupling regime reveals structure in canonical coverings of the spectrum that will prove useful in motivating conjectures regarding band combinatorics and fractal dimensions.

Typing of Panton-Valentine leukocidin-encoding phages carried by methicillin-susceptible and methicillin-resistant Staphylococcus aureus from Italy.

PubMed

Sanchini, A; Del Grosso, M; Villa, L; Ammendolia, M G; Superti, F; Monaco, M; Pantosti, A

2014-11-01

Panton-Valentine leukocidin (PVL) is the hallmark of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) but can also be found in methicillin-susceptible S. aureus (MSSA) sharing pathogenic and epidemiological characteristics of CA-MRSA. PVL is encoded by two co-transcribed genes that are carried by different staphylococcal bacteriophages. We applied an extended PCR-based typing scheme for the identification of two morphological groups (elongated-head group and icosahedral-head group I phages) and specific PVL phage types in S. aureus isolates recovered in Italy. We examined 48 PVL-positive isolates (25 MSSA and 23 MRSA) collected from different hospital laboratories from April 2005 to May 2011. spa typing, multilocus sequence typing and staphylococcal cassette chromosome mec typing were applied to categorize the isolates. Phage typeability was 48.0% in MSSA and 91.3% in MRSA, highlighting the limitation of the PCR typing scheme when applied to PVL-positive MSSA. Five different PVL phages and two variants of a known phage were detected, the most prevalent being ΦSa2usa, recovered in 15 out of 48 (31.2%) isolates, and carried by both MSSA and MRSA belonging to CC8 and CC5. The recently described ΦTCH60 was recovered in four isolates. A PVL phage (ΦSa119) from an ST772 MRSA, that was not detected using the previous typing scheme, was sequenced, and new primers were designed for the identification of the icosahedral-head group II PVL phages present in ST772 and ST59 MRSA. A comprehensive PVL-phage typing can contribute to the understanding of the epidemiology and evolution of PVL-positive MSSA and MRSA. © 2014 The Authors Clinical Microbiology and Infection © 2014 European Society of Clinical Microbiology and Infectious Diseases.

Role of string-like collective atomic motion on diffusion and structural relaxation in glass forming Cu-Zr alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Hao; Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 2V4; Zhong, Cheng

2015-04-28

We investigate Cu-Zr liquid alloys using molecular dynamics simulation and well-accepted embedded atom method potentials over a wide range of chemical composition and temperature as model metallic glass-forming (GF) liquids. As with other types of GF materials, the dynamics of these complex liquids are characterized by “dynamic heterogeneity” in the form of transient polymeric clusters of highly mobile atoms that are composed in turn of atomic clusters exhibiting string-like cooperative motion. In accordance with the string model of relaxation, an extension of the Adam-Gibbs (AG) model, changes in the activation free energy ΔG{sub a} with temperature of both the Cumore » and Zr diffusion coefficients D, and the alpha structural relaxation time τ{sub α} can be described to a good approximation by changes in the average string length, L. In particular, we confirm that the strings are a concrete realization of the abstract “cooperatively rearranging regions” of AG. We also find coexisting clusters of relatively “immobile” atoms that exhibit predominantly icosahedral local packing rather than the low symmetry packing of “mobile” atoms. These two distinct types of dynamic heterogeneity are then associated with different fluid structural states. Glass-forming liquids are thus analogous to polycrystalline materials where the icosahedrally packed regions correspond to crystal grains, and the strings reside in the relatively disordered grain boundary-like regions exterior to these locally well-ordered regions. A dynamic equilibrium between localized (“immobile”) and wandering (“mobile”) particles exists in the liquid so that the dynamic heterogeneity can be considered to be type of self-assembly process. We also characterize changes in the local atomic free volume in the course of string-like atomic motion to better understand the initiation and propagation of these fluid excitations.« less

Structural Studies of Adeno-Associated Virus Serotype 8 Capsid Transitions Associated with Endosomal Trafficking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nam, Hyun-Joo; Gurda, Brittney L.; McKenna, Robert

2012-09-17

The single-stranded DNA (ssDNA) parvoviruses enter host cells through receptor-mediated endocytosis, and infection depends on processing in the early to late endosome as well as in the lysosome prior to nuclear entry for replication. However, the mechanisms of capsid endosomal processing, including the effects of low pH, are poorly understood. To gain insight into the structural transitions required for this essential step in infection, the crystal structures of empty and green fluorescent protein (GFP) gene-packaged adeno-associated virus serotype 8 (AAV8) have been determined at pH values of 6.0, 5.5, and 4.0 and then at pH 7.5 after incubation at pHmore » 4.0, mimicking the conditions encountered during endocytic trafficking. While the capsid viral protein (VP) topologies of all the structures were similar, significant amino acid side chain conformational rearrangements were observed on (i) the interior surface of the capsid under the icosahedral 3-fold axis near ordered nucleic acid density that was lost concomitant with the conformational change as pH was reduced and (ii) the exterior capsid surface close to the icosahedral 2-fold depression. The 3-fold change is consistent with DNA release from an ordering interaction on the inside surface of the capsid at low pH values and suggests transitions that likely trigger the capsid for genome uncoating. The surface change results in disruption of VP-VP interface interactions and a decrease in buried surface area between VP monomers. This disruption points to capsid destabilization which may (i) release VP1 amino acids for its phospholipase A2 function for endosomal escape and nuclear localization signals for nuclear targeting and (ii) trigger genome uncoating.« less

Crystal structure of Au25(SePh)18 nanoclusters and insights into their electronic, optical and catalytic properties

NASA Astrophysics Data System (ADS)

Song, Yongbo; Zhong, Juan; Yang, Sha; Wang, Shuxin; Cao, Tiantian; Zhang, Jun; Li, Peng; Hu, Daqiao; Pei, Yong; Zhu, Manzhou

2014-10-01

The crystal structure of selenolate-capped Au25(SePh)18- nanoclusters has been unambiguously determined for the first time, and provides a solid basis for a deeper understanding of the structure-property relationships. The selenolate-capped Au25 cluster shows noticeable differences from the previously reported Au25(SCH2CH2Ph)18- counterpart, albeit both share the icosahedral Au13 core and semi-ring Au2(SeR)3 or Au2(SR)3 motifs. Distinct differences in the electronic structure and optical, catalytic and electrochemical properties are revealed by the coupling experiments with density functional theory (TD-DFT) calculations. Overall, the successful determination of the Au25(SePh)18- structure removes any ambiguity about its structure, and comparison with the thiolated Au25 counterpart helps us to further understand how the ligands affect the properties of the nanocluster.The crystal structure of selenolate-capped Au25(SePh)18- nanoclusters has been unambiguously determined for the first time, and provides a solid basis for a deeper understanding of the structure-property relationships. The selenolate-capped Au25 cluster shows noticeable differences from the previously reported Au25(SCH2CH2Ph)18- counterpart, albeit both share the icosahedral Au13 core and semi-ring Au2(SeR)3 or Au2(SR)3 motifs. Distinct differences in the electronic structure and optical, catalytic and electrochemical properties are revealed by the coupling experiments with density functional theory (TD-DFT) calculations. Overall, the successful determination of the Au25(SePh)18- structure removes any ambiguity about its structure, and comparison with the thiolated Au25 counterpart helps us to further understand how the ligands affect the properties of the nanocluster. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr04631e

Turnip yellow mosaic virus as a chemoaddressable bionanoparticle.

PubMed

Barnhill, Hannah N; Reuther, Rachel; Ferguson, P Lee; Dreher, Theo; Wang, Qian

2007-01-01

Viruses and virus-like particles (VLPs) have been demonstrated to be robust scaffolds for the construction of nanomaterials. In order to develop new nanoprobes for time-resolved fluoroimmuno assays as well as to investigate the two-dimensional self-assembly of viruses and VLPs, the icosahedral turnip yellow mosaic virus (TYMV) was investigated as a potential building block in our study. TYMV is an icosahedral plant virus with an average diameter of 28 nm that can be isolated inexpensively in gram quantities from turnips or Chinese cabbage. There are 180 coat protein subunits per TYMV capsid. The conventional N-hydroxysuccinimide-mediated amidation reaction was employed for the chemical modification of the viral capsid. Tryptic digestion with sequential MALDI-TOF MS analysis identified that the amino groups of K32 of the flexible N-terminus made the major contribution for the reactivity of TYMV toward N-hydroxysuccinimide ester (NHS) reagents. The reactivity was also monitored with UV-vis absorbance and fluorescence, which revealed that approximately 60 lysines per particle could be addressed. We hypothesized that the flexible A chain contains the reactive lysine because the crystal structure of TYMV has shown that chain A is much more flexible compared to B and C, especially at the N-terminal region where the Lys-32 located. In addition, about 90 to 120 carboxyl groups, located in the most exposed sequence, could be modified with amines catalyzed with 1-(3-dimethylaminopropyl-3-ethylcarbodiimide) hydrochloride (EDC) and sulfo-NHS. TYMV was stable to a wide range of reaction conditions and maintained its integrity after the chemical conjugations. Therefore, it can potentially be employed as a reactive scaffold for the display of a variety of materials for applications in many areas of nanoscience.

Mechanism of Membranous Tunnelling Nanotube Formation in Viral Genome Delivery

PubMed Central

Peralta, Bibiana; Gil-Carton, David; Castaño-Díez, Daniel; Bertin, Aurelie; Boulogne, Claire; Oksanen, Hanna M.; Bamford, Dennis H.; Abrescia, Nicola G. A.

2013-01-01

In internal membrane-containing viruses, a lipid vesicle enclosed by the icosahedral capsid protects the genome. It has been postulated that this internal membrane is the genome delivery device of the virus. Viruses built with this architectural principle infect hosts in all three domains of cellular life. Here, using a combination of electron microscopy techniques, we investigate bacteriophage PRD1, the best understood model for such viruses, to unveil the mechanism behind the genome translocation across the cell envelope. To deliver its double-stranded DNA, the icosahedral protein-rich virus membrane transforms into a tubular structure protruding from one of the 12 vertices of the capsid. We suggest that this viral nanotube exits from the same vertex used for DNA packaging, which is biochemically distinct from the other 11. The tube crosses the capsid through an aperture corresponding to the loss of the peripentonal P3 major capsid protein trimers, penton protein P31 and membrane protein P16. The remodeling of the internal viral membrane is nucleated by changes in osmolarity and loss of capsid-membrane interactions as consequence of the de-capping of the vertices. This engages the polymerization of the tail tube, which is structured by membrane-associated proteins. We have observed that the proteo-lipidic tube in vivo can pierce the gram-negative bacterial cell envelope allowing the viral genome to be shuttled to the host cell. The internal diameter of the tube allows one double-stranded DNA chain to be translocated. We conclude that the assembly principles of the viral tunneling nanotube take advantage of proteo-lipid interactions that confer to the tail tube elastic, mechanical and functional properties employed also in other protein-membrane systems. PMID:24086111

DOE Office of Scientific and Technical Information (OSTI.GOV)

Su, Qiudong; Yi, Yao; Guo, Minzhuo

Highlights: •The conformational HBV neutralization antigen domain was successfully displayed on the surface of truncated HBc particles. •Appropriate dialysis procedures to support the renaturing environment for the protein refolding. •Efficient purification procedures to obtain high purity and icosahedral particles of mosaic HBV antigen. •Strong immune responses not only including neutralization antibody response but also Th1 cell response were induced in mice. -- Abstract: Hepatitis B capsid protein expressed in Escherichia coli can reassemble into icosahedral particles, which could strongly enhance the immunogenicity of foreign epitopes, especially those inserted into its major immunodominant region. Herein, we inserted the entire ‘α’ antigenicmore » determinant amino acids (aa) 119–152 of HBsAg into the truncated HBc (aa 1–144), between Asp{sup 78} and Pro{sup 79}. Prokaryotic expression showed that the mosaic HBc was mainly in the form of inclusion bodies. After denaturation with urea, it was dialyzed progressively for protein renaturation. We observed that before and after renaturation, mosaic HBc was antigenic as determined by HBsAg ELISA and a lot of viruslike particles were observed after renaturation. Thus, we further purified the mosaic viruslike particles by (NH{sub 4}){sub 2}SO{sub 4} precipitation, DEAE chromatography, and Sepharose 4FF chromatography. Negative staining electron microscopy demonstrated the morphology of the viruslike particles. Immunization of Balb/c mice with mosaic particles induced the production of anti-HBs antibody and Th1 cell immune response supported by ELISPOT and CD4/CD8 proportions assay. In conclusion, we constructed mosaic hepatitis core particles displaying the entire ‘α’ antigenic determinant on the surface and laid a foundation for researching therapeutic hepatits B vaccines.« less

Morphogenesis of mimivirus and its viral factories: an atomic force microscopy study of infected cells.

PubMed

Kuznetsov, Yuri G; Klose, Thomas; Rossmann, Michael; McPherson, Alexander

2013-10-01

Amoebas infected with mimivirus were disrupted at sequential stages of virus production and were visualized by atomic force microscopy. The development of virus factories proceeded over 3 to 4 h postinfection and resulted from the coalescence of 0.5- to 2-μm vesicles, possibly bearing nucleic acid, derived from either the nuclear membrane or the closely associated rough endoplasmic reticulum. Virus factories actively producing virus capsids on their surfaces were imaged, and this allowed the morphogenesis of the capsids to be delineated. The first feature to appear on a virus factory surface when a new capsid is born is the center of a stargate, which is a pentameric protein oligomer. As the arms of the stargate grow from the pentamer, a rough disk the diameter of a capsid thickens around it. This marks the initial emergence of a protein-coated membrane vesicle. The capsid self-assembles on the vesicle. Hillocks capped by different pentameric proteins spontaneously appear on the emerging vesicle at positions that are ultimately occupied by 5-fold icosahedral vertices. A lattice of coat protein nucleates at each of the 5-fold vertices, but not at the stargate, and then spreads outward from the vertices over the surface, merging seamlessly to complete the icosahedral capsid. Filling with DNA and associated proteins occurs by the transfer of nucleic acid from the interior of the virus factory into the nearly completed capsids. The portal, through which the DNA enters, is sealed by a plug of protein having a diameter of about 40 nm. A layer of integument protein that anchors the surface fibers is acquired by the passage of capsids through a membrane enriched in the protein. The coating of surface fibers is similarly acquired when the integument protein-coated capsids pass through a second membrane that has a forest of surface fibers embedded on one side.

Morphogenesis of Mimivirus and Its Viral Factories: an Atomic Force Microscopy Study of Infected Cells

PubMed Central

Kuznetsov, Yuri G.; Klose, Thomas; Rossmann, Michael

2013-01-01

Amoebas infected with mimivirus were disrupted at sequential stages of virus production and were visualized by atomic force microscopy. The development of virus factories proceeded over 3 to 4 h postinfection and resulted from the coalescence of 0.5- to 2-μm vesicles, possibly bearing nucleic acid, derived from either the nuclear membrane or the closely associated rough endoplasmic reticulum. Virus factories actively producing virus capsids on their surfaces were imaged, and this allowed the morphogenesis of the capsids to be delineated. The first feature to appear on a virus factory surface when a new capsid is born is the center of a stargate, which is a pentameric protein oligomer. As the arms of the stargate grow from the pentamer, a rough disk the diameter of a capsid thickens around it. This marks the initial emergence of a protein-coated membrane vesicle. The capsid self-assembles on the vesicle. Hillocks capped by different pentameric proteins spontaneously appear on the emerging vesicle at positions that are ultimately occupied by 5-fold icosahedral vertices. A lattice of coat protein nucleates at each of the 5-fold vertices, but not at the stargate, and then spreads outward from the vertices over the surface, merging seamlessly to complete the icosahedral capsid. Filling with DNA and associated proteins occurs by the transfer of nucleic acid from the interior of the virus factory into the nearly completed capsids. The portal, through which the DNA enters, is sealed by a plug of protein having a diameter of about 40 nm. A layer of integument protein that anchors the surface fibers is acquired by the passage of capsids through a membrane enriched in the protein. The coating of surface fibers is similarly acquired when the integument protein-coated capsids pass through a second membrane that has a forest of surface fibers embedded on one side. PMID:23926353

The synthesis and characterization of iron nanoparticles

NASA Astrophysics Data System (ADS)

Bennett, Tyler

Nanoparticle synthesis has garnered attention for technological applications for catalysts, industrial processing, and medical applications. The size ranges for these is in the particles nanostructural domain. Pure iron nanoparticles have been of particular interest for their reactivity and relative biological inertness. Applications include cancer treatment and carrying medicine to a relevant site. Unfortunately, because of their reactivity, pure iron nanoparticles have been difficult to study. This is because of their accelerated tendency to form oxides in air, due to the increased surface area to volume ratio. Using synthesis processes with polyphenols or long chain amines, air stable iron nanoparticles have been produced with a diameter size range of ~ 2 to about ~10 nm, but apparently have transformed due to internal pressure and crystallographic defects to the FCC phase. The FCC crystals have been seen to form icosahedral and decahedral shapes. This size is within the range for use as a catalyst for the growth of both carbon nanotubes and boron nitride nanotubes as well for biomedical applications. The advantages of these kinds of catalysts are that nanotube growth can be for the first time separated from the catalyst formation. Additionally, the catalyst size can be preselected for a certain size nanotube to grow. In summary: (1) we found the size distributions of nanoparticles for various synthesis processes, (2) we discovered the right size range for growth of nanotubes from the iron nanoparticles, (3) the nanoparticles are under a very high internal pressure, (4) the nanoparticles are in the FCC phase, (5) they appear to be in icosahedral and decahedral structures, (6) they undergo room temperature twinning, (7) the FCC crystals are distorted due to carbon in octahedral sites, (8) the iron nanoparticles are stable in air, (9) adding small amounts of copper make the iron nanoparticles smaller.

Dynamics and asymmetry in the dimer of the norovirus major capsid protein.

PubMed

Tubiana, Thibault; Boulard, Yves; Bressanelli, Stéphane

2017-01-01

Noroviruses are the major cause of non-bacterial acute gastroenteritis in humans and livestock worldwide, despite being physically among the simplest animal viruses. The icosahedral capsid encasing the norovirus RNA genome is made of 90 dimers of a single ca 60-kDa polypeptide chain, VP1, arranged with T = 3 icosahedral symmetry. Here we study the conformational dynamics of this main building block of the norovirus capsid. We use molecular modeling and all-atom molecular dynamics simulations of the VP1 dimer for two genogroups with 50% sequence identity. We focus on the two points of flexibility in VP1 known from the crystal structure of the genogroup I (GI, human) capsid and from subsequent cryo-electron microscopy work on the GII capsid (also human). First, with a homology model of the GIII (bovine) VP1 dimer subjected to simulated annealing then classical molecular dynamics simulations, we show that the N-terminal arm conformation seen in the GI crystal structure is also favored in GIII VP1 but depends on the protonation state of critical residues. Second, simulations of the GI dimer show that the VP1 spike domain will not keep the position found in the GII electron microscopy work. Our main finding is a consistent propensity of the VP1 dimer to assume prominently asymmetric conformations. In order to probe this result, we obtain new SAXS data on GI VP1 dimers. These data are not interpretable as a population of symmetric dimers, but readily modeled by a highly asymmetric dimer. We go on to discuss possible implications of spontaneously asymmetric conformations in the successive steps of norovirus capsid assembly. Our work brings new lights on the surprising conformational range encoded in the norovirus major capsid protein.

Differential protein partitioning within the herpesvirus tegument and envelope underlies a complex and variable virion architecture

PubMed Central

Bohannon, Kevin Patrick; Jun, Yonggun; Gross, Steven P.; Smith, Gregory Allan

2013-01-01

The herpesvirus virion is a multilayered structure consisting of a DNA-filled capsid, tegument, and envelope. Detailed reconstructions of the capsid are possible based on its icosahedral symmetry, but the surrounding tegument and envelope layers lack regular architecture. To circumvent limitations of symmetry-based ultrastructural reconstruction methods, a fluorescence approach was developed using single-particle imaging combined with displacement measurements at nanoscale resolution. An analysis of 11 tegument and envelope proteins defined the composition and plasticity of symmetric and asymmetric elements of the virion architecture. The resulting virion protein map ascribes molecular composition to density profiles previously acquired by traditional ultrastructural methods, and provides a way forward to examine the dynamics of the virion architecture during infection. PMID:23569236

Liquid Aluminum: Atomic diffusion and viscosity from ab initio molecular dynamics

PubMed Central

Jakse, Noel; Pasturel, Alain

2013-01-01

We present a study of dynamic properties of liquid aluminum using density-functional theory within the local-density (LDA) and generalized gradient (GGA) approximations. We determine the temperature dependence of the self-diffusion coefficient as well the viscosity using direct methods. Comparisons with experimental data favor the LDA approximation to compute dynamic properties of liquid aluminum. We show that the GGA approximation induce more important backscattering effects due to an enhancement of the icosahedral short range order (ISRO) that impact directly dynamic properties like the self-diffusion coefficient. All these results are then used to test the Stokes-Einstein relation and the universal scaling law relating the diffusion coefficient and the excess entropy of a liquid. PMID:24190311

Recasting a model atomistic glassformer as a system of icosahedra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pinney, Rhiannon; Bristol Centre for Complexity Science, University of Bristol, Bristol BS8 1TS; Liverpool, Tanniemola B.

2015-12-28

We consider a binary Lennard-Jones glassformer whose super-Arrhenius dynamics are correlated with the formation of icosahedral structures. Upon cooling, these icosahedra organize into mesoclusters. We recast this glassformer as an effective system of icosahedra which we describe with a population dynamics model. This model we parameterize with data from the temperature regime accessible to molecular dynamics simulations. We then use the model to determine the population of icosahedra in mesoclusters at arbitrary temperature. Using simulation data to incorporate dynamics into the model, we predict relaxation behavior at temperatures inaccessible to conventional approaches. Our model predicts super-Arrhenius dynamics whose relaxation timemore » remains finite for non-zero temperature.« less

Mechanisms of Virus Assembly

PubMed Central

Perlmutter, Jason D.; Hagan, Michael F.

2015-01-01

Viruses are nanoscale entities containing a nucleic acid genome encased in a protein shell called a capsid, and in some cases surrounded by a lipid bilayer membrane. This review summarizes the physics that govern the processes by which capsids assembles within their host cells and in vitro. We describe the thermodynamics and kinetics for assembly of protein subunits into icosahedral capsid shells, and how these are modified in cases where the capsid assembles around a nucleic acid or on a lipid bilayer. We present experimental and theoretical techniques that have been used to characterize capsid assembly, and we highlight aspects of virus assembly which are likely to receive significant attention in the near future. PMID:25532951

Large scale structural optimization of trimetallic Cu-Au-Pt clusters up to 147 atoms

NASA Astrophysics Data System (ADS)

Wu, Genhua; Sun, Yan; Wu, Xia; Chen, Run; Wang, Yan

2017-10-01

The stable structures of Cu-Au-Pt clusters up to 147 atoms are optimized by using an improved adaptive immune optimization algorithm (AIOA-IC method), in which several motifs, such as decahedron, icosahedron, face centered cubic, sixfold pancake, and Leary tetrahedron, are randomly selected as the inner cores of the starting structures. The structures of Cu8AunPt30-n (n = 1-29), Cu8AunPt47-n (n = 1-46), and partial 75-, 79-, 100-, and 147-atom clusters are analyzed. Cu12Au93Pt42 cluster has onion-like Mackay icosahedral motif. The segregation phenomena of Cu, Au and Pt in clusters are explained by the atomic radius, surface energy, and cohesive energy.

Theoretical Problems in Materials Science

NASA Technical Reports Server (NTRS)

Langer, J. S.; Glicksman, M. E.

1985-01-01

Interactions between theoretical physics and material sciences to identify problems of common interest in which some of the powerful theoretical approaches developed for other branches of physics may be applied to problems in materials science are presented. A unique structure was identified in rapidly quenched Al-14% Mn. The material has long-range directed bonds with icosahedral symmetry which does not form a regular structure but instead forms an amorphous-like quasiperiodic structure. Finite volume fractions of second phase material is advanced and is coupled with nucleation theory to describe the formation and structure of precipitating phases in alloys. Application of the theory of pattern formation to the problem of dendrite formation is studied.

Structure and orientation of small particles of platinum deposited on NaCl and mica

NASA Technical Reports Server (NTRS)

Renou, A.; Gillet, M.

1979-01-01

The structure of small platinum particles condensed in vacuum onto NaCl (001), NaCl (111) and mica substrates was studied by electron diffraction and electron microscopy. Results show that above a certain substrate temperature decahedral or icosahedral particles are formed. These particles are practically absent with substrates cleaved in high vacuum. They are always much less numerous than in gold films prepared under the same conditions. Assumptions made to explain this phenomenon are: (1) the initial growth of an abnormal structure of the nuclei as opposed by the substrate; (2) the particles disappear before they attain a size which corresponds to the observations; and (3) the particles result from a coalescence mechanism leading to multiple twinned particles.

Iterative projection algorithms for ab initio phasing in virus crystallography.

PubMed

Lo, Victor L; Kingston, Richard L; Millane, Rick P

2016-12-01

Iterative projection algorithms are proposed as a tool for ab initio phasing in virus crystallography. The good global convergence properties of these algorithms, coupled with the spherical shape and high structural redundancy of icosahedral viruses, allows high resolution phases to be determined with no initial phase information. This approach is demonstrated by determining the electron density of a virus crystal with 5-fold non-crystallographic symmetry, starting with only a spherical shell envelope. The electron density obtained is sufficiently accurate for model building. The results indicate that iterative projection algorithms should be routinely applicable in virus crystallography, without the need for ancillary phase information. Copyright © 2016 Elsevier Inc. All rights reserved.

Differential protein partitioning within the herpesvirus tegument and envelope underlies a complex and variable virion architecture.

PubMed

Bohannon, Kevin Patrick; Jun, Yonggun; Gross, Steven P; Smith, Gregory Allan

2013-04-23

The herpesvirus virion is a multilayered structure consisting of a DNA-filled capsid, tegument, and envelope. Detailed reconstructions of the capsid are possible based on its icosahedral symmetry, but the surrounding tegument and envelope layers lack regular architecture. To circumvent limitations of symmetry-based ultrastructural reconstruction methods, a fluorescence approach was developed using single-particle imaging combined with displacement measurements at nanoscale resolution. An analysis of 11 tegument and envelope proteins defined the composition and plasticity of symmetric and asymmetric elements of the virion architecture. The resulting virion protein map ascribes molecular composition to density profiles previously acquired by traditional ultrastructural methods, and provides a way forward to examine the dynamics of the virion architecture during infection.

Composition Formulas of Inorganic Compounds in Terms of Cluster Plus Glue Atom Model.

PubMed

Ma, Yanping; Dong, Dandan; Wu, Aimin; Dong, Chuang

2018-01-16

The present paper attempts to identify the molecule-like structural units in inorganic compounds, by applying the so-called "cluster plus glue atom model". This model, originating from metallic glasses and quasi-crystals, describes any structure in terms of a nearest-neighbor cluster and a few outer-shell glue atoms, expressed in the cluster formula [cluster](glue atoms). Similar to the case for normal molecules where the charge transfer occurs within the molecule to meet the commonly known octet electron rule, the octet state is reached after matching the nearest-neighbor cluster with certain outer-shell glue atoms. These kinds of structural units contain information on local atomic configuration, chemical composition, and electron numbers, just as for normal molecules. It is shown that the formulas of typical inorganic compounds, such as fluorides, oxides, and nitrides, satisfy a similar octet electron rule, with the total number of valence electrons per unit formula being multiples of eight.

Photonic band gap in isotropic hyperuniform disordered solids with low dielectric contrast.

PubMed

Man, Weining; Florescu, Marian; Matsuyama, Kazue; Yadak, Polin; Nahal, Geev; Hashemizad, Seyed; Williamson, Eric; Steinhardt, Paul; Torquato, Salvatore; Chaikin, Paul

2013-08-26

We report the first experimental demonstration of a TE-polarization photonic band gap (PBG) in a 2D isotropic hyperuniform disordered solid (HUDS) made of dielectric media with a dielectric index contrast of 1.6:1, very low for PBG formation. The solid is composed of a connected network of dielectric walls enclosing air-filled cells. Direct comparison with photonic crystals and quasicrystals permitted us to investigate band-gap properties as a function of increasing rotational isotropy. We present results from numerical simulations proving that the PBG observed experimentally for HUDS at low index contrast has zero density of states. The PBG is associated with the energy difference between complementary resonant modes above and below the gap, with the field predominantly concentrated in the air or in the dielectric. The intrinsic isotropy of HUDS may offer unprecedented flexibilities and freedom in applications (i. e. defect architecture design) not limited by crystalline symmetries.

Bloch-like waves in random-walk potentials based on supersymmetry

NASA Astrophysics Data System (ADS)

Yu, Sunkyu; Piao, Xianji; Hong, Jiho; Park, Namkyoo

2015-09-01

Bloch's theorem was a major milestone that established the principle of bandgaps in crystals. Although it was once believed that bandgaps could form only under conditions of periodicity and long-range correlations for Bloch's theorem, this restriction was disproven by the discoveries of amorphous media and quasicrystals. While network and liquid models have been suggested for the interpretation of Bloch-like waves in disordered media, these approaches based on searching for random networks with bandgaps have failed in the deterministic creation of bandgaps. Here we reveal a deterministic pathway to bandgaps in random-walk potentials by applying the notion of supersymmetry to the wave equation. Inspired by isospectrality, we follow a methodology in contrast to previous methods: we transform order into disorder while preserving bandgaps. Our approach enables the formation of bandgaps in extremely disordered potentials analogous to Brownian motion, and also allows the tuning of correlations while maintaining identical bandgaps, thereby creating a family of potentials with `Bloch-like eigenstates'.

David Adler Lectureship Award: A Chance to Grow

NASA Astrophysics Data System (ADS)

Canfield, Paul

2014-03-01

Having a chance to grow has been a vital, key, aspect to my research career. A successful condensed matter, new materials group thrives when it can have multiple make-measure-think cycles running in parallel and series. The ability to explore phase space and design, discover and grow new compounds is the starting point for many research projects and, sometimes, new fields. In this talk I want to provide an overview of several of the motivations that can lead to sample growth and also provide some examples of how new materials can lead to the intellectual / technical growth of a group as well. Examples will be drawn, as time allows, from work on magnetic, non-magnetic, low-Tc, and high Tc superconductors as well as heavy Fermions, spin-glasses and quasicrystals. Much of this work was supported by the US DOE, Office of Basic Energy Science, Division of Materials Sciences and Engineering, under Contract No. DE-AC02-07CH11358.

Metallurgical reactions in two industrially strip-cast aluminum-manganese alloys

NASA Astrophysics Data System (ADS)

Hansen, V.; Andersson, B.; Tibballs, J. E.; Gjønnes, J.

1995-08-01

Precipitation, phase transformation, subgrain growth, and recrystallization that occur during heat treatment of two strip-cast, cold-rolled, high manganese aluminum alloys have been studied mainly by transmission electron microscopy (TEM). The alloys differ in silicon content. The isothermal heat treatments have been performed in a salt bath at temperatures between 330 °C and 530 °C for times up to 1000 hours. Size distributions for each type of secondary particle have been determined. After short annealing times, small quasicrystals precipitated and subsequently transformed to α phase. The densities of these precipitates controlled dislocation movement and regulated subgrain sizes. Prolonged heating resulted in peritectoid reactions to Al6Mn or Al12Mn. Recrystallization, which is associated with the formation of Al12Mn, is advanced by increasing the silicon content; the nucleation and growth of Al12Mn occurs only at the expense of other phases that stabilize the subgrain network.

Phase imaging using highly coherent X-rays: radiography, tomography, diffraction topography.

PubMed

Baruchel, J; Cloetens, P; Härtwig, J; Ludwig, W; Mancini, L; Pernot, P; Schlenker, M

2000-05-01

Several hard X-rays imaging techniques greatly benefit from the coherence of the beams delivered by the modern synchrotron radiation sources. This is illustrated with examples recorded on the 'long' (145 m) ID19 'imaging' beamline of the ESRF. Phase imaging is directly related to the small angular size of the source as seen from one point of the sample ('effective divergence' approximately microradians). When using the ;propagation' technique, phase radiography and tomography are instrumentally very simple. They are often used in the 'edge detection' regime, where the jumps of density are clearly observed. The in situ damage assessment of micro-heterogeneous materials is one example of the many applications. Recently a more quantitative approach has been developed, which provides a three-dimensional density mapping of the sample ('holotomography'). The combination of diffraction topography and phase-contrast imaging constitutes a powerful tool. The observation of holes of discrete sizes in quasicrystals, and the investigation of poled ferroelectric materials, result from this combination.

An explanation of resisted discoveries based on construal-level theory.

PubMed

Fang, Hui

2015-02-01

New discoveries and theories are crucial for the development of science, but they are often initially resisted by the scientific community. This paper analyses resistance to scientific discoveries that supplement previous research results or conclusions with new phenomena, such as long chains in macromolecules, Alfvén waves, parity nonconservation in weak interactions and quasicrystals. Construal-level theory is used to explain that the probability of new discoveries may be underestimated because of psychological distance. Thus, the insufficiently examined scope of an accepted theory may lead to overstating the suitable scope and underestimating the probability of its undiscovered counter-examples. Therefore, psychological activity can result in people instinctively resisting new discoveries. Direct evidence can help people judge the validity of a hypothesis with rational thinking. The effects of authorities and textbooks on the resistance to discoveries are also discussed. From the results of our analysis, suggestions are provided to reduce resistance to real discoveries, which will benefit the development of science.

NCAR global model topography generation software for unstructured grids

NASA Astrophysics Data System (ADS)

Lauritzen, P. H.; Bacmeister, J. T.; Callaghan, P. F.; Taylor, M. A.

2015-06-01

It is the purpose of this paper to document the NCAR global model topography generation software for unstructured grids. Given a model grid, the software computes the fraction of the grid box covered by land, the gridbox mean elevation, and associated sub-grid scale variances commonly used for gravity wave and turbulent mountain stress parameterizations. The software supports regular latitude-longitude grids as well as unstructured grids; e.g. icosahedral, Voronoi, cubed-sphere and variable resolution grids. As an example application and in the spirit of documenting model development, exploratory simulations illustrating the impacts of topographic smoothing with the NCAR-DOE CESM (Community Earth System Model) CAM5.2-SE (Community Atmosphere Model version 5.2 - Spectral Elements dynamical core) are shown.

A reconfigurable robot with tensegrity structure using nylon artificial muscle

NASA Astrophysics Data System (ADS)

Wu, Lianjun; de Andrade, Monica Jung; Brahme, Tarang; Tadesse, Yonas; Baughman, Ray H.

2016-04-01

This paper describes the design and experimental investigation of a self-reconfigurable icosahedral robot for locomotion. The robot consists of novel and modular tensegrity structures, which can potentially maneuver in unstructured environments while carrying a payload. Twisted and Coiled Polymer (TCP) muscles were utilized to actuate the tensegrity structure as needed. The tensegrity system has rigid struts and flexible TCP muscles that allow keeping a payload in the central region. The TCP muscles provide large actuation stroke, high mechanical power per fiber mass and can undergo millions of highly reversible cycles. The muscles are electrothermally driven, and, upon stimulus, the heated muscles reconfigure the shape of the tensegrity structure. Here, we present preliminary experimental results that determine the rolling motion of the structure.

Sheet-like assemblies of spherical particles with point-symmetrical patches.

PubMed

Mani, Ethayaraja; Sanz, Eduardo; Roy, Soumyajit; Dijkstra, Marjolein; Groenewold, Jan; Kegel, Willem K

2012-04-14

We report a computational study on the spontaneous self-assembly of spherical particles into two-dimensional crystals. The experimental observation of such structures stabilized by spherical objects appeared paradoxical so far. We implement patchy interactions with the patches point-symmetrically (icosahedral and cubic) arranged on the surface of the particle. In these conditions, preference for self-assembly into sheet-like structures is observed. We explain our findings in terms of the inherent symmetry of the patches and the competition between binding energy and vibrational entropy. The simulation results explain why hollow spherical shells observed in some Keplerate-type polyoxometalates (POM) appear. Our results also provide an explanation for the experimentally observed layer-by-layer growth of apoferritin--a quasi-spherical protein.

Hardness and Elastic Modulus on Six-Fold Symmetry Gold Nanoparticles

PubMed Central

Ramos, Manuel; Ortiz-Jordan, Luis; Hurtado-Macias, Abel; Flores, Sergio; Elizalde-Galindo, José T.; Rocha, Carmen; Torres, Brenda; Zarei-Chaleshtori, Maryam; Chianelli, Russell R.

2013-01-01

The chemical synthesis of gold nanoparticles (NP) by using gold (III) chloride trihydrate (HAuCl∙3H2O) and sodium citrate as a reducing agent in aqueous conditions at 100 °C is presented here. Gold nanoparticles areformed by a galvanic replacement mechanism as described by Lee and Messiel. Morphology of gold-NP was analyzed by way of high-resolution transmission electron microscopy; results indicate a six-fold icosahedral symmetry with an average size distribution of 22 nm. In order to understand the mechanical behaviors, like hardness and elastic moduli, gold-NP were subjected to nanoindentation measurements—obtaining a hardness value of 1.72 GPa and elastic modulus of 100 GPa in a 3–5 nm of displacement at the nanoparticle’s surface. PMID:28809302

ac impedance analysis of a Ni-Nb-Zr-H glassy alloy with femtofarad capacitance tunnels

NASA Astrophysics Data System (ADS)

Fukuhara, M.; Seto, M.; Inoue, A.

2010-01-01

A Nyquist diagram of a (Ni0.36Nb0.24Zr0.40)90H10 glassy alloy shows a semitrue circle, indicating that it is a conducting material with a total capacitance of 17.8 μF. The Bode plots showing the dependencies of its real and imaginary impedances, and phase on frequency suggest a simpler equivalent circuit having a resistor in parallel with a capacitor. Dividing the total capacitance (17.8 μF) by the capacitance of a single tunnel (0.9 fF), we deduced that this material has a high number of dielectric tunnels, which can be regarded as regular prisms separated from the electric-conducting distorted icosahedral Zr5Ni5Nb3 clusters by an average of 0.225 nm.

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source.

PubMed

Munke, Anna; Andreasson, Jakob; Aquila, Andrew; Awel, Salah; Ayyer, Kartik; Barty, Anton; Bean, Richard J; Berntsen, Peter; Bielecki, Johan; Boutet, Sébastien; Bucher, Maximilian; Chapman, Henry N; Daurer, Benedikt J; DeMirci, Hasan; Elser, Veit; Fromme, Petra; Hajdu, Janos; Hantke, Max F; Higashiura, Akifumi; Hogue, Brenda G; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A; Reddy, Hemanth K N; Lan, Ti-Yen; Larsson, Daniel S D; Liu, Haiguang; Loh, N Duane; Maia, Filipe R N C; Mancuso, Adrian P; Mühlig, Kerstin; Nakagawa, Atsushi; Nam, Daewoong; Nelson, Garrett; Nettelblad, Carl; Okamoto, Kenta; Ourmazd, Abbas; Rose, Max; van der Schot, Gijs; Schwander, Peter; Seibert, M Marvin; Sellberg, Jonas A; Sierra, Raymond G; Song, Changyong; Svenda, Martin; Timneanu, Nicusor; Vartanyants, Ivan A; Westphal, Daniel; Wiedorn, Max O; Williams, Garth J; Xavier, Paulraj Lourdu; Yoon, Chun Hong; Zook, James

2016-08-01

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.

Polymorphism in magic-sized Au144(SR)60 clusters

NASA Astrophysics Data System (ADS)

Jensen, Kirsten M. Ø.; Juhas, Pavol; Tofanelli, Marcus A.; Heinecke, Christine L.; Vaughan, Gavin; Ackerson, Christopher J.; Billinge, Simon J. L.

2016-06-01

Ultra-small, magic-sized metal nanoclusters represent an important new class of materials with properties between molecules and particles. However, their small size challenges the conventional methods for structure characterization. Here we present the structure of ultra-stable Au144(SR)60 magic-sized nanoclusters obtained from atomic pair distribution function analysis of X-ray powder diffraction data. The study reveals structural polymorphism in these archetypal nanoclusters. In addition to confirming the theoretically predicted icosahedral-cored cluster, we also find samples with a truncated decahedral core structure, with some samples exhibiting a coexistence of both cluster structures. Although the clusters are monodisperse in size, structural diversity is apparent. The discovery of polymorphism may open up a new dimension in nanoscale engineering.

Molecular symmetry with quaternions.

PubMed

Fritzer, H P

2001-09-01

A new and relatively simple version of the quaternion calculus is offered which is especially suitable for applications in molecular symmetry and structure. After introducing the real quaternion algebra and its classical matrix representation in the group SO(4) the relations with vectors in 3-space and the connection with the rotation group SO(3) through automorphism properties of the algebra are discussed. The correlation of the unit quaternions with both the Cayley-Klein and the Euler parameters through the group SU(2) is presented. Besides rotations the extension of quaternions to other important symmetry operations, reflections and the spatial inversion, is given. Finally, the power of the quaternion calculus for molecular symmetry problems is revealed by treating some examples applied to icosahedral symmetry.

Ab initio density-functional calculations in materials science: from quasicrystals over microporous catalysts to spintronics.

PubMed

Hafner, Jürgen

2010-09-29

During the last 20 years computer simulations based on a quantum-mechanical description of the interactions between electrons and atomic nuclei have developed an increasingly important impact on materials science, not only in promoting a deeper understanding of the fundamental physical phenomena, but also enabling the computer-assisted design of materials for future technologies. The backbone of atomic-scale computational materials science is density-functional theory (DFT) which allows us to cast the intractable complexity of electron-electron interactions into the form of an effective single-particle equation determined by the exchange-correlation functional. Progress in DFT-based calculations of the properties of materials and of simulations of processes in materials depends on: (1) the development of improved exchange-correlation functionals and advanced post-DFT methods and their implementation in highly efficient computer codes, (2) the development of methods allowing us to bridge the gaps in the temperature, pressure, time and length scales between the ab initio calculations and real-world experiments and (3) the extension of the functionality of these codes, permitting us to treat additional properties and new processes. In this paper we discuss the current status of techniques for performing quantum-based simulations on materials and present some illustrative examples of applications to complex quasiperiodic alloys, cluster-support interactions in microporous acid catalysts and magnetic nanostructures.

Computational Modeling of Bloch Surface Waves in One-Dimensional Periodic and Aperiodic Multilayer Structures

NASA Astrophysics Data System (ADS)

Koju, Vijay

Photonic crystals and their use in exciting Bloch surface waves have received immense attention over the past few decades. This interest is mainly due to their applications in bio-sensing, wave-guiding, and other optical phenomena such as surface field enhanced Raman spectroscopy. Improvement in numerical modeling techniques, state of the art computing resources, and advances in fabrication techniques have also assisted in growing interest in this field. The ability to model photonic crystals computationally has benefited both the theoretical as well as experimental communities. It helps the theoretical physicists in solving complex problems which cannot be solved analytically and helps to acquire useful insights that cannot be obtained otherwise. Experimentalists, on the other hand, can test different variants of their devices by changing device parameters to optimize performance before fabrication. In this dissertation, we develop two commonly used numerical techniques, namely transfer matrix method, and rigorous coupled wave analysis, in C++ and MATLAB, and use two additional software packages, one open-source and another commercial, to model one-dimensional photonic crystals. Different variants of one-dimensional multilayered structures such as perfectly periodic dielectric multilayers, quasicrystals, aperiodic multilayer are modeled, along with one-dimensional photonic crystals with gratings on the top layer. Applications of Bloch surface waves, along with new and novel aperiodic dielectric multilayer structures that support Bloch surface waves are explored in this dissertation. We demonstrate a slow light configuration that makes use of Bloch Surface Waves as an intermediate excitation in a double-prism tunneling configuration. This method is simple compared to the more usual techniques for slowing light using the phenomenon of electromagnetically induced transparency in atomic gases or doped ionic crystals operated at temperatures below 4K. Using a semi

Photoluminescence Investigation of the Indirect Band Gap and Shallow Impurities in Icosahedral B12As2

DTIC Science & Technology

2012-07-05

semiconductor that exhibits unusual properties as the result of the bonding within the 12-atom boron icosahe- dron that is an integral part of its crystal...aware that notwithstanding any other provision of law, no person shall be subject to a penalty for failing to comply with a collection of information if...LIMITATION OF ABSTRACT Same as Report (SAR) 18. NUMBER OF PAGES 13 19a. NAME OF RESPONSIBLE PERSON a. REPORT unclassified b. ABSTRACT

Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lokareddy, Ravi K.; Sankhala, Rajeshwer S.; Roy, Ankoor

Tailed bacteriophages and herpesviruses assemble infectious particles via an empty precursor capsid (or ‘procapsid’) built by multiple copies of coat and scaffolding protein and by one dodecameric portal protein. Genome packaging triggers rearrangement of the coat protein and release of scaffolding protein, resulting in dramatic procapsid lattice expansion. Here, we provide structural evidence that the portal protein of the bacteriophage P22 exists in two distinct dodecameric conformations: an asymmetric assembly in the procapsid (PC-portal) that is competent for high affinity binding to the large terminase packaging protein, and a symmetric ring in the mature virion (MV-portal) that has negligible affinitymore » for the packaging motor. Modelling studies indicate the structure of PC-portal is incompatible with DNA coaxially spooled around the portal vertex, suggesting that newly packaged DNA triggers the switch from PC- to MV-conformation. Thus, we propose the signal for termination of ‘Headful Packaging’ is a DNA-dependent symmetrization of portal protein.« less

UA-ICON - A non-hydrostatic global model for studying gravity waves from the troposphere to the thermosphere

NASA Astrophysics Data System (ADS)

Borchert, Sebastian; Zängl, Günther; Baldauf, Michael; Zhou, Guidi; Schmidt, Hauke; Manzini, Elisa

2017-04-01

In numerical weather prediction as well as climate simulations, there are ongoing efforts to raise the upper model lid, acknowledging the possible influence of middle and upper atmosphere dynamics on tropospheric weather and climate. As the momentum deposition of gravity waves (GWs) is responsible for key features of the large scale flow in the middle and upper atmosphere, the upward model extension has put GWs in the focus of atmospheric research needs. The Max Planck Institute for Meteorology (MPI-M) and the German Weather Service (DWD) have been developing jointly the non-hydrostatic global model ICON (Zängl et al, 2015) which features a new dynamical core based on an icosahedral grid. The extension of ICON beyond the mesosphere, where most GWs deposit their momentum, requires, e.g., relaxing the shallow-atmosphere and other traditional approximations as well as implementing additional physical processes that are important to the upper atmosphere. We would like to present aspects of the model development and its evaluation, and first results from a simulation of a period of the DEEPWAVE campaign in New Zealand in 2014 (Fritts et al, 2016) using grid nesting up to a horizontal mesh size of about 1.25 km. This work is part of the research unit: Multi-Scale Dynamics of Gravity Waves (MS-GWaves: sub-project GWING, https://ms-gwaves.iau.uni-frankfurt.de/index.php), funded by the German Research Foundation. Fritts, D.C. and Coauthors, 2016: "The Deep Propagating Gravity Wave Experiment (DEEPWAVE): An airborne and ground-based exploration of gravity wave propagation and effects from their sources throughout the lower and middle atmosphere". Bull. Amer. Meteor. Soc., 97, 425 - 453, doi:10.1175/BAMS-D-14-00269.1 Zängl, G., Reinert, D., Ripodas, P., Baldauf, M., 2015: "The ICON (ICOsahedral Non-hydrostatic) modelling framework of DWD and MPI-M: Description of the non-hydrostatic dynamical core". Quart. J. Roy. Met. Soc., 141, 563 - 579, doi:10.1002/qj.2378

Rigid-Cluster Models of Conformational Transitions in Macromolecular Machines and Assemblies

PubMed Central

Kim, Moon K.; Jernigan, Robert L.; Chirikjian, Gregory S.

2005-01-01

We present a rigid-body-based technique (called rigid-cluster elastic network interpolation) to generate feasible transition pathways between two distinct conformations of a macromolecular assembly. Many biological molecules and assemblies consist of domains which act more or less as rigid bodies during large conformational changes. These collective motions are thought to be strongly related with the functions of a system. This fact encourages us to simply model a macromolecule or assembly as a set of rigid bodies which are interconnected with distance constraints. In previous articles, we developed coarse-grained elastic network interpolation (ENI) in which, for example, only Cα atoms are selected as representatives in each residue of a protein. We interpolate distance differences of two conformations in ENI by using a simple quadratic cost function, and the feasible conformations are generated without steric conflicts. Rigid-cluster interpolation is an extension of the ENI method with rigid-clusters replacing point masses. Now the intermediate conformations in an anharmonic pathway can be determined by the translational and rotational displacements of large clusters in such a way that distance constraints are observed. We present the derivation of the rigid-cluster model and apply it to a variety of macromolecular assemblies. Rigid-cluster ENI is then modified for a hybrid model represented by a mixture of rigid clusters and point masses. Simulation results show that both rigid-cluster and hybrid ENI methods generate sterically feasible pathways of large systems in a very short time. For example, the HK97 virus capsid is an icosahedral symmetric assembly composed of 60 identical asymmetric units. Its original Hessian matrix size for a Cα coarse-grained model is >(300,000)2. However, it reduces to (84)2 when we apply the rigid-cluster model with icosahedral symmetry constraints. The computational cost of the interpolation no longer scales heavily with the size

Evaluation of structural vacancies for 1/1-Al-Re-Si approximant crystals by positron annihilation spectroscopy

NASA Astrophysics Data System (ADS)

Yamada, K.; Suzuki, H.; Kitahata, H.; Matsushita, Y.; Nozawa, K.; Komori, F.; Yu, R. S.; Kobayashi, Y.; Ohdaira, T.; Oshima, N.; Suzuki, R.; Takagiwa, Y.; Kimura, K.; Kanazawa, I.

2018-01-01

The size of structural vacancies and structural vacancy density of 1/1-Al-Re-Si approximant crystals with different Re compositions were evaluated by positron annihilation lifetime and Doppler broadening measurements. Incident positrons were found to be trapped at the monovacancy-size open space surrounded by Al atoms. From a previous analysis using the maximum entropy method and Rietveld method, such an open space is shown to correspond to the centre of Al icosahedral clusters, which locates at the vertex and body centre. The structural vacancy density of non-metallic Al73Re17Si10 was larger than that of metallic Al73Re15Si12. The observed difference in the structural vacancy density reflects that in bonding nature and may explain that in the physical properties of the two samples.

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source

PubMed Central

Munke, Anna; Andreasson, Jakob; Aquila, Andrew; Awel, Salah; Ayyer, Kartik; Barty, Anton; Bean, Richard J.; Berntsen, Peter; Bielecki, Johan; Boutet, Sébastien; Bucher, Maximilian; Chapman, Henry N.; Daurer, Benedikt J.; DeMirci, Hasan; Elser, Veit; Fromme, Petra; Hajdu, Janos; Hantke, Max F.; Higashiura, Akifumi; Hogue, Brenda G.; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A.; Reddy, Hemanth K.N.; Lan, Ti-Yen; Larsson, Daniel S.D.; Liu, Haiguang; Loh, N. Duane; Maia, Filipe R.N.C.; Mancuso, Adrian P.; Mühlig, Kerstin; Nakagawa, Atsushi; Nam, Daewoong; Nelson, Garrett; Nettelblad, Carl; Okamoto, Kenta; Ourmazd, Abbas; Rose, Max; van der Schot, Gijs; Schwander, Peter; Seibert, M. Marvin; Sellberg, Jonas A.; Sierra, Raymond G.; Song, Changyong; Svenda, Martin; Timneanu, Nicusor; Vartanyants, Ivan A.; Westphal, Daniel; Wiedorn, Max O.; Williams, Garth J.; Xavier, Paulraj Lourdu; Yoon, Chun Hong; Zook, James

2016-01-01

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here. PMID:27478984

Recent progress in boron nanomaterials

PubMed Central

Kondo, Takahiro

2017-01-01

Abstract Various types of zero, one, and two-dimensional boron nanomaterials such as nanoclusters, nanowires, nanotubes, nanobelts, nanoribbons, nanosheets, and monolayer crystalline sheets named borophene have been experimentally synthesized and identified in the last 20 years. Owing to their low dimensionality, boron nanomaterials have different bonding configurations from those of three-dimensional bulk boron crystals composed of icosahedra or icosahedral fragments. The resulting intriguing physical and chemical properties of boron nanomaterials are fascinating from the viewpoint of material science. Moreover, the wide variety of boron nanomaterials themselves could be the building blocks for combining with other existing nanomaterials, molecules, atoms, and/or ions to design and create materials with new functionalities and properties. Here, the progress of the boron nanomaterials is reviewed and perspectives and future directions are described. PMID:29152014

Polymorphism in magic-sized Au144(SR)60 clusters

DOE PAGES

Jensen, Kirsten M. O.; Juhas, Pavol; Tofanelli, Marcus A.; ...

2016-06-14

Ultra-small, magic-sized metal nanoclusters represent an important new class of materials with properties between molecules and particles. However, their small size challenges the conventional methods for structure characterization. We present the structure of ultra-stable Au144(SR)60 magic-sized nanoclusters obtained from atomic pair distribution function analysis of X-ray powder diffraction data. Our study reveals structural polymorphism in these archetypal nanoclusters. Additionally, in order to confirm the theoretically predicted icosahedral-cored cluster, we also find samples with a truncated decahedral core structure, with some samples exhibiting a coexistence of both cluster structures. Although the clusters are monodisperse in size, structural diversity is apparent. Finally,more » the discovery of polymorphism may open up a new dimension in nanoscale engineering.« less

pH-Induced Stability Switching of the Bacteriophage HK97 Maturation Pathway

PubMed Central

2015-01-01

Many viruses undergo large-scale conformational changes during their life cycles. Blocking the transition from one stage of the life cycle to the next is an attractive strategy for the development of antiviral compounds. In this work, we have constructed an icosahedrally symmetric, low-energy pathway for the maturation transition of bacteriophage HK97. By conducting constant-pH molecular dynamics simulations on this pathway, we identify which residues are contributing most significantly to shifting the stability between the states along the pathway under differing pH conditions. We further analyze these data to establish the connection between critical residues and important structural motifs which undergo reorganization during maturation. We go on to show how DNA packaging can induce spontaneous reorganization of the capsid during maturation. PMID:24495192