Information communication platform for the NBIC center at the Russian Research Center Kurchatov Institute

The problems of developing a unified information communication platform for the Nano-, Bio-, Info-, and Cognitive (NBIC) Technology Center at the Russian Research Center (RRC) Kurchatov Institute are considered. The distributed resources of the NBIC center are used based on grid technologies, which allow one to construct a distributed infrastructure on the basis of existing data transfer networks and computer equipment in accordance with the user’s requirements. This infrastructure makes it possible to uniformly offer combined computational resources for various scientific calculations and allows distant users to visually operate with very large amounts of data, high-resolution video streams, experimental equipment, and archival data sets.     

From aerogels to compact glasses: effect of the density on the dynamical structure factor

The dynamical structure factor, S(Q,E), of a model system, based on a percolator and using the harmonic approximation, has been calculated using the moments method especially in the smaller Q region. With this particular growth algorithm we calculate systems with densities as small as few percent of the complete lattice. The variation of the width of the Brillouin peak with density and its dependence on the exchanged wavevector are compared with the experimental data available for amorphous silica at different densities. The results show that the dynamical properties of sparse materials, such as aerogels and xerogels, can be reproduced considering only the dynamic of their network neglecting the contribution of the elemental units forming the network.     

Small-angle X-Ray analysis of macromolecular structure: the structure of protein NS2 (NEP) in solution

A complex structural analysis of nuclear export protein NS2 (NEP) of influenza virus A has been performed using bioinformatics predictive methods and small-angle X-ray scattering data. The behavior of NEP molecules in a solution (their aggregation, oligomerization, and dissociation, depending on the buffer composition) has been investigated. It was shown that stable associates are formed even in a conventional aqueous salt solution at physiological рН value. For the first time we have managed to get NEP dimers in solution, to analyze their structure, and to compare the models obtained using the method of the molecular tectonics with the spatial protein structure predicted by us using the bioinformatics methods. The results of the study provide a new insight into the structural features of nuclear export protein NS2 (NEP) of the influenza virus A, which is very important for viral infection development.     

The structure of nitrocubane: the last in the series of nitrocubanes

The structure of nitrocubane, C₈H₇NO₂, 1, reported herein, is the last to be reported in a series of nitrocubanes, ranging from mono- to octanitrocubane. Compound 1 crystallizes in the orthorhombic space group Pnma with cell dimensions a = 17.507(5), b = 6.584(2), and c = 5.832(2) Å and Z = 4. Thus the nitrocubane molecule possesses a crystallographically imposed mirror plane. Since the nitro group is in the mirror plane, it is coplanar with the C1–C6 bond in the cubane skeleton. As has been found previously, the C1–C6 bond in the cubane skeleton that is coplanar to its attached nitro groups is shortened (1.533(4) compared to an average value of 1.543(2) Å for all other cubane C–C bonds). In addition the single substitution of the nitro group into the cubane skeleton causes a tetrahedral distortion which is exhibited by alternating C–C–C angles which are greater than and less than 90°.     

Precision neutron diffraction structure determination of protein and nucleic acid components. VIII: the crystal and molecular structure of the β-form of the amino acidl-glutamic acid

A neutron diffraction study of the -form of L-glutamic acid, C₅H₉NO₄, has been carried out. The structure is orthorhombic: space groupP2₁2₁2₁,a= 5·159(5),b= 17·30(2),c= 6·948(7) Å andz = 4. Least-squares refinements based on 803 reflexions led to a final conventionalR value of 0·026, and bond lengths involving hydrogen atoms have been determined with an average precision of 0·004 Å. The molecule is in the zwitterion form, and no intramolecular hydrogen bonds have been found. The hydrogen atom involved in a strong hydrogen bond between two carboxyl groups in adjacent molecules (0 ... 0 distance 2·519(2) Å) is covalently bonded to the carboxyl group belonging to the side chain of the amino acid. This side chain is buckled with C gauche to C with respect to the C —C bond. The bond angles involving carbon atoms in the side chain are accordingly strained.Research performed under the auspices of the U.S. Atomic Energy Commission. Part VII is the crystal and molecular structure of the amino acid L-lysine monohydrochloride dihydrate bt T. F. Koetzle, M. S. Lehmann, J. J. Verbist & W. C. Hamilton (Acta Crystallogr, in Press).On leave from Kemisk Institut, Århus Universitet, Denmark, and supported in part by a grant from Statens Naturvidenskabelige Forskningsråd, Denmark.U.S. National Institutes of Health Postdoctoral Fellow.We are indebted to Drs. A. Sequeira, H. Rajagopal and R. Chidambaram for communicating their results for L-glutamicacid hydrochloride prior to publication.     

X-ray diffraction studies of fluid rubidium: From the liquid to a dense vapor

X-ray diffraction measurements have been carried out for fluid rubidium from the triple point up to supercritical conditions using synchrotron radiation at SPring-8. In order to achieve high- temperature diffraction experiments, we have developed a new sample cell made of molybdenum that is resistant to the highly corrosive nature of hot alkali metals. The use of the cell has made it possible to achieve stable and precise measurements at the supercritical region of fluid rubidium. It was observed that the position at the first peak of the pair distribution function starts to decrease around 1.0 g/cm³ with decreasing density, suggesting the possibility of dimerization in the density range where the fluid is still metallic.     

Onset of rigidity in glasses: From random to self-organized networks

In this paper, we review the signatures of a new elastic phase that is found in glasses with selected compositions. It is shown that in contrast with random networks, where rigidity percolates at a single threshold, networks that are able to self-organize to avoid stress will remain in an almost stress-free state during a compositional interval, a Boolchand intermediate phase, that is bounded by a flexible phase and a stressed rigid phase. We report the experimental signatures and describe the theoretical efforts that have been accomplished to characterize the Boolchand intermediate phase. We illustrate one of the methods used in more detail with the example of Group III chalcogenides and finally suggest further possible experimental signatures of self-organization.     

The crystal structure of vyuntspakhite: A redetermination

The crystal structure of the mineral vyuntspakhite (Y, TR)₆{Al₂(OH)₃[H_1.48Si_1.88O₇][SiO₄][SiO₃(OH)]}₂(a = 5.7551(11) Å, b = 14.752(3) Å, c = 15.906(4) Å, β = 96.046(4)°, sp. gr. P2₁/n, Z = 2), which had been established earlier in the pseudo-unit cell, is redetermined by X-ray diffraction (R = 0.040, T = 100 K). The redetermination of the structure shows that pronounced pseudotranslation along the axis c′ = c/3 is associated with the fact that Y(TR) atoms are related by a 1/3 translation along the [001] direction. Most of the hydrogen atoms are located. The crystal-chemical function of hydrogen bonds is analyzed. In the unit cell of vyuntspakhite, the cationic layers consisting of edge-sharing (Y,TR) eight-vertex polyhedra alternate along the b axis with mixed anionic layers composed of isolated Si tetrahedra (orthotetrahedra), Si₂O₇ double-tetrahedra (diortho) groups, Al five-vertex polyhedra, and Al₂O₈ double-tetrahedra groups linked by shared vertices and through hydrogen bonding.     

From heterogeneous probe rotation to the hydrodynamic limit

The recognition of heterogeneous dynamics in single component supercooled liquids has greatly advanced our understanding of the dynamics in glass-forming materials. However, details such as persistence times and length scales associated with dynamically distinct domains remain to be resolved. The rotational correlation function of probe molecules in viscous liquids is used as a tool for exploring the rate exchange or the time a domain memorizes its initial relaxation rate. With high precision dielectric experiments, the dynamics of probe molecules is observed to slow down with increasing size of the guest relative to the host molecules. For the case of di-n-butylether in 3-methylpentane, the situation of purely exponential probe dynamics within dispersive host relaxation is achieved as a result of time averaging. The results suggest that rate exchange occurs on a time scale which is equal to the longest structural relaxation time of the system.     

Breakdown of time–temperature superposition: From experiment to the coupling model and beyond

We studied chain and segmental relaxation in polyisoprene using broadband dielectric and light scattering spectroscopy. Our results demonstrate different temperature dependence of these processes (i.e. failure of the time–temperature superposition) in the entire temperature range studied. Segmental relaxation varies with temperature faster than chain relaxation at low temperatures while reverse is observed at high T. The transition between two regimes seems to occur around the dynamic crossover temperature. It appears that non-entangled and slightly entangled polymers exhibit the same behavior. The results are compared to predictions of the coupling model. We emphasize that current models cannot describe the data consistently.     

Organosilanols: The structure of 1,1,3,3-tetraphenyldisiloxane-1,3-diol

The title compound is triclinic, space groupP¯1, witha=13.468(2),b=20.289(2),c=14.247(1) Å,=98.92(1),=113.42(1),=99.52(1)°,V _c=3416(1) ų, andZ=6. The structure was solved by direct methods and refined by full-matrix least squares toR=0.078,R _w=0.089, for 6511 observed data. The molecules hydrogen-bond into helical chains parallel to [111], each oxygen being involved in one donor and one acceptor hydrogen bond. The geometry of the siloxane link is different in the three independent molecules present, with Si-O-Si angles of 147.8(3), 157.0(3), and 162.5(3)°.     

Two-photon sensitive photolabile protecting groups: From molecular engineering to nanostructuration

ABSTRACT

General molecular engineering rules for the optimization of two-photon sensitive cages are presented and examples for nitrobenzyl, indole and nitrophenethyl platforms are highlighted. The efficiency of electron donor and acceptor groups in dipolar structures and the length of the conjugated system in the photolabile protecting group on two-photon uncaging efficiency will be discussed, as well as the emergence of symmetrical platform based on bis-electron donor or on quadrupolar architectures. We will then present our first results on the nano-structuration of donor-acceptor systems based on nitrophenetyl platform using diethyleneglycol or pentaerythritol cores.     

Assessing the dynamics of liquid-phase solution growth via step growth models: From BCF to FEM

We examine the capability of the classical analyses of W.K. Burton, N. Cabrera and F.C. Frank (BCF) [Phil. Trans. Roy. Soc. London 243 (1951) 299–358], A.A. Chernov [Sov. Phys. Usp. 4 (1961) 116–148], G.H. Gilmer, R. Ghez and N. Cabrera [J. Cryst. Growth 8 (1971) 79–93], and R. Ghez and G.H. Gilmer [J. Cryst. Growth 21 (1974) 93–109] to model solution crystal growth and present a new formulation free of prior idealizations. Our model is based on an analysis of step motion along a vicinal crystal surface coupled with a detailed accounting of bulk and surface transport, thus representing phenomena ranging from the macro-scale to nanometers. The time-dependent governing equations of the model are solved simultaneously and self-consistently via a front-tracking Galerkin finite element method (FEM) in an arbitrary Lagrangian–Eulerian reference attached to the moving steps. Step motion and interactions are analyzed under several classical scenarios, and new results are shown to demonstrate the utility of the finite element model for studying the dynamics of growth. Such models promise to complement the rapidly advancing experimental tools applied to study solution crystal growth and provide a more rigorous underpinning of our understanding of these systems.     

From 3rd- to 4th-generation light sources: Free-electron lasers in the X-ray range

Activities on free-electron laser (FEL) x-ray sources, based on linear accelerators, to produce spatially coherent, ultra-short (∼100 fs) pulses with very high peak brilliance (10²⁸–10³² photons/s/mm²/mrad²/0.1% BW) are summarized. The scientific case includes time-resolved studies of dynamics on sub-ps scales, structural studies by imaging of non-periodic systems, and investigation of high energy-density phenomena such as non-linear x-ray optics and the production of warm dense matter. Examples are presented, with emphasis on the operational facilities, FLASH at DESY, Hamburg and LCLS in Stanford, California, and on the European XFEL project in Hamburg.     

Clathrate formation of gossypol: The structure of the complex of gossypol with tropolone

The clathrate of gossypol with tropolone is prepared for the first time and studied by X-ray diffraction. The structure is determined and refined using 7307 reflections (Siemens SMART/CCD diffractometer). The crystals are monoclinic, C₃₀H₃₀O₈ · 2C₇H₆O₂, a = 35.5892(1) Å, b = 12.8893(2) Å, c = 18.5910(2) Å, β = 118.54(3)°, Z = 8, space group C2/c, and R = 0.058. Each gossypol molecule is linked to two tropolone molecules through hydrogen bonds. The host (gossypol) and guest (tropolone) molecules form separate bilayers that are parallel to the bc plane and alternate along the a-axis.     

Diffraction studies of glass structure: (V). The structure of some arsenic chalcogenide glasses

X-ray and neutron diffraction experiments have been performed on vitreous arsenic sulphide close to the composition As₂S₃ and on a series of vitreous arsenic selenides including compositions both arsenic- and selenium-rich with respect to As₂Se₃. The data have been analysed by direct examination of the diffraction patterns, by Fourier analysis and by comparison both with quasi-crystalline calculations based on the orpiment structure and with models of the first neighbour correlations using the experimental peak functions. Sheet structures occur in all the glasses, the sheet separations being larger than in the corresponding orpiment structures, and the intersheet correlation perpendicular to the sheets extends for 15 Å in arsenic sulphide and 20 Å in arsenic selenide. For the selenide glasses the sheet structure becomes more pronounced with increasing arsenic concentration. For all the glasses the data are consistent with full satisfaction of the respective two- and threefold covalency requirements of chalcogenide and arsenic atoms, excess atoms being incorporated into the structure by the formation of covalent bonds between like atoms. The distribution of arsenic-chalcogen bond lengths is shown to be symmetrical about the average values of 2.24 Å and 2.44 Å for sulphide and selenide respectively. In the selenide glasses close to the As₂Se₃ composition, the average first SeSe distance is 3.65 Å. The advantages and limitations of the experimental and analytical techniques employed are discussed and a simple model based on steric considerations is advanced to account for the influence of arsenic concentration on the inter-sheet correlation.