Reconstructed Unit Cell Research Articles

Thermal shock resistance of 4D-inplane carbon/carbon composite based on micro-structurally informed effective properties

The thermal shock resistance of the 4D-inplane carbon/carbon composite has been predicted using the simulations of the laser irradiation test. Firstly, the effective homogenized temperature dependent properties of the carbon/carbon (c/c) composite have been predicted using realistic unit cell. The meso-scale unit cell has been reconstructed using the reconstructed images of the composite obtained through X-Ray computed tomography. The meso unit cell includes the realistic microstructural features such as fiber bundle distortions and irregular shaped big voids in the geometry. The bundles of the reconstructed unit cell are further considered as a unidirectional composite and micro unit cells are utilized to define their effective behavior. Two-scale asymptotic expansion homogenization method has been used along with finite element method and periodic boundary conditions for the prediction of effective properties. Later, thermo-mechanical transient two-dimensional analysis of a cylindrical specimen has been conducted. The irradiation laser beam parameters e.g. diameters of beam and heat flux have been varied to study the critical values of laser power density (LPD). The maximum shear strength failure criterion is used to define the ultimate state. The obtained trend of the variation of LPD is validated using the data available in the literature for 2D C/C composites. It has been observed that the present results are in good agreement with those existing in the literature. The thermal shock resistant capability of 4DIN C/C composite is found around 10–18 times higher than that of 2D C/C composite.

Computational mechanical characterization of geometrically transformed Schwarz P lattice tissue scaffolds fabricated via two photon polymerization (2PP)

Schwarz P unit cell-based tissue scaffolds comprised of poly(D,L-lactide-co- ε -caprolactone)(PLCL) fabricated via the additive manufacturing technique, two-photon polymerisation (2PP) were found to undergo geometrical transformations from the original input design. A Schwarz P unit cell surface geometry CAD model was reconstructed to take into account the geometrical transformations through CAD modeling techniques using measurements obtained from an image-based averaging technique before its implementation for micromechanical analysis. Effective modulus results obtained from computational mechanical characterization via micromechanical analysis of the reconstructed unit cell assigned with the same material model making up the fabricated scaffolds demonstrated excellent agreement with a small margin of error at 6.94% from the experimental mean modulus (0.69 ± 0.29 MPa). The possible sources for the occurrence of geometrical transformations are discussed in this paper. The inter-relationships between different dimensional parameters making up the Schwarz P architecture and resulting effective modulus are also assessed and discussed. With the ability to accommodate the geometrical transformations, maintain efficiency in terms of time and computational resources, micromechanical analysis has the potential to be implemented in tissue scaffolds with a periodic microstructure as well as other structures outside the field of tissue engineering in general.

C (4×4) Reconstruction on Arsenic-Rich GaAs (001) Surface after Phase Transition

C(4×4) reconstruction on arsenic-rich GaAs(001) surface after phase transition has been investigated from the experiment and simulation. We found that the c(4×4) As-rich reconstruction structure of the GaAs (001) surface can be best depicted with the model which there are three As-As dimers without Ga-As dimers in a reconstructed unit cell, and these dimers are found to be aligned perpendicular to the As dimers on β2(2×4) surface.

Atomistic Simulation Studies on the Dynamics and Thermodynamics of Nonpolar Molecules within the Zeolite Imidazolate Framework-8

Statistical-mechanics-based simulation studies at the atomistic level of argon (Ar), methane (CH(4)), and hydrogen (H(2)) sorbed in the zeolite imidazolate framework-8 (ZIF-8) are reported. ZIF-8 is a product of a special kind of chemical process, recently termed as reticular synthesis, which has generated a class of materials of critical importance as molecular binders. In this work, we explore the mechanisms that govern the sorption thermodynamics and kinetics of nonpolar sorbates possessing different sizes and strength of interactions with the metal-organic framework to understand the outstanding properties of this novel class of sorbents, as revealed by experiments published elsewhere. For this purpose, we have developed an in-house modeling procedure involving calculations of sorption isotherms, partial internal energies, various probability density functions, and molecular dynamics for the simulation of the sorbed phase over a wide range of occupancies and temperatures within a digitally reconstructed unit cell of ZIF-8. The results showed that sorbates perceive a marked energetic inhomogeneity within the atomic framework of the metal-organic material under study, resulting in free energy barriers that give rise to inflections in the sorption isotherms and guide the dynamics of guest molecules.

Computation of the dynamic thermal dissipation properties of porous media by Brownian motion simulation: Application to an open-cell aluminum foam

This paper reports simulation results of frequency dependent heat conduction through three-dimensional reconstructed unit cells of an open-cell aluminum foam under acoustic excitations. First, a three-dimensional random walk based algorithm is proposed to calculate the dynamic thermal permeability or dynamic bulk modulus of periodic complex porous geometries. Second, the error and convergence of the implemented calculation algorithm are quantified in terms of the random walk population, normalized trapping distance, and type of geometry. Finally, the algorithm is applied to the calculation of the dynamic bulk modulus of an aluminum foam and compared to laboratory measurements. Good agreement is obtained between simulations and measurements.

STM observation and first-principles determination of Ge nanoscale structures on Si(111)

Scanning tunneling microscopy observations and first-principles quantum mechanical calculations were employed to investigate the nanoscale structures formed on Si(111) surfaces upon germanium deposition at a coverage of $\ensuremath{\sim}0.3$ monolayer. At room temperature, Ge atoms form nanoclusters with sizes of $1.5--6\phantom{\rule{0.3em}{0ex}}\text{nanometers}$ in width. After annealing, the nanoclusters become two-dimensional islands with typical size of $\ensuremath{\sim}10$ nanometers in width. We propose that the annealing or high-$T$ deposition results in a partial transformation of $(7\ifmmode\times\else\texttimes\fi{}7)$ reconstructed unit cells to unreconstructed Si(111) configurations on which the Ge adatoms reside at the ${T}_{4}$ sites and form a $(\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})R30\ifmmode^\circ\else\textdegree\fi{}$ reconstruction.

Initial nucleation of Au on the [formula omitted]R45° reconstructed Fe 3O 4(0 0 1) surface

The initial nucleation of Au onto the ( 2 × 2 ) R45° reconstructed Fe 3O 4(0 0 1) surface has been studied using scanning tunnelling microscopy. Au clusters are formed, with a typical lateral dimension of ∼0.9 nm. The measured corrugation height of the clusters, ∼0.1 nm, suggests that they are a single atomic layer in height. The clusters nucleate on a specific surface site, which lies at the centre of a ( 2 × 2 ) R45° reconstructed unit cell. The size and spatial distribution of the Au clusters formed is shown to strongly correlate to the symmetry and periodicity of the reconstructed magnetite surface. It is also shown that even when the clusters are in close proximity they still only occupy this single nucleation site, and thus maintain the periodicity of the substrate. We relate the order and stability of this system to the fact that magnetite (0 0 1) is polar, and suggest that such surfaces offer ideal templates for self-assembly due to the stability of their polarity induced reconstructions.

Structure determination of the ( [formula omitted]) reconstructed α-Al 2O 3(0 0 0 1)

Grazing-incidence X-ray diffraction data are combined with energy-minimization calculations to analyse the atomic structure of the Al-rich ( 3 3 ×3 3 ) R30° reconstructed surface of sapphire α-Al 2O 3(0 0 0 1) . The experiments on the BM32 beamline of the ESRF provide the non-integer-order diffraction intensities and, after Fourier transform, an incomplete Patterson map. The computer simulations are implemented to obtain structural information from this map. In the simulations, the interactions between the Al overlayer atoms were described with the Sutton–Chen potential and the interactions between the overlayer and the sapphire substrate with a laterally modulated Lennard–Jones potential. We have shown that the hexagonal reconstructed unit cell is composed of triangles where the two layers of Al adatoms are FCC(1 1 1) ordered whereas between the triangles the stacking is FCC(0 0 1).

Surface structure of Si(100) with submonolayer coverages of C

We report a combined STM, LEED and AES study of Si(100) surfaces prepared by coevaporation from two MBE-sources with Si and SiC, respectively. The flux from the SiC source contains 10% C, enabling studies of deposited layers with C-concentrations in the range 0–10%. After room temperature deposition, the structures have been annealed at 600 °C to generate a c(4×4) reconstruction. This has previously been reported to contain from 0.0 to 0.5 monolayers (ML) of C. Annealing at 800 °C irreversibly transforms the c(4×4) surface to a 2×1-reconstructed surface that contains precipitates of SiC. Since only 0.07 ML of C is needed to have 98% of the surface covered with the c(4×4) reconstruction, we conclude that the c(4×4) reconstruction is impurity-induced rather than having C-atoms in well defined positions within each unit cell. The c(4×4) reconstruction is attributed to a basic structure containing buckled parallel ad-dimers, which in approximately 50% of the reconstructed unit cells is decorated with perpendicular dimers.

Energetic cluster deposition on a dislocation network: Ag 7 on 2 ML Ag/Pt(1 1 1)

Mass selected Ag 7 clusters have been deposited at two different impact energies (20 and 95 eV) on a dislocation network formed by evaporating 2 ML of Ag on Pt(1 1 1). The surface has been investigated by low temperature STM as a function of annealing temperature. The clusters adsorption site, stability and ordering depend on impact energies and annealing temperatures. We find that the hcp small triangle and dislocation region of the reconstructed unit cell form preferred pinning centers at low temperature, at higher temperature most clusters are situated in the fcc hexagon of the unit cell. The results are compared to experiments with thermal evaporated Ag atoms.

(3×3)R30°reconstruction of the6H−SiC(0001) surface: A simpleT4Si adatom structure solved by grazing-incidence x-ray diffraction

The atomic structure of the $(\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})$ $R30\ifmmode^\circ\else\textdegree\fi{}$ reconstructed surface of $6H\ensuremath{-}\mathrm{SiC}$ (0001) silicon terminated, is solved by grazing-incidence x-ray diffraction in ultrahigh vacuum. The simple adatom structure with one silicon atom per reconstructed unit cell sitting in a $T4$ site over the top SiC bilayer is the only one compatible with the data, thus ruling our other models involving Si adatoms in $H3$ site, Si trimers, C adatoms, or Si vacancies, and supporting the most recent theoretical predictions. The predominance on the surface of three bilayer steps with an A-type termination of the bulk stacking is fully confirmed. In addition, it is shown that varying the preparation conditions changes the density of faulted boundaries in the reconstructed surface but preserves a unique atomic structure within the $(\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})$ $R30\ifmmode^\circ\else\textdegree\fi{}$ ordered domains.

Preferential island nucleation at the elbows of the Au(111) herringbone reconstruction through place exchange

It has previously been shown that deposition of Fe, Co or Ni on Au(111) results in island formation preferentially at the elbows of the herringbone reconstruction, while other metals such as Al, Cu, Ag, and Au do not exhibit such behaviour. Here, new results of the Ni Au(111) system are presented which suggest an explanation for this disparity. STM images show a two-step process for the preferential nucleation of islands at certain points in the Au(111) reconstructed unit cell: first, place exchange of Ni adatoms with Au surface atoms, followed by nucleation of Ni islands on top of substitutional Ni atoms. It is argued that the preferential nucleation of islands results from a lower kinetic barrier to place exchange at these specific sites rather than slower (hopping) diffusion.

Structure of the hydrogen covered Cu(110) surface studied with thermal energy helium scattering

The adsorption of atomic hydrogen on the Cu(110) surface has been studied with thermal energy helium scattering. Upon hydrogen adsorption the structure exhibits a variety of structures: At temperatures above 140 K the helium diffraction spectra show a clear (1 × 2) structure even at very low H coverages. This phase is the well known (1 × 2) Cu(110)-H “missing row” reconstructed phase. Based on an analysis of the specularly reflected He-intensity as a function of hydrogen coverage we have characterized the nucleation and growth of this phase. After the formation of small reconstructed areas the development of the reconstructed phase proceeds via the growth of these nuclei into large (1 × 2) Cu(110)-H islands indicating an attractive interaction between adsorbed H atoms within the reconstructed unit cells. Adsorption at temperatures below 80 K yields a sequence of adsorbate phases as a function of hydrogen exposure: at low exposures a (1× 4) phase is observed. With increasing hydrogen exposure the (1 × 4) structure changes continuously into a well ordered (1 × 3) phase, which then evolves into a (1 × 2) phase at higher exposures. This (1 × 2) structure is only poorly ordered and transforms upon further hydrogen exposure into a (1 × 1) structure. This sequence of adsorbate phases, as well as the continuous transition between them, suggests a repulsive interaction between the adsorbed H atoms. All adsorbate phases formed at surface temperatures T s below 120 K undergo an irreversible transition into a disordered phase upon heating to 120 K < T s < 140 K. Heating above T s = 140 K irreversibly yields the (1 × 2) “missing row” phase.

Solving an interface structure by electron microscopy and x-ray diffraction: The GaAs(001)-CdTe(111) interface.

By a combination of high-resolution imaging and grazing-incidence x-ray diffraction at the GaAs(001)-CdTe(111) heterostructure we solve the atomic structure at the interface. We measure a \ensuremath{\surd}2 (2\ifmmode\times\else\texttimes\fi{}9) reconstructed unit cell and show that only three monolayers are involved in the interface relaxation. We deduce the first nearest neighbors of each atomic species at the interface and describe how they differ from the initial adsorbed layer on a bare GaAs(001) surface. This structure is compatible with two electrons per bond at any atom.

The initial stage of epitaxial growth of Ge on Ge(111) as studied by X-ray diffraction

We present an in situ X-ray scattering study of the evolution of surface structure and morphology during deposition of Ge on Ge(111). The substrate temperature (300 K) was such that the growth proceeds through two-dimensional nucleation. We determined the sites on the c(2 × 8) reconstructed Ge(111) surface to which the first deposited Ge atoms bond. The arrangement of the deposited atoms was inferred from an analysis of the diffracted intensities along the integer-order rods of Bragg scattering perpendicular to the surface plane. We find the first deposited Ge atoms to occupy adsorption sites above the “rest atoms” in the reconstructed unit cell. For higher coverages islands of bilayer height are formed.

Monte Carlo simulation of MBE growth of the 2 × 4 reconstructed GaAs(001) surface

A Monte Carlo model is used to simulate the MBE growth of the As-stabilized GaAs(001)2x4 surface. Atomistic detail of the bilayer growth cycle, derived from a proposed model of the growth, is incorporated in a phenomenological manner. Despite the large size of the reconstructed unit cell, this approach is not significantly more computationally-demanding in the updating of rates than simulations which neglect the reconstruction and the atomistic growth model details. Preliminary results indicate that the inclusion of these additional ingredients in the simulation produces significant differences in the grown surface. Simulated growth of the 2×4 system produces surfaces which reproduce features reported in STM studies of the real surface.

Chemical titration of clean silicon surfaces with N2O and O2: Atomic nature of ‘‘5×1’’ reconstructed Si(110)

Using spectroscopic differential reflectometry (SDR), Auger electron spectroscopy (AES), and low‐energy electron diffraction (LEED) we have studied the room temperature adsorption behavior of N2O and O2 at the clean low‐Miller index Si surfaces. Decomposition of the nitrous oxide molecule, resulting in Si–O bond formation, only occurs at the top layer Si atoms which have an unsaturated dangling bond. In this way it has been possible to determine the number of broken bonds at these clean reconstructed surfaces using AES. From a comparison of the site‐specific adsorption of N2O with the non‐site‐specific adsorption of O2 we propose a model of the atomic nature of the Si(110) surface showing a prominent 5×1 reconstruction which is in agreement with previously published LEED results and recent scanning tunneling microscopy (STM) and ultraviolet photoemission spectroscopy (UPS) work. This model is based on a reduction of dangling bonds which is due to the formation of adatoms. The model also includes a kind of rest atoms and atoms in nearest‐neighbor top layer chains along the [1̄10] direction (A type).We have found that the ratio adatoms/rest atoms/A atoms per reconstructed unit cell determines the primary superstructure. This ratio also accounts for a more or less ‘‘apparent’’ coexistence of higher order reconstructions very often reported in LEED studies, their presence being in the form of streaks at various fractional order positions along the [1̄10] direction. A real coexistence of various reconstructions with partial order at the Si(110) surface cannot be excluded as evidenced by STM, a result which makes it the most complicated low‐Miller index Si surface to study. Complementary information concerning the energy position of the unoccupied surface states has been obtained from SDR. Our clean Si(110) surface shows partial order along the [1̄10] direction, indicating the coexistence of 5×2 and 5×5 superstructures in addition to the observed prominent 5×1 LEED reconstruction. It has been derived that this surface has empty states at about 0.9 and 1.7 eV above the Fermi level (EF). The occupied states at about 0.8 and 2.4 eV below EF could be identified with rest atoms and A‐type atoms, respectively.

Bacteriophage T3 connector: Three-dimensional structure and comparison with other viral head-tail connecting regions

The bacteriophage T3 connector, which consists of 12 copies of protein gp8, has been studied by image processing of electron micrographs from negatively stained ordered aggregates. A three-dimensional reconstruction of T3 connectors was obtained by collection of tilted views and using the direct Fourier method, up to 2.3 nm resolution. The reconstructed unit cell contains two connectors whose main structural features are essentially identical, but facing in opposite directions. The T3 connector has a height of about 10.9 nm, with two clearly defined domains: a wider one 14.4 nm in diameter, with 12 morphological units in the periphery, and a narrower one, 9.7 nm in diameter. There is a channel clearly defined in the narrower domain that almost closes along the wider domain. Comparison of the three-dimensional structure obtained for the connector of phages T3 and φ29, and that of the neck extracted from phage φ29 particles, reveals striking similarities and significant differences. A model for a general connector to account for the common functions carried out by these viral assemblies is discussed together with the possible role of the channel for DNA translocation.

Three-dimensional structure of bovine NADH:Ubiquinone oxidoreductase of the mitochondrial respiratory chain

We have studied the structure of bovine heart mitochondrial NADH:ubiquinone (Q) oxidoreductase (EC 1.6.99.3) by image analysis of electron micrographs. A three-dimensional reconstruction was calculated from a tilt-series of a two-dimensional crystal of the molecule. Our interpretation of the position of the molecule in the unit cell of the crystal is supported by additional (low-resolution) analysis of images of single molecules. The three-dimensional reconstruction was calculated with the aid of an iterative real-space reconstruction algorithm. The various projections used as input to the algorithm were obtained by averaging the images of the tilted crystal through a Fourier-space peak-filtering procedure. The reconstructed unit cell measures 15.2 × 15.2 nm in the plane of the two-dimensional crystal and has a height of 10–11 nm. The unit cell contains one molecule consisting of four large subunits. At the present resolution of about 1.3 nm in the untilted projection, these four monomers are seen as two dimers related by a two-fold axis. Two views of the single particles have been recognized; they are the top and side view of the building block of the crystal. After computer image alignment and correspondence analysis, clusters of similar particles have been averaged. In the averages an uneven stain distribution is seen around the molecules, which may result from preferential staining of hydrophilic parts of the molecule. The molecular mass of the whole molecule was determined from scanning transmission electron microscopy measurements as (1.6 ± 0.2) · 10 6 daltons.

Symmetry of the Au (110) surface reconstruction studied by spin-polarized low-energy electron diffraction

Spin-polarized low-energy electron diffraction measurements of the analyzing power of two specular beams and the (0, 1/2 ) beam are presented. A theoretial argument relates the analyzing power S and polarizing power P of these beams for an unreconstructed Au (110) surface. This is used to deduce the symmetry of the reconstructed surface. In particualr, these results are inconsistent with the missing- and pairing-row models, suggesting rotation within the reconstructed unit cell.