Atomic picture of elastic deformation in a metallic glass.

The tensile behavior of a Ni60Nb40 metallic glass (MG) has been studied by using ab initio density functional theory (DFT) calculation with a large cell containing 1024 atoms (614 Ni and 410 Nb). We provide insight into how a super elastic limit can be achieved in a MG. Spatially inhomogeneous responses of single atoms and also major polyhedra are found to change greatly with increasing external stress when the strain is over 2%, causing the intrinsically viscoelastic behavior. We uncover the origin of the observed super elastic strain limit under tension (including linear and viscoelastic strains) in small-sized MG samples, mainly caused by inhomogeneous distribution of excess volumes in the form of newly formed subatomic cavities.

Electronic structure, stacking energy, partial charge, and hydrogen bonding in four periodic B-DNA models.

We present a theoretical study of the electronic structure of four periodic B-DNA models labeled (AT)(10), (GC)(10), (AT)(5)(GC)(5), and (AT-GC)(5) where A denotes adenine, T denotes thymine, G denotes guanine, and C denotes cytosine. Each model has ten base pairs with Na counterions to neutralize the negative phosphate group in the backbone. The (AT)(5)(GC)(5) and (AT-GC)(5) models contain two and five AT-GC bilayers, respectively. When compared against the average of the two pure models, we estimate the AT-GC bilayer interaction energy to be 19.015 Kcal/mol, which is comparable to the hydrogen bonding energy between base pairs obtained from the literature. Our investigation shows that the stacking of base pairs plays a vital role in the electronic structure, relative stability, bonding, and distribution of partial charges in the DNA models. All four models show a highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) gap ranging from 2.14 to 3.12 eV with HOMO states residing on the PO(4) + Na functional group and LUMO states originating from the bases. Our calculation implies that the electrical conductance of a DNA molecule should increase with increased base-pair mixing. Interatomic bonding effects in these models are investigated in detail by analyzing the distributions of the calculated bond order values for every pair of atoms in the four models including hydrogen bonding. The counterions significantly affect the gap width, the conductivity, and the distribution of partial charge on the DNA backbone. We also evaluate quantitatively the surface partial charge density on each functional group of the DNA models.

Theoretical nonlinear response of complex single crystal under multi-axial tensile loading.

The mechanical properties of single crystals are of interest as they represent the behavior of the basic building blocks. Using the density functional theory based ab initio technique we have devised an approach to analyze the behavior of single crystal so their mechanical properties can be studied beyond linear elasticity. Here we have applied the approach to investigate the mechanical properties of a single stoichiometric hydroxyapatite (HAP) crystal using a large supercell subjected to multi-axial tensile loading. The results reveal a complex nonlinear and loading-path dependent behavior with evolving anisotropy for the HAP crystal. Further, we have introduced a failure envelope index to quantify the strength behavior for comparison of similar materials. We have found that the complexities of the behavior of a single crystal originate from the local structural changes in these multi-component materials.

Mechanical properties, electronic structure and bonding of alpha- and beta-tricalcium phosphates with surface characterization.

The mechanical properties and electronic structure of alpha- and beta-tricalcium phosphate (TCP) crystals are studied by using two ab initio density functional methods, the Vienna Ab initio Simulation Package (VASP) and the orthogonalized linear combination of atomic orbitals method. Based on the VASP optimized crystal structures, the elastic constants of alpha- and beta-TCP are obtained using an effective stress-strain computational scheme. From the calculated elastic constants, the bulk modulus, shear modulus, Young's modulus and Poisson's ratios are obtained. The results show that the mechanical properties of the two crystals are comparable and that alpha-TCP is somewhat softer than beta-TCP. Comparison with experimental extrapolations of the elastic constants shows significant differences, which attest to the difficulty of obtaining single crystal samples. The calculated electronic structure results show that both crystals are large gap insulators with a direct band gap of 4.89 eV for alpha-TCP and 5.25 eV for beta-TCP. Effective charge calculations show that, on average, beta-TCP has slightly less charge transfer per Ca than alpha-TCP. The (010) ((001)) surface model for alpha-TCP (beta-TCP) is studied using a supercell slab geometry and fully relaxed to obtain the optimized structures. The estimated surface formation energies are 0.777 and 0.842 J m(-2) for alpha-TCP and beta-TCP, respectively. The electronic structures of the two surface models are compared with the bulk models. Charge density analysis shows that the surfaces of both TCP crystals are positively charged overall owing to the presence of Ca ions near the surfaces.

Optically anisotropic infinite cylinder above an optically anisotropic half space: Dispersion interaction of a single-walled carbon nanotube with a substrate.

A complete form of the van der Waals dispersion interaction between an infinitely long anisotropic semiconducting/insulating thin cylinder and an anisotropic half space is derived for all separations between the cylinder and the half space. The derivation proceeds from the theory of dispersion interactions between two anisotropic infinite half spaces as formulated in Phys. Rev. A 71, 042102 (2005). The approach is valid in the retarded as well as nonretarded regimes of the interaction and is coupled with the recently evaluated ab initio dielectric response functions of various semiconducting/insulating single wall carbon nanotubes, enables the authors to evaluate the strength of the van der Waals dispersion interaction for all orientation angles and separations between a thin cylindrical nanotube and the half space. The possibility of repulsive and/or nonmonotonic dispersion interactions is examined in detail.

Spectroscopic imaging of electron energy loss spectra using ab initio data and function field visualization.

We have devised a technique for spectral imaging using accurate ab initio electron energy loss near edge structure (ELNES) data and function field visualization. The technique is initially applied to a planar defect model in Si with different ring structures and no broken bonds where experimental probes are severely limited. The same model with B doping is also considered. It is shown that specific deviations in different energy ranges of the ELNES spectra are correlated with different structural components of the models.

Ab initio elastic properties and tensile strength of crystalline hydroxyapatite.

We report elastic constant calculation and a "theoretical" tensile experiment on stoichiometric hydroxyapatite (HAP) crystal using an ab initio technique. These results compare favorably with a variety of measured data. Theoretical tensile experiments are performed on the orthorhombic cell of HAP for both uniaxial and biaxial loading. The results show considerable anisotropy in the stress-strain behavior. It is shown that the failure behavior of the perfect HAP crystal is brittle for tension along the z-axis with a maximum stress of 9.6 GPa at 10% strain. Biaxial failure envelopes from six "theoretical" loading tests show a highly anisotropic pattern. Structural analysis of the crystal under various stages of tensile strain reveals that the deformation behavior manifests itself mainly in the rotation of the PO(4) tetrahedron with concomitant movements of both the columnar and axial Ca ions. These results are discussed in the context of mechanical properties of bioceramic composites relevant to mineralized tissues.

Spectral mixing formulations for van der Waals-London dispersion interactions between multicomponent carbon nanotubes.

Recognition of spatially varying optical properties is a necessity when studying the van der Waals-London dispersion (vdW-Ld) interactions of carbon nanotubes (CNTs) that have surfactant coatings, tubes within tubes, andor substantial core sizes. The ideal way to address these radially dependent optical properties would be to have an analytical add-a-layer solution in cylindrical coordinates similar to the one readily available for the plane-plane geometry. However, such a formulation does not exist nor does it appear trivial to be obtained exactly. The best and most pragmatic alternative for end-users is to take the optical spectra of the many components and to use a spectral mixing formulation so as to create effective solid-cylinder spectra for use in the far-limit regime. The near-limit regime at "contact" is dominated by the optical properties of the outermost layer, and thus no spectral mixing is required. Specifically we use a combination of a parallel capacitor in the axial direction and the Bruggeman effective medium in the radial direction. We then analyze the impact of using this mixing formulation upon the effective vdW-Ld spectra and the resulting Hamaker coefficients for small and large diameter single walled CNTs (SWCNTs) in both the near- and far-limit regions. We also test the spectra of a [16,0,s+7,0,s] multiwalled CNT (MWCNT) with an effective MWCNT spectrum created by mixing its [16,0,s] and [7,0,s] SWCNT components to demonstrate nonlinear coupling effects that exist between neighboring layers. Although this paper is primarily on nanotubes, the strategies, implementation, and analysis presented are applicable and likely necessary to any system where one needs to resolve spatially varying optical properties in a particular Lifshitz formulation.

Dependence of DNA electronic structure on environmental and structural variations.

We present experimental and theoretical evidence that varying the local environment and physical structure of dried DNA has a direct impact on its electronic structure. By preparing samples of DNA in various solutions, it was possible to alter the type of ions present during the production of the DNA samples. These variations resulted in differences in the local chemical environment of the dried DNA molecules. X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES) were used to probe the variations in the electronic structure of DNA samples. DFT calculations of a stack of 10 adenine (A)-thymine (T) nucleobase pairs show that slight structural variations in stacking height have a direct influence on the electronic structure and result in changes to the HOMO-LUMO gap. The effects of these differences in the local environment on the electronic structure are discussed and are related to the results of conductivity measurements of DNA.

Grain boundary strengthening in alumina by rare earth impurities.

Impurity doping often alters or improves the properties of materials. In alumina, grain boundaries play a key role in deformation mechanisms, particularly in the phenomenon of grain boundary sliding during creep at high temperatures. We elucidated the atomic-scale structure in alumina grain boundaries and its relationship to the suppression of creep upon doping with yttrium by using atomic resolution microscopy and high-precision calculations. We find that the yttrium segregates to very localized regions along the grain boundary and alters the local bonding environment, thereby strengthening the boundary against mechanical creep.

Complex nonlinear deformation of nanometer intergranular glassy films in beta-Si3N4.

The mechanical properties of a model of Y-doped intergranular glassy film in silicon nitride ceramics are studied by large-scale ab initio modeling. By linking directly to its electronic structure, it is shown that this microstructure has a complex nonlinear deformation under stress and Y doping significantly enhances the mechanical properties. The calculation of the electrostatic potential across the film supports the space charge model in ceramic microstructures.

Accurate redetermination of the X-ray structure and electronic bonding in adenosylcobalamin.

The electronic structure of adenosylcobalamin (B12 coenzyme, AdoCbl) has been calculated by a density functional method, using the orthogonalized linear combination of the atomic orbital method (OLCAO). Since a fixed accurately determined geometry was needed in such calculations, the crystal structure of adenosylcobalamin has been redone and refined to R = 0.065, using synchrotron diffraction data. Comparison with the recently reported electronic structures of cyano- (CNCbl) and methylcobalamin (MeCbl) shows that the net charges and bond orders vary only on the axial donors. The values in the three cobalamins suggest that the Co-C bond in MeCbl has a strength similar to that in AdoCbl, but it is significantly weaker that that in CNCbl. Present results are compared with those previously reported for the analogous corrin derivatives; i.e., simplified cobalamins with the side chains a-f replaced by H atoms. Despite a qualitative agreement, a discrepancy in the calculated HOMO-LUMO gap is found.

Theoretical prediction of ELNES/XANES and chemical bondings of AlN polytypes.

The first principles calculations of ELNES/XANES of AlN polytypes were carried out by the first-principles OLCAO method using large supercells composed of more than 100 atoms. It can quantitatively reproduce the experimental spectra from wurtzite AlN using a 108-atoms supercell. ELNES from rock-salt and zinc-blend AlN were predicted by using 128 atoms supercells. The spectral features of rock-salt phase are different from other phases, whereas that of zinc-blend phase have numerous similarities with that from wurtzite AlN. Characteristic differences between the wurtzite and zinc-blend phases are predicted to appear at the first peak of Al L(2,3) and K edges. The first peak of zinc-blend AlN is broader than that of wurtzite AlN. The same tendency was found in the case of SiC. In order to elucidate the cause of the broadness at the first peak, partial density of states and chemical bondings were investigated. The theoretical analysis revealed that the broadness of the first peak is related to the covalency of the compounds. This result suggests that the spectral features at the first peak of L(2,3) and K edges contain information about the covalency at the illuminated area.