Changes In Local Geometry Research Articles

Impurity and vacancy clustering at the Σ3(111)[1−10] grain boundary in strontium titanate

The interaction of selected point defects and the Σ3(1 1 1)[1 −1 0] symmetrical twin boundary in SrTiO3 is investigated by density-functional band-structure calculations. The pristine boundary is SrO3-terminated and exhibits electronic properties which are comparable with the pure bulk phase. Both the mirror-symmetric twin and some laterally shifted structures have low grain boundary energies, thus they may coexist in a real crystal if external stress is applied. With varying chemical potential of the electrons, the TiO3 sublattice of the pristine boundary is destabilised by both electron enrichment and electron depletion. These results may explain, why different translation states can be observed by electron microscopy within the same bicrystal. Substitutional doping of the Ti columns next to the boundary plane with formally 3+ cations yields a contraction compared with the pure boundary. The same result, accompanied by more pronounced local geometry changes, is obtained for the translation state in the presence of O vacancies. Neutral O vacancies in the boundary plane are the most stable species followed by positively charged O vacancies in the neighbouring Sr/O plane parallel to the boundary. The Fermi level is shifted either upward to metal-derived states by substitutional doping or downward into the O-2p manifold for O vacancies. These findings may rationalise both the observed low, mainly electronic, grain boundary conductivity of SrTiO3 boundaries and the changes in local potential found at the grain boundary by tunnelling and force microscopy experiments.

Probing the role of tryptophans in Aequorea victoria green fluorescent proteins with an expanded genetic code.

The expanded genetic code in combination with site-directed mutagenesis was used to probe spectroscopic and structural roles of tryptophan (Trp) residues in Aequorea victoria green fluorescent proteins (avGFPs). Nine different halogen-, chalcogen-, and methyl-containing Trp isosteric analogues and surrogates were incorporated into avGFPs containing indole moieties in, and outside of, the chromophore, by the use of the selective pressure incorporation method. Such isosteric replacements introduced minimal local geometry changes in indole moieties, often to the level of single atomic exchange ('atomic mutation') and do not affect three-dimensional structures of avGFPs but induce changes in spectral properties. Our approach offers a new platform to re-evaluate issues like resonance transfer, mechanisms of chromophore formation and maturation, as well as the importance of local geometry and weak sulphur-aromatic interactions for avGFP spectral properties and structural stability. The library of novel tailor-made avGFP mutants and variants generated in this work has demonstrated not only the potentials of the expanded genetic code to study spectroscopic functions, but also a new approach to generate tailor-made proteins with interesting and useful spectral properties.

Modeling the effects of prior exfoliation corrosion on fatigue life of aircraft wing skins

This paper presents a preliminary analytical model, which was developed to evaluate the effects of prior exfoliation corrosion on the residual fatigue life of wing skins. A literature review was completed on the effects of exfoliation corrosion and fatigue interaction and the most significant conclusions are presented in this paper. A number of coupons with fasteners were cut from naturally exfoliated upper wing skins fabricated from 7178-T6 alloy, and the maximum depth of exfoliation corrosion was determined using an ultrasonic inspection technique. These coupons were tested to failure using constant amplitude compression dominated loading and the fracture surfaces were examined to determine the cracking mechanisms. A three-dimensional (3D) finite element (FE) model associated with a ‘soft inclusion’ technique was developed to determine the local stress/strain distribution around the exfoliated fastener hole. The model included the local geometry change due to material loss, the contact effects between the fastener and the wing skin as well as the predominately compressive loading. It was found that the local stress around the cracking sites did not increase significantly with the current levels of exfoliation. A life prediction was then carried out based on the 3D FE and soft inclusion model, and the prediction agreed reasonably with the test.

230 kV Optical Voltage Transducers Using Multiple Electric Field Sensors

230 kV optical voltage transducers were constructed and tested. These transducers use three electric field sensors whose positions and outputs are selected and combined, respectively, in accordance with the quadrature method to obtain a voltage measurement. They meet IEC 0.2% class specifications and maintain 0.2% class accuracies even in the presence of electric field disturbances caused by local changes in geometry extemal to the transducer. The local changes in geometry used in the testing mimic those that may occur in a substation, e.g., installation or movement of equipment.

Pulsatile flow simulation in arterial vascular segments with intravascular ultrasound images

Previous studies have indicated a correlation between local variation in wall shear stress in arterial blood flow and atheroma development. The purpose of this study was to analyze the hemodynamics in vascular segments from morphologically realistic three-dimensional (3D) reconstruction, and to compare the computed wall shear stress in a compliant vascular segment model and the corresponding rigid walled model. Cross-sectional images of the segments of femoral and carotid arteries in five Yucatan miniswine were obtained using intravascular ultrasound (IVUS) imaging and the segment geometry was reconstructed at different times in the cardiac cycle. The actual measured wall motion from the reconstruction was employed to specify the moving boundaries for simulation of physiological distensibility. Velocity profiles and wall shear stress were computed using unsteady computational fluid dynamics analysis. The computed results revealed that the maximum wall shear stress in the compliant model was approximately 4–17 percent less than that in the rigid model if the wall motion is larger than 10 percent. Our analysis demonstrates that inaccuracies due to inflow velocity profile can be minimized by the extension of the model upstream. The phase angle between the diameter change and wall shear is affected by the local changes in geometry of the arteries. These simulations can be potentially used to analyze the effect of regional wall motion changes in the presence of atherosclerotic lesions on the local fluid dynamics and to correlate the same with subsequent growth of the lesions.

Biomechanics of Pediatric Cervical Spine: Compression, Flexion and Extension Responses

The objective of the present study was to develop three separate age-specific one, three, and six year old pediatric human cervical spine (C4-CS-C6) three-dimensional nonlinear finite element models and to quantify the biomechanical responses. The adult model was modified to create one, three, and six year old pediatric spines by incorporating the local geometrical and material characteristics of the developmental anatomy. The adult human cervical spine model was constructed from close-up computed tomography sections and sequential anatomic cryomicrotome sections, and validated with experimental data. The biomechanical responses were compared with the adult human cervical spine behavior under different loading modes using three approaches. Approach 1: using pure overall structural scaling (reduce size) of the adult model. Approach 2: using three separate age-specific pediatric models incorporating local component geometrical and material property changes. Approach 3: applying the overall structural scaling to the above three pediatric models. All pediatric structures were consistently more flexible than the adult spine under all loading modes. However, responses obtained using the pure overall structural scaling (Approach 1) increased the flexibilities slightly. In contrast, the inclusion of local component geometrical and material property changes to create the three individual pediatric cervical spine models (Approach 2) produced significantly higher changes in the flexibilities under all loading modes. When overall structural scaling effects were added to the three pediatric models (Approach 3), the increase was not considerably higher. White the one year old pediatric model was the most flexible followed by the three and six year old models in flexion and extension, the three year old pediatric model was the most flexible under compression followed by the six and one year old models. The differing biomechanical responses among different pediatric groups were ascribed to the individual developmental anatomical features. The present findings of significant increase in biomechanical response due to local geometry and material property changes emphasize the need to consider the developmental anatomical features in the pediatric structures to better predict their biomechanical behavior.

Computer-aided molecular modeling of the enantioselectivity of Pseudomonas cepacia lipase toward γ- and δ-lactones

Computer-aided molecular modeling was performed to investigate the experimentally determined enantioselectivities of Pseudomonas cepacia lipase (PCL) toward various saturated γ- and δ-lactones. Experimental data indicated that PCL preferentially hydrolyzes the ( R)-enantiomers of both types of substrates. Interactions between the non-polar aliphatic alkyl chain of the ( S)-enantiomers and the polar side chain of residue Y29 were identified to mediate enantioselectivity. Upon binding, the tyrosine was displaced, thus initiating a cascade of local geometry changes which led to the breakdown of the essential H-bond network at the active site H286. The lactone ring of the ( S)-δ-enantiomers further added to this process, since it was forced into an unfavorable position by repulsion from Y29, directly affecting the position of H286. In contrast, the respective ( R)-enantiomers fit without distorting side chains essential for catalysis in the binding pocket of PCL. In δ-lactones, the stereocenter was located close to the imidazole ring of H286, suggesting a more intense interaction with H286 as compared to γ-lactones. The length of the aliphatic chain adjacent to the stereocenter also affected the enantiopreference toward hydrolysis of δ-lactones, while for γ-lactones, the enantioselectivity did not significantly change with increasing alkyl chain length. In the cases of ( S)-δ-octa- and ( S)-δ-nonalactone, two alternative possible binding modes were examined, indicating that the respective substrate resolutions led to poor enantioselectivity as compared to the longer-chain δ-lactone substrates.

Atomic mutations at the single tryptophan residue of human recombinant annexin V: effects on structure, stability, and activity.

The single tryptophan residue (Trp187) of human recombinant annexin V, containing 320 residues and 5328 atoms, was replaced with three different isosteric analogues where hydrogen atoms at positions 4, 5, and 6 in the indole ring were exchanged with fluorine. Such single atom exchanges of H --> F represent atomic mutations that result in slightly increased covalent bond lengths and inverted polarities in the residue side-chain structure. These minimal changes in the local geometry do not affect the secondary and tertiary structures of the mutants, which were identical to those of wild-type protein in the crystal form. But the mutants exhibit significant differences in stability, folding cooperativity, biological activity, and fluorescence properties if compared to the wild-type protein. These rather large global effects, resulting from the minimal local changes, have to be attributed either to the relatively strong changes in polar interactions of the indole ring or to differences in the van der Waals radii or to a combination of both facts. The changes in local geometry that are below resolution of protein X-ray crystallographic studies are probably of secondary importance in comparison to the strong electronegativity introduced by the fluorine atom. Correspondingly, these types of mutations provide an interesting approach to study cooperative functions of integrated residues and modulation of particular physicochemical properties, in the present case of electronegativity, in a uniquely structured and hierarchically organized protein molecule.

The sensitivity of a Weibull failure criterion to singularity strength and local geometry variations

Previous experimental evidence has shown scale sensitivity of adhesives both in terms of ultimate stress and strain to failure; this sensitivity may be modelled using Weibull statistics. The implications of this on the sensitivity of strength predictions to mesh density around singularity points and small changes in local geometry is investigated using an idealised model of an enclosed corner in an adhesive joint. The sensitivity of two other failure criteria are also compared to the Weibull method. It is seen that there is a critical relationship between the Weibull shape parameter, m, and the singularity strength, λ. This relationship marks the transition between mesh insensitivity and mesh sensitivity, even with a singular stress (or strain) field present. If the singularity is removed by localised rounding, then the Weibull method of failure prediction shows much less sensitivity to the exact local geometry variation than other methods of failure prediction.

Frozen density matrix approach for electronic structure calculations

A frozen density matrix approach for determining local geometry changes of large molecules is proposed based on the density matrix divide-and-conquer method. This approach divides a large molecule into a small active part and the rest as the frozen part. After a single-point self-consistent field (SCF) calculation for the whole molecule, only the local molecular orbitals of the active part and its neighbor are updated when the geometry of the active part changes. The updated density matrix is calculated from the new local molecular orbitals of the active part and the stored local molecular orbitals of the frozen part. The electron transfer between the active and the frozen part is allowed via a common and variable chemical potential. The preliminary tests using semiempirical quantum chemical methods show this approach predicts the local geometry change well. The error in geometric parameters is less than 0.002 Å and less than 0.5° for bond length and bond angle, respectively. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 69: 397–404, 1998

Theoretical studies of CO adsorption on H-ZSM-5 and hydrothermally treated H-ZSM-5

The adsorption of CO on H-ZSM-5 and hydrothermally treated H-ZSM-5 is studied by means of quantum mechanical calculations. Good agreement with experimental FTIR data is established. The Al(OH) 3 dimer is found to account for the new bands that appear in the hydroxyl region of the FTIR spectra of H-ZSM-5 as a result of hydrothermal treatment. Effects of electron correlation (investigated through second-order Møller–Plesset perturbation and density-functional theory) are compared with Hartree–Fock results. Red shifts in the stretching frequency of bridging OH groups due to the CO interaction are best described by the density-functional approach. Frequency shifts are found to correlate with changes in local geometry.

Automated crack identification for cement paste

The development of an automated procedure for the identification of microcracks in cement paste using backscattered electron images of polished epoxy-impregnated specimens is described. Digitized images are acquired using an integrated scanning electron microscope/image acquisition system. Cracks are identified based on local changes in image intensity (gray level) and feature geometry. The gray level of epoxy-filled cracks is affected by the density of underlying and adjacent phases. As a result, cracks cannot be identified based on gray level alone. Combined procedures that establish the floor of the crack, a minimum gradient in the gray level adjacent to cracks, and minimum differences in gray level between the floor of a crack and adjacent solid phases provide a reproducible and consistent technique for crack identification in cement paste. The crack patterns observed using these procedures show that the denser phases within hydrated cement paste exhibited lower crack density than phases with lower density and that a significant portion of the cracking occurs through the softest phase, undesignated product (UDP), and at the boundary between UDP and other phases.

Growth habits and growth rates of snow crystals

Equations are derived for the growth rates of snow crystals as they fall through the atmosphere in terms of the air temperature, supersaturation and their terminal velocities. The predicted maximum attainable diameters of regular hexagonal plates(0.84 mm), sector plates (ca. 2 mm) and stellar dendrites (3.5 mm) are in good agreement with observations based on Nakaya’s large collection of snow crystal photographs. Masonet al. (Phil. Mag. 8, 505 (1963)) determined experimentally the average migration distancexBfor water molecules diffusing across the basal surface of ice crystals as a function of temperature. These measurements ofxBhave now been supplemented by calculations of the corresponding quantityxpfor the prism faces from measurements of the limitingc/aratios of small growing crystals whose shape is largely determined by the values of bothxpandxB. A theoretical treatment for the onset of dendritic growth leads to the result that a stationary thin regular hexagonal plate starts to sprout at the corners when its diameterdcexceeds 1.6 x 105x2p/Dv, whereDvis the diffusion coefficient of water vapour in air. Plates grow in the temperature range –8 °C to –23 °C, for whichdcranges from 50 µm at –15 °C to 670 µm at –8 °C. For falling ventilated plates the corresponding values ofdcare rather larger at 50 µm and 940 µm respectively, because the vapour concentration gradients around the crystal are enhanced. These latter values agree respectively with the observed minimum sizes of thin plates found at the centres of stellar dendritic crystals, and with the observed maximum size of regular plates. The observed maximum diameter (1.2 mm ) ofsectorplates at the centre of dendritic crystals agrees well with calculations based on the assumption that these originate at about the –20 °C level and develop into dendrites only after falling below the –16 °C level. A mechanism, based on the interplay between the external vapour diffusion field, which responds very rapidly to local changes in crystal geometry, and the much more sluggish process of surface diffusion, is suggested to account for the symmetrical dendritic growth of each of the six arms of a stellar crystal and also to explain the observation that once asymmetry is accidentally introduced on one side of an arm, it tends to persist.

Lattice relaxation of zeolites

Quantum-chemical cluster calculations as well as solid-state chemical lattice-calculations indicate that zeolitic SiO2- and AlPO4-structures are flexible structures. The structures reflect the subtle balance of electrostatic and covalent interactions. The different electrostatic interactions lower the symmetry of layered AlPO4-structures compared to that of the corresponding SiO2-compounds. The result is a smaller zeolite-channel dimension for the AlPO4-structure compared to that of the corresponding SiO2-network. Deprotonation of the zeolite-lattice leads to large local changes in geometry that changes acidity compared to that predicted for a non-flexible lattice. Changes in lattice vibrational frequencies are consistent with the theoretically predicted relaxation of the zeolite-lattice.

Tertiary structures in the platform cover strata of Nordenskiold Land, Svalbard

Air photo interpretation along with limited field work is the basis of a compilation map of Tertiary structures in the Upper Paleozoic through Mesozoic platform cover strata of Nordenskiold Land. Permian Kapp Starostin Formation strata form a continuous marker horizon delineating both a large NE-verging fold complex, which involves the basement (Hecla Hoek sequence) through basal Tertiary strata, and somewhat smaller scale folds, some of which may have formed in association with detachments and thrusts within the platform cover sequence. The map pattern is both a function of local structural plunge and changes in fold geometry along strike. Regional considerations suggest that subsurface basement-involved thrusts exist. In S Nordenskiold Land, to the E of folded Kapp Starostin Formation strata, a 3.5 km wide zone of folding and thrusting in Triassic and Jurassic strata above a subhorizontal decollement is inferred to occur. Further E is the W limb of the central Tertiary basin syncline.

The influence of local geometry on the strength of adhesive joints

This paper describes a two-part investigation into the effect of local geometry changes at the edges of the overlap in single lap joints. In the first part, finite element analysis has been used to model the effects on the stress distribution of geometry changes which are small in relation to the dimensions of the local geometry, in order to provide an improved model for failure prediction. The model used is that of an adhesive around a rigid corner, and the effect of rounding the corner has been considered. The second part deals with local geometry changes of the same order of magnitude as the dimensions of the geometry and their effect on joint strength. Three types of joint — one with a square-edged adhesive layer, one with a fillet of adhesive and one with an adhesive fillet plus a radiused adherend — were manufactured, tested and analysed. Improvements to the finite element models were also made following the results of part 1. It is found that finite element analysis is capable of predicting the significant strength increases that may be achieved in single lap joints by filleting the adhesive at the edges of the overlap and rounding the ends of the adherends.

Charge distributions and chemical effects. XXXVII. Note on tetracyclo[4.1.0.02,4.03,5]heptane

Full geometry and ζ optimizations are a must in the study of small cycles, as in tetracyclo[4.1.0.02.4.03.5]heptane. Indeed, nonoptimized STO-3G calculations suggest the 4-carbon to be electron richer than the carbon in 3 position, whereas the reverse is shown by optimized calculations ([Formula: see text] vs. −138 me forC-3 andC-4, respectively). The latter result is in accord with the general trends indicating that a gain in local 2s charge is accompanied by a downfield nmr shift (δ 22.1 for C-3 and −4.0 ppm for C-4, from tetramethylsilane). These charge and shift results can be directly compared to one another because the local geometries (namely, the angles) about these two carbon atoms are very similar. This, however, is not the case with other carbon atoms of 3-membered cycloalkanes, a situation restricting the validity of simple charge–shift correlations in this class of compounds because of the changes in local geometry affecting the hybridization of carbon.

Finite Element Techniques Applied to Cracks Interacting with Selected Singularities

The finite‐element method for computing the extensional stress‐intensity factor, K1, for cracks approaching selected singularities of varied geometry is described. Stress‐intensity factors are generated using both displacement and J‐integral techniques, and numerical results are compared to those obtained experimentally in a photoelastic investigation. The selected singularities considered are a colinear crack, a circular penetration, and a notched circular penetration. Results indicate that singularities greatly influence the crack‐tip stress‐intensity factor as the crack approaches the singularity. In addition, the degree of influence can be regulated by varying the overall geometry of the singularity. Local changes in singularity geometry have little effect on the stress‐intensity factor for the cases investigated.

Van der Waals forces between thin anisotropic cylinders

We calculate the van der Waals force between thin anisotropic dielectric cylinders immersed in an isotropic medium. For the special case where the cylinders possess only one absorption frequency and the intervening medium is a vacuum, our result reduces to a form derived by Zwanzig. For hydrocarbon chains immersed in water, numerical calculations show that the strong Debye relaxation of water gives an entropic contribution to the interaction energy, which is the same magnitude as that from the ultraviolet interactions. Furthermore, the contributions from the transverse chain susceptibility imply that local changes in geometry and side chains can give significant contributions to the interaction energy of macromolecules in biological systems.

Continuum Plasticity Theory in Relation to Solid Solution, Dispersion, and Precipitation Hardening

Small volume fractions of very small particles in a pure metal eliminate easy glide in a single crystal and produce very high yield strength in a polycrystal. The validity of a partial explanation provided by the application of ordinary continuum mechanics on the microscale is explored here. Size effect associated with inhomogeneity of the metal matrix is seen to play a major role because a small volume fraction of rigid spheroidal particles in any homogeneous elastic-plastic matrix can contribute little to engineering yield strength and to subsequent work-hardening. However, particle strength in itself cannot provide the yield strength and flow level of a structural metal. The increased resistance to additional slip must be due mainly to the expanding network of intersecting slip triggered by many particles of very small size. This and the elastic distortion in the immediate vicinity of solute atoms and extremely small particles represent significant large local changes in geometry. Consequently, such predictions of the general theorems of conventional plasticity as the lack of influence of initial stress on flow level need not be valid.