Average Geometry Research Articles

Stability of Ni sites across the pressure-induced insulator-to-metal transition in YNiO3

The local environment of nickel atoms in Y NiO3 across the pressure- induced insulator to metal (IM) transition was studied using X-ray absorption spectroscopy (XAS) supported by ab initio calculations. The monotonic contraction of the NiO6 units under applied pressure observed up to 13 GPa, stops in a limited pressure domain around 14 GPa, before resuming above 16 GPa. In this narrow pressure range, crystallographic modifications basically occur in the medium/long range, not in the NiO6 octahedron, whereas the evolution of the near-edge XAS features can be associated to metallization. Ab initio calculations show that these features are related to medium range order, provided that the Ni-O-Ni angle enables a proper overlap of the Ni eg and O 2p orbitals. Metallization is then not directly related to modifications in the average local geometry of the NiO6 units but more likely to an inter-octahedra rearrangement. These outcomes provides evidences of the bandwidth driven nature of the IM transition.

A flexible model for water based on TIP4P/2005

A new flexible water model, TIP4P/2005f, is developed. The idea was to add intramolecular degrees of freedom to the successful rigid model TIP4P/2005 in order to try to improve the predictions for some properties, and to enable the calculation of new ones. The new model incorporates flexibility by means of a Morse potential for the bond stretching and a harmonic term for the angle bending. The parameters have been fitted to account for the peaks of the infrared spectrum of liquid water and to produce an averaged geometry close to that of TIP4P/2005. As for the intermolecular interactions, only a small change in the σ parameter of the Lennard-Jones potential has been introduced. The overall predictions are very close to those of TIP4P/2005. This ensures that the new model may be used with the same confidence as its predecessor in studies where a flexible model is advisable.

How Do CAD Models Compare With Reverse Engineered Manufactured Components for Use in Wear Analysis?

To accurately quantify polyethylene wear in retrieved arthroplasty components, the original geometry of the component must be estimated accurately using a reference geometry such as a computer-aided design (CAD) model or a never-implanted insert. However, differences may exist between the CAD model and manufactured inserts resulting from manufacturing tolerances. We quantified the deviations between CAD models and newly manufactured inserts and determined how these deviations compared with using a never-implanted insert as a reference geometry. We obtained five cruciate-retaining (CR) and five posterior-stabilizing (PS) tibial inserts and their CAD models. The inserts were scanned and reconstructed using microcomputed tomography (micro-CT). Differences in volume and surface geometry were measured among (1) the individual inserts; (2) between the inserts and a CAD model; and (3) between the inserts and a reference geometry constructed from multiple scanned inserts averaged together. The micro-CT volumes were, on average, 0.4% smaller (34-178 mm(3)) than the CAD model volumes. The mean deviation between the CAD model and insert surface geometry was 25.7 μm smaller for CR and 36.8 μm smaller for PS. The mean deviation between the inserts and an averaged reference geometry was 1.4 μm larger for CR and 0.4 μm smaller for PS. Deviations exist between manufactured tibial inserts and CAD models that could cause errors in wear measurements. Scanned inserts may better represent the preimplantation geometry of worn inserts than CAD models, depending on the manufacturing variability between lots. The magnitude of the error in estimation of the preimplantation geometry of a retrieved component could add or subtract the equivalent of 1 year of wear.

Molecular structure of p-diisocyanobenzene from gas-phase electron diffraction and theoretical calculations and effects of intermolecular interactions in the crystal on the benzene ring geometry

In this study, the molecular structure of p-diisocyanobenzene has been determined by gas-phase electron diffraction and quantum chemical calculations. The electron diffraction intensities from a previous study by Colapietro et al. (J Mol Struct 125:19–32, 1984) have been reanalyzed using geometrical constraints and initial values of vibrational amplitudes from computations. The equilibrium structure of the molecule has D 2h symmetry, whereas the average geometry in the gaseous phase is best described by a non-planar model of C 2v symmetry. The lowering of symmetry is due to large-amplitude motion of the substituents out of the plane of the benzene ring. The non-planar model has an internal ring angle at the ipso position, ∠aC2–C1–C6 = 120.6 ± 0.2°, about 1° smaller than that from the previous study, but consistent with the quantum chemical calculations. The mean length of the ring C–C bonds and the length of the triple bond are accurately determined as 〈r g(C–C)〉 = 1.398 ± 0.003 A and r g(N≡C) = 1.177 ± 0.002 A, respectively. Comparison with the gaseous isoelectronic molecules p-diethynylbenzene and p-dicyanobenzene shows that the differences in the mean lengths of the ring C–C bonds and in the lengths of the triple bonds determined by electron diffraction are equal or closely similar to the corresponding differences from quantum chemical calculations. The present experimental value of the ipso angle in free p-diisocyanobenzene is slightly, but significantly smaller than that obtained by X-ray crystallography. The difference is confirmed by computational modeling of the crystal structure and appears to be due to –N≡C···H–C intermolecular interactions in the crystal.

Backreaction during Inflation: A Physical Gauge Invariant Formulation

Within a genuinely gauge invariant approach recently developed for the computation of the cosmological backreaction, we study, in a cosmological inflationary context and with respect to various observers, the impact of scalar fluctuations on the space-time dynamics in the long wavelength limit. We stress that such a quantum backreaction effect is evaluated in a truly gauge independent way using a set of effective equations which describe the dynamics of the averaged geometry. In particular we show under what conditions the free falling (geodetic) observers do not experience any scalar-induced backreaction in the effective Hubble rate and fluid equation of state.

In vivo dynamic strains of the ovine anterior mitral valve leaflet

Understanding the mechanics of the mitral valve is crucial in terms of designing and evaluating medical devices and techniques for mitral valve repair. In the current study we characterize the in vivo strains of the anterior mitral valve leaflet. On cardiopulmonary bypass, we sew miniature markers onto the leaflets of 57 sheep. During the cardiac cycle, the coordinates of these markers are recorded via biplane fluoroscopy. From the resulting four-dimensional data sets, we calculate areal, maximum principal, circumferential, and radial leaflet strains and display their profiles on the averaged leaflet geometry. Average peak areal strains are 13.8±6.3%, maximum principal strains are 13.0±4.7%, circumferential strains are 5.0±2.7%, and radial strains are 7.8±4.3%. Maximum principal strains are largest in the belly region, where they are aligned with the circumferential direction during diastole switching into the radial direction during systole. Circumferential strains are concentrated at the distal portion of the belly region close to the free edge of the leaflet, while radial strains are highest in the center of the leaflet, stretching from the posterior to the anterior commissure. In summary, leaflet strains display significant temporal, regional, and directional variations with largest values inside the belly region and toward the free edge. Characterizing strain distribution profiles might be of particular clinical significance when optimizing mitral valve repair techniques in terms of forces on suture lines and on medical devices.

Sex differences in anatomical parameters of acetabulum among asymptomatic Serbian population

Anatomical parameters of the bony components of the hip joint are essential for better understanding of etiopathogenesis of diseases like primary osteoarthrosis of the hip joint. The aim of this reserch was to examine the normal acetabular morphometry in Serbian population and to determine whether there are sex differences in anatomical parameters of the acetabulum among asymptomatic subjects. Pelvic radiographics of 320 adult asymptomatic patients (640 hips) were analyzed in 170 men and 150 women to determine the morphology of the acetabulum in Serbian population. For each hip the center edge angle of Wiberg (CEA), the acetabular angle of Sharp (AA), acetabular depth (AD), acetabular roof obliquity (ARO) and roof angle (RA) were measured. The following average measurements for acetabulum geometry were obtained (x +/- SD): CEA - 33.5 +/- 6.5 degrees (33.6 +/- 5.8 degrees in male, 33.3 +/- 6.9 degrees in female), AA - 38.0 +/- 3.8 degrees (37.5 +/- 3.6 degrees in male, 38.5 +/- 3.9 degrees in female), AD - 11.9 +/- 2.8 mm (12.5 +/- 2.7 mm in male, 11.2 +/- 2.7 mm in female), ARO - 7.6 +/- 5.7 degrees (6.2 +/- 4.9 degrees in male, 9.0 +/- 6.0 degrees in female) and RA - 18.4 +/- 10.0 degrees (19.6 +/- 8.5 degrees in male, 17.1 +/- 9.5 degrees in female). There were significant differences in the CEA, AA, AD, ARO and RA related to gender (p < 0.01, t-test). There are significant gender differences in Serbian population for all the examined anatomical parameters of acetabulum. We found sex-related differences in acetabular morphology, female acetabulum being marginally more dysplastic than male acetabulum. There is also a clear tendency of female hips to be more dysplastic than male ones.

Protein Free Energy Corrections in ONIOM QM:MM Modeling: A Case Study for Isopenicillin N Synthase (IPNS).

The protein environment can have significant effects on the enzyme catalysis even though the reaction occurs locally at the reaction center. In this paper, we describe an efficient scheme that includes a classical molecular dynamics (MD) free-energy perturbation (FEP) correction to the reaction energy diagram, as a complement to the protein effect obtained from static ONIOM (QM:MM) calculations. The method is applied to eight different reaction steps, from the O2-bound reactant to formation of a high-valent ferryl-oxo intermediate, in the nonheme iron enzyme isopenicillin N synthase (IPNS), for which the QM:MM energy diagram has previously been computed [ Lundberg , M. et al. J. Chem. Theory Comput. 2009 , 5 , 220 - 234 ]. This large span of the reaction coordinate is covered by dividing each reaction step into microsteps using a virtual reaction coordinate, thus only requiring ONIOM information about the stationary points themselves. Protein effects are important for C-H bond activation and heterolytic O-O bond cleavage because both these two steps involve charge transfer, and compared to a static QM:MM energies, the dynamics of the protein environment changes the barrier for O-O bond cleavage by several kcal/mol. The origin of the dynamical contribution is analyzed in two terms, the geometrical effect caused by the change in average protein geometry (compared to the optimized geometry) in the room temperature MD simulation with the solvent, and the statistical (entropic) effect resulting from fluctuations in the interactions between the active site and the protein environment. These two effects give significant contributions in different steps of the reaction.

The interplanetary magnetic field environment at Mercury's orbit

Mercury is exposed to the most dynamic heliospheric space environment of any planet in the solar system. The magnetosphere is particularly sensitive to variations in the interplanetary magnetic field (IMF), which control the intensity and geometry of the magnetospheric current systems that are the dominant source of uncertainty in determinations of the internal planetary magnetic field structure. The Magnetometer on the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft has made extensive magnetic field observations in the inner heliosphere over the heliocentric distances of Mercury's orbit, between 0.31 and 0.47 AU. In this paper, Magnetometer data from MESSENGER, obtained at rates of 2 and 20 vector samples per second, are used together with previous observations in the inner heliosphere by Helios and at Earth by the Advanced Composition Explorer, to study the characteristics of IMF variability at Mercury's orbit. Although the average IMF geometry and magnitude depend on heliocentric distance as predicted by Parker, the variability is large, comparable to the total field magnitude. Using models for the external current systems we evaluate the impact of the variability on the field near the planet and find that the large IMF fluctuations should produce variations of the magnetospheric field of up to 30% of the dipole field at 200 km altitude, corresponding to the planned periapsis of MESSENGER's orbit at Mercury. The IMF fluctuations in the frequency range 10 − 4 < f < 10 − 1 Hz are consistent with turbulence, whereas evidence for dissipation was observed for f > 1 Hz . The transition between the turbulent and dissipative regimes is indicated by a break in the power spectrum, and the frequency of this break point is proportional to the IMF magnitude.

Structural and Dynamical Properties and Vibrational Spectra of Bisulfate Ion in Water: A Study by Ab Initio Quantum Mechanical Charge Field Molecular Dynamics

The ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism was applied to simulate the bisulfate ion, HSO4-, in aqueous solution. The averaged geometry of bisulfate ion supports the separation of six normal modes of the O*-SO3 unit with C3v symmetry from three modes of the OH group in the evaluation of vibrational spectra obtained from the velocity autocorrelation functions (VACFs) with subsequent normal coordinate analyses. The calculated frequencies are in good agreement with the observations in Raman and IR experiments. The difference of the averaged coordination number obtained for the whole molecule (8.0) and the summation over coordinating sites (10.9) indicates some water molecules to be located in the overlapping volumes of individual hydration spheres. The averaged number of hydrogen bonds (H-bonds) during the simulation period (5.8) indicates that some water molecules are situated in the molecular hydration shell with an unsuitable orientation to form a hydrogen bond with the ion. The mean residence time in the surroundings of the bisulfate ion classify it generally as a weak structure-making ion, but the analysis of the individual sites reveals a more complex behavior of them, in particular a strong interaction with a water molecule at the hydrogen site.

Simulating thermal motion in crystalline phase-I ammonia

Path-integral molecular dynamics have been used to simulate the phase-I crystalline form of ammonia, using an empirical force field. This method allows quantum-mechanical effects on the average geometry and vibrational quantities to be evaluated. When these are used to adjust the output of a high-temperature density functional theory simulation, the results are consistent with those given by the most recent structural refinement based on powder neutron diffraction data. It is clear that the original refinement overestimated thermal motion, and therefore also overestimated the equilibrium N-{H/D} bond length.

Conformations of Some Large-Ring Cyclodextrins Derived from Conformational Search with Molecular Dynamics Simulations and Principal Component Analysis

Principal component analysis (PCA) was applied for postprocessing of trajectories from conformational search, based on 50.0 ns molecular dynamics (MD) simulations, with the purpose to elucidate the conformations of some large-ring cyclodextrins (LR-CDs), CDn (n = 24, 25, 26, 27, 28, 29). The dominant PCA modes for concerted motions of the macroring atoms were monitored in a lower-dimension subspace. The first 10 lowest indexed modes describe more than 90% of the total atomic motions in all cases, with about 85% (CD27, CD29) to more than 90% (CD24, CD25) contribution coming from the six highest-eigenvalue principal components. Representative average geometries of the cyclodextrin macrorings were also obtained for the whole simulation and for the five 10.0 ns time intervals of the simulation. Two conformations for CD26, the largest LR-CD for which X-ray data is available, are characterized by possessing, respectively, one and two helical turns. Resemblance to computed representative conformations of CD26 in water was found for CD27 and CD28, with the similarity being better expressed for the former case. Only CD24, among the two smaller size LR-CDs, displays resemblance during short simulation intervals to one of the conformations of CD26. The formation of small loops of six to seven glucose units is a favorable deformation mode of the macrorings. Besides, once a small loop of six to seven glucoses is formed, the next natural mode for deformation of the macromolecule is toward the creation of a short helix that further enhances the stability of the structure. The average geometry of CD29 has no likeness at all to the conformations of CD26. Thus, the difference of three glucose units between CD26 and CD29 already influences significantly the shape of the most probable conformation.

Quantitative detection of cartilage surfaces and ligament geometry of the wrist using an imaging cryomicrotome system

Biomechanical models may aid in improving diagnosis and treatment of wrist joint disorders. As input, geometrical information is required for model development. Previous studies acquired some elements of the average wrist joint geometry. However, there is a close geometric functional match between articulating surfaces and ligament geometry. Therefore, biomechanical models need to be fed with the geometric data of individual joints. This study is aimed at acquiring geometric data of cartilage surfaces and ligaments from individual wrist joints by using a cryomicrotome imaging system and the evaluation of inter- and intra-observer variability of the data. The 3D geometry of 30 cartilage surfaces and 15 ligaments in three cadaver wrists was manually detected and quantitatively reconstructed. The inter- and intra-observer variability of the cartilage surface detection was 0.14 and 0.19 mm, respectively. For the position of the radius attachment of the dorsal radiocarpal ligament (DRC), the observer variations were 0.12 and 0.65 mm, for intra-/inter-observer, respectively. For the DRC attachment on the triquetrum, the observer variations were 0.22 and 1.19 mm. Anatomic reconstruction from 3D cryomicrotome images offer a method to obtain unique geometry data of the entire wrist joint for modeling purposes.

Differences in Aortic Arch Geometry, Hemodynamics, and Plaque Patterns Between C57BL/6 and 129/SvEv Mice

Atherosclerotic plaques are distributed differently in the aortic arches of C57BL/6 (B6) and 129/SvEv (129) apolipoprotein E (apoE)-deficient mice. It is now recognized that hemodynamic wall shear stress (WSS) plays an important role in the localization of atherosclerotic development. Since the blood flow field in the vessel is modulated by the vascular geometry, we quantitatively examined the difference in the aortic arch geometry and hemodynamic WSS between the two corresponding wild-type mouse strains. The three-dimensional (3D) geometry of 14 murine aortic arches, seven from each strain, was characterized using casts and stereo microscopic imaging. Based on the geometry of each cast, an average 3D geometry of the aortic arch for each mouse strain was obtained, and computational fluid dynamic calculations were performed in the two average aortic arches. Many geometric features, including aortic arch shape, vessel diameter, and branch locations, were significantly different at p<0.05 between the two mouse strains. Lower shear stress was found at the inner curvature of the aortic arch in the 129 strain, corresponding to greater involvement in the corresponding apoE-deficient mice relative to the B6 strain. These results support the notion that heritable features of arterial geometry can contribute to individual differences in local susceptibility to arterial disease.

Cellular organization of the trophoblastic epithelium in elongating conceptuses of ruminants

We present a computational approach to analyze the cellular organization during the elongation process of the ovine conceptus. First, we selected a set of mathematical descriptors to quantify cell geometry and cell neighborhood within the external epithelial layer of the conceptus: the trophoblast. Second, we established a hybrid image segmentation framework, and analyzed the extracted features with statistical tools to describe and compare the spatio-temporal dynamics of cellular organization within this epithelium. The main results indicated that the average geometry and neighborhood of the trophoblast cells are relatively stable from a sampling position to another and from a stage of development to another. Further, their elongation axes are randomly distributed. The cellular organization fits the Poisson's process. Moreover, no clustering structures or grid-like regular point patterns are found inside the studied cell population. This suggests that the trophoblast elongation observed in ruminants is not due to the geometrical change of cell shape but might be the consequence of cell addition associated with peculiar plans of cell division or intercalation. To cite this article: J. Wang et al., C. R. Biologies 332 (2009).

OEDIPE: Software for Fast Construction of Computational Phantoms and MCNPX Calculation in Internal Dosimetry

Although great efforts have been made to improve the physical anthropomorphic phantoms used to calibrate in vivo measurement systems, each of these phantoms represents a single average counting geometry and usually contains a uniform distribution of a radionuclide in the tissue substitute. As a matter of fact, significant corrections must be made to phantom-based calibration factors in order to obtain absolute calibration efficiencies applicable to a given individual. The OEDIPE software has been developed at the Institute for Radiological Protection and Nuclear Safety. It allows the direct and fast construction of a voxel phantom from medical images with a realistic distribution of activity between organs and its conversion into computer files to be used online for Monte Carlo calculations. OEDIPE allows determining and visualizing the variation of activity retention in the segmented organs of the phantom and running MCNPX with these calculated source-organs at different times after intake. The influence of the biokinetics of radionuclides on the in vivo measurement as well as the uncertainty on the estimated activity is quantified by comparing the numerical calibration coefficients obtained by considering realistic and dynamic biokinetic distributions of activity with the counting efficiency commonly obtained from simple, homogeneous, and static activity distributions in organs or in the whole body. As an application, the effect of long-term retention tissues was studied through a case of inhalation of an insoluble compound where the thoracic lymph nodes make a significant contribution to the lung counting efficiency. Future work will concern contamination through other routes of intake, such as a wound, and mixtures of radionuclides.

Voidage distribution around bubbles in a fluidized bed: Influence on throughflow

In this work, a new method for measuring void fraction distribution around endogenous bubbles in a 2D fluidized bed is presented. The technique is based on illuminating a transparent-wall 2-dimensional bed with diffuse light from the rear and recording the distribution of light that penetrates the bed. The recording is made with a high speed video-camera, which gives frames with grey level corresponding to the light penetration and from which the voidage distribution around the bubbles can be determined. In this way, voidage distribution in the region very close to the bubble contour ( r/ R b ≲ 1.2) is obtained, which was not possible in previous studies due to limitations in spatial resolution. A correlation is proposed for the voidage at the contour of the bubble, with the voidage depending on the radial position and the polar angle ε( r, θ). In addition, the effect of the voidage distribution on the throughflow crossing the bubbles was studied and an increase of 20% was determined for the average bubble geometry of the more than 100 bubbles analysed.

Competing quantum effects in the dynamics of a flexible water model

Numerous studies have identified large quantum mechanical effects in the dynamics of liquid water. In this paper, we suggest that these effects may have been overestimated due to the use of rigid water models and flexible models in which the intramolecular interactions were described using simple harmonic functions. To demonstrate this, we introduce a new simple point charge model for liquid water, q-TIP4P/F, in which the O-H stretches are described by Morse-type functions. We have parametrized this model to give the correct liquid structure, diffusion coefficient, and infrared absorption frequencies in quantum (path integral-based) simulations. The model also reproduces the experimental temperature variation of the liquid density and affords reasonable agreement with the experimental melting temperature of hexagonal ice at atmospheric pressure. By comparing classical and quantum simulations of the liquid, we find that quantum mechanical fluctuations increase the rates of translational diffusion and orientational relaxation in our model by a factor of around 1.15. This effect is much smaller than that observed in all previous simulations of empirical water models, which have found a quantum effect of at least 1.4 regardless of the quantum simulation method or the water model employed. The small quantum effect in our model is a result of two competing phenomena. Intermolecular zero point energy and tunneling effects destabilize the hydrogen-bonding network, leading to a less viscous liquid with a larger diffusion coefficient. However, this is offset by intramolecular zero point motion, which changes the average water monomer geometry resulting in a larger dipole moment, stronger intermolecular interactions, and a slower diffusion. We end by suggesting, on the basis of simulations of other potential energy models, that the small quantum effect we find in the diffusion coefficient is associated with the ability of our model to produce a single broad O-H stretching band in the infrared absorption spectrum.

Cortical hypoperfusion in the B6.PS2APP mouse model for Alzheimer's disease: Comprehensive phenotyping of vascular and tissular parameters by MRI

Function and morphology of the cerebral vasculature were studied in the amyloid (Abeta) plaque-containing double-transgenic (TG) B6.PS2APP Alzheimer's disease (AD) mouse model with MRI at an age range of 10 to 17 months. Perfusion, blood volume, and average vessel geometry were assessed in the brain and compared to age-matched controls (wild-type [WT] C57Bl/6). Additionally, the MR relaxation times T(1), T(2), and T(2)* were measured to detect potential pathological changes that might be associated with Abeta plaque depositions. Both decreased perfusion and decreased blood volume were observed in the occipital cortex in B6.PS2APP mice as compared to controls. A significant decrease in T(1) and T(2) was found in the frontal cortex and in the subiculum/parasubiculum. Immunohistochemistry confirmed plaque depositions in the cortex and in the subiculum/parasubiculum. In summary, our data indicate a reduced blood supply of B6.PS2APP mice in the occipital cortex that parallels the findings in cortical regions of patients with AD.

Dependence of Deformability of Geometries and Characteristics of Intramolecular Hydrogen Bonds in Canonical 2′-Deoxyribonucleotides on DNA Conformations

The molecular structure and deformability (with respect to average geometry) of methyl ethers of canonical 2′-deoxyribonucleotides thymidine-5′-phosphate (mTMP), 2-deoxycytidine-5′- phosphate (mCMP), 2-deoxyadenosine-5′-phosphate (mAMP) and 2′-deoxyguanosine-5′- phosphate (mGMP) in different types of DNA have been calculated using B3LYP/cc-pvdz method. Comparison of energy at equilibrium conformations of nucleotides and conformations with torsion angles of backbone fixed to average values for different types of DNA reveals that incorporation of nucleotides to A-DNA macromolecules requires the minimum amount of deformation energy. Therefore, this type of DNA should be the least strained from viewpoint of intramolecular deformations of monomers. Modeling of environmental effects within the PCM approach reveals that the immersion of nucleotides in polar medium results in significant decrease of energy differences between anti conformers of all DNTs and syn conformers of mGMP This also leads to reduction by almost a half nucleotides' deformation energy facilitating formation of DNA macromolecule. Change of DNTs conformation causes switch between different types of intramolecular H bonds. Every type of DNA possesses unique set of intramolar hydrogen bonds in nucleotides.