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At least 1,513 records · Page 84

Kinetics of template-directed pyrophosphate-linked dideoxyguanylate synthesis as a function of 2-MeImpdG and poly(C) concentration: insights into the mechanism

Aqueous solutions of deoxyguanosine 5'-monophosphate 2-methylimidazolide, 2-MeImpdG, yield primarily deoxyguanosine 5'-monophosphate, 5'dGMP, and pyrophosphate-linked dideoxyguanylate, dG5'ppdG, abbreviated G2p (see Chart 1). The initial rate of G2p formation, d[G2p]/dt in M h-1, determined at 23 degrees C, pH 7.8, 1.0 M NaCl and 0.2 M Mg2+ by timed high-performance liquid chromatography (HPLC) analysis, exhibits a second-order dependence on 2-MeImpdG concentration, [G]o, indicating a bimolecular mechanism of dimerization in the range 0.02 M < or = [G]o < or = 0.09 M. In the presence of polycytidylate, poly(C), G2p synthesis is accelerated and oligodeoxyguanylate products are formed by incorporation of 2-MeImpdG molecules. The kinetics of G2p formation as a function of both monomer and polymer concentration, expressed in C equivalents, were also determined under the above conditions and exhibited a complex behavior. Specifically, at a constant [poly(C)], values of d[G2p]/dt typically increased with [G]o with a parabolic upward curvature. At a constant [G]o, values of d[G2p]/dt increase with [poly(C)], but level off at the higher poly(C) concentrations. As [G]o increases this saturation occurs at a higher poly(C) concentration, a result opposite to expectation for a simple complexation of two reacting monomers with the catalyst prior to reaction. Nevertheless, these results are shown to be quantitatively consistent with a template-directed (TD) mechanism of dimerization where poly(C) acts as the template to bind 2-MeImpdG in a cooperative manner and lead, for the first time, to the formulation of principles that govern template-directed chemistry. Analysis of the kinetic data via a proposed TD cooperative model provides association constants for the affinity between polymer and monomer and the intrinsic reactivity of 2-MeImpdG toward pyrophosphate synthesis. To the best of our knowledge, poly(C)/2-MeImpdG is the first system that could serve as a textbook example of a TD reaction under conditions such that the template is fully saturated by monomers and under conditions that it is not.

NASA Discipline Exobiology↗

An ab initio benchmark study of the H + CO --> HCO reaction

The H + CO --> HCO reaction has been characterized with correlation consistent basis sets at five levels of theory in order to benchmark the sensitivities of the barrier height and reaction ergicity to the one-electron and n-electron expansions of the electronic wave function. Single and multireference methods are compared and contrasted. The coupled cluster method RCCSD(T) was found to be in very good agreement with Davidson-corrected internally-contracted multireference configuration interaction (MRCI+Q). Second-order Moller-Plesset perturbation theory (MP2) was also employed. The estimated complete basis set (CBS) limits for the barrier height (in kcal/mol) for the five methods, including harmonic zero-point energy corrections, are MP2, 4.66; RCCSD, 4.78; RCCSD(T), 4.15; MRCI, 5.10; and MRCI+Q, 4.07. Similarly, the estimated CBS limits for the ergicity of the reaction are: MP2, -17.99; RCCSD, -13.34; RCCSD(T), -13.79; MRCI, -11.46; and MRCI+Q, -13.70. Additional basis set explorations for the RCCSD(T) method demonstrate that aug-cc-pVTZ sets, even with some functions removed, are sufficient to reproduce the CBS limits to within 0.1-0.3 kcal/mol.

NASA Discipline Exobiology↗

Air oxidation of hydrazine. 1. Reaction kinetics on natural kaolinites, halloysites, and model substituent layers with varying iron and titanium oxide and O- center contents

Air oxidation of hydrazine was studied by using a group of kaolinites, halloysites, and substituent oxides as models for the tetrahedral and octahedral sheets. The rate was found to be linear with oxygen. The stoichiometry showed that oxygen was the primary oxidant and that dinitrogen was the only important nitrogen-containing product. The rates on kaolinites were strongly inhibited by water. Those on three-dimensional silica and gibbsite appeared not to be. That on a supposedly layered silica formed from a natural kaolinite by acid leaching showed transitional behavior--slowed relative to that expected from a second-order reaction relative to that on the gibbsite and silica but faster than those on the kaolinites. The most striking result of the reaction was the marked increase in the rate of reaction of a constant amount of hydrazine as the amount of clay was increased. The increase was apparent (in spite of the water inhibition at high conversions) over a 2 order of magnitude variation of the clay weight. The weight dependence was taken to indicate that the role of the clay is very important, that the number of reactive centers is very small, or that they may be deactivated over the course of the reaction. In contrast to the strong dependence on overall amount of clay, the variation of amounts of putative oxidizing centers, such as structural Fe(III), admixed TiO2 or Fe2O3, or O- centers, did not result in alteration of the rate commensurate with the degree of variation of the entity in question. Surface iron does play some role, however, as samples that were pretreated with a reducing agent were less active as catalysts than the parent material. These results were taken to indicate either that the various centers interact to such a degree that they cannot be considered independently or that the reaction might proceed by way of surface complexation, rather than single electron transfers.

NASA Discipline Number 52-20↗

Space proton transport in one dimension

An approximate evaluation procedure is derived for a second-order theory of coupled nucleon transport in one dimension. An analytical solution with a simplified interaction model is used to determine quadrature parameters to minimize truncation error. Effects of the improved method on transport solutions with the BRYNTRN data base are evaluated. Comparisons with Monte Carlo benchmarks are given. Using different shield materials, the computational procedure is used to study the physics of space protons. A transition effect occurs in tissue near the shield interface and is most important in shields of high atomic number.

NASA Discipline Number 45-10↗

Aerodynamic Design Optimization on Unstructured Grids with a Continuous Adjoint Formulation

A continuous adjoint approach for obtaining sensitivity derivatives on unstructured grids is developed and analyzed. The derivation of the costate equations is presented, and a second-order accurate discretization method is described. The relationship between the continuous formulation and a discrete formulation is explored for inviscid, as well as for viscous flow. Several limitations in a strict adherence to the continuous approach are uncovered, and an approach that circumvents these difficulties is presented. The issue of grid sensitivities, which do not arise naturally in the continuous formulation, is investigated and is observed to be of importance when dealing with geometric singularities. A method is described for modifying inviscid and viscous meshes during the design cycle to accommodate changes in the surface shape. The accuracy of the sensitivity derivatives is established by comparing with finite-difference gradients and several design examples are presented.

Anderson, W. Kyle↗

Hindlimb unweighting decreases endothelium-dependent dilation and eNOS expression in soleus not gastrocnemius

We tested the hypothesis that hindlimb unweighting (HLU) decreases endothelium-dependent vasodilation and expression of endothelial nitric oxide synthase (eNOS) and superoxide dismutase-1 (SOD-1) in arteries of skeletal muscle with reduced blood flow during HLU. Sprague-Dawley rats (300-350 g) were exposed to HLU (n = 15) or control (n = 15) conditions for 14 days. ACh-induced dilation was assessed in muscle with reduced [soleus (Sol)] or unchanged [gastrocnemius (Gast)] blood flow during HLU. eNOS and SOD-1 expression were measured in feed arteries (FA) and in first-order (1A), second-order (2A), and third-order (3A) arterioles. Dilation to infusion of ACh in vivo was blunted in Sol but not Gast. In arteries of Sol muscle, HLU decreased eNOS mRNA and protein content. eNOS mRNA content was significantly less in Sol FA (35%), 1A arterioles (25%) and 2A arterioles (18%). eNOS protein content was less in Sol FA (64%) and 1A arterioles (65%) from HLU rats. In arteries of Gast, HLU did not decrease eNOS mRNA or protein. SOD-1 mRNA expression was less in Sol 2A arterioles (31%) and 3A arterioles (29%) of HLU rats. SOD-1 protein content was less in Sol FA (67%) but not arterioles. SOD-1 mRNA and protein content were not decreased in arteries from Gast. These data indicate that HLU decreases endothelium-dependent vasodilation, eNOS expression, and SOD-1 expression primarily in arteries of Sol muscle where blood flow is reduced during HLU.

NASA Discipline Cardiopulmonary↗

Characteristics of the Shuttle Orbiter Leeside Flow During A Reentry Condition

A study of the leeside flow characteristics of the Shuttle Orbiter is presented for a reentry flight condition. The flow is computed using a point-implicit, finite-volume scheme known as the Langley Aerothermodynamic Upwind Relaxation Algorithm (LAURA). LAURA is a second-order accurate, laminar Navier-Stokes solver, incorporating finite-rate chemistry with a radiative equilibrium wall temperature distribution and finite-rate wall catalysis. The resulting computational solution is analyzed in terms of salient flow features and the surface quantities are compared with flight data.

Kleb, William L.↗

Evolution of the vestibulo-ocular system

The evolutionary and developmental changes in the eye muscle innervation, the inner ear, and the vestibulo-ocular reflex are examined. Three eye muscle patterns, based on the innervation by distinct ocular motoneurons populations, can be identified: a lamprey, an elasmobranch, and a bony fish/tetrapod pattern. Four distinct patterns of variation in the vestibular system are described: a hagfish pattern, a lamprey pattern, an elasmobranch pattern, and a bony fish/tetrapod pattern. Developmental data suggest an influence of the hindbrain on ear pattern formation, thus potentially allowing a concomitant change of eye muscle innervation and ear variation. The connections between the ear and the vestibular nuclei and between the vestibular nuclei and ocular motoneurons are reviewed, and the role of neurotrophins for pattern specification is discussed. Three patterns are recognized in central projections: a hagfish pattern, a lamprey pattern, and a pattern for jawed vertebrates. Second-order connections show both similarities and differences between distantly related species such as lampreys and mammals. For example, elasmobranchs lack an internuclear system, which is at best poorly developed in lampreys. It is suggested that the vestibulo-ocular system shows only a limited degree of variation because of the pronounced functional constraints imposed on it.

Non-NASA Center↗

Coupling of fingertip somatosensory information to head and body sway

Light touch contact of a fingertip with a stationary surface can provide orientation information that enhances control of upright stance. Slight changes in contact force at the fingertip provide sensory cues about the direction of body sway, allowing attenuation of sway. In the present study, we asked to which extent somatosensory cues are part of the postural control system, that is, which sensory signal supports this coupling? We investigated postural control not only when the contact surface was stationary, but also when it was moving rhythmically (from 0.1 to 0.5 Hz). In doing so, we brought somatosensory cues from the hand into conflict with other parts of the postural control system. Our focus was the temporal relationship between body sway and the contact surface. Postural sway was highly coherent with contact surface motion. Head and body sway assumed the frequency of the moving contact surface at all test frequencies. To account for these results, a simple model was formulated by approximating the postural control system as a second-order linear dynamical system. The influence of the touch stimulus was captured as the difference between the velocity of the contact surface and the velocity of body sway, multiplied by a coupling constant. Comparison of empirical results (relative phase, coherence, and gain) with model predictions supports the hypothesis of coupling between body sway and touch cues through the velocity of the somatosensory stimulus at the fingertip. One subject, who perceived movement of the touch surface, demonstrated weaker coupling than other subjects, suggesting that cognitive mechanisms introduce flexibility into the postural control scheme.

NASA Discipline Neuroscience↗

A dynamical model for reflex activated head movements in the horizontal plane

We present a controls systems model of horizontal-plane head movements during perturbations of the trunk, which for the first time interfaces a model of the human head with neural feedback controllers representing the vestibulocollic (VCR) and the cervicocollic (CCR) reflexes. This model is homeomorphic such that model structure and parameters are drawn directly from anthropomorphic, biomechanical and physiological studies. Using control theory we analyzed the system model in the time and frequency domains, simulating neck movement responses to input perturbations of the trunk. Without reflex control, the head and neck system produced a second-order underdamped response with a 5.2 dB resonant peak at 2.1 Hz. Adding the CCR component to the system dampened the response by approximately 7%. Adding the VCR component dampened head oscillations by 75%. The VCR also improved low-frequency compensation by increasing the gain and phase lag, creating a phase minimum at 0.1 Hz and a phase peak at 1.1 Hz. Combining all three components (mechanics, VCR and CCR) linearly in the head and neck system reduced the amplitude of the resonant peak to 1.1 dB and increased the resonant frequency to 2.9 Hz. The closed loop results closely fit human data, and explain quantitatively the characteristic phase peak often observed.

NASA Discipline Neuroscience↗

The Parametrized Post-Newtonian Gravitational Redshift

A derivation of the gravitational redshift effect to order c ^(-4) is presented. The calculation isperformed within the framework of the parametrized post-Newtonian formalism for analyzing metrictheories of gravity, which includes corrections to second- order in the Newtonian potential,gravitomagnetic contributions, and preferred-frame terms. We briefly discuss how to generalize ourresults to include possible violations of local Lorentz invariance or local position invariance which canarise in nonmetric theories. Our results are useful for analyzing possible new redshift experimentswhich may be sensitive to second-order effects, such as a close solar flyby mission.

Krisher, T. P.↗

The Effects of Noise on Polarimetric SAR Data

Polarimetric SAR data can provide a great deal of information about the scattering behavior of the surface under observation. Polarimetric SAR systems often measure the scattering matrices of the areas under observation in linear polarizations (H and V). From the scattering matrix commonly used forms such as the covariance matrix and the Stokes matrix can be easily derived. Other measures derived from polarimetric SAR data include correlation coefficients between scattering matrix terms and the mode and variance of phase differences between scattering matrix terms. The effects of additive system noise on these measurements is not often considered in the literature on this subject. In this paper, the effects of additive system noise on measurements derived from polarimetric SAR data will be examined. It will be shown how first-order noise effects can be removed and how second-order noise effects can be reduced for some measurements...

Freeman, A.↗

A Parallel Incompressible Navier-Stokes Solver with Multigrid Iterations

We developed a parallel, numerically accurate and stable, and computationally efficient finate-difference incompressible Navier-Stokes (N-S) fluid flow solver. The solver runs on both sequential and massively parallel computers. The numerical method used here is a second-order projection method on a staggered grid. The code is highly modular and it can be used either as a stand-alone flow solver and or a template code which can be adapted or expanded to a specific application. Numerical results and parallel performances of our code on Intel Delta and Paragon are reported.

Navier-Stokes solver↗

Method for suppressing noise in measurements

Techniques of combining separate but correlated measurements to form a second-order or higher order correlation function to suppress the effects of noise in the initial condition of a system capable of retaining memory of an initial state of the system with a characteristic relaxation time. At least two separate measurements are obtained from the system. The temporal separation between the two separate measurements is preferably comparable to or less than the characteristic relaxation time and is adjusted to allow for a correlation between two measurements.

Carson, Paul J.↗

Resonance Cases and Small Divisors in a Third Integral of Motion

In this paper a general discussion of the resonance cases in an axially-symmetric potential field is presented, when the unperturbed frequencies in the radial and z direction have a rational ratio. The general form of the third integral is not valid in these cases because of the appearance of divisors of the form (m(exp 2)P-n(exp 2)Q), which become zero in the resonance cases. However, a new isolating integral of the unperturbed case is available, and this can be used to construct a third integral in the form of a power series and eliminate all secular terms. Three cases are distinguished, (alpha) m+n>4, (beta) m+n=4, and (gamma) m+n<4. In the first case the orbits are rather similar to those of the general irrational case. In the third case th e orbits show a quite peculiar character, which, however, can be explained rather accurately by a first-order theory of the third integral. Numerical integrations were made for the cases P=16Q, 4P=9Q, and P=4Q. The third integral, given in first- or second-order approximation, is rather well conserved. Case beta and the cases of small divisors, when m(exp 2)P-n(exp 2)Q is near zero but not equal to zero, are discussed in Paper II.

Contopoulos, George↗

An analysis of digital phase-locked loops

This report focuses on second-order digital phase-locked loops (DPLLs) with uniformly sampled input, an amplitude-insenstive phase extractor and a conventional loop filter.

Thomas, J. B.↗

Higher-Order Ionospheric Effects on the GPS Observables and Means of Modeling Them

Based on realistic modeling of the electron density of the ionosphere and using a dipole moment approximation for the earth magnetic field, we are able to estimate the effect of the ionosphere on the GPS signal for a ground user. Our study implies reduction of the second-order ionospheric error to less than 2 mm on the average and, therefore, potential improvement of orbit determination and baseline solutions.

ionosphere↗

Resolution requirements for high-speed droplet impact along a rigid wall

The mechanical and thermal loads that are produced on high-speed projectiles from a droplet are key in the projectile development.To accurately predict the pressure produced along the wall surface during impact, it is important to correctly model the air/water interface of the droplet. Novel modeling approaches such as the Phase-Field enable control of the (numerical) interface thickness. However, the interplay between the grid resolution (including potential adaptive mesh refinement) and the interface thickness is unclear. In this work, the resolution requirements for numerical simulations of a two-dimensional cylindrical water droplet impacting a rigid wall at Mach four are computationally investigated. Numerical simulations are performed using a second-order accurate scheme with adaptive mesh refinement and a Phase-Field interface model. The choice of numerical interface thickness and resolution parameters affects the maximum pressure and location of the maximum pressure along the wall. The overall maximum pressure does not converge even at high resolutions. The number of levels and thickness (number of cells across the interface) play a role in obtaining a well behaved solution.

Burrell, E.↗