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At least 505 records · Page 28

Predicting functional divergence in protein evolution by site-specific rate shifts

Most modern tools that analyze protein evolution allow individual sites to mutate at constant rates over the history of the protein family. However, Walter Fitch observed in the 1970s that, if a protein changes its function, the mutability of individual sites might also change. This observation is captured in the "non-homogeneous gamma model", which extracts functional information from gene families by examining the different rates at which individual sites evolve. This model has recently been coupled with structural and molecular biology to identify sites that are likely to be involved in changing function within the gene family. Applying this to multiple gene families highlights the widespread divergence of functional behavior among proteins to generate paralogs and orthologs.

Review↗

Line strengths, collision strengths and excitation rates for multiply-charged silicon ions

In the present paper, the line strengths, collision strengths, and rate coefficients are calculated for a variety of transitions in multiply charged silicon ions from Si(VI) to Si(XIV). The line strengths are obtained by using Clementi wave functions for the ground-state configuration, and excited-state wave functions generated by a semiempirical method. The collision strengths are calculated in an LS coupling scheme in the distorted-wave approximation, neglecting exchange except for the helium-like transitions. These results are then integrated over a Maxwellian velocity distribution function to yield rate coefficients. The rates are presented graphically and also in terms of a two-parameter fit.

Davis, J.↗

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↗

Microscopic Foundation and Simulation of Coupled Carrier-Temperature Diffusions in Semiconductor Lasers

A typical semiconductor-based optoelectronic device, such as a diode laser, consists of three subsystems: an optical field, an electron-hole plasma (EHP), and a host crystal lattice. The physics of such a device involves the interplay of optical, electrical and thermal processes. A proper description of such a device requires that all three processes are treated on equal footing and in a self-consistent fashion. Furthermore, since a semiconductor laser has intrinsic spatial inhomogeneity, such a self-consistency naturally leads to a set of partial differential equations in space and time. There is a significant lacking of research interest and results on the transport aspects of optical devices in the literature with only a few exceptions. Even the most important carrier diffusion coefficient has not been properly derived and studied so far for optically excited plasma, while most of the work adopted results from electronics community where heavily doped semiconductors with mainly one type of carriers are dealt with. The corresponding transport equation for plasma energy or temperature has received even less attention. In this talk we describe our recent results on such a self-consistent derivation of temperature and carrier-density diffusion equations coupled with the lasing process. Starting from the microscopic semiconductor Bloch equations (SBEs) including the Boltzmann transport terms in the distribution function equations for electrons and holes, we derived a closed set of diffusion equations for carrier densities and temperatures with self-consistent coupling to Maxwell's equation and to an effective optical polarization equation. The coherent many-body effects are included within the screened Hartree-Fock approximation, while scatterings are treated within the second Born approximation including both the in- and out-scatterings. Microscopic expressions for electron-hole (e-h) and carrier-LO (c-LO) phonon scatterings are directly used to derive the momentum and energy relaxation rates. These rates expressed as functions of temperatures and densities lead to microscopic expressions for self- and mutual-diffusion coefficients in the coupled density-temperature diffusion equations. Approximations for reducing the general two-component description of the electron-hole plasma (EHP) to a single-component one are discussed. In particular, we show that a special single-component reduction is possible when e-h scattering dominates over c-LO phonon scattering. The ambipolar diffusion approximation is also discussed and we show that the ambipolar diffusion coefficients are independent of e-h scattering, even though the diffusion coefficients of individual components depend sensitively on the e-h scattering rates. Our discussions lead to new perspectives into the roles played in the single-component reduction by the electron-hole correlation in momentum space induced by scatterings and the electron-hole correlation in real space via internal static electrical field. Finally, the theory is completed by coupling the diffusion equations to the lattice temperature equation and to the effective optical polarization which in turn couples to the laser field. The equations derived above are implemented in various limiting cases to a typical diode laser to study the consequences of nonlinear diffusion and the cross diffusion terms on laser behavior, especially the dynamic behavior of a diode laser under modulation. Detailed results will be presented by comparing with the standard rate equation results.

Li, J.↗

Design of an Event-Driven Random-Access-Windowing CCD-Based Camera

Commercially available cameras are not design for the combination of single frame and high-speed streaming digital video with real-time control of size and location of multiple regions-of-interest (ROI). A new control paradigm is defined to eliminate the tight coupling between the camera logic and the host controller. This functionality is achieved by defining the indivisible pixel read out operation on a per ROI basis with in-camera time keeping capability. This methodology provides a Random Access, Real-Time, Event-driven (RARE) camera for adaptive camera control and is will suited for target tracking applications requiring autonomous control of multiple ROI's. This methodology additionally provides for reduced ROI read out time and higher frame rates compared to the original architecture by avoiding external control intervention during the ROI read out process.

event driven↗

LSPRAY-V: A Lagrangian Spray Module

LSPRAY-V is a Lagrangian spray solver developed for application with unstructured grids and massively parallel computers. It is mainly designed to predict the flow, thermal and transport properties of a rapidly vaporizing spray encountered over a wide range of operating conditions in modern aircraft engine development. It could easily be coupled with any existing gas-phase flow and/or Monte Carlo Probability Density Function (PDF) solvers. The manual provides the user with an understanding of various models involved in the spray formulation, its code structure and solution algorithm, and various other issues related to parallelization and its coupling with other solvers. With the development of LSPRAY-V, we have advanced the state-of-the-art in spray computations in several important ways.

CFD↗

Vibration-rotation line shifts for 1 sigma g + H2/V,J/-1S/0/ He computed via close coupling - Temperature dependence

The density shifting of vibration-rotation transitions of H2 perturbed by He was computed (as a function of temperature) with no adjustable parameters. The calculation was carried out using the framework of the impact theory of Baranger with S-matrix elements obtained via close coupling calculations which incorporated the ab initio H2-H2 system potential of Tsapline et al.(1977). Vibrational and rotational inelasticity were neglected in the calculations; nevertheless good agreement with experimental data was obtained, up to moderate temperatures, for the density shift. A much poorer comparison was obtained for the density broadening.

Hahne, G. E.↗

Langmuir Probe Measurements of Inductively Coupled CHF3/Ar and Ar/CHF3/O2 Plasmas

Plasma parameters, such as, electron number density (ne), electron temperature (Te), y electron energy distribution function (EEDF), mean electron energy (Ee), ion number density (ni), and plasma potential (Vp), have been measured by using Langmuir probe in low-pressure (10-50 mTorr) inductively coupled CHF3/Ar and CHF3/Ar/O2 plasmas generated in the GEC cell. The measurements were made at the center of the plasma, keeping the lower electrode grounded, for various CHF3/Ar and Ar/CHF3/O2 mixtures operating at 10-50 mTorr pressures and two input RF power levels, 200 and 300 W. EEDF data show a strong Druyvesteyn distribution with relatively lower number of low energy electrons as compared to a Maxwell distribution and a large electron population with energies higher than the plasma potential. The results further show that at low CHF3 concentrations (less than 50%) the electron number density remains nearly constant with increase in pressure. At higher CHF3 concentrations, however, it decreases with increase in pressure. Plasma potential and electron temperature increase with decrease in pressure and with increase in CHF3 concentration. An analysis of the above observations and mechanisms will be presented.

Sharma, S. P.↗

HFGMC Enhancement of MAC/GMC

Additional information about a mathematical model denoted the high-fidelity generalized method of cells (HFGMC) and implementation of the HFGMC within version 4.0 of the MAC/GMC software has become available. MAC/GMC (Micromechanics Analysis Code With Generalized Method of Cells) was a topic of several prior NASA Tech Briefs articles, version 4.0 having been described in "Comprehensive Micromechanics-Analysis Code - Version 4.0" (LEW-17495-1), NASA Tech Briefs, Vol. 29, No. 9 (September 2005), page 54. MAC/GMC predicts elastic and inelastic thermomechanical responses of composite materials. MAC/GMC utilizes the generalized method of cells (GMC) - a model of micromechanics that predicts macroscopic responses of a composite material as functions of the properties, sizes, shapes, and responses of its constituents (e.g., matrix and fibers). The accuracy of the GMC is limited by neglect of coupling between normal and shear stresses. The HFGMC was developed by combining elements of the GMC and a related model, denoted the higher-order theory for functionally graded materials (HOTFGM), that can account for this coupling. Hence, the HFGMC enables simulation of stress and strain with greater accuracy. Some alterations of the MAC/GMC data structure were necessitated by the greater computational complexity of the HFGMC.

Arnold, Steven M.↗

Electron Impact Excitation of Forbidden and Allowed Transitions in O(II)

The B-spline R-matrix method is used to investigate the electron impact excitation of forbidden and allowed transitions in singly ionized oxygen. The relativistic effects have been incorporated in the Breit-Pauli Hamiltonian. Flexible non-orthogonal sets of radial functions are used to obtain accurate target description and to represent the scattering functions. The 47 fine-structure levels of the 2s(sup 2)2p(sup 3), 2s2p(sup 4), 2s(sup 2)2p(sup 2)3s, 2s(sup 2)2p(sup 2)3p and 2s(sup 2)2p(sup 2)3d configurations have been included in the scattering calculation. A calculation with 62 levels in the close-coupling expansion using the Breit-Pauli R-matrix (BPRM) method with orthogonal radial functions has also been carried out to check electron correlation, relativistic and channel coupling effects. The present results are in good agreement with the previous 16-level BPRM calculation by Montenegro et a1 (2006 J. Phys. B: At. Mol. Opt. Phys. 39 1863-77) for the forbidden transitions, but differ from the 21-level BPRM calculation by McLaughlin and Bell (1998 J. Phys. B: At. Mol. Opt. Phys. 31 4317-29). Our cross sections for the first forbidden (sup 4)S(sup o)-(sup 2)D(sup o)and resonance (sup 4)S(sup o)-2s(sup 2)p(sup 4) (sup 4)P transitions are in reasonably good agreement with the electron energy-loss and merged-beams experiment.

Tayal, S. S.↗

Extension-bend-twist coupling behavior of thin-walled advanced composite beams with initial twist

An analytical model is developed for assessing the extension-bend-twist coupling behavior of nonhomogeneous anisotropic beams with initial twist. The model is formulated as a coupled two-dimensional boundary value problem, where the displacement solutions are defined with pretwist-dependent functions that represent the extension, bending, and torsion, and unknown functions that represent local in-plane deformations and out-of-plane cross-section warping. The unknown deformation functions are determined by applying the principle of minimum potential energy to a discretized representation of the cross section. Numerical results are presented that fully verify this approach and illustrate the strong extension-twist coupling behavior present in pretwisted beams with thin-wall laminated composite cross sections as a function of ply angle, initial twist level, and initial twist axis location. Cross-sections analyzed include; thin laminated rectangles with either asymmetric or symmetric ply stacking sequences and a thin-wall single cell D-section composed of a graphite/epoxy woven cloth.

Kosmatka, J. B.↗

Reliable Spectroscopic Constants for CCH-, NH2- and Their Isotopomers from an Accurate Potential Energy Function

Accurate quartic force fields have been determined for the CCH- and NH2- molecular anions using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, CCSD(T). Very large one-particle basis sets have been used including diffuse functions and up through g-type functions. Correlation of the nitrogen and carbon core electrons has been included, as well as other "small" effects, such as the diagonal Born-Oppenheimer correction, and basis set extrapolation, and corrections for higher-order correlation effects and scalar relativistic effects. Fundamental vibrational frequencies have been computed using standard second-order perturbation theory as well as variational methods. Comparison with the available experimental data is presented and discussed. The implications of our research for the astronomical observation of molecular anions will be discussed.

Lee, Timothy J.↗

Contractile function is unaltered in diaphragm from mice lacking calcium release channel isoform 3

Skeletal muscle expresses at least two isoforms of the calcium release channel in the sarcoplasmic reticulum (RyR1 and RyR3). Whereas the function of RyR1 is well defined, the physiological significance of RyR3 is unclear. Some authors have suggested that RyR3 participates in excitation-contraction coupling and that RyR3 may specifically confer resistance to fatigue. To test this hypothesis, we measured contractile function of diaphragm strips from adult RyR3-deficient mice (exon 2-targeted mutation) and their heterozygous and wild-type littermates. In unfatigued diaphragm, there were no differences in isometric contractile properties (twitch characteristics, force-frequency relationships, maximal force) among the three groups. Our fatigue protocol (30 Hz, 0.25 duty cycle, 37 degrees C) depressed force to 25% of the initial force; however, lack of RyR3 did not accelerate the decline in force production. The force-frequency relationship was shifted to higher frequencies and was depressed in fatigued diaphragm; lack of RyR3 did not exaggerate these changes. We therefore provide evidence that RyR3 deficiency does not alter contractile function of adult muscle before, during, or after fatigue.

Non-NASA Center↗

Vestibular Stochastic Resonance as a Method to Improve Balance Function: Optimization of Stimulus Characteristics

Stochastic resonance (SR) is a mechanism by which noise can assist and enhance the response of neural systems to relevant sensory signals. Application of imperceptible SR noise coupled with sensory input through the proprioceptive, visual, or vestibular sensory systems has been shown to improve motor function. Specifically, studies have shown that that vestibular electrical stimulation by imperceptible stochastic noise, when applied to normal young and elderly subjects, significantly improved their ocular stabilization reflexes in response to whole-body tilt as well as balance performance during postural disturbances. The goal of this study was to optimize the characteristics of the stochastic vestibular signals for balance performance during standing on an unstable surface. Subjects performed a standardized balance task of standing on a block of 10 cm thick medium density foam with their eyes closed for a total of 40 seconds. Stochastic electrical stimulation was applied to the vestibular system through electrodes placed over the mastoid process behind the ears during the last 20 seconds of the test period. A custom built constant current stimulator with subject isolation delivered the stimulus. Stimulation signals were generated with frequencies in the bandwidth of 1-2 Hz and 0.01-30 Hz. Amplitude of the signals were varied in the range of 0- +/-700 micro amperes with the RMS of the signal increased by 30 micro amperes for each 100 micro amperes increase in the current range. Balance performance was measured using a force plate under the foam block and inertial motion sensors placed on the torso and head segments. Preliminary results indicate that balance performance is improved in the range of 10-25% compared to no stimulation conditions. Subjects improved their performance consistently across the blocks of stimulation. Further the signal amplitude at which the performance was maximized was different in the two frequency ranges. Optimization of the frequency and amplitude of the signal characteristics of the stochastic noise signals on maximizing balance performance will have a significant impact in its development as a unique system to aid recovery of function in astronauts after long duration space flight or for people with balance disorders.

Mulavara, Ajitkumar↗

Novel polymers and method of preparing same

Polymers are prepared with terminal functional groups by reacting a compound selected from the group consisting of lithium p-lithiophenoxide and tetrabutylammonium p-lithiophenoxide as an initiator with material such as butadiene. The resulting functionally terminated new polymers are then capable of reacting with coupling agents to form star polymers.

Hirshfield, S. M.↗

An analysis of auroral E region neutral winds based on incoherent scatter radar observations at Chatanika

The physical origin of auroral E-region neutral winds during geomagnetic disturbances is investigated by comparing incoherent-backscatter radar observations made at Chatanika, Alaska, during such disturbances with detailed theoretical calculations of neutral velocities for these conditions. In the analysis, an ion-drag collisional-coupling model is adopted as the primary driving force for the neutral winds. Electric fields and electron number densities observed by the radar facility are used in the calculations, and the coupled ion and neutral momentum equations are solved numerically as functions of altitude and time in the ion-drag approximation. The altitude structure of the velocity field is examined, and the detailed response of the neutral gas to the ion-drag mechanism is delineated. Weighted altitude averages of the calculated velocities are obtained, the accuracy of the procedure for deriving neutral winds from incoherent-scatter radar observations is evaluated, and the comparison is carried out. It is concluded that both ion drag and pressure gradients appear to be required to explain the neutral winds observed in the auroral E-region during geomagnetic disturbances.

Comfort, R. H.↗

A digital computer simulation and study of a direct-energy-transfer power-conditioning system

An investigation of the behavior of the power-conditioning system as a whole is a necessity to ensure the integrity of the aggregate system in the case of space applications. An approach for conducting such an investigation is considered. A description is given of the application of a general digital analog simulator program to the study of an aggregate power-conditioning system which is being developed for use on the International Ultraviolet Explorer spacecraft. The function of the direct energy transfer system studied involves a coupling of a solar array through a main distribution bus to the spacecraft electrical loads.

Burns, W. W., III↗