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At least 397 records · Page 22

Better, Cheaper, Faster Molecular Dynamics

Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.

Pohorille, Andrew↗

High-temperature properties of gases

Computational chemistry is being applied at NASA Ames Research Center to a variety of problems in chemistry, physics, and materials sciences. Supercomputers and modern computational chemistry techniques have provided a powerful new tool to help fill NASA's continuing need for information about the properties of gases and materials as well as their interaction. For example, radiative transition probabilities, spectroscopic constants, bond dissociation energies, transport properties, and chemical reaction rates for molecules can be determined computationally just as reliably as by experiment. Recent results on the radiative transition probabilities of the strongly radiating systems of air species, based on state-of-the-art computational chemistry calculations, are presented and compared with experimental data.

Cooper, David M.↗

Impact of Universal Plasma and Energetic Particle Processes on Icy Bodies of the Kuiper Belt and the Oort Cloud

Modeling of space plasma and energetic particle interactions with icy bodies of the outer solar system is simplified when there is commonality of the underlying source, acceleration, and transport processes in spatially distinct regions from the supersonic heliosphere through the heliosheath into the local interstellar medium (LISM). Current trends in the Voyager heliosheath measurements suggest strong commonality to processes in the LISM. The Fisk-Gloeckler "universal" spectrum at suprathermal energies apparently plays a strong role in coupling the plasma and high energy particle regimes in the spatial and energetic transitions from the outer heliosphere to the LISM. Dominant processes in consecutive energy regimes project to varying effects versus irradiation depth on exposed upper surfaces of airless small icy bodies and to upper atmospheres of larger bodies such as Titan and Pluto. Relative absence of the universal suprathermal spectrum in the mid-heliospheric region of the classical Kuiper Belt may profoundly affect surface color diversity of icy bodies in this region.

Cooper, John F.↗

Analytic Method to Estimate Particle Acceleration in Flux Ropes

The mechanism that accelerates particles to the energies required to produce the observed high-energy emission in solar flares is not well understood. Drake et al. (2006) proposed a kinetic mechanism for accelerating electrons in contracting magnetic islands formed by reconnection. In this model, particles that gyrate around magnetic field lines transit from island to island, increasing their energy by Fermi acceleration in those islands that are contracting. Based on these ideas, we present an analytic model to estimate the energy gain of particles orbiting around field lines inside a flux rope (2.5D magnetic island). We calculate the change in the velocity of the particles as the flux rope evolves in time. The method assumes a simple profile for the magnetic field of the evolving island; it can be applied to any case where flux ropes are formed. In our case, the flux-rope evolution is obtained from our recent high-resolution, compressible 2.5D MHD simulations of breakout eruptive flares. The simulations allow us to resolve in detail the generation and evolution of large-scale flux ropes as a result of sporadic and patchy reconnection in the flare current sheet. Our results show that the initial energy of particles can be increased by 2-5 times in a typical contracting island, before the island reconnects with the underlying arcade. Therefore, particles need to transit only from 3-7 islands to increase their energies by two orders of magnitude. These macroscopic regions, filled with a large number of particles, may explain the large observed rates of energetic electron production in flares. We conclude that this mechanism is a promising candidate for electron acceleration in flares, but further research is needed to extend our results to 3D flare conditions.

Energetic particle acceleration↗

Vibration-translation energy transfer in anharmonic diatomic molecules. I - A comparative evaluation of the semiclassical approximation

The semiclassical approximation (quantum oscillator, classical path) is applied to anharmonic diatomic oscillators in excited initial states. Multistate numerical solutions giving the vibrational transition probabilities for collinear collisions with an inert atom are compared with equivalent, exact quantum-mechanical calculations. Several symmetrization methods are shown to correlate accurately the predictions of both theories for all initial states, transitions, and molecular types tested, but only if coupling of the oscillator motion and the classical trajectory of the incident particle is considered. In anharmonic heteronuclear molecules, the customary semiclassical method of computing the classical trajectory independently leads to transition probabilities with anomalous low-energy resonances. Proper accounting of the effects of oscillator compression and recoil on the incident particle trajectory removes the anomalies and restores the applicability of the semiclassical approximation.

Mckenzie, R. L.↗

The chromosphere and transition region

The physical processes occurring as a result of the transfer of energy and momentum from the primary solar flare energy release site in the corona to the underlying chromosphere and transition region during the course of the flare are investigated through a comparison of theoretical models and observational data. Static, dynamic and hydrodynamic models of the lower-temperature chromospheric flare are reviewed. The roles of thermal conduction, radiation, fast particles and mass motion in chromosphere-corona interactions are analyzed on the basis of Skylab UV, EUV and X-ray data, and empirical and synthetic models of the chromospheric and upper photospheric responses to flares are developed. The canonical model of chromospheric heating during flares as a result of primary energy release elsewhere is found to be justified in the chromosphere as a whole, although not entirely as the temperature minimum, and a simplified model of horizontal chromospheric flare structure based on results obtained is presented.

Canfield, R. C.↗

The effect of thickness on fatigue crack propagation in 7475-T731 aluminum alloy sheet

Tests were conducted on three thicknesses of 7475-T731 aluminum alloy sheet to investigate the effect of thickness on fatigue crack propagation under constant amplitude loading conditions and on retardation following a single peak overload. Constant amplitude loading tests were performed at stress ratios of 0.05 and 0.75 to obtain data for conditions with crack closure and without crack closure, respectively. At both stress ratios a thickness effect was clearly evident, with thicker specimens exhibiting higher growth rates in the transition from plane strain to plane stress region. The effect of thickness for a stress ratio of 0.05 corresponded well with the fracturing mode transitions observed on the specimens. A model based on the strain energy release rate which accounted for the fracture mode transition was found to correlate the thickness effects well. The specimens tested at the stress ratio of 0.75 did not make the transition from tensile mode to shear mode, indicating that another mechanism besides crack closure or fracture mode transition was active.

Daiuto, R. A.↗

Atomic Data and Spectral Line Intensities for CA XVII

Electron impact collision strengths, energy levels, oscillator strengths and spontaneous radiative decay rates are calculated for Ca XVII. The configurations used are 2s(sup 2), 2s2p, 2p(sup 2), 2l3l', 214l' and 2s5l', with l = s,p and l' = s,p, d giving rise to 92 fine-structure levels in intermediate coupling. Collision strengths are calculated at seven incident energies (15, 30, 75, 112.5, 150, 187.5 and 225 Ry) for the transitions within the three lowest configurations corresponding to the 10 lowest energy levels, and five incident energies (75, 112.5, 150, 187.5 and 225 Ry) for transitions between the lowest five levels and the n = 3,4,5 configurations. Calculations have been carried out using the distorted wave approximation. Excitation rate coefficients are calculated as a function of electron temperature by assuming a Maxwellian electron velocity distribution. Using the excitation rate coefficients and the radiative transition rates of the present work, and R-Matrix results for the 2s2, 2s2p, 2p2 configurations available in the literature, statistical equilibrium equations for level populations are solved at electron densities covering the range of 10(exp 8)-10(exp 14)/cu cm at an electron temperature of log Te(K)=6.7, corresponding to the maximum abundance of Ca XVII. Spectral line intensities are calculated, and their diagnostic relevance L; discussed. This dataset will be made available in the next version of the CHIANTI database.

Bhatia, A.K.↗

Relativistic electron transport and bremsstrahlung production in solar flares

A Monte Carlo simulation of ultrarelativistic electron transport in solar flare magnetic loops has been developed. It includes Coulomb, synchrotron, and bremsstrahlung energy losses; pitch-angle scattering by Alfven and whistler turbulence in the coronal region of the loop; and magnetic mirroring in the converging magnetic flux tubes beneath the transition region. Depth distributions, time profiles, energy spectra, and angular distributions of the resulting bremsstrahlung emission are calculated. It is found that both the preferential detection of solar flares with greater than 10 MeV emission near the limb of the sun and the observation of ultrarelativistic electron bremsstrahlung from flares on the disk are consequences of the loop transport model. The declining portions of the observed time profiles of greater than 10 MeV emission from solar flares can also be accounted for, and it is proposed that these portions are determined by transport and not acceleration.

Miller, James A.↗

System Identification of X-33 Neural Network

Modern flight control research has improved spacecraft survivability as its goal. To this end we need to have a failure detection system on board. In case the spacecraft is performing imperfectly, reconfiguration of control is needed. For that purpose we need to have parameter identification of spacecraft dynamics. Parameter identification of a system is called system identification. We treat the system as a black box which receives some inputs that lead to some outputs. The question is: what kind of parameters for a particular black box can correlate the observed inputs and outputs? Can these parameters help us to predict the outputs for a new given set of inputs? This is the basic problem of system identification. The X33 was supposed to have the onboard capability of evaluating the current performance and if needed to take the corrective measures to adapt to desired performance. The X33 is comprised of both rocket and aircraft vehicle design characteristics and requires, in general, analytical methods for evaluating its flight performance. Its flight consists of four phases: ascent, transition, entry and TAEM (Terminal Area Energy Management). It spends about 200 seconds in ascent phase, reaching an altitude of about 180,000 feet and a speed of about 10 to 15 Mach. During the transition phase which lasts only about 30 seconds, its altitude may increase to about 190,000 feet but its speed is reduced to about 9 Mach. At the beginning of this phase, the Main Engine is Cut Off (MECO) and the control is reconfigured with the help of aerosurfaces (four elevons, two flaps and two rudders) and reaction control system (RCS). The entry phase brings down the altitude of X33 to about 90,000 feet and its speed to about Mach 3. It spends about 250 seconds in this phase. Main engine is still cut off and the vehicle is controlled by complex maneuvers of aerosurfaces. The last phase TAEM lasts for about 450 seconds and the altitude and speed, both are reduced to zero. The present attempt, as a start, focuses only on the entry phase. Since the main engine remains cut off in this phase, there is no thrust acting on the system. This considerably simplifies the equations of motion. We introduce another simplification by assuming the system to be linear after some non-linearities are removed analytically from our consideration. Under these assumptions, the problem could be solved by Classical Statistics by employing the least sum of squares approach. Instead we chose to use the Neural Network method. This method has many advantages. It is modern, more efficient, can be adapted to work even when the assumptions are diluted. In fact, Neural Networks try to model the human brain and are capable of pattern recognition.

Aggarwal, Shiv↗

Ultrasonic investigation of the superconducting properties of the Nb-Mo system

The superconducting properties of single crystals of Nb and two alloys of Nb with Mo were investigated by ultrasonic techniques. The results of measurements of the ultrasonic attenuation and velocities as a function of temperature, Mo composition, crystallographic direction, and ultrasonic frequency are reported. The attenuation and small velocity changes associated with the superconductivity of the samples are shown to be dependent on the sample resistivity ratio which varied from 4.3 for Nb-9% Mo to 6500 for pure Nb. The ultrasonic attenuation data are analyzed in terms of the superconducting energy gap term of the BCS theory. A new model is proposed for the analysis of ultrasonic attenuation in pure superconductors with two partially decoupled energy bands. To analyze the attenuation in pure superconducting Nb, the existence of two energy gaps was assumed to be associated with the two partially decoupled energy bands. One of the gaps was found to have the normal BCS value of 3.4 and the other gap was found to have the anomalously large value of 10. No experimental evidence was found to suggest that the second energy gap had a different transition temperature. The interpretation of the results for the Nb-Mo alloys is shown to be complicated by the possible existence of a second superconducting phase in Nb-Mo alloys with a transition temperature of 0.35 of the transition temperature of the first phase. The elastic constants of Nb and Nb-Mo alloys are shown to be approximately independent of Mo composition to nine atomic percent Mo. These results do not agree with the current microscopic theory of transition temperature for the transition elements.

Lacy, L. L.↗

Deformed Brueckner-Hartree-Fock calculations

The renormalized Brueckner-Hartree-Fock (RBHF) theory for many-body nuclear systems is generalized to permit calculations for intrinsic states having permanent deformation. Both Hartree-Fock and Brueckner self-consistencies are satisfied, and details of the numerical techniques are discussed. The Hamada-Johnston interaction is used in a study of deformations, binding, size, and separation energies for several nuclei. Electromagnetic transition rates, moments, and electron scattering form factors are calculated using nuclear wave functions obtained by angular momentum projection. Comparison is made to experiment as well as to predictions of ordinary and density-dependent Hartree-Fock Theory.

Ford, W. F.↗

Deformed Brueckner-Hartree-Fock calculations.

The renormalized Brueckner-Hartree-Fock (RBHF) theory for many-body nuclear systems has been generalized to permit calculations for intrinsic states having permanent deformation. Both Hartree-Fock and Brueckner self-consistencies are satisfied, and details of the numerical techniques are discussed. The Hamada-Johnston interaction is used in a study of deformations, binding, size, and separation energies for several nuclei. Electromagnetic transition rates, moments, and electron scattering form factors are calculated using nuclear wave functions obtained by angular momentum projection. Comparison is made to experiment as well as to predictions of ordinary and density-dependent Hartree-Fock theory.

Ford, W. F.↗

O2/1-Sigma sub g/+// relaxation in collisions - Temperature dependence of the interaction with HBr

Rate constants for the quenching of O2(1-Sigma sub g(+)) in the temperature range 170-400 K were obtained by observing the change in the rate of decay of this oxygen emission as a function of HBr concentration. At each temperature the decay was observed at eight different HBr concentrations ranging from 0 to 6 x 10 to the -6th moles/l. It is found that long range multipolar interactions make a major contribution to the quenching of the oxygen molecule by H2, with the quenching shown to be most effective at low temperatures. Short range repulsive interactions may also contribute to the quenching process, especially at high temperatures. The suggestion that the quenching process is dominated by the ability of the quencher to take up the energy of the oxygen molecule transition in vibrational and rotational motion is confirmed.

Braithwaite, M.↗

Electronic states of Zn2 - Ab initio calculations of a prototype for Hg2

The electronic states of Zn2 are investigated by ab initio polarization configuration-interaction calculations. Molecular states dissociating to Zn(1S) + Zn(1S, 3P, 1P) and Zn(3P) + Zn(3P) are treated. Important effects from states arising from Zn(+)(25) + Zn(-)(2P) are found in the potential-energy curves and electronic-transition moments. A model calculation for Hg2 based on the Zn2 curves and including spin-orbit coupling leads to a new interpretation of the emission bands in Hg vapor.

Hay, P. J.↗