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At least 577 records · Page 32
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NASA NTRSDate not supplied

REACTER 2.0: Quantum-Informed Reaction Constraints and Automated Interaction Typing

REACTER is a heuristic method for modeling chemical reactions in classical molecular dynamics simulations, implemented in LAMMPS as fix bond/react. The authors recently extended LAMMPS to support alphanumeric labels for atom types, bond types etc., which enables the pre- and post-reaction templates required by the REACTER protocol to be portable between different simulations and greatly simplifies the task of creating simulation-ready reaction templates. To further increase the generality of reaction templates, support for wildcard characters within atom types has been added, along with the automatic assignment of interaction types for new bonds, angles, etc. based on the involved atom types. In some cases, this feature can express a class of reactions with one pair of reaction templates, where previously dozens may have been required. Advanced reaction constraints have also been added, including an Arrhenius constraint to enforce an effective activation energy, a root-mean-square-deviation option for complex geometrical constraints, as well as a custom constraint that leverages LAMMPS’ powerful built-in variable framework. Other new features include variable support for various inputs (e.g., to allow reaction rates or cutoffs to be dependent on overall conversion), on-the-fly update of molecule IDs, and the ability to create new atoms positioned with respect to the reaction site. The new features are applied to modeling polymeric, thermosetting and composite materials, and advanced applications of the new reaction constraints are demonstrated. For example, REACTER is shown to accurately reproduce mechanically-induced bond breaking, as characterized by third-order DFT-based tight-binding (DFTB3) simulations, via a constraint on the total potential energy of the involved atoms.

polymer simulations↗
NASA NTRS2017

Revised Models of Interstellar Nitrogen Isotopic Fractionation

Nitrogen-bearing molecules in cold molecular clouds exhibit a range of isotopic fractionation ratios and these molecules may be the precursors of 15N enrichments found in comets and meteorites. Chemical model calculations indicate that atom-molecular ion and ion-molecule reactions could account for most of the fractionation patterns observed. However, recent quantum-chemical computations demonstrate that several of the key processes are unlikely to occur in dense clouds. Related model calculations of dense cloud chemistry show that the revised 15N enrichments fail to match observed values. We have investigated the effects of these reaction rate modifications on the chemical model of Wirstrom et al. (2012) for which there are significant physical and chemical differences with respect to other models. We have included 15N fractionation of CN in neutral-neutral reactions and also updated rate coefficients for key reactions in the nitrogen chemistry. We find that the revised fractionation rates have the effect of suppressing 15N enrichment in ammonia at all times, while the depletion is even more pronounced, reaching 14N/15N ratios of >2000. Taking the updated nitrogen chemistry into account, no significant enrichment occurs in HCN or HNC, contrary to observational evidence in dark clouds and comets, although the 14N/15N ratio can still be below 100 in CN itself. However, such low CN abundances are predicted that the updated model falls short of explaining the bulk 15N enhancements observed in primitive materials. It is clear that alternative fractionating reactions are necessary to reproduce observations, so further laboratory and theoretical studies are urgently needed.

Wirstrom, E. S.↗
NASA NTRS2012

Large Eddy Simulation (LES) of Particle-Laden Temporal Mixing Layers

High-fidelity models of plume-regolith interaction are difficult to develop because of the widely disparate flow conditions that exist in this process. The gas in the core of a rocket plume can often be modeled as a time-dependent, high-temperature, turbulent, reacting continuum flow. However, due to the vacuum conditions on the lunar surface, the mean molecular path in the outer parts of the plume is too long for the continuum assumption to remain valid. Molecular methods are better suited to model this region of the flow. Finally, granular and multiphase flow models must be employed to describe the dust and debris that are displaced from the surface, as well as how a crater is formed in the regolith. At present, standard commercial CFD (computational fluid dynamics) software is not capable of coupling each of these flow regimes to provide an accurate representation of this flow process, necessitating the development of custom software. This software solves the fluid-flow-governing equations in an Eulerian framework, coupled with the particle transport equations that are solved in a Lagrangian framework. It uses a fourth-order explicit Runge-Kutta scheme for temporal integration, an eighth-order central finite differencing scheme for spatial discretization. The non-linear terms in the governing equations are recast in cubic skew symmetric form to reduce aliasing error. The second derivative viscous terms are computed using eighth-order narrow stencils that provide better diffusion for the highest resolved wave numbers. A fourth-order Lagrange interpolation procedure is used to obtain gas-phase variable values at the particle locations.

Bellan, Josette↗
NASA NTRS2017

Revised Models of Interstellar Nitrogen Isotopic Fractionation

Nitrogen-bearing molecules in cold molecular clouds exhibit a range of isotopic fractionation ratios and these molecules may be the precursors of (15)N enrichments found in comets and meteorites. Chemical model calculations indicate that atom-molecular ion and ion-molecule reactions could account for most of the fractionation patterns observed. However, recent quantum-chemical computations demonstrate that several of the key processes are unlikely to occur in dense clouds. Related model calculations of dense loud chemistry show that the revised (15)N enrichments fail to match observed values. We have investigated the effects of these reaction rate modifications on the chemical model of Wirstrom et al. (2012) for which there are significant physical and chemical differences with respect to other models. We have included (15)N fractionation of CN in neutral-neutral reactions and also updated rate coefficients for key reactions in the nitrogen chemistry. We find that the revised fractionation rates have the effect of suppressing (15)N enrichment in ammonia at all times, while the depletion is even more pronounced, reaching (14)N/(15)N ratios of > 2000. Taking the updated nitrogen chemistry into account, no sigificant enrichment occurs in HCN or HNC, contrary to observational evidence in dark clouds and comets, although the (14)N/(15)N ratio can still be below 100 in CN itself. However, such low CN abundances are predicted that the updated model falls short of explaining the bulk (15)N enhancements observed in primitive materials. It is clear that alternative fractionating reactions are necessary to reproduce observations, so further laboratory and theoretical studies are urgently needed.

Astrochemistry↗
NASA NTRS2009

A Continuum-Atomistic Analysis of Transgranular Crack Propagation in Aluminum

A concurrent multiscale modeling methodology that embeds a molecular dynamics (MD) region within a finite element (FEM) domain is used to study plastic processes at a crack tip in a single crystal of aluminum. The case of mode I loading is studied. A transition from deformation twinning to full dislocation emission from the crack tip is found when the crack plane is rotated around the [111] crystallographic axis. When the crack plane normal coincides with the [112] twinning direction, the crack propagates through a twinning mechanism. When the crack plane normal coincides with the [011] slip direction, the crack propagates through the emission of full dislocations. In intermediate orientations, a transition from full dislocation emission to twinning is found to occur with an increase in the stress intensity at the crack tip. This finding confirms the suggestion that the very high strain rates, inherently present in MD simulations, which produce higher stress intensities at the crack tip, over-predict the tendency for deformation twinning compared to experiments. The present study, therefore, aims to develop a more realistic and accurate predictive modeling of fracture processes.

Yamakov, V.↗
NASA NTRS1994

Using FU Orionis outbursts to constrain self-regulated protostellar disk models

One-dimensional, convective, vertical structure models and one dimensional time-dependent, radial diffusion models are combined to create a self-consistent picture in which FU Orionis outbursts occur in young stellar objects (YSOs) as the result of a large-scale, self-regulated, thermal ionization instability in the surrounding protostellar accretion disk. Although active accretion disks have long been postulated to be ubiqitous among low-mass YSOs, few constraints have until now been imposed on physical conditions in these disks. By fitting the results of time-dependent disk models to observed timescales of FU Orionis events, we estimate the magnitude of the effective viscous stress in the inner disk (r approximately less than 1 AU) to be, in accordance with an ad hoc 'alpha' prescription, the product of the local sound speed, pressure scale height, and an efficiency factor alpha of 10(exp -4) where hydrogen is neutral and 10(exp 3) where hydrogen is ionized. We hypothesize that all YSOs receive infall onto their outer disks which is steady (or slowly declining with time) and that FU Orionis outbursts are self-regulated, disk outbursts which occur only in systems which transport matter inward at a rate sufficiently high to cause hydrogen to be ionized in the inner disk. We estimate a critical mass flux of dm(sub crit)/dt = 5 x 10(exp 7) solar mass/yr independent of the magnitude of alpha for systems with one solar mass, three solar radius central objects. Infall accretion rates in the range of dm(sub in)/dt = 1-10) x 10(exp -6) solar mass/yr produce observed FU Orionis timescales consistent with estimates of spherical molecular cloud core collapse rates. Modeled ionization fronts are typically initiated near the inner edge of the disk and propogate out to a distance of several tens of stellar radii. Beyond this region, the disk transports mass steadily inward at the supplied constant infall rate. Mass flowing through the innermost disk annulus is equal to dm(sub in)/dt only in a time-averaged sense and is regulated by the ionization of hydrogen in the inner disk such that long intervals (approximately 1000 yr) of low-mass flux: (1-30) x 10(exp -8) solar mass/yr are punctuated by short intervals (approximately 100 yr) of high-mass flux: (1-30) x 10(exp -5) solar mass/yr. Timescales and mass fluxes derived for quiescent and outburst stages are consistent with estimates from observations of T Tauri and FU Orionis systems, respectively.

Bell, K. R.↗
NASA NTRS2003

Genetic control of Drosophila nerve cord development

The Drosophila ventral nerve cord has been a central model system for studying the molecular genetic mechanisms that control CNS development. Studies show that the generation of neural diversity is a multistep process initiated by the patterning and segmentation of the neuroectoderm. These events act together with the process of lateral inhibition to generate precursor cells (neuroblasts) with specific identities, distinguished by the expression of unique combinations of regulatory genes. The expression of these genes in a given neuroblast restricts the fate of its progeny, by activating specific combinations of downstream genes. These genes in turn specify the identity of any given postmitotic cell, which is evident by its cellular morphology and choice of neurotransmitter.

Review↗
NASA NTRSDate not supplied

Solid-state Precipitation in Molecular Dynamics: KMC-MD Hybrid Simulations

A critical drawback of molecular dynamics (MD) simulations when modeling physical properties is the limitation to short timescales. Solid state precipitation is one behavior that is not significantly observable at timescales accessible to MD, and thus has been difficult to simulate at an MD scale. Taking inspiration from Kinetic Monte-Carlo (KMC) methods for simulating diffusion on a rigid lattice, we have developed a hybrid KMC-MD approach to enable simulation of solid-state precipitation during MD simulation implemented in LAMMPS. This method incorporates the atomic neighbor hopping behavior utilized by KMC simulations into a MD simulation with a variable local lattice configuration. By accelerating nearest-neighbor atomic hopping with this technique, solid-state precipitation can be observed at an MD timescale. Utilizing theory based on persistent-embryo methods for liquid-solid precipitation in MD we demonstrate the calculation of critical nucleus size for the gamma’ precipitation out of gamma phase in the Ni-Al system.

Molecular Dynamics↗
NASA NTRSDate not supplied

Solid-state Precipitation in Molecular Dynamics: kMC-MD Hybrid Simulations

A critical drawback of molecular dynamics (MD) simulations when modeling physical properties is the limitation to short timescales. Solid state precipitation is one behavior that is not significantly observable at timescales accessible to MD, and thus has been difficult to simulate at an MD scale. Taking inspiration from Kinetic Monte-Carlo (KMC) methods for simulating diffusion on a rigid lattice, we have developed a hybrid KMC-MD approach to enable simulation of solid-state precipitation during MD simulation implemented in LAMMPS. This method incorporates the atomic neighbor hopping behavior utilized by KMC simulations into a MD simulation with a variable local lattice configuration. By accelerating nearest-neighbor atomic hopping with this technique, solid-state precipitation can be observed at an MD timescale. Utilizing theory based on persistent-embryo methods for liquid-solid precipitation in MD we demonstrate the calculation of critical nucleus size for the gamma’ precipitation out of gamma phase in the Ni-Al system.

Molecular Dynamics↗
NASA NTRS1995

One-dimensional hybrid satellite track model for the Dynamics Explorer 2 (DE 2) satellite

A one-dimensional hybrid satellite track model has been developed to calculate the high-latitude thermospheric/ionospheric structure below the satellite altitude using Dynamics Explorer 2 (DE 2) satellite measurements and theory. This model is based on Emery et al. (1985) satellite track code but also includes elements of Roble et al. (1987b) global mean thermosphere/ionosphere model. A number of parameterizations and data handling techniques are used to input satellite data from several DE 2 instruments into this model. Profiles of neutral atmospheric densities are determined from the Mass Spectrometer Incoherent Scatter 1990 (MSIS-90) model and measured neutral temperatures. Measured electron precipitation spectra are used in an auroral model to calculate particle impact ionization rates below the satellite. These rates are combined with a solar ionization rate profile and used to solve the O(+) diffusion equation, with the measured electron density as an upper boundary condition. The calculated O(+) density distribution, as well as the ionization profiles, are then used in a photochemical equilibrium model to calculate the electron and molecular ion densities. The electron temperature is also calculated by solving the electron energy equation with an upper boundary condition determined by the DE 2 measurement. The model enables calculations of altitude profiles of conductivity and Joule heating rate along and below the satellite track. In a first application of the new model, a study is made of thermospheric and ionospheric structure below the DE 2 satellite for a single orbit which occurred on October 25, 1981. The field-aligned Poynting flux, which is independently obtained for this orbit, is compared with the model predictions of the height-integrated energy conversion rate. Good quantitative agreement between these two estimates has been reached. In addition, measurements taken at the incoherent scatter radar site at Chatanika (65.1 deg N, 147.4 deg W) during a DE 2 overflight are compared with the model calculations. A good agreement was found in lower thermospheric conductivities and Joule heating rate.

Deng, Wei↗
NASA NTRS1995

One-Dimensional Hybrid Satellite Track Model for the Dynamics Explorer 2 (DE 2) Satellite

A one-dimensional hybrid satellite track model has been developed to calculate the high-latitude thermospheric/ionospheric structure below the satellite altitude using Dynamics Explorer 2 (DE 2) satellite measurements and theory. This model is based on Emery et al. satellite track code but also includes elements of Roble et al. global mean thermosphere/ionosphere model. A number of parameterizations and data handling techniques are used to input satellite data from several DE 2 instruments into this model. Profiles of neutral atmospheric densities are determined from the MSIS-90 model and measured neutral temperatures. Measured electron precipitation spectra are used in an auroral model to calculate particle impact ionization rates below the satellite. These rates are combined with a solar ionization rate profile and used to solve the O(+) diffusion equation, with the measured electron density as an upper boundary condition. The calculated O(+) density distribution, as well as the ionization profiles, are then used in a photochemical equilibrium model to calculate the electron and molecular ion densities. The electron temperature is also calculated by solving the electron energy equation with an upper boundary condition determined by the DE 2 measurement. The model enables calculations of altitude profiles of conductivity and Joule beating rate along and below the satellite track. In a first application of the new model, a study is made of thermospheric and ionospheric structure below the DE 2 satellite for a single orbit which occurred on October 25, 1981. The field-aligned Poynting flux, which is independently obtained for this orbit, is compared with the model predictions of the height-integrated energy conversion rate. Good quantitative agreement between these two estimates has been reached. In addition, measurements taken at the incoherent scatter radar site at Chatanika (65.1 deg N, 147.4 deg W) during a DE 2 overflight are compared with the model calculations. A good agreement was found in lower thermospheric conductivities and Joule heating rate.

Deng, Wei↗
NASA NTRS1995

Thermal Balance in Dense Molecular Clouds: Radiative Cooling Rates and Emission-Line Luminosities

We consider the radiative cooling of fully shielded molecular astrophysical gas over a wide range of temperatures ( 10 K < T < 2500 K) and H2 densities ( 10(exp 3)/cc < n(H2) < 10(exp 10)/cc). Our model for the radiative cooling of molecular gas includes a detailed treatment of the interstellar chemistry that determines the abundances of important coolant molecules, and a detailed treatment of the excitation of the species H2, CO, H2O, HCl, O2, C, O, and their isotopic variants where important. We present results for the total radiative cooling rate and for the cooling rate due to individual coolant species, as a function of the gas temperature, density, and optical depth. We have also computed the individual millimeter, submillimeter, and far-infrared line strengths that contribute to the total radiative cooling rate, and we have obtained example spectra for the submillimeter emission expected from molecular cloud cores. Many of the important cooling lines will be detectable using the Infrared Space Observatory and the Submillimeter Wave Astronomy Satellite.

Neufeld, David A.↗
NASA NTRS2004

Tissue Engineering and Cellular Regeneration at NASA Report to Regenetech SAB

A project overview describing three dimensional tissue models is shown. The topics include: 1) cellular regeneration; 2) haemopoietic replacement; 3) novel vaccine development; 4) pharmacology and toxicology interventions; 5) development of synthetic viruses; and 6) molecular genetics and proteomics of recapitulated models.

Goodwin, Thomas J.↗
NASA NTRS1992

Experimental dehydration of natural obsidian and estimation of DH2O at low water contents

Water diffusion experiments were carried out by dehydrating rhyolitic obsidian from Valles Caldera (New Mexico, USA) at 510-980 degrees C. The starting glass wafers contained approximately 0.114 wt% total water, lower than any glasses previously investigated for water diffusion. Weight loss due to dehydration was measured as a function of experiment duration, which permits determination of mean bulk water diffusivity, mean Dw. These diffusivities are in the range of 2.6 to 18 X 10(-14) m2/s and can be fit with the following Arrhenius equation: ln mean Dw (m2/s) = -(25.10 +/- 1.29) - (46,480 +/- 11,400) (J/mol) / RT, except for two replicate runs at 510 degrees C which give mean Dw values much lower than that defined by the above equation. When interpreted according to a model of water speciation in which molecular H2O is the diffusing species with concentration-independent diffusivity while OH units do not contribute to the transport but react to provide H2O, the data (except for the 510 degrees C data) are in agreement with extrapolation from previous results and hence extend the previous data base and provide a test of the applicability of the model to very low water contents. Mean bulk water diffusivities are about two orders of magnitude less than molecular H2O diffusivities because the fraction of molecular H2O out of total water is very small at 0.114 wt% total water and less. The 510 degrees C experimental results can be interpreted as due to slow kinetics of OH to H2O interconversion at low temperatures.

NASA Program Exobiology↗
NASA NTRS1969

Dipole properties of molecular hydrogen.

Molecular hydrogen electron scattering, optical refractivity and molecular anisotropy used to construct model dipole spectrum consistent with oscillator strength rules

Dalgarno, A.↗