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At least 955 records · Page 53
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Molecular Dynamics Simulation of Pore-Size Effects on Gas Adsorption Kinetics in Zeolites

Strong gas-mineral interactions or slow adsorption kinetics require a molecular-level understanding of both adsorption and diffusion for these interactions to be properly described in transport models. In this combined molecular simulation and experimental study, noble gas adsorption and mobility is investigated in two naturally abundant zeolites whose pores are similar in size (clinoptilolite) and greater than (mordenite) the gas diameters. Simulated adsorption isotherms obtained from grand canonical Monte Carlo simulations indicate that both zeolites can accommodate even the largest gas (Rn). However, gas mobility in clinoptilolite is significantly hindered at pore-limiting window sites, as seen from molecular dynamics simulations in both bulk and slab zeolite models. Further, experimental gas adsorption isotherms for clinoptilolite confirm the presence of a kinetic barrier to Xe uptake, resulting in the unusual property of reverse Kr/Xe selectivity. Finally, a kinetic model is used to fit the simulated gas loading profiles, allowing a comparison of trends in gas diffusivity in the zeolite pores.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Coulomb field correction due to virtual $e$ + $e$ - production in heavy ion collisions

The correction to the Coulomb energy due to virtual production of $e$ + $e$ - pairs, which is on the order of one percent of the Coulomb energy at nuclear scales is discussed. The effects of including a pair-production term in the semi-empirical mass formula and the correction to the Coulomb barrier for a handful of nuclear collisions using the Bass and Coulomb potentials are studied. Furthermore, with an eye toward future work using Constrained Molecular Dynamics (CoMD) model, we also calculate the correction to the Coulomb energy and force between protons after folding with a Gaussian spatial distribution.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1986

Numerical studies of collapsing interstellar clouds

Numerical simulation of the structure and evolution of interstellar clouds was initiated. Steps were taken toward an integrated treatment of the dynamical, thermal, and chemical processes entering model calculations. A detailed study was made of radiative transfer in molecular lines to allow model predictions to be tested against empirical data. The calculations have successfully reproduced and explained several observed cloud properties, including abundances of complex molecular species and the apparent depletion of CO in dense cores.

Bodenheimer, P. H.↗
DOE OSTI2020

Lithium in T Coronae Borealis

T Coronae Borealis is a recurrent, symbiotic nova system currently in quiescence between its periodic ≈80 yr cycle of eruptions. Observations during inter-outburst epochs provide an opportunity to study properties of the accretion disk and the M red giant. Here we present new irradiated (blackbody veiling) models, incorporating modern molecular opacities and line lists, of spectra derived from high-resolution (22,000 ≲ R ≲ 120,000) optical echelle observations obtained at two epochs, one prior to and one post the 2015 rebrightening event at similar spectroscopic system phase. We find a lithium abundance in the secondary at both epochs to be comparable. The non-irradiated (classical) model atmospheres yield a lithium abundance, A(Li) = 1.3 ± 0.1. The irradiated model (veiled) atmospheres, which are likely a better representation of the system in which the white dwarf and accretion disk illuminate the red giant, give A(Li) = 2.4 ± 0.1.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Molecular dynamics study on interface formation and bond strength of impact-welded Mg-steel joints

It was recently demonstrated that the vaporizing foil actuator welding (VFAW) method can directly join immiscible magnesium and steel alloys without coating or a third chemical element based intermetallic compound layer. The VFAW Mg/steel joint exhibits a mixed interface layer of up to 200μm thickness consisting of Mg matrix and Fe particles. Computer simulations have suggested the formation of the interlayer is from the high-velocity frictional shearing between the Mg/steel substrates during the oblique impact in the VFAW process. This paper investigates the formation of Mg-Fe interlayer under VFAW condition with different shearing velocities using molecular dynamics (MD) model, and studies the bonding strength under different scenarios. Finally, the results elucidate the critical role of shearing velocity and surface roughness in achieving Mg/Fe joint.

36 MATERIALS SCIENCE↗
NASA NTRS1976

An analysis of the interstellar material in the line of sight toward Omicron Persei

Chemical abundances and physical conditions in the interstellar gas toward Omicron Per are analyzed using Copernicus UV spectrophotometric data on 69 lines due to ions and atoms as well as 19 lines of H2 and HD. The UV extinction toward the star is determined along with the column densities of atomic and molecular hydrogen, the atomic column densities and temperature in the H I region, and the nature of the ionized regions along the line of sight. It is concluded that: (1) Omicron Per is apparently embedded in the near edge of an extended dense molecular cloud, the outer parts of which give rise to the observed absorption lines; (2) the H I region may consist of more than one cloud; (3) the far-UV extinction rise is unusually steep, indicating a high proportion of small grains; (4) the element depletions are somewhat greater than in Zeta Oph, particularly for sulfur and argon; and (5) the molecular abundances are generally consistent with gas-phase formation models rather than with molecular formation on grain surfaces, unless a substantial amount of small grains is present to increase the available surface area.

Snow, T. P., Jr.↗
NASA NTRS1987

Numerical studies of collapsing interstellar clouds

Numerical simulation of the structure and evolution of interstellar clouds was conducted. Steps were taken toward an integrated treatment of the dynamical, thermal, and chemical processes entering model calculations, and a detailed study was made of radiative transfer in molecular lines to allow model predictions to be tested against empirical data. It is shown that the shapes of molecular lines are sensitive to details of the cloud structure and evolutionary state and are thus useful in inferring the cloud density, temperature, chemical composition, age, and initial conditions. The calculations have successfully reproduced and explained several observed cloud properties, including abundances of complex molecular species and the apparent depletion of CO in dense cores.

Bodenheimer, Peter↗
NASA NTRS2002

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↗
NASA NTRS2019

Isotopologue Consistency of Semi-Empirically Computed InfraRed Line Lists and Further Improvement for Rare Isotopologues: CO2 and SO2 Case Studies.

The semi-empirical molecular rovibrational IR line lists, such as ExoMol, TheoReTs, and Ames, combine the experimental accuracy and theoretical power to reach better than 0.1 cm-1 accuracy for line positions and better than 80-90% agreement for line intensities. The quality of these existing semi-empirical IR lists allows further improvements of intensity and line positions for those unobserved minor isotopologues. This paper presents our new BTRHE (Best Theory + Reliable High-resolution Experiment) strategy implementation. For line intensity, the isotopologue consistency and the patterns of mass dependence in the Ames-296K SO2 and CO2 IR lists are quantitatively presented along the mass-inverse coordinates. The consistency and patterns are better than those in existing experimental data. The methodology proposed here can be used to identify inconsistencies, outliers, and mistakes in intensities, and help improve Effective Dipole Model (EDM) and molecular IR databases. We call for an experimental study on the 50006 and 60007 bands of CO2 628. For line position predictions, a simple approach combining the variational IR line lists with Effective Hamiltonian (EH) model may refine the effective rotational constants A0/B0/C0 and quartic centrifugal distortion constants of minor isotopologues. The prediction accuracy may be improved by two orders of magnitude, i.e. reaching 0-5 MHz prediction accuracy in the range of J<20-30, Ka<10-20, and 0.01-0.02 MHz accuracy for A0/B0/C0. Several important factors have been systematically investigated and discussed, e.g. convergence, uncertainties, higher order terms, fixing EH parameters, mass coordinates, etc. Amicrowave (MW) line set consisting of 644,636 strong transitions for all 30 isotopologues and corresponding refined EH(Ames) parameters are reported in the supplementary material. This approach may be easily extended to rovibrational bands, hot bands, and other molecular systems.

Xinchuan Huang↗
DOE OSTI2020

Methodology for Generating Covariance Data of Thermal Neutron Scattering Cross Sections

This paper details and implements a framework for evaluating thermal neutron scattering cross sections that provide S(α,β) data and covariance data for hydrogen in light water. This methodology involves perturbing model parameters of molecular dynamics potentials and fitting the simulation results to experimental data. The framework is general and can be applied to any material or simulation method. The fit is made using the Unified Monte Carlo method to experimentally measure double-differential scattering cross sections of light water at the Spallation Neutron Source at Oak Ridge National Laboratory. Mean values and covariance data were generated for model parameters, phonon density of states, double-differential cross sections, and total scattering cross sections. These posterior parameter values were very similar to their prior values with a maximum relative error of 0.54%. This falls within in the Unified Monte Carlo–calculated uncertainties on the order of 2.7%. Additionally, posterior double-differential cross sections agree favorably with ENDF/B-VIII.0 cross sections. The new thermal scattering law was tested by comparing it against benchmarks from the International Criticality Safety Benchmark Evaluation Project Handbook, which showed a slight improvement over the ENDF/B-VIII.0 library. Additionally, the covariance matrix of the phonon density of states was validated to confirm that the spread of k eff from the density of states used to generate the covariance matrix was similar to the spread of k eff from the density of states of the sampled covariance matrix.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Can Third-Body Stabilization of Bimolecular Collision Complexes in Cold Molecular Clouds Happen?

For more than half a century, networks of radiative association, dissociative recombination, and bimolecular reactions have been postulated to drive the low-temperature chemistry of cold molecular clouds. Third-body stabilizations of collision complexes have been assumed to be 'irrelevant' due to short lifetime of such complexes. Here, we conduct crossed molecular beam studies of ground state atomic silicon with diacetylene in combination with electronic structure calculations and microcanonical kinetics models operating under cold molecular cloud conditions. Our combined experimental, electronic structure, and microcanonical kinetics modelling investigations provide compelling evidence that three-body collisions of molecular hydrogen with long-lived reaction intermediates accessed through intersystem crossing are prevalent deep inside molecular clouds. This concept might be exportable to reactions involving polycyclic aromatic hydrocarbons thus affording a versatile machinery to complex organics via third-body stabilizations of bimolecular collision complexes deep inside cold molecular clouds.

astrochemistry↗
NASA NTRS1997

First astronomical detection of the cumulene carbon chain molecule H2C6 in TMC-1

The cumulene carbenes are important components of hydrocarbon chemistry in low-mass star-forming cores. Here we report the first astronomical detection of the long-chain cumulene carbene H2C6 in the interstellar cloud TMC-1, from observations of two of its rotational transitions: J(K,K') = 7(1,7) --> 6(1,6) at 18.8 GHz and 8(1,8) --> 7(1,7) at 21.5 GHz, using NASA's Deep Space Network 70 m antenna at Goldstone, California. In addition we also observed the shorter cumulene carbene H2C4 at the same position. The fractional abundance of H2C6 relative to H2 is about 4.7 x 10(-11) and that of H2C4 is about 4.1 x 10(-9). The abundance of H2C6 is in fairly good agreement with gas-phase chemical models for young molecular cloud cores, but the abundance of H2C4 is significantly larger than predicted.

NASA Discipline Exobiology↗
NASA NTRS1999

Sensitivity of Temperature Profiles Retrieved from Mars Global Surveyor Thermal Emission Spectrometer (MGS/TES) Observations to the GSFC Synthetic Mars Model Atmosphere

Part of the task of interpreting IR spectral features observed by MGS/TES due to surface minerals requires distinguishing those IR signatures from atmospheric signatures of gas and dust. Surface-atmosphere separation for MGS/TES depends on knowledge of the retrieved temperature profile. In turn, the temperature retrieval Erom the observed data depends on molecular parameters including 15 micron CO2 line shape or line intensities which contribute to defining the Mars synthetic radiative transfer model. Using a simple isothermal, homogeneous single layer model of Pinnock and Shine, we find the ratio of (the error in degrees Kelvin of the retrieved temperature profile) to (the percentage error in the absorption coefficient) (deg K/percent) to be 0.4 at 200K. This ratio at 150K and 250K is 0.2 and 0.6, respectively. A more refined model, incorporating observed MGS/TES retrieved temperature profiles, the TES instrumental resolution and the most recent molecular modelling, will yield an improved knowledge of this error sensitivity. We present results of such a sensitivity study to determine the dependence of temperature profiles inverted from MGS/TES on these and other molecular parameters. This work was supported in part by NASA's Mars Data Analysis Program.

Maguire, William C.↗
NASA NTRS1993

Magnetic Field Structure in Monoceros R2

For some time now it has been suspected that magnetic fields play a major role in determining the mass spectrum of stars formed in molecular clouds. Theoretical models of protostellar evolution in a quiescent environment invoke magnetic fields as one form of cloud support and one which has a decisive effect on the minimum stellar mass formed (cf. Shu, Adams and Lizano 1987; Shu et al. 1988). The magnetic field also might act as an angular momentum dampening mechanism---a vital requirement for gravitational collapse and subsequent star formation (Gillis, Mestel and Paris 1974; Mouschovias 1978). Empirical evidence of the contribution of magnetic fields to the total energetics of molecular clouds comes from analysis of Zeeman splitting of OH absorption and thermal emission lines originating from dense (n greater than 10^4 cm^(-3)) cloud cores (Myers and Goodman 1988; Heiles et al. 1991, and references therein)...

Goldsmith, P.F.↗
DOE OSTI2022

Atomic-scale mechanism of carbon nucleation from a deep crustal fluid by replica exchange reactive molecular dynamics simulation

Here we present a mechanistic model of carbon nucleation and growth from a fluid at elevated temperature (T) and pressure conditions, typical of those found in the shallow Earth’s lithosphere. Our model uses a replica exchange reactive molecular dynamics framework in which molecular configurations are swapped between adjacent T replica at regular intervals according to underlying statistical mechanics. This framework allows predicting complex molecular structures and thermodynamics while remaining computationally efficient. Here we simulate the reactivity of an unstable mixture of CO 2 and CH 4 at 1000 K and 1 GPa. We find that the path to thermodynamic equilibrium is initially entropy-driven, producing a diversity of short-lived species, including various alcohols with intermediate carbon oxidation states. Cyclic and polycyclic radicals that are sometimes resonance-stabilized form next and set the stage for carbon nucleation. The carbon exsolution process releases abundant water, is exothermic and starts with the nucleation of a large aggregate of hydrogenated graphene flakes from covalently bonded polycyclic units. The carbon backbone of this nucleus subsequently grows into a hydrogen-depleted fullerene-like structure, before evolving toward a partially bilayered graphene layer. Overall, our results show that the mechanism of graphitic C formation is certainly not bimolecular, and that it may involve a combination of key condensation and radical chain reactions. This will help understand the isotopic, and reactive characteristics of carbon-bearing fluids during their upward transit through the Earth’s mantle and crust. Moreover, the mechanistic insights outlined here present intriguing similarities with the process of soot and interstellar dust formation, which suggests that the widespread distribution of abiotic polyaromatic and graphitic material on Earth and beyond may reflect the prevalence of a fundamental chemical pathway.

58 GEOSCIENCES↗
DOE OSTI2026

Long-Range Fit: A Software Package for the Representation and Study of Long-Range Molecular Interactions

Describing intermolecular forces is fundamental to modeling and predicting the behavior of molecular systems. In particular, long-range molecular interactions─with electrostatic, induction, and dispersion as the main components─play a critical role, especially for low-temperature and low-density regimes. Long-range interactions are often described through perturbation theory, representing the electronic charge distribution via a multipolar series of the moments and polarizability tensors corresponding to each molecule. However, while the theory is well established, obtaining the resulting analytical expressions (and their practical implementation) constitutes a highly complex and system-dependent task. To address this challenge, we developed long-range-fit (LRF), an interactive and user-friendly software package designed to automate the generation and fitting of long-range interaction terms for arbitrary molecules in nondegenerate (ground or excited) electronic states. We have derived and implemented all terms up to 15th order, without approximations, via a spherical tensor representation, with symmetry adaptation to all molecular point-group symmetries. The resulting potential energy surface is compatible with most representations of the close interaction region.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Molecular dynamics analysis of the binding of human interleukin-6 with interleukin-6 α-receptor

Human interleukin-6 (hIL-6) is a multifunctional cytokine that regulates immune and inflammatory responses in addition to metabolic and regenerative processes and cancer. hIL-6 binding to the IL-6 receptor (IL-6Rα) induces homodimerization and recruitment of the glycoprotein (gp130) to form a hexameric signaling complex. Anti-IL-6 and IL-6R antibodies are clinically approved inhibitors of IL-6 signaling pathway for treating rheumatoid arthritis and Castleman's disease, respectively. There is a potential to develop novel small molecule IL-6 antagonists derived from understanding the structural basis for IL-6/IL-6Rα interactions. In this work, we combine homology modeling with extensive molecular dynamics (MD) simulations to examine the association of hIL-6 with IL-6Rα. A comparison with MD of apo hIL-6 reveals that the binding of hIL-6 to IL-6Rα induces structural and dynamic rearrangements in the AB loop region of hIL-6, disrupting intraprotein contacts and increasing the flexibility of residues 48 to 58 of the AB loop. In contrast, due to the involvement of residues 59 to 78 in forming contacts with the receptor, these residues of the AB loop are observed to rigidify in the presence of the receptor. The binary complex is primarily stabilized by two pairs of salt bridges, Arg181 (hIL-6)- Glu182 (IL-6Rα) and Arg184 (hIL-6)- Glu183 (IL-6Rα) as well as hydrophobic and aromatic stacking interactions mediated essentially by Phe residues in both proteins. An interplay of electrostatic, hydrophobic, hydrogen bonding, and aromatic stacking interactions facilitates the formation of the hIL-6/IL-6Rα complex.

59 BASIC BIOLOGICAL SCIENCES↗