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Results for “MOLECULAR INTERACTION”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
NASA NTRS2004

Computational studies of Ras and PI3K

Until recently, experimental techniques in molecular cell biology have been the primary means to investigate biological risk upon space radiation. However, computational modeling provides an alternative theoretical approach, which utilizes various computational tools to simulate proteins, nucleotides, and their interactions. In this study, we are focused on using molecular mechanics (MM) and molecular dynamics (MD) to study the mechanism of protein-protein binding and to estimate the binding free energy between proteins. Ras is a key element in a variety of cell processes, and its activation of phosphoinositide 3-kinase (PI3K) is important for survival of transformed cells. Different computational approaches for this particular study are presented to calculate the solvation energies and binding free energies of H-Ras and PI3K. The goal of this study is to establish computational methods to investigate the roles of different proteins played in the cellular responses to space radiation, including modification of protein function through gene mutation, and to support the studies in molecular cell biology and theoretical kinetics models for our risk assessment project.

Ren, Lei↗
NASA NTRS1991

Star formation - A theoretician's view

The present evaluation of the hypothesis that the birth of a sunlike star occurs in four stages, with a critical bipolar outflow phase, notes that observed molecular outflows cannot be initiated from circumstellar disks and must instead represent swept-up shells of gas that are driven by strong protostellar winds. The star can resolve its growing angular-momentum problem only by rejecting a fraction of the material that is fed through the disk in a powerful, magnetocentrifugally-driven wind. Empirical properties measured for well-collimated outflow sources can be accounted for by the interaction of this anisotropic wind with the ambient molecular cloud core.

Shu, Frank H.↗
DOE OSTI2024

Graph neural networks for CO 2 solubility predictions in Deep Eutectic Solvents

Deep Eutectic Solvents (DESs) are a promising class of solvents for CO 2 capture. DESs are complex mixtures that can be designed to optimize CO solubility and overall capture process efficiency. However, the vast design landscape of DES mixtures makes experimental investigation prohibitive; as such, there is a need for computational models that can quickly and efficiently navigate the design space and inform data collection efforts. In this work, we propose Graph Neural Network (GNN) models for predicting CO 2 solubility for DESs; the GNN leverages a mixture graph representation that captures the molecular structure of the DES components as well as their intermolecular interactions. Here, we compare the GNN framework against alternative architectures (neural networks, graph convolution networks, and random forests) and data representations (molecular fingerprints, sigma profiles, and graphs). We show that the proposed approach offers superior predictive performance; specifically, we show that solubility can be predicted reliably directly from molecular structure (without the need of using sigma profiles as proposed in previous studies). This result is important, as obtaining sigma profiles requires expensive density functional theory computations. We also explored the ability of GNNs to predict solubility for new DES mixtures and operating conditions. We found that the model extrapolates across temperature reliably. However, we also found deficiencies in the ability of the model to predict solubility for DES mixtures, pressures, and molar ratio not included in the training sets; we show that this is due to an inherent lack of chemical diversity in datasets available in the literature. The proposed computational capabilities can thus help navigate the design space of DES and inform data collection efforts. Our models, data, and benchmarks are shared as Python code implemented in Jupyter notebooks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2001

Carbon Nanotubes in Water: MD Simulations of Internal and External Flow, Self Organization

We have developed computational tools, based on particle codes, for molecular dynamics (MD) simulation of carbon nanotubes (CNT) in aqueous environments. The interaction of CNTs with water is envisioned as a prototype for the design of engineering nano-devices, such as artificial sterocillia and molecular biosensors. Large scale simulations involving thousands of water molecules are possible due to our efficient parallel MD code that takes long range electrostatic interactions into account. Since CNTs can be considered as rolled up sheets of graphite, we expect the CNT-water interaction to be similar to the interaction of graphite with water. However, there are fundamental differences between considering graphite and CNTs, since the curvature of CNTs affects their chemical activity and also since capillary effects play an important role for both dynamic and static behaviour of materials inside CNTs. In recent studies Gordillo and Marti described the hydrogen bond structure as well as time dependent properties of water confined in CNTs. We are presenting results from the development of force fields describing the interaction of CNTs and water based on ab-initio quantum mechanical calculations. Furthermore, our results include both water flows external to CNTs and the behaviour of water nanodroplets inside heated CNTs. In the first case (external flows) the hydrophobic behaviour of CNTs is quantified and we analyze structural properties of water in the vicinity of CNTs with diagnostics such as hydrogen bond distribution, water dipole orientation and radial distribution functions. The presence of water leads to attractive forces between CNTs as a result of their hydrophobicity. Through extensive simulations we quantify these attractive forces in terms of the number and separation of the CNT. Results of our simulations involving arrays of CNTs indicate that these exhibit a hydrophobic behaviour that leads to self-organising structures capable of trapping water clusters. In the second case (internal flows) we study the behaviour of water droplets confined inside CNTs. Constant temperature simulations allow us to capture structural properties such as the contact angles and density profiles of the equilibrated drops. By heating and subsequently cooling of the CNT, we are able to measure the evaporation and the condensation rate of the entrapped water.

Jaffe, Richard L.↗
NASA NTRS1996

Formation of Ordered Arrays of Proteins on Surfaces

Van der Waals (dispersion) forces contribute to interactions of proteins with other molecules or with surfaces, but because of the structural complexity of protein molecules, the magnitude of these effects is usually estimated based on idealized models of the molecular geometry, e.g., spheres or spheroids. The calculations reported here seek to account for both the geometric irregularity of protein molecules and the material properties of the interacting media. While the latter are found to fall in the generally accepted range, the molecular shape is shown to cause the magnitudes of the interactions to differ significantly from those calculated using idealized models, with important consequences. First, the roughness of the molecular surface leads to much lower average interaction energies for both protein-protein and protein-surface cases relative to calculations in which the protein molecule is approximated as a sphere. These results indicate that a form of steric stabilization may be an important effect in protein solutions. Underlying this behavior is appreciable orientational dependence, one reflection of which is that molecules of complementary shape are found to exhibit very strong attractive dispersion interactions. Although this has been widely discussed previously in the context of molecular recognition processes, the broader implications of these phenomena may also be important at larger molecular separations, e.g., in the dynamics of aggregation, precipitation and crystal growth.

Lenhoff, A. M.↗
NASA NTRS1996

Van der Waals Interactions Involving Proteins

Van der Waals (dispersion) forces contribute to interactions of proteins with other molecules or with surfaces, but because of the structural complexity of protein molecules, the magnitude of these effects is usually estimated based on idealized models of the molecular geometry, e.g., spheres or spheroids. The calculations reported here seek to account for both the geometric irregularity of protein molecules and the material properties of the interacting media. Whereas the latter are found to fall in the generally accepted range, the molecular shape is shown to cause the magnitudes of the interactions to differ significantly from those calculated using idealized models. with important consequences. First, the roughness of the molecular surface leads to much lower average interaction energies for both protein-protein and protein-surface cases relative to calculations in which the protein molecule is approximated as a sphere. These results indicate that a form of steric stabilization may be an important effect in protein solutions. Underlying this behavior is appreciable orientational dependence, one reflection of which is that molecules of complementary shape are found to exhibit very strong attractive dispersion interactions. Although this has been widely discussed previously in the context of molecular recognition processes, the broader implications of these phenomena may also be important at larger molecular separations, e.g., in the dynamics of aggregation, precipitation, and crystal growth.

Roth, Charles M.↗
NASA NTRS1984

A low Earth orbit molecular beam space simulation facility

A brief synopsis of the low Earth orbit (LEO) satellite environment is presented including neutral and ionic species. Two ground based atomic and molecular beam instruments are described which are capable of simulating the interaction of spacecraft surfaces with the LEO environment and detecting the results of these interactions. The first detects mass spectrometrically low level fluxes of reactively and nonreactively surface scattered species as a function of scattering angle and velocity while the second ultrahigh velocity (UHV) molecular beam, laser induced fluorescence apparatus is capable of measuring chemiluminescence produced by either gas phase or gas-surface interactions. A number of proposed experiments are described.

Cross, J. B.↗
DOE OSTI2024

Effect of helium bubbles on the mobility of edge dislocations in copper

Abstract Helium bubbles can form in materials upon exposure to irradiation. It is well known that the presence of helium bubbles can cause changes in the mechanical behavior of materials. To improve the lifetime of nuclear components, it is important to understand deformation mechanisms in helium-containing materials. In this work, we investigate the interactions between edge dislocations and helium bubbles in copper using molecular dynamics (MD) simulations. We focus on the effect of helium bubble pressure (equivalently, the helium-to-vacancy ratio) on the obstacle strength of helium bubbles and their interaction with dislocations. Our simulations predict significant differences in the interaction mechanisms as a function of helium bubble pressure. Specifically, bubbles with high internal pressure are found to exhibit weaker obstacle strength as compared to low-pressure bubbles of the same size due to the formation of super-jogs in the dislocation. Activation energies and rate constants extracted from the MD data confirm this transition in mechanism and enable upscaling of these phenomena to higher length-scale models.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Phase field dislocation dynamics formulation coupled with Fourier based micromechanics solver and its application to grain boundary–dislocation interactions

A new phase field dislocation dynamics (PFDD) formulation for homogeneous and heterogeneous materials is presented, which couples micromechanical solvers and the time-dependent Ginzburg–Landau equation. The strain fields are obtained from the micromechanical solver by solving the Lippmann–Schwinger equation and then used to define energy terms to model the evolution of the dislocations. Grain boundary (GB)–dislocation interactions are studied using the coupled PFDD formulation and by describing GBs as inclusions. GB energy and stiffness tensors are computed from molecular statics simulations, and a newly proposed lattice energy term that is dependent on the GB energy is considered in the calculations. Interaction of a screw dislocation with minimum energy and metastable states of low and high angle ⟨110⟩ symmetric tilt grain boundaries are studied. We show good agreement between predictions from our PFDD formulation and molecular dynamics simulations of grain boundary–dislocation interactions.

36 MATERIALS SCIENCE↗
NASA NTRS2001

A Model for Macromolecular Crystallization

Macromolecular crystallization is a complex process. involving a system which typically has 5 or more components (macromolecule, water, buffer + counter ion, and precipitant). Whereas small molecules have only several well defined contacts in the crystal lattice, macromolecules generally have 10's or even 100's of contacts between molecules. These can range from hydrogen bonds (direct or water-mediated), through van der Waals, hydrophobic, salt bridges, and ion-mediated contacts. The latter interactions are stronger and require some specificity in the molecular alignment, while the others are weaker, more prevalent, and more promiscuous, i.e., can often be readily broken and reformed between other sites. Formation of a consistent, ordered, 3D structure may be impossible in the absence of any or presence of too many strong interactions. Further complicating the process is the inherent structural asymmetry of monomeric single chain macromolecules. The process of crystal nucleation and growth involves the ordered assembly of growth units into a defined 3D lattice. We suggest that for many macromolecules, particularly those that are monomeric, this involves a preliminary solution-phase assembly process into a growth unit having some symmetry prior to addition to the lattice, recapitulating the initial stages of the nucleation process. If this model is correct then fluids and crystal growth models assuming a strictly monodisperse nutrient solution need to be revised. Experimental evidence, based upon face growth rate, AFM, and fluorescence energy transfer data, for a postulated model of the nucleation of tetragonal lysozyme crystals and how it transitions into crystal growth will be presented.

Pusey, Marc L.↗
NASA NTRS1988

The evolution of the system of globular clusters

The physical processes affecting the evolution of the system of globular clusters are reviewed. Aspects of internal structure evolution discussed include evaporation, core collapse, expansion, tidal shocks, and interaction with other massive components of the Galaxy such as black holes, molecular clouds, and other clusters. The evolution of orbital parameters is examined, including dynamical friction, scattering by massive subcomponents, and interactions with nearby systems. In addition, an overview of the system evolution is presented.

Ostriker, Jeremiah P.↗
NASA NTRS2002

A Model for Tetragonal Lysozyme Crystal Nucleation and Growth

Macromolecular crystallization is a complex process, involving a system that typically has 5 or more components (macromolecule, water, buffer + counter ion, and precipitant). Whereas small molecules have only a few contacts in the crystal lattice, macromolecules generally have 10's or even 100's of contacts between molecules. These can range from hydrogen bonds (direct or water-mediated), through van der Waals, hydrophobic, salt bridges, and ion-mediated contacts. The latter interactions are stronger and require some specificity in the molecular alignment, while the others are weaker, more prevalent, and more promiscuous, i.e., can be readily broken and reformed between other sites. Formation of a consistent, ordered, 3D structure may be difficult or impossible in the absence of any or presence of too many strong interactions. Further complicating the process is the inherent structural asymmetry of monomeric (single chain) macromolecules. The process of crystal nucleation and growth involves the ordered assembly of growth units into a defined 3D lattice. We suggest that for many macromolecules, particularly those that are monomeric, this involves a preliminary solution-phase assembly process into a growth unit having some symmetry prior to addition to the lattice, recapitulating the initial stages of the nucleation process. If this model is correct then fluids and crystal growth models assuming a strictly monodisperse nutrient solution need to be revised. This model has been developed from experimental evidence based upon face growth rate, AFM, and fluorescence energy transfer data for the nucleation and growth of tetragonal lysozyme crystals.

Pusey, Marc L.↗
DOE OSTI2024

Electroweak Nuclear Properties from Single Molecular Ions in a Penning Trap

Here, we present a novel technique to probe electroweak nuclear properties by measuring parity violation (PV) in single molecular ions in a Penning trap. The trap’s strong magnetic field Zeeman shifts opposite-parity rotational and hyperfine molecular states into near degeneracy. The weak interaction-induced mixing between these degenerate states can be larger than in atoms by more than 12 orders of magnitude, thereby vastly amplifying PV effects. The single molecule sensitivity would be suitable for applications to nuclei across the nuclear chart, including rare and unstable nuclei.

electronic structure of atoms & molecules↗
DOE OSTI2024

Axial H-Bonding Solvent Controls Inhomogeneous Spectral Broadening, While Peripheral H-Bonding Solvent Controls Vibronic Broadening: Cresyl Violet in Methanol

The dynamics of the nuclei of both a chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore–solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore–solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both force field and ab initio molecular dynamics trajectories along with the inclusion of only certain solvent molecules in the excited-state calculations, we determine that the methanol molecules axial to the chromophore are responsible for the majority of inhomogeneous broadening, with a single methanol molecule that forms an axial hydrogen bond dominating the response. Furthermore, the strong peripheral hydrogen bonds do not contribute to spectral broadening, as they are very stable throughout the dynamics and do not lead to increased energy-gap fluctuations. We also find that treating the strong peripheral hydrogen bonds as molecular mechanical point charges during the molecular dynamics simulation underestimates the vibronic coupling. Including these peripheral hydrogen bonding methanol molecules in the quantum-mechanical region in a geometry optimization increases the vibronic coupling, suggesting that a more advanced treatment of these strongly interacting solvent molecules during the molecular dynamics trajectory may be necessary to capture the full vibronic spectral broadening.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

The interaction of edge dislocations with hydrogen-helium bubbles in tungsten

In fusion reactors, plasmas-facing components undergo degradation due to displacement damage and injection of gas impurities. Significant amounts of hydrogen (H) and helium (He) impurities can be introduced into materials through plasma exposure and nuclear transmutation, and their synergistic effects lead to the formation of mixed He/H bubbles under irradiation, changing their hardening mechanisms. In this study, molecular dynamics (MD) models were developed to study the interaction between ½<111> edge dislocations with mixed He/H-bubbles in W. The critical resolved shear stress (CRSS) that is required for dislocation breakaway increases with He/H-to-vacancy ratio at 600 K, indicating strong pinning effects of mixed He/H bubbles. However, as the temperature increases up to 1400 K, the mixed He/H bubbles become unstable as the H atoms are increasingly emitted from the mixed He/H bubbles and migrate into W matrix, which lowers bubble pressure and CRSS. Overall, these results highlight the synergistic effects of He and H on dislocation behavior in irradiated W during deformation.

36 - MATERIALS SCIENCE↗
NASA NTRS1994

An X-ray and optical study of the supernova remnant W44

We report the results of a 8000 s observation of the supernova remnant W44 using the ROSAT Position Sensitive Proportional Counter (PSPC). The image shows the same centrally peaked morphology observed by the Einstein IPC and contrasts with the shell-like radio morphology. The eastern limb shows a lack of X-ray emission within the radio shell, probably due to the interaction between the Supernova Remnants (SNR) and a molecular cloud. No counterpart to the pulsar 1853 + 01 in W44 has been detected, with L(sub X) less than 1.3 x 10(exp 32) ergs/s in the 0.2 to 2.4 keV band. The spectral analysis of the central part of W44, combining EXOSAT ME and Einstein SSS data, shows that the shocked plasma has not reached ionization equilibrium. The best nonequilibrium fit to PSPC, ME, and SSS spectra gives Eta = 10(exp 51) ergs cm(exp -6), T(sub s) = 10(exp 7) K with T(sub e) = T(sub i), suggesting conditions are approaching ionization equilibrium. There is no evidence of enhanced abundances of Mg, Si, S, or Fe. The variation of temperature and column density was obtained region by region using the PSPC and Einstein IPC. The temperature is largely uniform over the remnant, but strong column density variations are found to be consistent with molecular clouds in the line of sight. An evaporation model with a two-phase interstellar medium structure of clumps and interclump gas (White & Long 1991) can explain the X-ray centrally peaked morphology of W44. The clumps remaining behind a SN shock provide a reservoir of material, and evaporat e to increase the density of X-ray emitting gas in the interior of a SNR. The uniform temperature distribution of W44 strongly supports the predictions of this model. In addition, mosaiced H alpha and (S II) images of W44, taken using the prime focus universal extragalactic instrument (PFUEI) camera on the Palomar 60 sec telescope, reveal the first discovery of optical filaments (both H alpha and (S II)) in the northwestern and southeastern portion of the remnant, within the X-ray emitting region. The optical filaments and the X-ray image showing locally brighter emission and clumps along the filaments suggest both are produced by the interaction between the supernova shock front and regions of enhanced ambient density.

Rho, Jeongee↗
NASA NTRS2020

Inter-species molecular attraction effect in the development of a two-species mixing layer

Simulations of fluid mixing occurring at high-pressures mandate the use of real-fluid equations of state to capture the effect of boh intermolecular repulsive forces and attractive forces which are neglected in perfect gases. Dedicated mixing rules account for these forces by providing a generic mapping of the mixture state-space onto a pure fluid domain. However, the specific inter-species molecular forces depend on the particular characteristics of the molecular pairs under consideration, and typically require the knowledge of binary interaction coefficients k_{αβ}. The impact of k_{αβ} on a flow field is as of now unclear; further, k_{αβ} is unknown for many molecular pairs and when unknown, set to be null. This study addresses the impact of k_{αβ} on the temporal evolution of a real-fluid mixing layer and uses Direct Numerical Simulation (DNS) to explore this impact. The results show differences between augmented attraction (k_{αβ}<0) and diminished attraction (k_{αβ}>0), affecting both fluid dynamics and diffusion processes. Specifically, in a binary mixing layer, it is observed that augmented attraction leads to delayed transition and mixing layer growth, manifested in the momentum layer thickness. The fractal dimension, which is a manifestation of interface corrugation, is calculated. These results provide an hitherto undocumented mechanism affecting the development of mixing layers.

Banuti, Daniel↗
DOE OSTI2026

Local Spin Density Approximation Strongly Improved by a Better-Informed Local Scaling of Its Self-Interaction Correction

The Perdew−Zunger self-interaction correction (PZSIC) makes density functional approximations (DFAs) exact for all one-electron densities. However, it overcorrects in manyelectron regions, introducing errors for the uniform-density limit, where uncorrected DFAs are exact. The locally scaled PZSIC (LSIC), based on the iso-orbital indicator zσ [which distinguishes single-orbital and slowly varying density regions and is used with the local spin density approximation (LSDA)], restores the uniform-density limit and significantly improves results for many properties, including chemical reaction barrier heights, atomization energies, and ionization potentials. Yet, LSIC performs poorly for weakly bonded systems, leaving many unbound, due to limitations of its iso-orbital indicator. To correct this, in this work we propose a new local scaling, LSIC-α, based on the iso-orbital indicator ασ (which additionally identifies regions of overlapping density tails). A two-parameter scaling function of ασ is fitted to a subset of the nonbonded appropriate norms for the SCAN and r2SCAN meta- GGAs, and tested on many properties of main-group atoms, molecules, and molecular complexes. LSIC-α greatly improves the interaction energies of weakly bonded systems in the S22 data set while retaining LSIC’s accuracy for other properties. This work shows that the errors of LSDA (and presumably of higher-level DFAs) can be largely but not entirely repaired by a proper “do no harm” self-interaction correction.

Approximation↗