Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular modelling”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Extended Lagrangian Born–Oppenheimer molecular dynamics for orbital-free density-functional theory and polarizable charge equilibration models

We report extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) is formulated for orbital-free Hohenberg–Kohn density-functional theory and for charge equilibration and polarizable force-field models that can be derived from the same orbital-free framework. The purpose is to introduce the most recent features of orbital-based XL-BOMD to molecular dynamics simulations based on charge equilibration and polarizable force-field models. These features include a metric tensor generalization of the extended harmonic potential, preconditioners, and the ability to use only a single Coulomb summation to determine the fully equilibrated charges and the interatomic forces in each time step for the shadow Born–Oppenheimer potential energy surface. The orbital-free formulation has a charge-dependent, short-range energy term that is separate from long-range Coulomb interactions. This enables local parameterizations of the short-range energy term, while the long-range electrostatic interactions can be treated separately. The theory is illustrated for molecular dynamics simulations of an atomistic system described by a charge equilibration model with periodic boundary conditions. The system of linear equations that determines the equilibrated charges and the forces is diagonal, and only a single Ewald summation is needed in each time step. The simulations exhibit the same features in accuracy, convergence, and stability as are expected from orbital-based XL-BOMD.

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

Permeation of CO 2 and N 2 through glassy poly(dimethyl phenylene) oxide under steady- and presteady-state conditions

Glassy polymers are often used for gas separations because of their high selectivity. Although the dual-mode permeation model correctly fits their sorption and permeation isotherms, its physical interpretation is disputed, and it does not describe permeation far from steady state, a condition expected when separations involve intermittent renewable energy sources. To develop a more comprehensive permeation model, we combine experiment, molecular dynamics, and multiscale reaction–diffusion modeling to characterize the time-dependent permeation of N 2 and CO 2 through a glassy poly(dimethyl phenylene oxide) membrane, a model system. Simulations of experimental time-dependent permeation data for both gases in the presteady-state and steady-state regimes show that both single- and dual-mode reaction–diffusion models reproduce the experimental observations, and that sorbed gas concentrations lag the external pressure rise. The results point to environment-sensitive diffusion coefficients as a vital characteristic of transport in glassy polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1987

Low Reynolds number modeling of turbulent flows with and without wall transpiration

A full Reynolds-stress closure that is capable of describing the flow all the way to the wall is formulated. The closure is based on the conventional high Reynolds number form of the redistribution model, the inclusion of molecular diffusion, and a modified dissipation model to account for viscous effects near a wall. Two dissipation models are investigated along with two gradient diffusion and two redistribution models. Their respective effects on the calculated flow properties are assessed by comparing them with the data of fully developed turbulent flows and a developing pipe flow with wall transpiration. The near-wall behavior is very well predicted; however, the wall correction to the redistribution modeling is found to have little effect on the calculated results. The overall behavior of the fully developed turbulent flows is best described by a nonisotropic gradient diffusion model, a return-to-isotropy redistribution model, and a dissipation model that accounts for viscous behavior near a wall. This same closure also gives the best prediction of the axial pressure drop behavior along a pipe with a uniform wall suction. Furthermore, the near-wall behavior of such a flow is very well predicted by this closure.

So, Ronald M. C.↗
NASA NTRS1993

The abundance of CH(+) in translucent molecular clouds - Further tests of shock models

Observations of interstellar absorption lines of CH(+) in the (0, 0) and (1, 0) bands of the A 1Pi - X 1Sigma(+) system are presented for 17 stars with reddenings up to E(B-V) about 1.5 mag. Complementary data on interstellar CH in the (0, 0) bands of the A 2Delta - X 2Pi and B 2Sigma(-) - X 2Pi systems and C2 in the A 1Pi(u) - X 1Sigma(g)(+) red system have been obtained as well. The derived CH(+) column densities continue to increase with total column density, and values up to 10 exp 14/sq cm are reported for highly-reddened lines of sight. In most cases, the CH(+) and CH absorptions are dominated by a single strong component, with weaker features displaced by a few km/s. No significant velocity difference is found between CH(+) and neutral species such as CH and CN for this sample of randomly oriented lines of sight. In contrast with CN, the CH(+) abundance does not increase with the density in the cloud as derived from the observed C2 excitation. For the two clouds with the largest density, HD 62542 and HD 94413, no CH(+) absorption is found with CH(+)/CH less than 0.03 and 0.14, respectively. The CH(+) findings do not support a single-shock origin for the formation of the ion.

Gredel, R.↗
NASA NTRS1976

Theoretical analysis of the density within an orbiting molecular shield

An analytical model based on the kinetic theory of a drifting Maxwellian gas is used to determine the nonequilibrium molecular density distribution within a hemispherical shell open aft with its axis parallel to its velocity. Separate numerical results are presented for the primary and secondary density distribution components due to the drifting Maxwellian gas for speed ratios between 2.5 and 10. An analysis is also made of the density component due to gas desorbed from the wall of the hemisphere, and numerical results are presented for the density distribution. It is shown that the adsorption process may be completely ignored. The results are applicable to orbital trajectories in any planet-atmosphere system and interplanetary transfer trajectories. Application to the earth's atmosphere is mentioned briefly.

Hueser, J. E.↗
NASA NTRS1987

Kinetic model for the vibrational energy exchange in flowing molecular gas mixtures

The present study is concerned with the development of a computational model for the description of the vibrational energy exchange in flowing gas mixtures, taking into account a given number of energy levels for each vibrational degree of freedom. It is possible to select an arbitrary number of energy levels. The presented model uses values in the range from 10 to approximately 40. The distribution of energy with respect to these levels can differ from the equilibrium distribution. The kinetic model developed can be employed for arbitrary gaseous mixtures with an arbitrary number of vibrational degrees of freedom for each type of gas. The application of the model to CO2-H2ON2-O2-He mixtures is discussed. The obtained relations can be utilized in a study of the suitability of radiation-related transitional processes, involving the CO2 molecule, for laser applications. It is found that the computational results provided by the model agree very well with experimental data obtained for a CO2 laser. Possibilities for the activation of a 16-micron and 14-micron laser are considered.

Offenhaeuser, F.↗
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 NTRS1988

Computer modeling of polymers

A Polymer Molecular Analysis Display System (p-MADS) was developed for computer modeling of polymers. This method of modeling allows for the theoretical calculation of molecular properties such as equilibrium geometries, conformational energies, heats of formations, crystal packing arrangements, and other properties. Furthermore, p-MADS has the following capabilities: constructing molecules from internal coordinates (bonds length, angles, and dihedral angles), Cartesian coordinates (such as X-ray structures), or from stick drawings; manipulating molecules using graphics and making hard copy representation of the molecules on a graphics printer; and performing geometry optimization calculations on molecules using the methods of molecular mechanics or molecular orbital theory.

Green, Terry J.↗
DOE OSTI2021

Phase field dislocation dynamics (PFDD) modeling of non-Schmid behavior in BCC metals informed by atomistic simulations

Body-Centered Cubic (BCC) metals exhibit anomalous mechanical properties such as twinning/anti-twinning and tension/compression asymmetry, which are attributed to asymmetric behavior of screw dislocations. Unlike Face-Centered Cubic (FCC) metals, the Critical Resolved Shear Stress (CRSS) of BCC metals deviates from the Schmid law. Here, we use a mesoscale modeling approach called Phase Field Dislocation Dynamics (PFDD) to understand the critical factors that control this non-Schmid behavior and reproduce atomistic predictions of the CRSS (Peierls stress). All inputs to the PFDD model are obtained from Molecular Statics (MS) simulations. Multiple pathways for modeling the non-Schmid behavior are investigated by incorporating the representative dislocation properties into different energy terms in the PFDD model. One way to understand non-Schmid behavior is to incorporate stress components projected on inclined planes into the external energy term within PFDD. Alternatively, we propose that non-Schmid behavior can also be accounted for by considering the variation of the {110} unstable stacking fault energy and the dislocation core width as a function of the applied tensorial stress field. The CRSS predicted using PFDD modeling is in excellent agreement with MS predictions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

The evolution of HCO + in molecular clouds using a novel chemical post-processing algorithm

Modelling the chemistry of molecular clouds is critical to accurately simulating their evolution. To reduce computational cost, 3D simulations generally restrict their chemistry to species with strong heating and cooling effects. Time-dependent information about the evolution of other species is therefore often neglected. We address this gap by post-processing tracer particles in the SILCC-Zoom molecular cloud simulations. Using a chemical network of 39 species and 301 reactions (including freeze-out of CO and H 2 O) and a novel algorithm to reconstruct a density grid from sparse tracer particle data, we produce time-dependent density distributions for various species. We focus upon the evolution of HCO + , which is a critical formation reactant of CO but is not typically modelled on the fly. We find that ∼ 90 per cent of the HCO + content of the cold molecular gas forms in situ around n HCO + ∼ 10 3 –10 4 cm −3 , over a time-scale of approximately 1 Myr. The remaining ∼ 10 per cent forms at high extinction sites, with minimal turbulent mixing out into the less dense gas. We further show that the dominant HCO + formation pathway is dependent on the visual extinction, with the reaction H 3 + + CO contributing 90 per cent of the total HCO + production above A V, 3D = 3. We produce the very first maps of the HCO + column density, N(HCO + ), and show that it reaches values as high as 10 15 cm −2 . We find that 50 per cent of the HCO + mass is located within AV ∼ 10–30 in a density range of 10 3.5 –10 4.5 cm −3 . Our maps of N(HCO + ) are shown to be in good agreement with recent observations of the W49A star-forming region.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Deep learning-based quasi-continuum theory for structure of confined fluids

Predicting the structural properties of water and simple fluids confined in nanometer scale pores and channels is essential in, for example, energy storage and biomolecular systems. Classical continuum theories fail to accurately capture the interfacial structure of fluids. In this work, we develop a deep learning-based quasi-continuum theory (DL-QT) to predict the concentration and potential profiles of a Lennard-Jones (LJ) fluid and water confined in a nanochannel. The deep learning model is built based on a convolutional encoder–decoder network (CED) and is applied for high-dimensional surrogate modeling to relate the fluid properties to the fluid–fluid potential. The CED model is then combined with the interatomic potential-based continuum theory to determine the concentration profiles of a confined LJ fluid and confined water. Further, we show that the DL-QT model exhibits robust predictive performance for a confined LJ fluid under various thermodynamic states and for water confined in a nanochannel of different widths. The DL-QT model seamlessly connects molecular physics at the nanoscale with continuum theory by using a deep learning model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1996

A dynamic response model for pressure sensors in continuum and high Knudsen number flows with large temperature gradients

This paper develops a dynamic model for pressure sensors in continuum and rarefied flows with longitudinal temperature gradients. The model was developed from the unsteady Navier-Stokes momentum, energy, and continuity equations and was linearized using small perturbations. The energy equation was decoupled from momentum and continuity assuming a polytropic flow process. Rarefied flow conditions were accounted for using a slip flow boundary condition at the tubing wall. The equations were radially averaged and solved assuming gas properties remain constant along a small tubing element. This fundamental solution was used as a building block for arbitrary geometries where fluid properties may also vary longitudinally in the tube. The problem was solved recursively starting at the transducer and working upstream in the tube. Dynamic frequency response tests were performed for continuum flow conditions in the presence of temperature gradients. These tests validated the recursive formulation of the model. Model steady-state behavior was analyzed using the final value theorem. Tests were performed for rarefied flow conditions and compared to the model steady-state response to evaluate the regime of applicability. Model comparisons were excellent for Knudsen numbers up to 0.6. Beyond this point, molecular affects caused model analyses to become inaccurate.

Whitmore, Stephen A.↗
DOE OSTI2023

Efficient 3D Molecular Design with an E(3) Invariant Transformer VAE

This work introduces a three-dimensional (3D) invariant graph-to-string transformer variational autoencoders (VAE) (Vagrant) for generating molecules with accurate density functional theory (DFT)-level properties. Vagrant learns to model the joint probability distribution of a 3D molecular structure and its properties by encoding molecular structures into a 3D-aware latent space. Directed navigation through this latent space implicitly optimizes the 3D structure of a molecule, and the latent embedding can be used to condition a generative transformer to predict the candidate structure as a one-dimensional (1D) sequence. Additionally, we introduce two novel sampling methods that exploit the latent characteristics of a VAE to improve performance. Here, we show that our method outperforms comparable 3D autoregressive and diffusion methods for predicting quantum chemical property values of novel molecules in terms of both sample quality and computational efficiency.

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

Tuning the Molecular Structure and Reaction Mechanism of Olefin Metathesis by Model Bilayered Supported MoO x /AlO x /SiO 2 Catalysts

The molecular structure and activity of supported MoO x olefin metathesis catalysts are heavily impacted by the choice of catalyst support. In this study, surface modification of the SiO 2 support with AlO x and selective anchoring of the MoO x on the surface AlO x sites were used to tune the structure, activation, and reactivity of the resulting surface MoO x sites. Extensive in situ molecular characterization, chemical probe studies, and density functional theory (DFT) calculations reveal that the enhanced activity of the supported MoO x /AlO x /SiO 2 catalyst over the MoO x / SiO 2 catalyst is associated with more favorable activation and kinetics of surface MoO x anchored at AlO x sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗