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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 1,657 records · Page 92
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Near-continuum, hypersonic oxygen flow over a double cone simulated by direct simulation Monte Carlo informed from quantum chemistry

A large-scale, fully resolved direct simulation Monte Carlo (DSMC) computation of a non-equilibrium, reactive flow of pure oxygen over a double cone is presented. Under the simulated near-continuum conditions, the computational demands are shown to be significant because of the wide range of length scales that must be resolved. Therefore, robust grid adaption capabilities and efficient parallelization of the Stochastic PArallel Rarefied-gas Time-accurate Analyzer (SPARTA) code that is utilized in this work are essential. The thermochemical and transport collision models were selected for efficiency and simplicity. First-principles data, obtained from the highly accurate direct molecular simulation method, were used to inform the collision models’ parameters. Importantly, because SPARTA implements molecular collision models using collision-specific energies, the resulting macroscopic relaxation rates were evaluated a posteriori via zero-dimensional heat bath simulations. The comparisons of surface properties, namely heat flux and pressure, show very close agreement with previous computational fluid dynamics (CFD) results. Differences with the measurements were found to be similar to the CFD simulations. The unresolved discrepancy with the measurements could be due to inconsistent free stream conditions with the actual experimental data or missing physical phenomena altogether, for example atomic and molecular oxygen electronically excited states, three-dimensional effects, or more complex gas–surface interactions. As shown in this work, the advantages of obtaining a DSMC particle solution for these flows reside in the method's ability to be directly informed from first principles and to seamlessly describe internal energy non-equilibrium for all modes. With the advent of exascale computing and beyond, particle methods will be an increasingly important tool to verify the validity of physical assumptions in reduced-order models via fully resolved, experimental-scale simulations, down to the level of molecular-level distributions.

Mechanics↗
DOE OSTI2020

Transport phenomena in electrolyte solutions: Nonequilibrium thermodynamics and statistical mechanics

The theory of transport phenomena in multicomponent electrolyte solutions is presented here through the integration of continuum mechanics, electromagnetism, and nonequilibrium thermodynamics. The governing equations of irreversible thermodynamics, including balance laws, Maxwell's equations, internal entropy production, and linear laws relating the thermodynamic forces and fluxes, are derived. Green–Kubo relations for the transport coefficients connecting electrochemical potential gradients and diffusive fluxes are obtained in terms of the flux–flux time correlations. Furthermore, the relationship between the derived transport coefficients and those of the Stefan–Maxwell and infinitely dilute frameworks are presented, and the connection between the transport matrix and experimentally measurable quantities is described. To exemplify the application of the derived Green–Kubo relations in molecular simulations, the matrix of transport coefficients for lithium and chloride ions in dimethyl sulfoxide is computed using classical molecular dynamics and compared with experimental measurements.

42 ENGINEERING↗
DOE OSTI2015

Extension of the BMCSL equation of state for hard spheres to the metastable disordered region: Application to the SAFT approach

A simple modification of the Boublík-Mansoori-Carnahan-Starling-Leland equation of state is proposed for an application to the metastable disordered region. The new model has a positive pole at the jamming limit and can accurately describe the molecular simulation data of pure hard in the stable fluid region and along the metastable branch. The new model has also been applied to binary mixtures hard spheres, and an excellent description of the fluid and metastable branches can be obtained by adjusting the jamming packing fraction. The new model for hard sphere mixtures can be used as the repulsive term of equations of state for real fluids. In this case, the modified equations of state give very similar predictions of thermodynamic properties as the original models, and one can remove the multiple liquid density roots observed for some versions of the Statistical Associating Fluid Theory (SAFT) at low temperature without any modification of the dispersion term.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Light-induced dilation in nanosheets of charge-transfer complexes

We observe a sizable photostrictive effect of 5.7% with fast, submillisecond response times, arising from a light-induced lattice dilation of a molecular nanosheet, composed of the molecular charge-transfer compound dibenzotetrathiafulvalene (DBTTF) and C 60 . An interfacial self-assembly approach is introduced for the thickness-controlled growth of the thin films. From photoabsorption measurements, molecular simulations, and electronic structure calculations, we suggest that photostriction within these films arises from a transformation in the molecular structure of constituent molecules upon photoinduced charge transfer, as well as the accommodation of free charge carriers within the material. Additionally, we find that the photostrictive properties of the nanosheets are thickness-dependent, a phenomenon that we suggest arises from surface-induced conformational disorder in the molecular components of the film. Moreover, because of the molecular structure in the films, which results largely from interactions between the constituent π-systems and the sulfur atoms of DBTTF, the optoelectronic properties are found to be anisotropic. This work enables the fabrication of 2D molecular charge-transfer nanosheets with tunable thicknesses and properties, suitable for a wide range of applications in flexible electronic technologies.

2D nanosheets↗
DOE OSTI2024

Early Career Researcher Support for Foundations of Molecular Modeling and Simulation Conference

This project enabled 14 early career researchers, including graduate students and postdocs, to attend the 8th triennial conference on Foundations of Molecular Modeling and Simulation (FOMMS 2022), which took place in Delavan, WI (Lake Geneva area), from July 17 to 21, 2022. Molecular-level modeling and simulation, which serve as critical tools for advancing science and engineering in a myriad of applications, were at the forefront of discussions. These ranged from the design of new materials for various energy applications to insights into the interaction between drug molecules and protein receptors within the body.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Constructing polyatomic potential energy surfaces by interpolating diabatic Hamiltonian matrices with demonstration on green fluorescent protein chromophore

Simulating molecular dynamics directly on quantum chemically obtained potential energy surfaces is generally time consuming. The cost becomes overwhelming especially when excited state dynamics is aimed with multiple electronic states. The interpolated potential has been suggested as a remedy for the cost issue in various simulation settings ranging from fast gas phase reactions of small molecules to relatively slow condensed phase dynamics with complex surrounding. Here, we present a scheme for interpolating multiple electronic surfaces of a relatively large molecule, with an intention of applying it to studying nonadiabatic behaviors. The scheme starts with adiabatic potential information and its diabatic transformation, both of which can be readily obtained, in principle, with quantum chemical calculations. The adiabatic energies and their derivatives on each interpolation center are combined with the derivative coupling vectors to generate the corresponding diabatic Hamiltonian and its derivatives, and they are subsequently adopted in producing a globally defined diabatic Hamiltonian function. As a demonstration, we employ the scheme to build an interpolated Hamiltonian of a relatively large chromophore, para-hydroxybenzylidene imidazolinone, in reference to its all-atom analytical surface model. We show that the interpolation is indeed reliable enough to reproduce important features of the reference surface model, such as its adiabatic energies and derivative couplings. In addition, nonadiabatic surface hopping simulations with interpolation yield population transfer dynamics that is well in accord with the result generated with the reference analytic surface. With these, we conclude by suggesting that the interpolation of diabatic Hamiltonians will be applicable for studying nonadiabatic behaviors of sizeable molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 million deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for COVID-19 includes: (1) designing a vaccine as future protection; (2) de novo drug discovery; and (3) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determine two apo structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial femtosecond X-ray crystallography. We employ detailed molecular simulations of selected known main protease inhibitors with the structures and compare binding modes and energies. The combined structural and molecular modeling studies not only reveal the dynamics of small molecules targeting the main protease but also provide invaluable opportunities for drug repurposing and structure-based drug design strategies against SARS-CoV-2.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Simulation of supersonic molecular beam injection fueling into H-mode plasmas on EAST using BOUT++

Transport dynamic 2D simulations for supersonic molecular beam injection (SMBI) fueling into H-mode deuterium plasmas on the Experimental Advanced Superconducting Tokamak (EAST) is first simulated using a seven-field two-fluid model in the BOUT++ framework. The SMB is assumed to be injected into plasma from the midplane at the low field side with a fixed width and constant molecular flux. The different densities and injection velocities of SMBI are investigated within the upper single-null geometry of EAST. The simulations indicate that the SMBI has a self-shielding effect on molecules' inward transport into the plasma, and the deposition of SMBI leads to a large increase in plasma density and decrease in plasma temperature. There is a velocity threshold for SMB penetrating the pedestal and depositing at the top of density pedestal. However, the deposition point would be back toward the plasma boundary after SMB arriving at the deepest penetration position. Comparing the different molecular injection velocities and densities, the outcomes demonstrate that the depth of deposition is closely related to the injection velocity rather than the molecular density. The simulated results show good agreement with the EAST experiments by comparing the electron density profiles obtained by simulation and experiment, respectively. These results will be helpful for guiding future experiments, as well as the design of the SMBI system.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Incorporating Electronic Information into Machine Learning Potential Energy Surfaces via Approaching the Ground-State Electronic Energy as a Function of Atom-Based Electronic Populations

Machine learning (ML) approximations to density functional theory (DFT) potential energy surfaces (PESs) are showing great promise for reducing the computational cost of accurate molecular simulations, but at present, they are not applicable to varying electronic states, and in particular, they are not well suited for molecular systems in which the local electronic structure is sensitive to the medium to long-range electronic environment. With this issue as the focal point, we present a new machine learning approach called "BpopNN" for obtaining efficient approximations to DFT PESs. Conceptually, the methodology is based on approaching the true DFT energy as a function of electron populations on atoms; in practice, this is realized with available density functionals and constrained DFT (CDFT). Additionally, the new approach creates approximations to this function with neural networks. These approximations thereby incorporate electronic information naturally into a ML approach, and optimizing the model energy with respect to populations allows the electronic terms to self-consistently adapt to the environment, as in DFT. We confirm the effectiveness of this approach with a variety of calculations on LinHn clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Highly Selective Supported Graphene Oxide Membranes for Water-Ethanol Separation

Polyethersulfone (PES)-supported graphene oxide (GO) membrane has been developed by a simple casting approach. This stable membrane is applied for ethanol/water separation at different temperatures. The 5.0 µm thick GO film coated on PES membrane showed a long-term stability over a testing period of one month and excellent water/ethanol selectivity at elevated temperatures. The water/ethanol selectivity is dependent on the ethanol weight percentage in the water/ethanol feed mixtures and the operating temperature. The water/ethanol selectivity was enhanced with an increase of ethanol weight percentage in water/ethanol mixtures and from below 100 at RT to close to 874 at 90 ºC for 90% ethanol/10% water mixture. Molecular simulations of water-ethanol mixtures in graphene bilayers that are considered to play a key role in transport revealed that molecular transport is negligible for layer spacing below 1 nm. The differences in the diffusion of ethanol and water in the bilayer are not consistent with the large selectivity value experimentally observed. The entry of water and ethanol into the interlayer space may be the crucial step controlling the selectivity.

36 MATERIALS SCIENCE↗
DOE OSTI2015

A review on nanomechanical resonators and their applications in sensors and molecular transportation

Nanotechnology has opened a new area in science and engineering, leading to the development of novel nano-electromechanical systems such as nanoresonators with ultra-high resonant frequencies. The ultra-high-frequency resonators facilitate wide-ranging applications such as ultra-high sensitive sensing, molecular transportation, molecular separation, high-frequency signal processing, and biological imaging. This paper reviews recent studies on dynamic characteristics of nanoresonators. A variety of theoretical approaches, i.e., continuum modeling, molecular simulations, and multiscale methods, in modeling of nanoresonators are reviewed. The potential application of nanoresonators in design of sensor devices and molecular transportation systems is introduced. The essence of nanoresonator sensors for detection of atoms and molecules with vibration and wave propagation analyses is outlined. The sensitivity of the resonator sensors and their feasibility in detecting different atoms and molecules are particularly discussed. Furthermore, the applicability of molecular transportation using the propagation of mechanical waves in nanoresonators is presented. An extended application of the transportation methods for building nanofiltering systems with ultra-high selectivity is surveyed. The article aims to provide an up-to-date review on the mechanical properties and applications of nanoresonators, and inspire additional potential of the resonators.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Reticular Materials and AI-Driven Computer Simulations for Seawater Mining of Valuable Metals (Final Technical Report)

This Final Technical Report describes our exploratory efforts that combine reticular materials synthesis (hydrolytically robust metal–organic frameworks, MOFs) with AI‑enabled molecular simulations to develop mechanistic, quantitative design rules for recovering lithium and other alkali-metal ions from highly dilute, competitive aqueous resources (e.g., seawater). The central outcome is a joint experimental–computational study of ion uptake in MOF‑808 (Chemical Science, 2025) that quantifies both thermodynamics and kinetics of Li + , Na + , and K + uptake and identifies how pore size, pore hydration state, dehydration penalties, and pore-window transport barriers govern selectivity. Guided by these insights, we synthesized and tested functionalized MOF‑808 and multivariate MOFs incorporating ion-recognition motifs (including carboxylates and crown-ether linkers) and evaluated uptake in synthetic seawater, highlighting framework topology and pore chemistry as levers for improved Li + /Na + discrimination. We also developed transferable simulation models, enhanced-sampling protocols, and automated workflows that enable systematic screening of porous sorbents.

42 ENGINEERING↗
DOE OSTI2025

Beyond real: alternative unitary cluster Jastrow models for molecular electronic structure calculations on near-term quantum computers

Near-term quantum devices require wavefunction ansätze that are expressive while also of shallow circuit depth in order to both accurately and efficiently simulate molecular electronic structure. While the unitary coupled cluster ansatz (e.g., UCCSD) has become a standard, the high gate count associated with the implementation of this limits its feasibility on noisy intermediate-scale quantum (NISQ) hardware. k -Fold unitary cluster Jastrow (uCJ) ansätze mitigate this challenge by providing O( kN 2 ) circuit scaling and favorable linear depth circuit implementation. Previous work has focused on the real orbitalrotation (Re-uCJ) variant of uCJ, which allows an exact (Trotter-free) implementation. Here we extend and generalize the k -fold uCJ framework by introducing two new variants, Im-uCJ and g-uCJ, which incorporate imaginary and fully complex orbital rotation operators, respectively. Similar to Re-uCJ, both of the new variants achieve quadratic gate-count scaling. Our results focus on the simplest k = 1 model, and show that the uCJ models frequently maintain energy errors within chemical accuracy (∼1 kcal mol −1 ). Both g-uCJ and Im-uCJ are more expressive in terms of capturing electron correlation and are also more accurate than the earlier Re-uCJ ansatz. We further show that Im-uCJ and g-uCJ circuits can also be implemented exactly, without any Trotter decomposition. Numerical tests using k = 1 on H 2 , H 3 + , Be 2 , C 2 H 4 , C 2 H 6 and C 6 H 6 in various basis sets confirm the practical feasibility of these shallow Jastrow-based ansätze for applications on near-term quantum hardware.

Tkachenko, Nikolay V. [University of California, B↗
DOE OSTI2026

Deriving effective electrode–ion interactions from free-energy profiles at electrochemical interfaces

Understanding ion adsorption at electrified metal–electrolyte interfaces is essential for accurate modeling of electrochemical systems. Here, in this study, we systematically investigate the free energy profiles of Na + , Cl − , and F − ions at the Au(111)–water interface using enhanced sampling molecular dynamics with both classical force fields and machine-learned interatomic potentials (MLIPs). Our classical metadynamics results reveal a strong dependence of predicted ion adsorption on the Lennard-Jones parameters, highlighting that—without due care—standard mixing rules can lead to qualitatively incorrect descriptions of ion–metal interactions. We present a systematic methodology for tuning the cross term LJ parameters to control adsorption energetics in agreement with more accurate models. As a surrogate for an ab initio model, we employed the recently released Universal Models for Atoms MLIP, which validates classical trends and displays strong specific adsorption for chloride, weak adsorption for fluoride, and no specific adsorption for sodium, in agreement with experimental and theoretical expectations. By integrating molecular-level adsorption free energies into continuum models of the electric double layer, we show that specific ion adsorption substantially alters the interfacial ion population, the potential of zero charge, and the differential capacitance of the system. Our results underscore the critical importance of force field parameterization and advanced interatomic potentials for the predictive modeling of ion-specific effects at electrified interfaces and provide a robust framework for bridging molecular simulations and continuum electrochemical models.

Roncoroni, Fabrice [Lawrence Berkeley National Lab↗
DOE OSTI2015

Stout: Cloudy’s atomic and molecular database

We describe a new atomic and molecular database we developed for use in the spectral synthesis code Cloudy. The design of Stout is driven by the data needs of Cloudy, which simulates molecular, atomic, and ionized gas with kinetic temperatures 2.8 K<T<10{sup 10} K and densities spanning the low-to high-density limits. The radiation field between photon energies 10{sup −8} Ry and 100 MeV is considered, along with all atoms and ions of the lightest 30 elements, and ∼10{sup 2} molecules. For ease of maintenance, the data are stored in a format as close as possible to the original data sources. Few data sources include the full range of data we need. We describe how we fill in the gaps in the data or extrapolate rates beyond their tabulated range. We tabulate data sources both for the atomic spectroscopic parameters and for collision data for the next release of Cloudy. This is not intended as a review of the current status of atomic data, but rather a description of the features of the database which we will build upon.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Communication: Probing anomalous diffusion in frequency space

Anomalous diffusion processes are usually detected by analyzing the time-dependent mean square displacement of the diffusing particles. The latter evolves asymptotically as W(t) ∼ 2D{sub α}t{sup α}, where D{sub α} is the fractional diffusion constant and 0 < α < 2. In this article we show that both D{sub α} and α can also be extracted from the low-frequency Fourier spectrum of the corresponding velocity autocorrelation function. This offers a simple method for the interpretation of quasielastic neutron scattering spectra from complex (bio)molecular systems, in which subdiffusive transport is frequently encountered. The approach is illustrated and validated by analyzing molecular dynamics simulations of molecular diffusion in a lipid POPC bilayer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗