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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 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Discussion on molecular dynamics (MD) simulations of the asphalt materials

The application of asphalt materials in pavement engineering has been increasingly widespread and sophisticated over the past several decades. Variations in the properties of asphalt binder during mixing, transportation, and paving can affect the performance of asphalt pavement. However, the asphalt material is a non-homogeneous and complex organic substance, consisting of various molecules with widely various molecular weights, elemental compositions, and structures. This complexity leads to difficulties for researchers to clearly and immediately understand the properties of asphalt materials and their variations. The multi-scale research approach combines macroscopic experimental data and microscopic simulation results from a practical engineering perspective. It helps to improve the understanding of asphalt materials. The molecular dynamics (MD) simulation proposes a corresponding molecular model of asphalt material based on experimental data, and the simulation algorithm is able to derive properties similar to those of real asphalt. Here, this paper provides a comprehensive review of the current studies on MD simulation of asphalt materials, including modeling, properties, and multi-scale analysis. As a key part of the computational simulation, this paper discusses the typical asphalt binder and asphalt-aggregate interface models constructed by different groups, and also presents their differences from real samples and their feasibility based on fundamental properties. After the introduction of molecular models, the extensive work made by researchers based on molecular models is categorically reviewed and discussed. The strengths and weaknesses of MD simulation methods in the study of asphalt materials are also summarized in order to provide the reader with a more comprehensive understanding of the relevant contents and to guide subsequent research.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Molecular Modes Elucidate the Nuclear Magnetic Resonance Relaxation of Viscous Fluids

The Bloembergen, Purcell, and Pound (BPP) theory of nuclear magnetic resonance (NMR) relaxation in fluids dating back to 1948 continues to be the linchpin in interpreting NMR relaxation data in applications ranging from characterizing fluids in porous media to medical imaging (MRI). The BPP theory is founded on assuming molecules are hard spheres with 1 H– 1 H dipole pairs reorienting randomly; assumptions that are severe in light of modern understanding of liquids. Nevertheless, it is intriguing to this day that the BPP theory was consistent with the original experimental data for glycerol, a hydrogen-bonding molecular fluid for which the hard-sphere-rigid-dipole assumption is inapplicable. To better understand this incongruity, atomistic molecular simulations are used to compute 1 H NMR T 1 relaxation dispersion (i.e., frequency dependence) in two contrasting cases: glycerol, and a (non hydrogen-bonding) viscosity standard. At high viscosities, simulations predict distinct functional forms of T 1 for glycerol compared to the viscosity standard, in agreement with modern measurements, yet both in contrast to BPP theory. The cause of these departures from BPP theory is elucidated, without assuming any relaxation models and without any free parameters, by decomposing the simulated T 1 response into dynamic molecular modes for both intramolecular and intermolecular interactions. The decomposition into dynamic molecular modes provides an alternative framework to understand the physics of NMR relaxation for viscous fluids.

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

Dynamic separation of gases using microsieves

Separation of light weight molecules, such as nitrogen, argon, and oxygen, from heavier compounds can have significant impacts on energy capture, environmental monitoring, or isotopic applications. Large-scale gas separation techniques, like gas centrifugation and membrane mitigation, can be problematic as they impart tremendous energy and induce high mechanical stress onto the instrumentation. Microsieves, also known as micronozzles or microfunnels, are developed to create physical barriers to separate specific isotopes and gases. Separation is achieved using a converging and diverging micronozzle to impose supersonic gas flow around a curved wall, and it has been used for the separation of heavy actinide isotopes in low weight gas as well as separation of low weight gas compositions of nitrogen and argon back in 1900s. However, systematic reviews of this unique technology are lacking. The application of the Laval style nozzle, which has a converging/diverging entrance fundamental to the micronozzle, is included in this review due to its importance in industrial applications in uranium (U) isotope refinement. Using advanced computational fluid dynamic (CFD) simulations, the extent of gas separation can be modelled. Herein, we first examine the literature and survey recent advances on fabrication techniques for creating curved micronozzles, methods and separation principles used to design devices. Furthermore, we then follow with highlights of CFD simulations applied to evaluate the separation effects using microsieves. Finally, identification of the gap and recommendation for future development and applications are suggested for using intrinsic molecular features and fluidic dynamics in formulating separation strategies.

30 Microfluidics↗
DOE OSTI2022

Modeling the Solvation and Acidity of Carboxylic Acids Using an Ab Initio Deep Neural Network Potential

Formic and acetic acid constitute the simplest of carboxylic acids, yet they exhibit fascinating chemistry in the condensed phase such as proton transfer and dimerization. The go-to method of choice for modeling these rare events have been accurate but expensive ab-initio molecular dynamics simulations. Here, we present a deep neural network potential trained using accurate ab-initio data that can be used in tandem with enhanced-sampling methods to perform an efficient exploration of the free-energy surface of aqueous solutions of weak carboxylic acids. In particular, we show that our model captures proton dissociation and provides a good estimate of the pK a , as well as the dimerization of formic and acetic acid. This provides a suitable starting point for applications in different research areas where computational efficiency coupled with the accuracy of ab-initio methods is required.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

An ab initio molecular dynamics investigation of the thermophysical properties of molten NaCl-MgCl 2

Molten salts have many applications in the nuclear and solar energy industries for thermal storage and heat transfer applications. However, there is a knowledge gap in molten salt thermophysical properties which hinders the technical readiness level of molten salt applications, especially in the nuclear industry. A common method of investigating new materials is through ab initio Molecular Dynamics (AIMD) simulations which is an effective tool to investigate structural and thermophysical properties at realistic temperatures. NaCl-MgCl 2 is an inexpensive salt that is a good candidate for use as a heat transfer medium in solar power applications or in the secondary loop of a nuclear reactor. In this article, the thermophysical properties of NaCl-MgCl 2 are computed via AIMD calculations to supplement the limited experimental studies in the literature. Here a wide range of compositions and temperatures for the pseudo-binary NaCl-MgCl 2 were used to calculate the density, heat capacity, compressibility, enthalpy of mixing, and volumetric thermal expansion coefficient. AIMD is shown to accurately model the densities of molten NaCl-MgCl 2 as there is good agreement with the available literature. This work observed a transition to a monotonic increase of the density with respect to MgCl 2 composition occurring above 1100 K. The heat capacity values increase uniformly with respect to concentration of MgCl 2 at a rate of 2.85 J/mol-K per 10 mol% of MgCl 2 . Select thermophysical properties are fit to a Redlich-Kister expansion for utilization in multiphysics simulations.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Unravelling Microstructure Selection in an Additively Manufactured Eutectic High‐Entropy Alloy

High-entropy alloys (HEAs) are promising candidates for advanced structural applications due to their excellent mechanical properties. Additive manufacturing (AM), with its rapid solidification conditions, enables the creation of unique nonequilibrium microstructures. To fully leverage the synergy between AM and HEAs, understanding how processing affects structure and properties is essential. Here, how solidification rate influences microstructure evolution and phase transformation pathway in laser additively manufactured AlCrFe2Ni2 eutectic HEAs is investigated. By increasing the laser scan speed and hence the solidification rate, distinct solidification modes evolving from coupled eutectic to anomalous eutectic and eventually to single-phase solidification are revealed. These transitions result in distinct microstructures and a wide range of mechanical properties. Thermodynamic modeling and molecular dynamics simulations reveal that low cooling rates allow for sufficient atomic diffusion and phase separation, facilitating coupled eutectic growth. In contrast, rapid cooling suppresses diffusion and destabilizes the solid–liquid interface, promoting anomalous or single-phase solidification. This integrated experimental and computational approach provides a multiscale understanding of solidification mechanisms in HEAs and underscores how kinetic effects can over-ride thermodynamic predictions under nonequilibrium conditions. Furthermore, these results demonstrate that AM can serve as a powerful tool to design HEAs with tailored microstructures and properties.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Modeling separation of lanthanides via heterogeneous ligand binding

Individual lanthanide elements have physical/electronic/magnetic properties that make each useful for specific applications. Several of the lanthanides cations (Ln 3+ ) naturally occur together in the same ores. They are notoriously difficult to separate from each other due to their chemical similarity. Predicting the Ln 3+ differential binding energies (ΔΔE) or free energies (ΔΔG) at different binding sites, which are key figures of merit for separation applications, will help design of materials with lanthanide selectivity. We apply ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) to calculate ΔΔG for Ln 3+ coordinated to ligands in water and embedded in metal–organic frameworks (MOFs), and ΔΔE for Ln 3+ bonded to functionalized silica surfaces, thus circumventing the need for the computational costly absolute binding (free) energies ΔG and ΔE. Perturbative AIMD simulations of water-inundated simulation cells are applied to examine the selectivity of ligands towards adjacent Ln 3+ in the periodic table. Static DFT calculations with a full Ln 3+ first coordination shell, while less rigorous, show that all ligands examined with net negative charges are more selective towards the heavier lanthanides than a charge-neutral coordination shell made up of water molecules. Amine groups are predicted to be poor ligands for lanthanide-binding. Finally, we also address cooperative ion binding, i.e., using different ligands in concert to enhance lanthanide selectivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration

Abstract Motivation Volumetric 3D object analyses are being applied in research fields such as structural bioinformatics, biophysics, and structural biology, with potential integration of artificial intelligence/machine learning (AI/ML) techniques. One such method, 3D Zernike moments, has proven valuable in analyzing protein structures (e.g., protein fold classification, protein–protein interaction analysis, and molecular dynamics simulations). Their compactness and efficiency make them amenable to large-scale analyses. Established methods for deriving 3D Zernike moments, however, can be inefficient, particularly when higher order terms are required, hindering broader applications. As the volume of experimental and computationally-predicted protein structure information continues to increase, structural biology has become a “big data” science requiring more efficient analysis tools. Results This application note presents a Python-based software package, ZMPY3D, to accelerate computation of 3D Zernike moments by vectorizing the mathematical formulae and using graphical processing units (GPUs). The package offers popular GPU-supported libraries such as CuPy and TensorFlow together with NumPy implementations, aiming to improve computational efficiency, adaptability, and flexibility in future algorithm development. The ZMPY3D package can be installed via PyPI, and the source code is available from GitHub. Volumetric-based protein 3D structural similarity scores and transform matrix of superposition functionalities have both been implemented, creating a powerful computational tool that will allow the research community to amalgamate 3D Zernike moments with existing AI/ML tools, to advance research and education in protein structure bioinformatics. Availability and implementation ZMPY3D, implemented in Python, is available on GitHub (https://github.com/tawssie/ZMPY3D) and PyPI, released under the GPL License.

Lai, Jhih-Siang (ORCID:0000000156775890)↗
DOE OSTI2021

Molecular Dynamics Simulations of a Catalytic Multivalent Peptide–Nanoparticle Complex

Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide–nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure–function relationship, for technological and nanomedical applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Insight into Pyroelectricity and Phase Transitions in Ferroelectrics from Nonequilibrium Approach: The Case of PbTiO 3

Computational methodology is proposed to simulate time dependent temperature variations via thermostat approach. Here, the methodology is applied to study pyroelectricity under nonequilibrium conditions in prototypical ferroelectric PbTiO 3 . It is found that at room temperature the nonequilibrium effects in pyroelectricity begin manifesting above 1.0 THz and originate from the overlap with the intrinsic soft mode frequency. Therefore, the proposed computational methodology can be used to predict equilibrium pyroelectric response by choosing a frequency of temperature variation below the intrinsic polar mode frequencies for the material. Probing the dynamics of ferroelectric phase transition with the proposed methodology revealed that it takes about a nanosecond for the computational supercell to undergo phase transition. It is concluded that computational techniques capable of simulating picoseconds can be used to compute pyroelectric response from nonequilibrium dynamical approach while those that can reach nanoseconds are suitable for simulating phase transitions in ferroelectrics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Active Learning Framework

Machine learning (ML) of interatomic potentials show great promise to accelerate scientific simulation, e.g., by emulating expensive computations at a high accuracy but much reduced computational cost. Training datasets are calculated from computationally expensive ab initio quantum mechanics methods, density functional theory (DFT). Trained on this data, an ML model can be very successful in predicting energy and forces for new atomic configurations. A critical factor is the quality and diversity of the training dataset. Thus, a highly automated approach to dataset construction based on active learning framework is designed suitable for material physics. The active learning scheme begins with fully randomized atomic configurations. Then, many Molecular Dynamics (MD) trajectories are simulated using current ML potentials, where each MD trajectory is initialized to a random disordered configuration. The temperature is varied in order to diversify the sampled configuration during these simulations. The variance of predictions for eight neural networks within an ensemble is analyzed to determine whether the model is operating as expected. This helps in determining whether collecting more data would be helpful to the model by checking the ensemble variance is greater than the threshold. In this case, the MD trajectory is terminated and the final atomic configuration is placed on a queue (SQL database) for DFT calculations and added to training dataset. Periodically, ML model is retrained to the updated training model. This Active Learning loop is iterated until the cost of MD simulations becomes prohibitively expensive. The MD simulations will hopefully be sufficiently robust to support nucleation after many active learning iterations. In this sense, active learning scheme must automatically discover the important low energy and nonequilibrium physics.

Nebgen, Benjamin↗
DOE OSTI2025

Fast methods for multisite charge transfer processes. I. Constrained, state averaged CASSCF(1,n) and CASSCF(2n − 1,n) simulations

We design a dynamically weighted state-averaged constrained complete active space self-consistent field (DW-SA-cCASSCF) algorithm to treat electrons or holes moving between n molecular fragments (where n can be larger than 2). Within such a so-called eDSCn/hDSCn approach, we consider configurations that are mutually single excitations of each other, and we apply a generalized set of constraints to tailor the method for studying charge transfer problems. The constrained optimization problem is efficiently solved using a DIIS-SQP algorithm, thus maintaining computational efficiency. We demonstrate the method for a finite Su–Schrieffer–Heeger chain, successfully reproducing the expected exponential decay of diabatic couplings with distance. When combined with a gradient, the current extension immediately enables efficient nonadiabatic dynamics simulations of complex multi-state charge transfer processes.

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

A Holistic Approach for Elucidating Local Structure, Dynamics, and Speciation in Molten Salts with High Structural Disorder

To examine ion solvation, exchange, and speciation for minority components in molten salts (MS) typically found as corrosion products, we propose a multimodal approach combining extended X-ray absorption fine structure (EXAFS) spectroscopy, optical spectroscopy, ab initio molecular dynamics (AIMD) simulations, and rate theory of ion exchange. Going beyond conventional EXAFS analysis, our method can accurately quantify populations of different coordination states of ions with highly disordered coordination environments via linear combination fitting of the EXAFS spectra of these coordination states computed from AIMD to the experimental EXAFS spectrum. In a case study of dilute Ni(II) dissolved in the ZnCl 2 +KCl melts, our method reveals heterogeneous distributions of coordination states of Ni(II) that are sensitive to variations in temperature and melt composition. These results are fully explained by the difference in the chloride exchange dynamics at varied temperatures and melt compositions. Finally, this insight will enable a better understanding and control of ion solubility and transport in MS.

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

Berni Julian Alder, theoretical physicist and inventor of molecular dynamics, 1925–2020

Berni Julian Alder, one of the leading figures in the invention of molecular dynamics simulations used for a wide array of problems in physics and chemistry, died on September 7th, 2020. His career, spanning more than 65 years, transformed statistical mechanics, many body physics, the study of chemistry and the microscopic dynamics of fluids, by making atomistic computational simulation (in parallel with traditional theory and experiment) a new pathway to unexpected discoveries. Among his many honors, the CECAM prize, recognizing exceptional contributions to the simulation of the microscopic properties of matter is named for him. He was awarded the National Medal of Science by President Obama in 2008.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Mechanistic Studies of a Primitive Homolog of Nitrogenase Involved in Coenzyme F430 Biosynthesis

Methyl-coenzyme M reductase (MCR) is the key enzyme in the biological formation and anaerobic oxidation of methane (AOM). Methane is a potent greenhouse gas and the major component of natural gas. Given the abundance of natural gas reserves in remote areas, there is great current interest in a scalable bio-based process for the conversion of methane to liquid fuel or other high-value commodity chemicals. MCR holds much promise for use in such a methane bioconversion strategy. However, MCR cannot currently be produced in an active form in a heterologous host, due in large part to the lack of genetic and biochemical information about the production of holo MCR. In an effort to overcome this deficiency, our laboratory elucidated the biosynthetic pathway of the unique nickel-containing coenzyme of MCR, F430. The key step in coenzyme F430 biosynthesis (Cfb) was found to involve an unprecedented reductive cyclization reaction that converts Ni-sirohydrochlorin a , c -diamide to 15,17 3 -seco-F430-17 3 -acid. This remarkable transformation, which involves a 6-electron reduction of the isobacteriochlorin ring system, cyclization of the c -acetamide side chain to form a γ-lactam ring, and the formation of 7 stereocenters, is catalyzed by a primitive homolog of nitrogenase (CfbCD). Nitrogenase is a two-component metalloenzyme that catalyzes the ATP-dependent reduction of dinitrogen to ammonia (nitrogen fixation). Homologs of nitrogenase are also involved in the biosynthesis of the photosynthetic pigments chlorophyll and bacteriochlorophyll. Phylogenetic analysis of the CfbCD complex suggests that it is representative of a more ancient lineage of the nitrogenase superfamily, and a thorough investigation of its structure and function is likely to shed light on the mechanisms and evolution of these important metalloenzymes that catalyze multi-electron redox reactions. Moreover, a detailed understanding of the mechanism of the CfbCD complex may aid in the development of specific inhibitors to help reduce natural greenhouse gas emissions and can be exploited for the heterologous production of MCR for methane bioconversion. Towards these goals, the following Specific Aims will be pursued to determine the: 1) Identity of the CfbCD reaction product. The exact reaction catalyzed by CfbCD, including the number of electrons transferred and whether it involves enzymatic cyclization, is unclear. Several approaches, including reaction stoichiometry measurements, spectroelectrochemistry, and magnetic resonance spectroscopy will be applied to elucidate the structure of the reaction product and establish whether CfbCD is a reductase or reductive cyclase. 2) Structure, conformational dynamics, and oligomerization state changes of CfbCD. Significant insight into the mechanism and allosteric regulation of CfbCD can be obtained by assessing changes in the structure and dynamics of the complex during the catalytic cycle. To accomplish this, a combination of size-exclusion chromatography, hydrogen-deuterium exchange mass spectrometry, molecular dynamics simulations, and high-resolution structural methods will be employed. 3) Source, order, and stereochemistry of proton additions during CfbCD catalysis. Details regarding the order and stereochemistry of proton additions during the CfbCD reaction will be uncovered using a combined spectroscopic and computational approach. Complementary mechanistic studies employing site-directed mutagenesis and substrate analogs will establish the identity of active site acid residues and the possible involvement of substrate-assisted catalysis during the CfbCD reaction.

09 BIOMASS FUELS↗
DOE OSTI2022

Computational Insights into Malononitrile-Based Carbanions for CO 2 Capture

Although anionic N and O sites have been widely used in chemisorption of CO 2 , carbanions are much less explored for CO 2 capture. Here, in this study, we employ ab initio calculations and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations to examine the interaction between CO 2 and the malononitrile carbanion, [CH(CN) 2 ] – . We have explored the potential energy surface of CO 2 binding by scanning the C–C distance between CO 2 and the central C site of the carbanion. We find that CO 2 prefers to bind to the nitrile group physically rather than to form a C–C bond via the carboxylation reaction at the sp 2 C site. Moreover, the two –CN groups can attract two CO 2 molecules at equal strength. The presence of an alkali metal ion enhances both physical and chemical interactions of CO 2 with the malononitrile carbanion. QM/MM MD simulations further confirm the preference of physical interaction in the condensed ionic liquid phase with a phosphonium cation. Our findings suggest that ionic liquids based on the malononitrile carbanion may have a high CO 2 solubility for carbon capture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗