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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 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Effective Fragment Potential-Based Molecular Dynamics Studies of Diffusion in Acetone and Hexane

To facilitate more reliable descriptions of transport properties in liquids, molecular dynamics (MD) simulations are performed based on the effective fragment potential (EFP) method derived from first-principles quantum mechanics (in contrast to MD based upon empirically fitted potentials). The EFP method describes molecular interactions in terms of Coulomb, polarization/induction, dispersion, exchange-repulsion, and charge-transfer interactions. The EFP MD simulations described in this paper, performed on hexane and acetone, are able to track the mean-square displacement of molecules for sufficient time to reliably extract translational diffusion coefficients. Finally, the results reported here are in reasonable agreement with experiment.

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

Anharmonic phonons, thermal expansion, and nuclear quantum effects in Zn

The anharmonic behavior of phonons and thermal expansion of hexagonal zinc were studied from 15 to 690 K by inelastic neutron scattering (INS) and ab initio simulations. Phonon spectra were measured for Q-points covering the full Brillouin zone, giving the phonon density of states (DOS) and dispersions along high-symmetry directions. The dispersions were sharp at 15 K, but diffuse intensity was observed at energies above them. The dispersions broadened with temperature T and the diffuse intensity became stronger. This diffuse intensity appeared in all INS measurements and simulations, except for classical molecular dynamics at 15 K. The temperature-dependent effective potential (TDEP) method, which included the nuclear quantum effect from zero-point vibrational dynamics, was used to calculate the free energy and thermal expansion. For T < 100 K nuclear quantum effects were important for obtaining the correct negative thermal expansion, and path integral molecular dynamics (PIMD) was particularly effective for obtaining the negative thermal expansion in the basal plane. A Heisenberg-Langevin model for interacting phonons coupled to a thermal bath was able to reproduce the shape and intensity of the diffuse spectral features.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Ab initio molecular dynamics with enhanced sampling in heterogeneous catalysis

Ab initio molecular dynamics simulations combined with enhanced sampling techniques are becoming widespread methods to investigate chemical phenomena in catalytic systems. These techniques automatically include finite temperature effects, anharmonicity, and collective dynamics in their robust description of enthalpic and entropic contributions, which can have significant impact on reaction free energy landscapes. This contrasts with standard ab initio static approaches that are based on assessing reaction free energies from various coarse-grained descriptions of the reaction potential energy surface. Enhanced sampling ab initio molecular dynamics opens the way to first principles simulations of systems of increasing complexity like solid/liquid catalytic interfaces. Here, we aim at guiding the reader through the basis of these techniques, summarizing their fundamental theoretical and practical aspects, and reviewing the relevant literature in the field. After a brief introduction to the problem, we will illustrate the advantage of using molecular simulations to include finite temperature effects, examine the most common ab initio techniques currently in use, describe their application to solid state heterogeneous catalysts, and finally critically review the most popular enhanced sampling techniques used in computational catalysis.

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

CTRAMER: An open-source software package for correlating interfacial charge transfer rate constants with donor/acceptor geometries in organic photovoltaic materials

In this paper, we present CTRAMER (Charge-Transfer RAtes from Molecular dynamics, Electronic structure, and Rate theory)—an opensource software package for calculating interfacial charge-transfer (CT) rate constants in organic photovoltaic (OPV) materials based on ab initio calculations and molecular dynamics simulations. The software is based on identifying representative donor/acceptor geometries within interfacial structures obtained from molecular dynamics simulation of donor/acceptor blends and calculating the corresponding Fermi’s golden rule CT rate constants within the framework of the linearized-semiclassical approximation. While the methods used are well established, the integration of these state-of-the-art tools originating from different disciplines to study photoinduced CT processes with explicit treatment of the environment, in our opinion, makes this package unique and innovative. The software also provides tools for investigating other observables of interest. After outlining the features and implementation details, the usage and performance of the software are demonstrated with results from an example OPV system.

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

Rotational and translational diffusion of liquid n-hexane: EFP-based molecular dynamics analysis

Molecular Dynamics (MD) simulations based on the Effective Fragment Potential (EFP) method are utilized to provide a comprehensive assessment of diffusion in liquid n-hexane. We decompose translational diffusion into components along and orthogonal to the long axis of the molecule. Rotational diffusion is decomposed into tumbling and spinning motions about this axis. Our analysis yields four corresponding diffusion coefficients which are related to diagonal entries in the complete 6 × 6 diffusion tensor accounting for the three rotational and three translational degrees of freedom and for the potential coupling between them. However, coupling between different degrees of freedom is expected to be minimal for a natural choice of the molecular body-fixed axis, so then off-diagonal entries in the tensor are negligible. This expectation is supported by a hydrodynamic analysis of the diffusion tensor which treats the liquid surrounding the molecule being tracked as a viscous continuum. Thus, the EFP MD analysis provides a comprehensive characterization of diffusion and also reveals expected shortcomings of the hydrodynamic treatment, particularly for rotational diffusion, when applied to neat liquids.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Geometrically necessary dislocation fingerprints of dislocation loop absorption at grain boundaries

Here we present a numerical methodology to compute the Nye-tensor fingerprints of dislocation loop absorption at grain boundaries (GBs) for comparison with TEM observations of irradiated polycrystals. Our approach links atomistic simulations of self-interstitial atom (SIA) prismatic loops gliding toward and interacting with GBs in body-centered cubic iron with experimentally extracted geometrically necessary dislocation (GND) maps to facilitate the interpretation of damage processes. The Nye-tensor analysis is strongly mesh-size dependent—corresponding to resolution-dependent TEM observations. The method computes GND fingerprints from discretized dislocation line segments extracted from molecular dynamics simulations of dislocation loops being absorbed at a GB. Specifically, we perform MD simulation of prismatic loops of two diameters and monitor the three stages of the absorption process: loop glide, the partial, and full absorption of the loops at a [1 0 0] symmetric tilt GB. These methods provide a framework for future investigations of the nature of defect absorption by grain boundaries under irradiation conditions.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Insights into the Properties of MXenes and MXene Analogs from Atomistic Simulation

We review the properties that have been predicted for MXenes and MXene analogs from computational simulation with a focus on structural and electronic properties, energy storage, and ion transport. Methods considered range from quantum mechanical approaches to classical molecular dynamics. We conclude by reviewing current limitations and outstanding questions for simulation and MXene properties that have been little explored to-date.

Muraleedharan, Murali Gopal↗
DOE OSTI2020

The relation between lignin sequence and its 3D structure

Background: Lignin, the second most abundant biopolymer on earth, plays a major structural role in plants, conferring mechanical strength and regulating water conduction. Understanding the three-dimensional structure of lignin is important for fundamental reasons as well as engineering plants towards lignin valorization. Lignin lacks a specific primary sequence, making its average chemical composition the focus of most recent studies. However, it remains unclear whether the 3D structure of lignin molecules depends on their sequence. Methods: In this work, we performed all-atom molecular dynamics simulation of three S/G-lignin molecules with the same average composition but different sequence. Results: A detailed statistical analysis of the radius of gyration and relative shape anisotropy reveals that the lignin sequence has no statistically significant effect on the global three-dimensional structure. We found however, that homopolymers of C-lignin with the same molecular weight have smaller radii of gyration than S/G-lignin. We attribute this to lower hydroxyl content of C-lignin, which makes it more compact and rigid. Conclusions: The 3D structure of lignin is influenced by the overall content of monomeric units and interunit linkages and not by its precise primary sequence. General Significance: Lignin is assumed to not have a well-defined primary structure. The results presented here demonstrate there are no significant differences in the global 3D structure of lignin molecules with the same average composition but different primary sequence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

On the integration of molecular dynamics, data science, and experiments for studying solvent effects on catalysis

Computational workflows that combine molecular dynamics (MD) simulations and emerging data-centric (DC) methods can accelerate the screening and analysis of solvent systems experimentally and computationally. Here, MD simulations provide atomic positions and velocities of reactant, solvent, and catalyst materials that can be manipulated into data representations that in turn can be used by DC techniques to conduct predictive modeling, feature extraction, and experimental design. For liquid-phase catalytic applications, emerging DC techniques such as Convolutional and Graph Neural Networks (CNN/GNN), Topological Data Analysis (TDA), and Active Learning (AL) can leverage MD and experimental data to quickly predict solvent effects on reaction outcomes. For instance, in recent studies, 3D solvent environments obtained with MD have been exploited by CNNs to predict experimental reaction rates for homogeneous acid-catalyzed lignocellulosic processes. In this perspective, we discuss basic principles of DC methods and how these can be combined with MD to enable high-throughput screening of solvent selection for diverse catalysis applications.

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

Effect of Confinement of SIA Cluster Diffusion by Impurities on Radiation Defect Accumulation due to 14MeV neutrons in Tungsten

Impurities acting as traps, reduce the self-interstitial atom (SIA) cluster mobility, thereby increasing recombination and in turn enhancing radiation-resistance of polycrystalline materials. However, at elevated temperatures, depending on SIA-trap (impurity) binding energy, SIA clusters may trap and detrap (detach) numerous times. In tungsten, SIA clusters of all sizes glide one-dimensionally (1D) along their Burgers vector direction. Hence, detrapped SIAs would retrace their path, confining their 1D-glide between traps. However, small SIA clusters can change the direction of their 1D-glide by overcoming a rotation barrier. In addition, impurities or solutes are known to reduce this barrier. A lower rotation barrier can result in detrapped SIA clusters that diffuse in a random 1D direction, effectively leading to 3D (net-3D) diffusion. Here we investigate the effect of two cases of SIA diffusion, namely confined-1D diffusion and net-3D diffusion, on the damage accumulation in polycrystalline tungsten under 14 MeV neutron irradiation using the object kinetic Monte Carlo method. Simulations were performed using cascade debris obtained from molecular dynamics simulations with primary knock-on atom (PKA) energies corresponding to 14 MeV neutrons. In the simulations with net-3D diffusion, SIA clusters of all sizes diffuse in a random 1D direction after the clusters detrap. While for the confined 1D diffusion case, SIA clusters larger than size 5 retain their original direction of 1D-glide. In both types of simulations, trapped vacancies are assumed to be permanently immobilized. Unexpectedly, the damage accumulation was lower with confined 1D diffusion than that with net-3D. We present a systematic comparison of the influence of the two cases of SIA diffusion on the radiation damage accumulation as a function of dose rate, detrapping barrier, and impurity concentration at 1025 K.

Accumulation and recovery of lattice damage, tungs↗
DOE OSTI2022

Thermophysical properties of FLiBe using moment tensor potentials

Fluoride salts are prospective materials for applications in some next-generation nuclear reactors and their thermophysical properties at various conditions are of interest. Experimental measurement of the properties of these salts is often difficult and, in some cases, unfeasible due to challenges from high temperatures, impurity control, and corrosivity. Therefore, accurate theoretical methods are needed for fluoride salt property prediction. In this work, we used moment tensor potentials (MTP) to approximate the potential energy surface of eutectic FLiBe (66.6% LiF – 33.3% BeF2) predicted by the ab initio (DFT-D3) method. Here, we then used the developed potential and molecular dynamics to obtain several thermophysical properties of FLiBe, including radial distribution functions, density, self-diffusion coefficients, thermal expansion, specific heat capacity, bulk modulus, viscosity, and thermal conductivity. Our results show that the MTP potential approximates the potential energy surface accurately and the overall approach yields very good agreement with experimental values. The converged fitting can be obtained with less than 600 configurations generated from DFT calculations, which data can be generated in just 1200 core hours on today's typical processors. The MTP potential is faster than many machine learning potentials and about one order of magnitude slower than widely used empirical molten salt potentials such as Tosi/Fumi.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Unraveling Local Structure of Molten Salts via X-ray Scattering, Raman Spectroscopy, and Ab Initio Molecular Dynamics

In this work, we resolve a long-standing issue concerning the local structure of molten MgCl 2 by employing a multimodal approach, including X-ray scattering and Raman spectroscopy, along with the theoretical modeling of the experimental spectra based on ab initio molecular dynamics (AIMD) simulations utilizing several density functional theory (DFT) methods. We demonstrate the reliability of AIMD simulations in achieving excellent agreement between the experimental and simulated spectra for MgCl 2 and 50 mol % MgCl 2 + 50 mol % KCl, and ZnCl 2 , thus allowing structural insights not directly available from experiment alone. A thorough computational analysis using five DFT methods provides a convergent view that octahedrally coordinated magnesium in pure MgCl 2 upon melting preferentially coordinates with five chloride anions to form distorted square pyramidal polyhedra that are connected via corners and to a lesser degree via edges. This is contrasted with the results for ZnCl 2 , which does not change its tetrahedral coordination on melting. Although the five-coordinate MgCl 5 3– complex was not considered in the early literature, together with an increasing tendency to form a tetrahedrally coordinated complex with decreasing the MgCl 2 content in the mixture with alkali metal chloride systems, current work reconciles the results of most previous seemingly contradictory experimental studies.

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

Nonadditive Interactions Unlock Small-Particle Mobility in Binary Colloidal Monolayers

We examine the organization and dynamics of binary colloidal monolayers composed of micron-scale silica particles interspersed with smaller-diameter silica particles that serve as minority component impurities. These binary monolayers are prepared at the surface of ionic liquid droplets over a range of size ratios (σ = 0.16–0.66) and are studied with low-dose minimally perturbative scanning electron microscopy (SEM). The high resolution of SEM imaging provides direct tracking of all particle coordinates over time, enabling a complete description of the microscopic state. In these bidisperse size mixtures, particle interactions are nonadditive because interfacial pinning to the droplet surface causes the equators of differently sized particles to lie in separate planes. By varying the size ratio, we control the extent of nonadditivity in order to achieve phase behavior inaccessible to additive 2D systems. Across the range of size ratios, we tune the system from a mobile small-particle phase (σ < 0.24) to an interstitial solid (0.24 < σ < 0.33) and furthermore to a disordered glass (σ > 0.33). These distinct phase regimes are classified through measurements of hexagonal ordering of the large-particle host lattice and the lattice’s capacity for small-particle transport. Altogether, we explain these structural and dynamic trends by considering the combined influence of interparticle interactions and the colloidal packing geometry. Our measurements are reproduced in molecular dynamics simulations of 2D nonadditive disks, suggesting an efficient method for describing confined systems with reduced dimensionality representations.

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

Elasticity of two-dimensional ferroelectrics across their paraelectric phase transformation

The mechanical behavior of two-dimensional (2D) materials across 2D phase changes is unknown, and the finite temperature (T) elasticity of paradigmatic SnSe monolayers—ferroelectric 2D materials turning paraelectric as their unit cell turns from a rectangle into a square—is described here in a progressive manner. To begin with, their zero–T total energy landscape gives way to (Boltzmann-like) averages from which the elastic behavior is determined. Furthermore, these estimates are complemented with results from the strain-fluctuation method, which employs the energy landscape or ab initio molecular dynamics data. All approaches capture the coalescence of elastic moduli < C 11 (T) > = < C 22 (T) > due to the structural transformation. The broad evolution and sudden changes of elastic parameters < C 11 (T) >, < C 22 (T) >, and < C 12 (T) > of these atomically thin phase-change membranes establishes a heretofore overlooked connection among 2D materials and soft matter.

2-dimensional systems↗
DOE OSTI2023

FASDA: An FPGA-Aided, Scalable and Distributed Accelerator for Range-Limited Molecular Dynamics

Conducting long-term simulations of small molecules using Molecular Dynamics (MD) is crucial in drug design. However, traditional methods to accelerate the process including ASICs or GPUs, have limitations. ASICs are difficult to access, while publicly accessible GPU packages for MD have issues with more GPUs when processing small molecules, causing decreased performance. Conversely, FPGAs are renowned for their scalability and have been commonly used as accelerators for various applications, making them suitable for the task. Moreover, with the availability of FPGAs in the cloud, pharmaceutical developers can now access FPGA devices. The only missing piece is a design deployed for MD acceleration. Therefore, we present FASDA, the first FPGA-based MD accelerator available for community development. FASDA is designed to evaluate range-limited MD, which is the most resource-intensive and computationally demanding component in MD. It outperforms the state of-the-art GPU solution by 4.67x, significantly reducing the time for MD in drug design.

Wu, Chunshu↗
DOE OSTI2025

Impact of solvation on the electronic resonances in uracil

Interactions of low-energy electrons with the DNA and RNA nucleobases are known to form metastable states, known as electronic resonances. In this work, we study electron attachment to solvated uracil, an RNA nucleobase, using the orbital stabilization method at the Equation of Motion-Coupled Cluster for Electron Affinities with Singles and Doubles (EOM-EA-CCSD) level of theory with the Effective Fragment Potential (EFP) solvation method. We benchmarked the approach using multireference methods, as well as by comparing EFP and full quantum calculations. The impact of solvation on the first one particle (1p) shape resonance, formed by electron attachment to the π* LUMO orbital, as well as the first two particle one hole (2p1h) resonance, formed by electron attachment to neutral uracil's π–π* excited state, was investigated. We used molecular dynamics simulations for solvent configurations and applied charge stabilization technique-based biased sampling to procure configurations adequate to cover the entire range of the electron attachment energy distribution. The electron attachment energy in solution is found to be distributed over a wide range of energies, between 4.6 eV to 6.8 eV for the 2p1h resonance, and between −0.1 eV to 2 eV for the 1p resonance. The solvent effects were similar for the two resonances, indicating that the exact electron density of the state is not as important as the solvent configurations. Multireference calculations extended the findings showing that solvation effects are similar for the lowest four resonances, further indicating that the specific solute electron density is not as important, but rather the water configurations play the most important role in solvation effects. Lastly, by comparing bulk solvation to clusters of uracil with a few water molecules around it, we find that the impact of microsolvation is very different from that of bulk solvation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1985

The exact eigenfunctions and eigenvalues of a two-dimensional rigid rotor obtained using Gaussian wave packet dynamics

Exact eigenfunctions for a two-dimensional rigid rotor are obtained using Gaussian wave packet dynamics. The wave functions are obtained by propagating, without approximation, an infinite set of Gaussian wave packets that collectively have the correct periodicity, being coherent states appropriate to this rotational problem. This result leads to a numerical method for the semiclassical calculation of rovibrational, molecular eigenstates. Also, a simple, almost classical, approximation to full wave packet dynamics is shown to give exact results: this leads to an a posteriori justification of the De Leon-Heller spectral quantization method.

Reimers, J. R.↗