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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 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Uncertainty Quantification in Dynamic Simulations of Large-scale Power System Models using the High-Order Probabilistic Collocation Method on Sparse Grids

This paper proposes a probabilistic collocation method (PCM) to quantify the uncertainties with dynamic simulations in power systems. The appraoch was tested on a single-machine-infinite-bus system and the over 15,000 -bus Western Electricity Coordinating Council (WECC) system. Comparing to classic Monte-Carlo (MC) method, the proposed PCM applies the Smolyak algorithm to reduce the number of simulations that have to be performed. Therefore, the computational cost can be greatly reduced using PCM. The algorithm and procedures are described in the paper. Comparison was made with MC method on the single machine as well as the WECC system. The simulation results shows that using PCM only a small number of sparse grid points need to be sampled even when dealing with systems with a relatively large number of uncertain parameters. PCM is, therefore, computationally more efficient than MC method.

Uncertainty quantification, parameter estimation, ↗
DOE OSTI2015

Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo

Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Spin dynamics simulation of electron spin relaxation in Ni{sup 2+}(aq)

The ability to quantitatively predict and analyze the rate of electron spin relaxation of open-shell systems is important for electron paramagnetic resonance and paramagnetic nuclear magnetic resonance spectroscopies. We present a combined molecular dynamics (MD), quantum chemistry (QC), and spin dynamics simulation method for calculating such spin relaxation rates. The method is based on the sampling of a MD trajectory by QC calculations, to produce instantaneous parameters of the spin Hamiltonian used, in turn, to numerically solve the Liouville-von Neumann equation for the time evolution of the spin density matrix. We demonstrate the approach by simulating the relaxation of electron spin in an aqueous solution of Ni{sup 2+} ion. The spin-lattice (T{sub 1}) and spin-spin (T{sub 2}) relaxation rates are extracted directly from the simulations of the time dependence of the longitudinal and transverse magnetization, respectively. Good agreement with the available, indirectly obtained experimental data is obtained by our method.

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

Molecular Dynamics Simulation on the Effect of MgO/Al{sub 2}O{sub 3} Ratio on Structure and Properties of Blast Furnace Slag Under Different Basicity Conditions

The SiO{sub 2}-Al{sub 2}O{sub 3}-CaO-MgO is the basic structural system of blast furnace slag and the composition directly affects the performance of the slag. Molecular dynamics simulations were carried out to analyze the local structure, structural unit, bond angle, transport properties, and enthalpy of the slag with the increase of MgO/Al{sub 2}O{sub 3} mass ratio under different basicity conditions. It was found that the change of MgO/Al{sub 2}O{sub 3} ratio does not affect the short-range order structure, but it will reduce the overall stability of the network structure. Through the analysis of the structural unit of the slag, it was found that the polymerization degree of the system decreases with the increase of MgO/Al{sub 2}O{sub 3} ratio, indicating that the complex network structure of the system is partially depolymerized. Besides, the self-diffusion coefficients of each ion were concluded and the magnitudes were observed to be in the following order: Mg{sup 2+}>Ca{sup 2+}>Al{sup 3+}>O{sup 2-}>Si{sup 4+}. The diffusivity of the slag increases with the increase of MgO/Al{sub 2}O{sub 3} ratio and the corresponding viscosity decreases. And the enthalpy of the slag is increased with the increase of MgO/Al{sub 2}O{sub 3} ratio or basicity, therefore the fuel consumption should also be properly adjusted during the operation of blast furnace to ensure the target temperature.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Initial position optimization in molecular dynamics simulations for a Coulomb system

A new algorithm for molecular dynamics (MD) simulations is developed to optimize plasma particle distributions at given initial temperatures. By combining velocity scaling and reassignment, the method effectively eliminates the initial rise and oscillation in temperatures observed with randomly distributed positions. These rises and oscillations are undesired numerical artifacts observed in conventional plasma MD simulations, arising from unoptimized particle positions. The algorithm demonstrates temperature relaxation without initial rises or oscillations, as well as precise flow velocity relaxation, enabling accurate measurement of relaxation times. The code is accelerated using graphics processing units for parallel processing, enhancing the study of plasma dynamics. The proposed method for distributing physically valid particles in MD simulations enables accurate studies of intrinsic collision processes in plasmas, including the dynamics of strongly coupled plasmas, plasma–wave interactions, and transport phenomena in magnetized plasmas. The paper concludes with a discussion of potential applications and future enhancements to the algorithm.

Jo, Jawon (ORCID:0009000924193285)↗
DOE OSTI2021

Initial hydration process of calcium silicates in Portland cement: A comprehensive comparison from molecular dynamics simulations

As the main components of Portland cement, calcium silicates show substantial differences in their hydration reactivity which have not been fully explained. A comprehensive comparison of the initial hydration process of calcium silicates, namely dicalcium silicate (C{sub 2}S) and tricalcium silicate (C{sub 3}S), was conducted using molecular dynamics simulations. The initial hydration process was divided into three stages using cut-off times of 0.001 ns and 3 ns. The hydration of M{sub 3}-C{sub 3}S (010) was more evident than that of β-C{sub 2}S (100), supported by the hydroxylation degree, radial distribution function, atomic density profile, etc. The coordination number of the surface Ca atoms might be the underlying reason for such a difference. Interactions between cement surfaces and water molecules were mainly characterised by solid OH bonding and Ca-water O bonding. Dissolution of Ca atoms was observed, although quite scarce, while no dissolution of Si atoms was observed.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Molecular dynamics simulations of shock waves in hydroxyl-terminated polybutadiene melts: Mechanical and structural responses

The mechanical and structural responses of hydroxyl-terminated cis-1,4-polybutadiene melts to shock waves were investigated by means of all-atom non-reactive molecular dynamics simulations. The simulations were performed using the OPLS-AA force field but with the standard 12-6 Lennard-Jones potential replaced by the Buckingham exponential-6 potential to better represent the interactions at high compression. Monodisperse systems containing 64, 128, and 256 backbone carbon atoms were studied. Supported shock waves were generated by impacting the samples onto stationary pistons at impact velocities of 1.0, 1.5, 2.0, and 2.5 km s{sup −1}, yielding shock pressures between approximately 2.8 GPa and 12.5 GPa. Single-molecule structural properties (squared radii of gyration, asphericity parameters, and orientational order parameters) and mechanical properties (density, shock pressure, shock temperature, and shear stress) were analyzed using a geometric binning scheme to obtain spatio-temporal resolution in the reference frame centered on the shock front. Our results indicate that while shear stress behind the shock front is relieved on a ∼0.5 ps time scale, a shock-induced transition to a glass-like state occurs with a concomitant increase of structural relaxation times by several orders of magnitude.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Water around fullerene shape amphiphiles: A molecular dynamics simulation study of hydrophobic hydration

Fullerene C{sub 60} sub-colloidal particle with diameter ∼1 nm represents a boundary case between small and large hydrophobic solutes on the length scale of hydrophobic hydration. In the present paper, a molecular dynamics simulation is performed to investigate this complex phenomenon for bare C{sub 60} fullerene and its amphiphilic/charged derivatives, so called shape amphiphiles. Since most of the unique properties of water originate from the pattern of hydrogen bond network and its dynamics, spatial, and orientational aspects of water in solvation shells around the solute surface having hydrophilic and hydrophobic regions are analyzed. Dynamical properties such as translational-rotational mobility, reorientational correlation and occupation time correlation functions of water molecules, and diffusion coefficients are also calculated. Slower dynamics of solvent molecules—water retardation—in the vicinity of the solutes is observed. Both the topological properties of hydrogen bond pattern and the “dangling” –OH groups that represent surface defects in water network are monitored. The fraction of such defect structures is increased near the hydrophobic cap of fullerenes. Some “dry” regions of C{sub 60} are observed which can be considered as signatures of surface dewetting. In an effort to provide molecular level insight into the thermodynamics of hydration, the free energy of solvation is determined for a family of fullerene particles using thermodynamic integration technique.

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

Predicting CaO-(MgO)-Al2O3-SiO2 glass reactivity in alkaline environments from force field molecular dynamics simulations

In this investigation, force field-based molecular dynamics (MD) simulations have been employed to generate detailed structural representations for a range of amorphous quaternary CaO-MgO-Al{sub 2}O{sub 3}-SiO{sub 2} (CMAS) and ternary CaO-Al{sub 2}O{sub 3}-SiO{sub 2} (CAS) glasses. Comparison of the simulation results with select experimental X-ray and neutron total scattering and literature data reveals that the MD-generated structures have captured the key structural features of these CMAS and CAS glasses. Based on the MD-generated structural representations, we have developed two structural descriptors, specifically (i) average metal oxide dissociation energy (AMODE) and (ii) average self-diffusion coefficient (ASDC) of all the atoms at melting. Both structural descriptors are seen to more accurately predict the relative glass reactivity than the commonly used degree of depolymerization parameter, especially for the eight synthetic CAS glasses that span a wide compositional range. Hence these descriptors hold great promise for predicting CMAS and CAS glass reactivity in alkaline environments from compositional information.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Determination of the structure of lithium niobosilicate glasses by molecular dynamics simulation with a new Nb-O potential

A partial charge empirical potential for the Nb-O pair has been developed based on existing parameters of other pairs in a Teter potential to enable molecular dynamics simulations of both lithium niobate crystal and lithium niobosilicate glasses. The developed potential is capable of describing structural features of lithium niobosilicate glasses in a wide composition range, including niobium coordination number and bond length, density, bond angle distribution, polyhedral distribution and fraction of bridging oxygen. Furthermore, the results obtained using this new potential show good agreement with experimental data of density and structure from Raman spectroscopy of lithium niobosilicate glasses and X-ray absorption spectroscopy near Nb K-edge.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Determination of bimetallic architectures in nanometer-scale catalysts by combining molecular dynamics simulations with x-ray absorption spectroscopy

In this study, we present an approach for the determination of an atomic structure of small bimetallic nanoparticles by combining extended X-ray absorption fine structure spectroscopy and classical molecular dynamics simulations based on the Sutton-Chen potential. The proposed approach is illustrated in the example of PdAu nanoparticles with ca 100 atoms and narrow size and compositional distributions. Using a direct modeling approach and no adjustable parameters, we were able to reproduce the size and shape of nanoparticles as well as the intra-particle distributions of atoms and metal mixing ratios and to explore the influence of these parameters on the local structure and dynamics in nanoparticles.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Machine Learning‐Augmented Molecular Dynamics Simulations (MD) Reveal Insights Into the Disconnect Between Affinity and Activation of ZTP Riboswitch Ligands

Abstract The challenge of targeting RNA with small molecules necessitates a better understanding of RNA–ligand interaction mechanisms. However, the dynamic nature of nucleic acids, their ligand‐induced stabilization, and how conformational changes influence gene expression pose significant difficulties for experimental investigation. This work employs a combination of computational and experimental methods to address these challenges. By integrating structure‐informed design, crystallography, and machine learning‐augmented all‐atom molecular dynamics simulations (MD), we synthesized, biophysically and biochemically characterized, and studied the dissociation of a library of small molecule activators of the 5‐aminoimidazole–4–carboxamide ribonucleotide triphosphate (ZTP) riboswitch, a ligand‐binding RNA motif that regulates bacterial gene expression. We uncovered key interaction mechanisms, revealing valuable insights into the role of ligand binding kinetics on riboswitch activation. Further, we established that ligand on‐rates determine activation potency as opposed to binding affinity and elucidated RNA structural differences, which provide mechanistic insights into the interplay of RNA structure on riboswitch activation.

Chemistry↗
DOE OSTI2014

Molecular Dynamics Simulations of Laser-Materials Interactions: General and Material-Specific Mechanisms of Material Removal and Generation of Crystal Defects. In: Veiko V., Konov V. (eds) Fundamentals of Laser-Assisted Micro- and Nanotechnologies

Molecular dynamics simulations of laser-materials interactions are capable of providing detailed information on the complex processes induced by the fast laser energy deposition and can help in the advancement of laser-driven applications. This chapter provides a brief overview of recent progress in the atomic- and molecular-level modeling of laser-materials interactions and presents several examples of the application of atomistic simulations for investigation of laser melting and resolidification, generation of crystal defects, photomechanical spallation, and ablation of metals and molecular targets. A particular focus of the analysis of the computational results is on revealing the general and material-specific phenomena in laser-materials interactions and on making connections to experimental observations.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Dynamic simulation of a reverse Brayton refrigerator

A test refrigerator based on the modified Reverse Brayton cycle has been developed in the Chinese Academy of Sciences recently. To study the behaviors of this test refrigerator, a dynamic simulation has been carried out. The numerical model comprises the typical components of the test refrigerator: compressor, valves, heat exchangers, expander and heater. This simulator is based on the oriented-object approach and each component is represented by a set of differential and algebraic equations. The control system of the test refrigerator is also simulated, which can be used to optimize the control strategies. This paper describes all the models and shows the simulation results. Comparisons between simulation results and experimental data are also presented. Experimental validation on the test refrigerator gives satisfactory results.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2013

Quantify Water Extraction by TBP/Dodecane via Molecular Dynamics Simulations

The purpose of this project is to quantify the interfacial transport of water into the most prevalent nuclear reprocessing solvent extractant mixture, namely tri-butyl- phosphate (TBP) and dodecane, via massively parallel molecular dynamics simulations on the most powerful machines available for open research. Specifically, we will accomplish this objective by evolving the water/TBP/dodecane system up to 1 ms elapsed time, and validate the simulation results by direct comparison with experimentally measured water solubility in the organic phase. The significance of this effort is to demonstrate for the first time that the combination of emerging simulation tools and state-of-the-art supercomputers can provide quantitative information on par to experimental measurements for solvent extraction systems of relevance to the nuclear fuel cycle. Results: Initially, the isolated single component, and single phase systems were studied followed by the two-phase, multicomponent counterpart. Specifically, the systems we studied were: pure TBP; pure n-dodecane; TBP/n-dodecane mixture; and the complete extraction system: water-TBP/n-dodecane two phase system to gain deep insight into the water extraction process. We have completely achieved our goal of simulating the molecular extraction of water molecules into the TBP/n-dodecane mixture up to the saturation point, and obtained favorable comparison with experimental data. Many insights into fundamental molecular level processes and physics were obtained from the process. Most importantly, we found that the dipole moment of the extracting agent is crucially important in affecting the interface roughness and the extraction rate of water molecules into the organic phase. In addition, we have identified shortcomings in the existing OPLS-AA force field potential for long-chain alkanes. The significance of this force field is that it is supposed to be optimized for molecular liquid simulations. We found that it failed for dodecane and/or longer chains for this particular solvent extraction application. We have proposed a simple way to circumvent the artificial crystallization of the chains at ambient temperature.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2014

Molecular dynamics simulation of Coulomb explosion, melting and shock wave creation in silicon after an ionization pulse

Strong electronic stopping power of swift ions in a semiconducting or insulating substrate can lead to localized electron stripping. The subsequent repulsive interactions among charged target atoms can cause Coulomb explosion. Using molecular dynamics simulation, we simulate Coulomb explosion in silicon by introducing an ionization pulse lasting for different periods, and at different substrate temperatures. We find that the longer the pulse period, the larger the melting radius. The observation can be explained by a critical energy density model assuming that melting required thermal energy density is a constant value and the total thermal energy gained from Coulomb explosion is linearly proportional to the ionization period. Our studies also show that melting radius is larger at higher substrate temperatures. The temperature effect is explained due to a longer structural relaxation above the melting temperature at original ionization boundary due to lower heat dissipation rates. Furthermore, simulations show the formation of shock waves, created due to the compression from the melting core.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Thermal conductivity of MoS 2 monolayers from molecular dynamics simulations

Quantification of lattice thermal conductivity of two-dimensional semiconductors like MoS 2 is necessary for the design of electronic and thermoelectric devices, but direct experimental measurements on free-standing samples is challenging. Molecular dynamics simulations, with appropriate corrections, can provide a reference value for thermal conductivity for these material systems. Here, we construct a new empirical forcefield of the Stillinger-Weber form, parameterized to phonon dispersion relations, lattice constants and elastic moduli and we use it to compute a material-intrinsic thermal conductivity of 38.1 W/m-K at room temperature and estimate a maximum thermal conductivity of 85.4 W/m-K at T = 200 K. We also identify that phonon scattering by the large isotopic mass distribution of Mo and S contributes a significant correction (>45%) to the thermal conductivity at low temperatures.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Molecular dynamics simulation of phase competition in terbium

The competition among multiple solid phases determines the final microstructures of a material. Such competition can originate at the very beginning of the solidification process. We report the results of molecular dynamics simulation of the phase competition between the hexagonal close-packed (hcp), face-centered cubic (fcc), and body-centered cubic (bcc) phases during the solidification of pure Tb. We found that the liquid supercooled below the hcp melting temperature has both bcc and hcp/fcc nuclei, but only the bcc nuclei grow such that the liquid always solidifies into the bcc phase, even at temperatures where the hcp phase is more stable. The hcp phase can only form in the last liquid droplet or at the bcc grain boundaries. Depending on the bcc grain orientations, the hcp phase jammed between the bcc grains either completely disappears or slowly grows via a solid-state massive transformation mechanism. Once the hcp phase becomes large enough, the stresses associated with its appearance can trigger a martensitic transformation. Yet, not the entire bcc phase is consumed by the martensitic transformation and the remaining bcc phase is transformed into the hcp phase via the solid-state massive transformation mechanism. If the supercooling is too large, the nucleation becomes almost barrier free and the liquid solidifies into a structure consisting of ultra-fine hcp and bcc grains after which the bcc phase quickly disappears.

36 MATERIALS SCIENCE↗