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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 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
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 OSTI2012

Collision induced dissociation of doubly-charged ions: Coulomb explosion vs. neutral loss in [Ca(urea)]{sup 2+} gas phase unimolecular reactivity via chemical dynamics simulations

In this paper we report different theoretical approaches to study the gas-phase unimolecular dissociation of the doubly-charged cation [Ca(urea)]{sup 2+}, in order to rationalize recent experimental findings. Quantum mechanical plus molecular mechanical (QM/MM) direct chemical dynamics simulations were used to investigate collision induced dissociation (CID) and rotational-vibrational energy transfer for Ar{sup +} [Ca(urea)]{sup 2+} collisions. For the picosecond time-domain of the simulations, both neutral loss and Coulomb explosion reactions were found and the differences in their mechanisms elucidated. The loss of neutral urea subsequent to collision with Ar occurs via a shattering mechanism, while the formation of two singly-charged cations follows statistical (or almost statistical) dynamics. Vibrational-rotational energy transfer efficiencies obtained for trajectories that do not dissociate during the trajectory integration were used in conjunction with RRKM rate constants to approximate dissociation pathways assuming complete intramolecular vibrational energy redistribution (IVR) and statistical dynamics. This statistical limit predicts, as expected, that at long time the most stable species on the potential energy surface (PES) dominate. These results, coupled with experimental CID from which both neutral loss and Coulomb explosion products were obtained, show that the gas phase dissociation of this ion occurs by multiple mechanisms leading to different products and that reactivity on the complicated PES is dynamically complex. (authors)

74 ATOMIC AND MOLECULAR PHYSICS↗
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↗
DOE OSTI2014

Anion pairs in room temperature ionic liquids predicted by molecular dynamics simulation, verified by spectroscopic characterization

Molecular-level spectroscopic analyses of an aprotic and a protic room-temperature ionic liquid, BMIM OTf and BMIM HSO4, respectively, have been carried out with the aim of verifying molecular dynamics simulations that predict anion pair formation in these fluid structures. Fourier-transform infrared spectroscopy, Raman spectroscopy and nuclear magnetic resonance spectroscopy of various nuclei support the theoretically-determined average molecular arrangements.

ionic liquids↗
DOE OSTI2021

Ion Pairing, Clustering and Transport in a LiFSI-TMP Electrolyte as Functions of Salt Concentration using Molecular Dynamics Simulations

Battery capacity is highly related to ion-pairing mechanisms in electrolytes, since a cluster formation can lead to dead Li formation, reducing the number of charge carriers and leading to capacity fading. We use molecular dynamics simulations to model an electrolyte comprising trimethyl phosphate (TMP) solvent and a lithium bis(fluorosulfonyl)imide (LiFSI) salt, exploring effects of salt concentration on solvation and ion-transport. We simulate the LiFSI-TMP electrolyte for salt concentrations of 0.7, 1.43 and 3.82 molar. A statistical analysis was performed to study ion-pairing, clustering, diffusivity, conductivity, and coordination of Li-ions, providing insights into relations between molecular structures and transport properties. Molecular structure of ionic components changes as concentration increases, from a predominant solvent separated ion pair (SSIP) and contact ion pair (CIP) to aggregate salt (AGG) and ionic cluster formation. Given the formation of the ionic cluster, the diffusion mechanism followed by Li-ions changes from a hopping/exchange to a vehicular mechanism as concentration increases; this is reflected in a decrease of ionic conductivities. Ionicity was also calculated to reveal how the ionic motion changes from an uncorrelated to a correlated one as the salt concentration increases. Furthermore, we also compared our results with experimental calculations performed for similar electrolyte systems

25 ENERGY STORAGE↗
NASA NTRS1975

Dispersion analysis and linear error analysis capabilities of the space vehicle dynamics simulation program

Previous error analyses conducted by the Guidance and Dynamics Branch of NASA have used the Guidance Analysis Program (GAP) as the trajectory simulation tool. Plans are made to conduct all future error analyses using the Space Vehicle Dynamics Simulation (SVDS) program. A study was conducted to compare the inertial measurement unit (IMU) error simulations of the two programs. Results of the GAP/SVDS comparison are presented and problem areas encountered while attempting to simulate IMU errors, vehicle performance uncertainties and environmental uncertainties using SVDS are defined. An evaluation of the SVDS linear error analysis capability is also included.

Snow, L. S.↗
DOE OSTI2023

Quantum mechanics based non-bonded force field functions for use in molecular dynamics simulations of materials and systems: The nitrogen and oxygen columns

Accurate Force Fields (FFs) are essential for Molecular Dynamics (MD) simulations of the dynamics of realistic materials in terms of atomic-level interactions. The FF parameters of short-range valence interactions can be derived through Quantum Mechanical (QM) calculations on model systems practical for QM (<300 atoms). Similarly, the dynamic electrostatic interactions can be described with methods such as QEq or PQEq that allow charges and polarization to adjust dynamically. However, accurately extracting long-range van der Waals (vdW) interactions from QM calculations poses challenges due to the absence of a definitive method to distinguish between the different energetic components of electrostatics, polarization, vdW, hydrogen bonding, and valence interactions. To do this we use the Perdew–Burke–Ernzerhof flavor of Density Functional Theory, including empirical D3 vdW corrections, to predict the Equation of State for each element (keeping any covalent bonds fixed), from which we obtain the two-body vdW nonbond potential. Here, we extend these calculations to include non-bonded parameters for the N and O columns of the periodic table so that we now describe columns 15 (N), 16 (O), 17 (F), and 18 (Ne) of the periodic table. For these 20 elements, we find that the two-body vdW potentials can all be mapped to a single universal two-body curve, with just three scaling parameters: Re, De, and L. We refer to this as the Universal NonBond (UNB) potential. We expect this to be useful for new MD simulations and a helpful starting point to obtain UNB parameters for the remainder of the periodic table.

Chemistry↗
DOE OSTI2020

Molecular dynamics simulations of alkaline earth metal ions binding to DNA reveal ion size and hydration effects

The identity of metal ions surrounding DNA is key to its biological function and materials applications. In this work, we compare atomistic molecular dynamics simulations of double strand DNA (dsDNA) with four alkaline earth metal ions (Mg 2+ , Ca 2+ , Sr 2+ , and Ba 2+ ) to elucidate the physical interactions that govern DNA–ion binding. Simulations accurately model the ion–phosphate distance of Mg 2+ and reproduce ion counting experiments for Ca 2+ , Sr 2+ , and Ba 2+ . Our analysis shows that alkaline earth metal ions prefer to bind at the phosphate backbone compared to the major groove and negligible binding occurs in the minor groove. Larger alkaline earth metal ions with variable first solvation shells (Ca 2+ , Sr 2+ , and Ba 2+ ) show both direct and indirect binding, where indirect binding increases with ion size. Mg 2+ does not fit this trend because the strength of its first solvation shell predicts indirect binding only. Ions bound to the phosphate backbone form fewer contacts per ion compared to the major groove. Within the major groove, metal ions preferentially bind to guanine–cystosine base pairs and form simultaneous contacts with the N7 and O6 atoms of guanine. Overall, we find that the interplay among ion size, DNA–ion interaction, and the size and flexibility of the first solvation shell are key to predicting how alkaline earth metal ions interact with DNA.

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

Molecular dynamics simulation of hollow thick-walled cylinder collapse

The generation and evolution of plastic deformation in a hollow single-crystal cylinder under high-rate axisymmetric loading were studied. An advantage of the proposed loading scheme is that all loading modes are applied simultaneously within the chosen crystallographic plane of the cylinder base and different strain degrees are achieved along the specimen cross section. Molecular dynamics simulation was performed to show that the achievement of a certain strain causes the formation of structural defects on the inner surface of the specimen. The obtained results can be used to explain the main plastic deformation mechanisms of crystalline solids.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗