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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Path integral Monte Carlo and density functional molecular dynamics simulations of warm dense MgSiO 3

In order to provide a comprehensive theoretical description of MgSiO 3 at extreme conditions, we combine results from path integral Monte Carlo and density functional molecular dynamics simulations and generate a consistent equation of state for this material. We consider a wide range of temperature and density conditions from 10 4 to 10 8 K and from 0.321 to 64.2 g/cm -3 (0.1- to 20-fold the ambient density). We study how the L and K shell electrons are ionized with increasing temperature and pressure. We derive the shock Hugoniot curve and compare with experimental results. Our Hugoniot curve is in good agreement with the experiments, and we predict a broad compression maximum that is dominated by the K shell ionization of all three nuclei while the peak compression ratio of 4.70 is obtained when the Si and Mg nuclei are ionized. To conclude, we analyze the heat capacity and structural properties of the liquid.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2020

Extrapolation of thermal conductivity in non-equilibrium molecular dynamics simulations to bulk scale

Predictions of the bulk scale thermal conductivity of solids using non-equilibrium molecular dynamics (MD) simulations have relied on the linear extrapolation of the thermal resistivity versus the reciprocal of the system length in the simulations. Several studies have reported deviation of the extrapolation from linearity near the micro-scale, raising a concern of its applicability to large systems. To investigate this issue, present work conducted extensive MD simulations of silicon with two different potentials (EDIP and Tersoff-II) for unprecedented length scales up to 10.3 μm and simulation times up to 530 ns. For large systems ≥0.35 μm in size the non-linearity of the extrapolation of the reciprocal of the thermal conductivity is mostly due to ignoring the dependence of the thermal conductivity on temperature. To account for such dependence, the present analysis fixes the temperature range for determining the gradient for calculating the thermal conductivity values. However, short systems ≤0.23 μm in size show significant non-linearity in the calculated thermal conductivity values using a temperature window of 500 ± 10 K from the simulations results with the EDIP potential. Since these system sizes are shorter than the mean phonon free path in EDIP (~0.22 μm), the nonlinearity may be attributed to phonon transport. For the MD simulations with the Tersoff-II potential there is no significant non-linearity in the calculated thermal conductivity values for systems ranging in size from 0.05 to 5.4 μm.

42 ENGINEERING↗
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 OSTI2024

Insights on the structure and properties of sodium iron phosphate glasses from molecular dynamics simulations

Iron phosphate glasses are promising nuclear waste forms while more detailed understanding of their structures and structure-property relations are still needed to better design waste glass compositions. In this work we report studies of three series of sodium iron phosphate (NFP) glasses: 60P 2 O 5 -(40-x)Fe 2 O 3 -xNa 2 O (x = 0→40), (100–2x)P 2 O 5 -xFe 2 O 3 -xNa 2 O (x = 5→17.5) and one with different iron redox ratio, to understand the composition as well as the iron redox effects on the structure and properties of these glasses using molecular dynamics simulations with effective two-body and three-body potentials. Structural analyses, including pair distribution function, bond angle distribution, Q n distribution, and polyhedral connectivity, were performed to obtain in-depth information on short-range and medium-range structural features. The P-O pair distributions showed a first peak splitting with phosphorus-bridging and non-bridging oxygen contributions. This and the average P-O and other cation-oxygen bond distances are in excellent agreement with experiments. The coordination number of P 5+ remained four while that of Fe 3+ increased from 4.30 to 4.72 with decreasing Fe/Na ratio. Polyhedral linkage analysis showed [PO 4 ] units linked with [PO 4 ] and [FeO x ] through corner-sharing while the [PO 4 ]-[FeO x ] linkages become dominant for compositions with Fe 2 O 3 larger than 15 mol%. The effect of iron redox ratio on the structure of NFP glasses was also studied and it was found that bond lengths and coordination numbers were not strongly affected, while the reduction of iron introduced higher network distortions, as evident by O-P-O bond angle and Q n distribution. The glass transition temperature (T g ) showed a monotonic increase with Fe 2 O 3 in the first series, in good agreement with experiments, while those of the second series showed a maximum at P 2 O 5 = 82 mol%. Here, calculated elastic moduli were found to increase with Fe 2 O 3 in the first glass series, which was be explained by the increase of network connectivity, while those of the second series decrease with Fe 2 O 3 due to decrease of P 2 O 5 .

36 MATERIALS SCIENCE↗
DOE OSTI2020

Development of interatomic potential for Al–Tb alloys using a deep neural network learning method

An interatomic potential for the Al–Tb alloy around the composition of Al 90 Tb 10 is developed using the deep neural network (DNN) learning method. The atomic configurations and the corresponding total potential energies and forces on each atom obtained from ab initio molecular dynamics (AIMD) simulations are collected to train a DNN model to construct the interatomic potential for the Al–Tb alloy. Here we show that the obtained DNN model can well reproduce the energies and forces calculated by AIMD simulations. Molecular dynamics (MD) simulations using the DNN interatomic potential also accurately describe the structural properties of the Al 90 Tb 10 liquid, such as partial pair correlation functions (PPCFs) and bond angle distributions, in comparison with the results from AIMD simulations. Furthermore, the developed DNN interatomic potential predicts the formation energies of the crystalline phases of the Al–Tb system with an accuracy comparable to ab initio calculations. The structure factors of the Al 90 Tb 10 metallic liquid and glass obtained by MD simulations using the developed DNN interatomic potential are also in good agreement with the experimental X-ray diffraction data. The development of short-range order (SRO) in the Al 90 Tb 10 liquid and the undercooled liquid is also analyzed and three dominant SROs, i.e., Al-centered distorted icosahedron (DISICO) and Tb-centered ‘3661’ and ‘15551’ clusters, respectively, are identified.

36 MATERIALS SCIENCE↗
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 OSTI2023

Ab-Initio molecular dynamics simulations of binary NaCl-ThCl 4 and ternary NaCl-ThCl 4 -UCl 3 molten salts

Molten salt reactor (MSR) with Thorium (Th) fuel cycle has attracted growing attention due to its merits such as safety, low radioactive waste production, and non-proliferation. The design and safe operation of MSR rely on a thorough understanding of the thermophysical properties of molten salts over a wide range of composition and temperature. However, experimental data of Th-based molten salts are limited due to the inherent challenges of dealing with corrosive molten salts and the radioactive nature of actinides. Here, in this work, thermophysical properties including density, heat capacity, thermal expansion coefficient, and mixing energy of binary NaCl-ThCl 4 and ternary NaCl-ThCl 4 -UCl 3 molten salts are explored using ab-initio molecular dynamic simulations (AIMD) with the dDsC dispersion correction. The calculated mixing energy of binary NaCl-ThCl 4 exhibits a minimum close to the eutectic composition. The heat capacity of the mixtures is linearly dependent on the mole fraction of each component. 7-fold and 6-fold coordinated Th complexes are dominant in the mixtures. 8-fold coordinated Th complex increases with ThCl 4 fraction due to the formation of network structures. The average coordination number of Th exhibits a minimum near the eutectic composition. The minimum mixing energy for the ternary mixtures is observed in systems with a composition close to [NaCl] 0.5 [ThCl 4 ] 0.25 [UCl 3 ] 0.25 . The density positively deviates from the ideal solution in mixtures near this composition. These results are important to fill the data and knowledge gap of ThCl 4 molten salts.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
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 OSTI2020

Structures of fluoride containing aluminosilicate low activity nuclear waste glasses: A molecular dynamics simulations study

Fluorine and other halides commonly exist in nuclear waste forms, and due to their volatile nature, halide retention poses an issue affecting waste loading during vitrification. The compositional effect on fluorine incorporation in aluminosilicate glasses is investigated through molecular dynamics simulations. Oxygen and fluorine coordination numbers around glass former and modifier cations, bond angle distributions, and medium range structure features such as Q n distributions, ring size distributions and neutron diffraction structure factors were calculated. It was found that fluorine has higher preference to bond to Ca 2+ than to Na + , both in the melt and the glass, and there is no Si-F bond formation in the glass but they do exist in the melt. Consequently, CaO for Na 2 O substitution can be an effective way to help fluorine retention without significantly changing the glass chemistry. Furthermore, these results thus provide insights on fluorine incorporation in the aluminosilicate nuclear waste glasses and the strategy on how to improve fluorine retention both in the glass and the melt.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Effects of sodium and calcium chloride ionic stresses on model yeast membranes revealed by molecular dynamics simulation

As efforts to move a renewable economy grow, it will be necessary to make use of microbial conversion strategies for the production of novel materials or the upgrading of waste to high-value products. One critical technical challenge currently limiting waste upgrading remains the difficulty in obtaining single-pot conversion techniques where physical, chemical, and biological conversion are performed in a single step. To overcome this challenge, a detailed understanding of how different stresses impact microbial membrane stability will be necessary. In this work, using all-atom molecular dynamics simulations, we examine the impacts of moderate concentrations of NaCl and CaCl 2 on a model yeast plasma membrane. Weak, though statistically significant, changes in membrane morphology and dynamics functions are observed that are consistent with swelling and stiffening. Additionally, an examination of the ion-lipid contacts and the behavior of water at the water-membrane interface suggests that the impacts of these common salts may, in part, be mediated through changes to water-membrane hydrogen-bonding and hydration water dynamics.

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

Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model

In this work, we describe the development and implementation of a quasi-equilibrium hydration shell model of biomolecular solvation with adaptive boundaries. Applying the model to microsecond-long molecular dynamics simulations of several protein systems of varying complexity, we find that the model simulation results are of comparable quality to those obtained from simulations of fully solvated systems, but at a reduced computational cost. We discuss the dominant sources of error in the model and outline directions for future improvements.

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

Capacitance of Carbon Nanotube/Graphene Composite Electrodes with [BMIM + ][BF$_4^–$]/Acetonitrile: Fixed Voltage Molecular Dynamics Simulations

The capacitance of nanoporous carbon electrode materials is dictated by the physical interactions with electrolyte ions and molecules at the accessible interior electrode surface. While significant progress has been made in designing and synthesizing carbon materials with well-defined and relatively homogeneous nanoporosity, the majority of materials remain heterogeneous, and the resulting properties reflect an average over this distribution. In this regard, computer simulations can be a valuable tool to predict or validate structure/property relationships by systematically investigating well-defined, model electrode morphologies. In this work, we utilize fixed-voltage molecular dynamics simulations to predict structure/capacitance relationships for five different model morphologies of carbon nanotube/graphene (CNT/G) composite electrodes with 1-butyl-3-methylimidazolium tetrafluoroborate/acetonitrile electrolyte. The CNT/G electrode models are inspired by experimental “layer-by-layer” syntheses and strike a balance between realism and computational tractability. Comparison between different model electrode architectures elucidates important structure/property relationships. We find that CNT/graphene contact points serve as “hot spots” with significantly enhanced charge separation relative to the rest of the electrode. Furthermore, we demonstrate a specific nanoconfinement motif that provides substantial 3–4$\times$ enhancement of local capacitance, resulting in a ~40% increase of the total electrode differential capacitance. Because the accessible surface area of the model CNT/G electrodes is precisely determined, a comparison of per-area capacitance across systems is unambiguous. Our results thus complement a prior computational demonstration of capacitance enhancement in nanoconfinement while elucidating additional interaction motifs at CNT/G electrochemical interfaces.

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

Molecular Dynamics Simulation and Theoretical Analysis of Structural Relaxation, Bond Exchange Dynamics, and Glass Transition in Vitrimers

Vitrimers are a class of polymer networks featuring dynamic covalent cross-links that can undergo associative bond exchange. There has been recent interest in these materials due to their promise as recyclable thermosets or self-healing polymers because of the ability of vitrimer networks to rearrange at the molecular level and undergo macroscopic flow. However, the practical use of these materials often occurs in the supercooled regime or glassy state, where the implications of dynamic bonds are complicated by the interplay between slow activated segmental dynamics, cross-link (i.e., bond-exchange) kinetics, and ultimately material properties. Here, in this paper, we combine coarse-grained molecular dynamics simulation and microscopic statistical mechanical theory to understand how cross-linking kinetics affect material dynamics and how this couples to segmental relaxation of the polymeric network strands across a spectrum of length and time scales, especially in the supercooled regime. We characterize the Kuhn segmental alpha relaxation time and bond exchange time for vitrimer systems across various cross-link densities, temperatures, and bond exchange rates. Simulation and theory both exhibit a bending-up behavior for bond exchange time upon cooling, suggesting a coupling between bond exchange dynamics and segmental relaxation that intensifies with faster bond exchange kinetics. We also found bond exchange dynamics have an impact on Kuhn segment alpha relaxation time, which is most significant at higher cross-link densities. Both these effects are most prominent when the bond exchange time is similar to the Kuhn segment alpha relaxation time, and the resulting coupling of these two relaxation processes is tied to both the probability of a free end to find a bonded pair and the time scale of the constraints imposed by the dynamic cross-links. This relationship is reflected by a cross-link dependence of a theoretical parameter which represents the quantitative degree of coupling between bond exchange and segmental dynamics. Overall, the combination of simulation and theory clarifies the intricate interaction between bond kinetics and segmental relaxation and demonstrates the ability to provide molecular-level insights into vitrimer dynamics over a wide temperature range.

dynamic relaxation↗
DOE OSTI2025

Proton radiation effects in indium oxide using cascade molecular dynamics simulations

Metal oxide (MO) semiconductors, characterized by their wide band gaps and notable charge transport properties, are promising candidates for electronic applications in extreme environments, including near-Earth space. However, atomistic simulations of radiation–matter interactions in MOs remain challenging due to the limitations of existing interatomic potentials, which often fail to capture both the short-range repulsive forces essential for radiation damage modeling and the long-range electrostatic effects governing defect evolution. In this work, we develop a customized interatomic potential tailored for radiation damage simulations in indium oxide (In 2 O 3 ) as a model system, a representative MO material. Our potential integrates the Ziegler-Biersack-Littmark potential to accurately describe short-range interactions with Buckingham and Coulombic potentials to account for long-range forces. We perform molecular dynamics simulations of low-energy proton irradiation using this custom potential. We employ the primary knock-on atom (PKA) cascade method to study atomic displacements and primary defect formation. Simulations were conducted for 1 keV proton irradiation in four randomly chosen directions, and PKA-driven defect analyses at 5, 10, and 15 keV to examine the effects of direction and energy level on damage generation. Our results provide insight into the impact of irradiation direction and energy level on the cascade evolution and defect formation mechanisms.

Atomistic simulations↗
DOE OSTI2025

Reorganization of Water at Aqueous Aluminum Chloride (AlCl 3 ) Interfaces: Vibrational Sum Frequency Generation and Molecular Dynamics Simulations

AlCl 3 hydration states and complexation are not well understood both in solutions and at the air–aqueous interface despite their potential significance in natural waters and their industrial and energy-related applications. Here, we investigated Al 3+ and Cl – ion behaviors in an AlCl 3 aqueous bulk solution and at the air–aqueous interface using interface-selective vibrational sum frequency generation (SFG), Raman and infrared spectroscopies, molecular dynamics (MD) simulation, as well as molecular-informed reduced modeling. Our reduced modeling reveals relatively long-range effects for Al 3+ as compared to monovalent ions such as Na + indicating that the interfacial depth of trivalent ions can be significantly larger than that of monovalent ions at the air–water interface. MD simulations reveal interfacial stratification and multiple layering of the ions. Compression of the Al 3+ and Cl – distributions with increasing concentrations from 0.5 to 2.5 m is also observed in the subsurface regions. Significant SSP- and PPP-polarized SFG OH spectral intensity increases are observed from 0.5 to 1.5 m and 0.5 to 2.5 m, respectively, indicative of interfacial depth increases and a change in average orientation above 1.5 m. Extensive evaluation of SFG spectra, Fresnel-corrected using several approaches, shows the same trends. The nonmonotonic trend points to a changing structure in surface and subsurface water orientation and hydrogen bonding environment generally consistent with the MD simulation of stratification and water orientation changes. Furthermore, solvent-shared ion pairing is implicated with MD simulation radial distribution analysis and consistent with infrared spectral identification of the hexaaqua aluminum ion in the solution phase. Spectral evidence of a strong Al 3+ hydration shell and the acidic behavior of the Al 3+ ions is obvious in the Raman and infrared spectra of the bulk solution. In conclusion, we show that the MD dipole potential is directly related to the MD second-order susceptibility of the interface, χ SFG–MD (2) , both of which correlate up to ∼35 Å with the spectral observations of increasing and then saturating intensities, suggesting that both ion stratification and interfacial depth determine the water orientations at an air–water interface of 1-3 electrolyte solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗