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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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New discoveries on polymer and polyelectrolyte brush systems and the corresponding brush-supported ions and water, arising from employing all-atom molecular dynamics simulations, have been thoroughly reviewed.
Nonadiabatic excited-state molecular dynamics underpin many photophysical and photochemical phenomena, such as exciton dynamics, charge separation and transport. In this work, we present an efficient nonadiabatic molecular dynamic (NAMD) simulation method based on time-dependent density functional tight-binding (TDDFTB) theory. Specifically, the adiabatic electronic structure, an essential NAMD input, is described at the TDDFTB level. Here, the nonadiabatic effects originating from the coupled motions of electrons and nuclei are treated by the trajectory surface hopping algorithm. To improve the computational efficiency, nonadiabatic couplings between excited states within the TDDFTB method are derived and implemented using an analytical approach. Further, the time-dependent nonadiabatic coupling scalars are calculated based on the overlap between molecular orbitals rather than the Slater determinants to speed up the simulations. In addition, the electronic decoherence scheme and a state reassigned unavoided crossings algorithm, which has been implemented in the NEXMD software, are used to improve the accuracy of the simulated dynamics and handle trivial unavoided crossings. Finally, the photoinduced nonadiabatic dynamics of a benzene molecule are simulated to demonstrate our implementation. The results for excited state NAMD simulations of benzene molecule based on TDDFTB method compare well that obtained with numerically expensive time-dependent density functional theory. The proposed methodology provides an attractive theoretical simulation tool for predicting the photophysical and photochemical properties of complex materials.
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
This work quantifies the core–shell structure of nano-confined CO 2 molecules under pressure in silica pores using in operando small-angle neutron scattering (SANS) measurements and molecular dynamics simulations.
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.
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 .
The automobile industry is incorporating more lightweight content in car designs to boost fuel-economy. New structural adhesives are needed to mitigate the corrosion and thermal expansion issues associated with joining dissimilar lightweight materials, but adhesive developers lack a fundamental understanding of the chemistry that occurs in the adhesive as the joint ages. In this study, we developed structural adhesive molecular models and applied classical molecular dynamics simulations and density functional theory calculations to gain molecular insights into the influence of water molecules on the properties of epoxy-based adhesives (DGEBA + Jeffamine (JD230)). The simulations were complemented by experimental synthesis and characterization. Our work underscores the impact of water molecules on the local structure of the epoxy network as well as resulting mechanical properties. Water molecules were mainly coordinated with hydroxyls, primary amines and secondary amines, but also weakly coordinated with ether linkages, which were found most probable to be labile. Simulated stress–strain data indicates that increasing the water content deteriorates the mechanical properties. The Young’s modulus decreased by ~ 30% when the water content increased to 3 wt%. We conclude, this integration of molecular-level chemical insights with mechanical property simulations of the hydrated epoxy system and experimental validation holds the promise to advance lightweight joint technologies.
Heparin is a highly charged, polysulfated polysaccharide and serves as an anticoagulant. Heparin binds to multiple proteins throughout the body, suggesting a large range of potential therapeutic applications. Although its function has been characterized in multiple physiological contexts, heparin’s solution conformational dynamics and structure–function relationships are not fully understood. Molecular dynamics (MD) simulations facilitate the analysis of a molecule’s underlying conformational ensemble, which then provides important information necessary for understanding structure–function relationships. However, for MD simulations to afford meaningful results, they must both provide adequate sampling and accurately represent the energy properties of a molecule. The aim of this study is to compare heparin’s conformational ensemble using two well-developed force fields for carbohydrates, known as GLYCAM06 and CHARMM36, using replica exchange molecular dynamics (REMD) simulations, and to validate these results with NMR experiments. In this work, the anticoagulant sequence, an ultra-low-molecular-weight heparin, known as Arixtra (fondaparinux, sodium), was simulated with both parameter sets. The results suggest that GLYCAM06 matches experimental nuclear magnetic resonance three-bond J-coupling values measured for Arixtra better than CHARMM36. In addition, NOESY and ROESY experiments suggest that Arixtra is very flexible in the sub-millisecond time scale and does not adopt a unique structure at 25 C. Moreover, GLYCAM06 affords a much more dynamic conformational ensemble for Arixtra than CHARMM36.
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.
Source code implementation for "SurgGBSA: Learning Representations From Molecular Dynamics Trajectories".
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.
Machine learning approaches to potential generation for molecular dynamics (MD) simulations of low-temperature plasma-surface interactions could greatly extend the range of chemical systems that can be modeled. Empirical potentials are difficult to generalize to complex combinations of multiple elements with interactions that might include covalent, ionic, and metallic bonds. This work demonstrates that a specific machine learning approach, Deep Potential Molecular Dynamics (DeepMD), can generate potentials that provide a good model of plasma etching in the Si-Cl-Ar system. Comparisons are made between MD results using DeepMD models and empirical potentials, as well as experimental measurements. Pure Si properties predicted by the DeepMD model are in reasonable agreement with experimental results. Simulations of Si bombardment by Ar + ions demonstrate the ability of the DeepMD method to predict sputtering yields as well as the depth of the amorphous-crystalline interface. Etch yields as a function of flux ratio and ion energy for simultaneous Cl 2 and Ar + impacts are in good agreement with previous simulation results and experiment. Predictions of etch yields and etch products during plasma-assisted atomic layer etching of Si-Cl 2 -Ar are shown to be in good agreement with MD predictions using empirical potentials and with experiment. Finally, good agreement was also seen with measurements for the spontaneous etching of Si by Cl atoms at 300 K. Further, the demonstration that DeepMD can reproduce results from MD simulations using empirical potentials is a necessary condition to future efforts to extend the method to a much wider range of systems for which empirical potentials may be difficult or impossible to obtain.
We have performed quasielastic neutron scattering (QENS) experiments up to 1243 K and ab initio molecular dynamics (AIMD) simulations to investigate the Na diffusion in various phases of NaAlSiO4 (NASO), namely, low-carnegieite (L-NASO; trigonal), high-carnegieite (H-NASO; cubic) and nepheline (N-NASO; hexagonal) phases. The QENS measurements reveal Na ions localized diffusion behavior in L-NASO and N-NASO, but long-range diffusion behavior in H-NASO. Furthermore, the AIMD simulation supplemented the QENS measurements and showed that excess Na ions in H-NASO enhance the host network flexibility and activate the AlO 4 /SiO 4 tetrahedra rotational modes. These framework modes enable the long-range diffusion of Na across a pathway of interstitial sites. The simulations also show Na diffusion in Na-deficient N-NASO through vacant Na sites along the hexagonal c-axis.
Calcite (CaCO 3 ) is one of the most common minerals in geologic and engineered systems. It is often in contact with aqueous solutions, causing chemically assisted fracture that is critical to understanding the stability of subsurface systems and manmade structures. Calcite fracture was evaluated with reactive molecular dynamics simulations, including the impacts of crack tip geometry (notch), the presence of water, and surface hydroxyl groups. Chemo-mechanical weakening was assessed by comparing the loads where fracture began to propagate. Our analyses show that in the presence of a notch, the load at which crack growth begins is lower, compared to the effect of water or surface hydroxyls. Additionally, the breaking of two adjacent Ca–O bonds is the kinetic limitation for crack initiation, since transiently broken bonds can reform, not resulting in crack growth. In aqueous environments, fresh (not hydroxylated) calcite surfaces exhibited water strengthening. Manual addition of H + and/or OH – species on the (104) calcite surface resulted in chemo-mechanical weakening of calcite by 9%. Achieving full hydroxylation of the calcite surface was thermodynamically and kinetically limited, with only 0.17–0.01 OH/nm 2 surface hydroxylation observed on the (104) surface at the end of the simulations. In conclusion, the limited reactivity of pure water with the calcite surface restricts the chemo-mechanical effects and suggests that reactions between physiosorbed water and localized structural defects may be dominating the chemo-mechanical process in the studies where water weakening has been reported.
The diffusivity of fission gas xenon (Xe) at UO 2 grain-boundaries is one of the most important parameters in mechanistic modeling of fission gas diffusion in UO 2 based nuclear fuels. In this report, we use molecular dynamics simulations to investigate the Xe diffusivity in UO 2 grain-boundaries, employing the many-body potential developed by Cooper, Rushton and Grimes for UO 2 . Three different types of grain-boundaries are investigated, twist Σ5, tilt Σ5, and a random grain-boundary. Diffusion activation energies in the range of 0.39 – 1.46 eV are obtained for the Xe diffusivity. Comparison to results for the uranium vacancy diffusivity from MD simulations employing the same methodology suggests a weak to moderate attractive Xe-uranium vacancy binding energy depending on the grain-boundary type.
Choline chloride (ChCl) is used extensively as a hydrogen bond donor in deep eutectic solvents (DESs). However, determining its melting properties experimentally is challenging due to decomposition upon melting, leading to widely varying literature values. Accurate melting properties are crucial for understanding the solid–liquid phase behavior of ChCl-containing DESs. Here, we employ molecular dynamics simulations to compute the phase transitions of ChCl, testing a variety of atomistic force fields. We find that the results are sensitive to the choice of force field, but a melting temperature of 627 K and a melting enthalpy of 7.8 kJ/mol seem most reasonable, in good agreement with some literature values. Furthermore, we suggest these as the likely melting properties of ChCl, though the results are tentative due to limited experimental data for the liquid ChCl phase.
Here, understanding the size- and shape-dependent properties of platinum nanoparticles is critical for enabling the design of nanoparticle-based applications with optimal and potentially tunable functionality. Toward this goal, we evaluated nine different empirical potentials with the purpose of accurately modeling faceted platinum nanoparticles using molecular dynamics simulation. First, the potentials were evaluated by computing bulk and surface properties - surface energy, lattice constant, stiffness constants, and the equation of state - and comparing these to prior experimental measurements and quantum mechanics calculations. Then, the potentials were assessed in terms of the stability of cubic and icosahedral nanoparticles with faces in the {100} and {111} planes, respectively. Although none of the force fields predicts all the evaluated properties with perfect accuracy, one potential - the embedded atom method formalism with a specific parameter set - was identified as best able to model platinum in both bulk and nanoparticle forms.
Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semipermeable shell proteins and are packed full of enzyme cargoes and metabolites as they fulfill their function. Coupling together recent SAXS and proteomics work, it is possible to develop molecular models for these microcompartments and interrogate enzyme and metabolite dynamics within. Our primary goal of this study is to quantify the permeability of metabolite glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP) across the BMC shell through classical molecular dynamics simulation. The Haliangium ochraceum model of BMC shell (PDB: 6MZX) was used to model an intact BMC of approximately 10 million atoms. Working at this scale presented its own challenges in managing large data sets, with multiple challenges and hardware advances discussed that facilitated this work. Over approximately 750 ns of aggregate simulation, we see multiple permeation events for these metabolites that were added at high concentration through the pores present within BMC shell tiles. When compared to independent permeability estimates for the same metabolites determined through replica exchange umbrella sampling simulations, the permeabilities varied by approximately 3 orders of magnitude. Regardless, the permeability coefficients for both G3P and DHAP are highly similar and very high, such that only very small concentration gradients can be maintained across the BMC shell between the cytosol and BMC interior. The large simulation systems also facilitated comparisons for molecular diffusivity in the crowded environment within the BMC shell. By our estimates, the viscosity within a packed BMC shell is at least 10-fold higher than it would be in neat solution and is the real driver for varying permeability estimates we obtained through simulation. These findings will be used as design inputs for future bioengineering efforts to make products from BMCs, highlighting how permeable BMC shells can be.