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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

Molecular Simulation of Water Extraction into a Tri-n-Butyl-Phosphate/n-Dodecane Solution

Abstract: Molecular dynamics simulations were performed to investigate water extraction into a solution of 30 vol% tri-n-butyl-phosphate (TBP) in n-dodecane. This solvent extraction mixture is commonly used in hydrometallurgical and nuclear fuel recycling operations for recovering metals from aqueous streams. It is known that water is coextracted in the organic phase and that it competes with metal ions for the available extractant agent (TBP). Therefore investigating pure water extraction provides a realistic prototype to test molecular simulation methods for the first time in this area. Our computational results indicate that the TBP electric dipole moment has a significant effect on the predicted water solubility. A larger TBP dipole moment decreases the aqueous-organic interfacial tension, leading to increased roughness of the aqueous-organic interface. Interfacial roughness has a significant effect on disrupting the interfacial water hydrogen bonding structure, resulting in a greater number of dangling water molecules at the interface. This enhances the probability of water molecules to break away from the aqueous phase and to migrate into the bulk of the organic phase. Therefore, the magnitude of the TBP dipole moment is a crucial factor in controlling water hydrogen bond breaking at the aqueous-organic interface. By slightly lowering the atomic partial charges of the TBP atoms, to produce a dipole moment that better agrees with experimental data, we were able to predict water solubility in close agreement with experimental measurements. Hence we demonstrate that a molecular modeling and simulation approach may provide quantitative support to experimental programs in this area. In addition, our simulation results shed light into the molecular mechanism of water extraction, the critical role of TBP, and the structural forms of water molecules both at the interface and in the bulk of the organic phase. Specifically, it is found that water molecules are extracted either as single molecules or as clusters. Furthermore, within the organic phase, the extracted water forms clusters with up to 20 water molecules, however, more than 70% of these water clusters contain less than 5 water molecules when the water extraction process reaches saturation.

de Almeida, Valmor F↗
DOE OSTI2020

Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein

Molecular Dynamics (MD) simulations seek to provide atomic-level insights into conformationally dynamic biological systems at experimentally relevant time resolutions, such as those afforded by single-molecule fluorescence measurements. However, limitations in the time scales of MD simulations and the time resolution of single-molecule measurements have challenged efforts to obtain overlapping temporal regimes required for close quantitative comparisons. Achieving such overlap has the potential to provide novel theories, hypotheses, and interpretations that can inform idealized experimental designs that maximize the detection of the desired reaction coordinate. Here, we report MD simulations at time scales overlapping with in vitro single-molecule Förster (fluorescence) resonance energy transfer (smFRET) measurements of the amino acid binding protein LIV-BP SS at sub-millisecond resolution. Computationally efficient all-atom structure-based simulations, calibrated against explicit solvent simulations, were employed for sampling multiple cycles of LIV-BP SS clamshell-like conformational changes on the time scale of seconds, examining the relationship between these events and those observed by smFRET. The MD simulations agree with the smFRET measurements and provide valuable information on local dynamics of fluorophores at their sites of attachment on LIV-BP SS and the correlations between fluorophore motions and large-scale conformational changes between LIV-BP SS domains. We further utilize the MD simulations to inform the interpretation of smFRET data, including Förster radius (R 0 ) and fluorophore orientation factor (κ 2 ) determinations. The approach we describe can be readily extended to distinct biochemical systems, allowing for the interpretation of any FRET system conjugated to protein or ribonucleoprotein complexes, including those with more conformational processes, as well as those implementing multi-color smFRET.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Understanding Gas Solubility of Pure Component and Binary Mixtures within Multivalent Ionic Liquids from Molecular Simulations

Understanding the molecular-level solubility of CO 2 and its mixtures is essential to the progress of gas treating technologies. Herein, we use grand canonical Monte Carlo simulations to study the single component gas absorption of SO 2 , N 2 , CH 4 , and H 2 , and binary mixtures of CO 2 /SO 2 , CO 2 /N 2 , CO 2 /CH 4 , and CO 2 /H 2 of varying mole fractions within multivalent ionic liquids (ILs). Our results highlight the importance of the free volume effect and the anion effect when interpreting the absorption behavior of these mixtures, similar to the behavior of CO 2 found in our previous study. The deviation of the gas solubility between the pure component absorption versus the binary absorption, as well as the solubility selectivity, highlight the importance of the relative affinity of gas species within a mixture to the different anions. Further, the absorption selectivity within a specific IL system can be predicted based on the relative gas affinity to the anion.

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

STOCK: Structure mapper and online coarse-graining kit for molecular simulations

We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, e.g. all-atom, to low, i.e. coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, e.g. VOTCA and DL_CGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, e.g. radial distribution functions, of the underlying higher resolution model. The required distribution functions can be provided by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at http://stock.cmm.ki.si.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Molecular simulation of liquid–vapor coexistence for NaCl: Full-charge vs scaled-charge interaction models

Scaled-charge models have been recently introduced for molecular simulations of electrolyte solutions and molten salts to attempt to implicitly represent polarizability. Although these models have been found to accurately predict electrolyte solution dynamic properties, they have not been tested for coexistence properties, such as the vapor pressure of the melt. In this work, we evaluate the vapor pressure of a scaled-charge sodium chloride (NaCl) force field and compare the results against experiments and a non-polarizable full-charge force field. The scaled-charge force field predicts a higher vapor pressure than found in experiments, due to its overprediction of the liquid-phase chemical potential. Reanalyzing the trajectories generated from the scaled-charge model with full charges improves the estimation of the liquid-phase chemical potential but not the vapor pressure.

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

Ettringite hysteresis under sorption from molecular simulations

Highlights: • Hybrid Grand Canonical Monte Carlo (GCMC) and Molecular Dynamics (MD) simulations are performed. • Anisotropic large strain coefficient of crystal shrinkage of ettringite is provided. • Entropy increases when ettringite converts into metaettringite. • Sorption-induced stress may lead to columns collapse upon drying. • H-bonds involving OH groups in columns play a role in hysteresis. The response of ettringite under sorption is critical for the utilization of this mineral as an energy storage material and to understand the concrete durability problems associated with ettringite formation. We report molecular simulations directly sampling the osmotic ensemble to understand the sorption processes and structural changes in ettringite-metaettringite transition. Desorption branch and sorption-induced volume changes from simulations agree with the experiments. The structural changes at low relative humidity are analyzed, revealing for the first time details of metaettringite structure. The reversibility under sorption observed experimentally is captured by simulation in the ettringite domain. The reversibility in the conversion of metaettringite into ettringite is not captured by the direct simulations in the osmotic ensemble due to the large volume changes associated with ettringite desorption. Finally, we discuss the role of hydrogen bonds on the hysteresis in ettringite.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Avoiding pitfalls in molecular simulation of vapor sorption: Example of propane and isobutane in metal–organic frameworks for adsorption cooling applications

This study introduces recommendations for conducting molecular simulations of vapor adsorption, with an emphasis on enhancing the accuracy, reproducibility, and comparability of results. The first aspect we address is consistency in the implementation of some details of typical molecular models, including tail corrections and cutoff distances, due to their significant influence on generated data. We highlight the importance of explicitly calculating the saturation pressures at relevant temperatures using methods such as Gibbs ensemble Monte Carlo simulations and illustrate some pitfalls in extrapolating saturation pressures using this method. For grand canonical Monte Carlo (GCMC) simulations, the input fugacity is usually calculated using an equation of state, which often requires the critical parameters of the fluid. We show the importance of using critical parameters derived from the simulation with the same model to ensure internal consistency between the simulated explicit adsorbate phase and the implicit bulk phase in GCMC. We show the advantages of presenting isotherms on a relative pressure scale to facilitate easier comparison among models and with experiment. Extending these guidelines to a practical case study, we evaluate the performance of various isoreticular metal–organic frameworks (MOFs) in adsorption cooling applications. This includes examining the advantages of using propane and isobutane as working fluids and identifying MOFs with a superior performance.

36 MATERIALS SCIENCE↗
NASA NTRS2020

Molecular Simulations of Ultrafast Radiation Induced Melting at Metal-Semiconductor Interfaces

Understanding radiation induced ultrafast melting at material interfaces is essential in designing robust electronic devices for aviation/space applications and in laser machining. While it is difficult to achieve the spatial and temporal resolution required to quantify the phenomenon experimentally, simulations can provide the detailed mechanisms of the structural changes that happen during phase transition. In this work, we use molecular simulations to study the effect of radiation damage on silicon carbide (SiC) - tungsten (W) interfaces which is of interest in high power electronics. A multi-scale approach is involved wherein the reactions at the interfaces are quantified using ab-initio molecular dynamics (MD) simulations and classical MD simulations are employed to understand the structural and diffusional changes across the material interface. Finally, coarse-grained Lennard-Jones type models are used to study the larger scale mechanisms and structures obtained due to the induced damages. We show that the response of the material to radiation damage depends on factors such as energy of the incident radiation, thermal properties, and molecular structure of the material.

Ravichandran, Ashwin↗
DOE OSTI2024

Effect of layer bending on montmorillonite hydration and structure from molecular simulation

Conceptual models of smectite hydration include planar (flat) clay layers that undergo stepwise expansion as successive monolayers of water molecules fill the interlayer regions. However, X-ray diffraction (XRD) studies indicate the presence of interstratified hydration states, suggesting non-uniform interlayer hydration in smectites. Additionally, recent theoretical studies have shown that clay layers can adopt bent configurations over nanometer-scale lateral dimensions with minimal effect on mechanical properties. Therefore, in this study we used molecular simulations to evaluate structural properties and water adsorption isotherms for montmorillonite models composed of bent clay layers in mixed hydration states. Results are compared with models consisting of planar clay layers with interstratified hydration states (e.g. 1W–2W). The small degree of bending in these models (up to 1.5 Å of vertical displacement over a 1.3 nm lateral dimension) had little or no effect on bond lengths and angle distributions within the clay layers. Except for models that included dry states, porosities and simulated water adsorption isotherms were nearly identical for bent or flat clay layers with the same averaged layer spacing. Similar agreement was seen with Na- and Ca-exchanged clays. In conclusion, while the small bent models did not retain their configurations during unconstrained molecular dynamics simulation with flexible clay layers, we show that bent structures are stable at much larger length scales by simulating a 41.6×7.1 nm 2 system that included dehydrated and hydrated regions in the same interlayer.

58 GEOSCIENCES↗
DOE OSTI2016

What can molecular simulation do for global warming?

Carbon capture is necessary to reduce CO 2 emissions from burning fossil fuels, which has led to global warming. Molecular simulations offer chemical insights and design principles for new separation media and for understanding the separation process. In this review, we summarize recent applications of simulation methods from ab initio and density functional theory to classical molecular dynamics and Grand canonical Monte Carlo in understanding ionic liquids and porous carbonaceous materials for CO 2 separation, especially the postcombustion CO 2 / N 2 separation. We highlight design and simulation of the porous two‐dimensional ( 2D ) materials as the highly selective membranes for CO 2 separation. Simulated structure–property relationships for the materials are discussed in connection to the corresponding chemisorption, physisorption, or membrane process. In chemisorption, the focus is on reducing the heat of reaction with CO 2 ; in physisorption, the key is to increase the binding strength via CO 2 ‐philic groups; in membrane process, the key is to increase solubility for ionic‐liquid membranes and to control pore size for 2D materials. Challenges and opportunities for simulating emerging materials are also discussed. WIREs Comput Mol Sci 2016, 6:173–197. doi: 10.1002/wcms.1241 This article is categorized under: Structure and Mechanism > Computational Materials Science Electronic Structure Theory > Density Functional Theory Molecular and Statistical Mechanics > Molecular Interactions

Tian, Ziqi↗
DOE OSTI2020

Predicting chemical reaction equilibria in molten carbonate fuel cells via molecular simulations

It has been recently suggested that hydroxide ions can be formed in the electrolyte of molten carbonate fuel cells when water vapor is present. The hydroxide can replace carbonate in transporting electrons across the electrolyte, thereby reducing the CO 2 separation efficiency of the fuel cell although still producing electricity. In this work, we obtain the equilibrium concentration of hydroxide in five molten alkali carbonate salts from molecular simulations. The results reveal that there can be a substantial amount of hydroxide in the electrolyte at low partial pressures of CO 2 . In addition, we find that the equilibrium concentration of molecular water dissolved in the electrolyte is over two orders of magnitude higher than that of CO 2 . Increasing the size and polarizability (or in other words reducing the “hardness”) of the cations present in the electrolyte can reduce the hydroxide fraction, but at the cost of lowering ionic conductivity.

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

Computational Molecular Simulation of the Oxidative Adsorption of Ferrous Iron at the Hematite (001)-Water Interface

The interaction of Fe(II) with ferric oxide/oxyhydroxide phases is central to the biogeochemical redox chemistry of iron. Molecular simulation techniques were employed to determine the mechanisms and quantify the rates of Fe(II) oxidative adsorption at the hematite (001)-water interface. Molecular dynamics potential of mean force calculations of Fe(II) adsorbing on the hematite surface revealed the presence of three free energy minima corresponding to Fe(II) adsorbed in an outersphere complex, a monodentate innersphere complex, and a tridentate innersphere complex. The free energy barrier for adsorption from the outersphere position to the monodentate innersphere site was calculated to be similar to the activation enthalpy for water exchange around aqueous Fe(II). Adsorption at both innersphere sites was predicted to be unfavorable unless accompanied by release of protons. Molecular dynamics umbrella sampling simulations and ab initio cluster calculations were performed to determine the rates of electron transfer from Fe(II) adsorbed as an innersphere and outersphere complex. The electron transfer rates were calculated to range from 10^-4 to 10^2 s-1, depending on the adsorption site and the potential parameter set, and were generally slower than those obtained in the bulk hematite lattice. The most reliable estimate of the rate of electron transfer from Fe(II) adsorbed as an outersphere complex to lattice Fe(III) was commensurate with the rate of adsorption as an innersphere complex suggesting that adsorption does not necessarily need to precede oxidation.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

Growth of bi- and tri-layered graphene on silicon carbide substrate via molecular dynamics simulation

Molecular dynamics (MD) simulation with simulated annealing method is used to study the growth process of bi- and tri-layered graphene on a 6H-SiC (0001) substrate via molecular dynamics simulation. Tersoff-Albe-Erhart (TEA) potential is used to describe the inter-atomic interactions among the atoms in the system. The formation temperature, averaged carbon-carbon bond length, pair correlation function, binding energy and the distance between the graphene formed and the SiC substrate are quantified. The growth mechanism, graphitization of graphene on the SiC substrate and characteristics of the surface morphology of the graphene sheet obtained in our MD simulation compare well to that observed in epitaxially grown graphene experiments and other simulation works.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Advances in Clayff Molecular Simulation of Layered and Nanoporous Materials and Their Aqueous Interfaces

As a general-purpose force field for molecular simulations of layered materials and their fluid interfaces, Clayff continues to see broad usage in atomistic computational modeling for numerous geoscience and materials science applications due to its (1) success in predicting properties of bulk nanoporous materials and their interfaces, (2) transferability to a range of layered and nanoporous materials, and (3) simple functional form which facilitates incorporation into a variety of simulation codes. Here, we review applications of Clayff to model bulk phases and interfaces not included in the original parameter set and recent modifications for modeling surface terminations such as hydroxylated nanoparticle edges. Overall, we conclude with a discussion of expectations for future developments.

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

Development of EEM based silicon–water and silica–water wall potentials for non-reactive molecular dynamics simulations

Molecular dynamics simulations of heat transfer in gases are computationally expensive when the wall molecules are explicitly modeled. To save computational time, an implicit boundary function is often used. Steele's potential has been used in studies of fluid–solid interface for a long time. In this work, the conceptual idea of Steele's potential was extended in order to simulate water–silicon and water–silica interfaces. A new wall potential model is developed by using the electronegativity-equalization method (EEM), a ReaxFF empirical force field and a non-reactive molecular dynamics package PumMa. Contact angle simulations were performed in order to validate the wall potential model. Contact angle simulations with the resulting tabulated wall potentials gave a silicon–water contact angle of 129°, a quartz–water contact angle of 0°, and a cristobalite–water contact angle of 40°, which are in reasonable agreement with experimental values.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Wettability of Two-Dimensional Carbon Allotropes from Molecular Simulations

Force-field Monte Carlo and Molecular Dynamics simulations are used to compare wetting behaviors of model carbon sheets mimicking neat graphene, its saturated derivative, graphane, and related planar allotropes penta-graphene, γ-graphyne, and ψ-graphene in contact with aqueous droplets or an aqueous film confined between parallel carbon sheets. Atomistic and area-integrated surface/water potentials are found to be essentially equivalent in capturing moderate differences between the wetting free energies of tested substrates. Despite notable differences in mechanical and electric properties of distinct allotropes, the predicted allotrope/water contact angles span a narrow window of weakly hydrophilic values. Contact angles in the range of 80 ± 10° indicate modest hydration repulsion incapable of competing with van der Waals attraction between carbon particles. Poor dispersibility in neat water is hence a common feature of studied materials.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Depletion of the Protein Hydration Shell with Increasing Temperature Observed by Small-Angle X-ray Scattering and Molecular Simulations

The hydration shell is an integral part of proteins since it plays key roles in conformational transitions, molecular recognition, and enzymatic activity. While the dynamics of the hydration shell have been described by spectroscopic techniques, the structure of the hydration shell remains less understood due to the lack of hydration shell-sensitive structural probes with high spatial resolution. We combined temperature-ramp small-angle X-ray scattering (T-ramp SAXS) from 255 to 335 K with molecular simulations to demonstrate that the hydration shells of the IgG-binding domain of Protein G (GB3) and the villin headpiece are remarkably temperature-sensitive. For proteins in the folded state, T-ramp SAXS data and explicit-solvent SAXS predictions consistently demonstrate decays of protein contrasts and radii of gyration with increasing temperature, which are shown to reflect predominantly temperature-sensitive, depleting hydration shells. The depletion is caused not merely by enhanced disorder within the hydration shells but also by partial displacements of surface-coordinated water molecules. Together, T-ramp SAXS and explicit-solvent SAXS calculations provide a novel structural view of the protein hydration shell, which underlies temperature-dependent processes such as cold denaturation, thermophoresis, or biomolecular phase separation.

electron density↗