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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Thermodynamic stability and contributions to the Gibbs free energy of nanocrystalline Ni 3 Fe

In this work, the heat capacities of nanocrystalline Ni 3 Fe and control materials with larger crystallites were measured from 0.4–300 K. The heat capacities were integrated to obtain the enthalpy, entropy, and Gibbs free energy and to quantify how these thermodynamic functions are altered by nanocrystallinity. From the phonon density of states (DOS) measured by inelastic neutron scattering, we find that the Gibbs free energy is dominated by phonons and that the larger heat capacity of the nanomaterial below 100 K is attributable to its enhanced phonon DOS at low energies. Besides electronic and magnetic contributions, the nanocrystalline material has an additional contribution at higher temperatures, consistent with phonon anharmonicity. The nanocrystalline material shows a stronger increase with temperature of both the enthalpy and entropy compared to the bulk sample. Its entropy exceeds that of the bulk material by 0.4 $k_B$/atom at 300 K. This is insufficient to overcome the enthalpy of grain boundaries and defects in the nanocrystalline material, making it thermodynamically unstable with respect to the bulk control material.

36 MATERIALS SCIENCE↗
NASA NTRS2015

Free-Energy Calculations. A Mathematical Perspective

Ion channels are pore-forming assemblies of transmembrane proteins that mediate and regulate ion transport through cell walls. They are ubiquitous to all life forms. In humans and other higher organisms they play the central role in conducting nerve impulses. They are also essential to cardiac processes, muscle contraction and epithelial transport. Ion channels from lower organisms can act as toxins or antimicrobial agents, and in a number of cases are involved in infectious diseases. Because of their important and diverse biological functions they are frequent targets of drug action. Also, simple natural or synthetic channels find numerous applications in biotechnology. For these reasons, studies of ion channels are at the forefront of biophysics, structural biology and cellular biology. In the last decade, the increased availability of X-ray structures has greatly advanced our understanding of ion channels. However, their mechanism of action remains elusive. This is because, in order to assist controlled ion transport, ion channels are dynamic by nature, but X-ray crystallography captures the channel in a single, sometimes non-native state. To explain how ion channels work, X-ray structures have to be supplemented with dynamic information. In principle, molecular dynamics (MD) simulations can aid in providing this information, as this is precisely what MD has been designed to do. However, MD simulations suffer from their own problems, such as inability to access sufficiently long time scales or limited accuracy of force fields. To assess the reliability of MD simulations it is only natural to turn to the main function of channels - conducting ions - and compare calculated ionic conductance with electrophysiological data, mainly single channel recordings, obtained under similar conditions. If this comparison is satisfactory it would greatly increase our confidence that both the structures and our computational methodologies are sufficiently accurate. Channel conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.

free energy↗
NASA NTRS1976

Statistical mechanics of light elements at high pressure. IV - A model free energy for the metallic phase

A large quantity of data on the thermodynamic properties of hydrogen-helium metallic liquids have been obtained in extended computer calculations in which a Monte Carlo code essentially identical to that described by Hubbard (1972) was used. A model free energy for metallic hydrogen with a relatively small mass fraction of helium is discussed, taking into account the definition of variables, a procedure for choosing the free energy, values for the fitting parameters, and the evaluation of the entropy constants. Possibilities concerning a use of the obtained data in studies of the interiors of the outer planets are briefly considered.

Dewitt, H. E.↗
DOE OSTI2025

Fully thermal meta-GGA exchange correlation free-energy density functional

The application of density functional theory to materials in the warm dense matter regime has motivated the development of exchange-correlation functionals which incorporate proper, explicit temperature dependence. Previous work has yielded fully-thermal exchange-correlation free energy functionals at the local density approximation (LDA) and generalized gradient approximation (GGA) levels of refinement. Recently an additive thermal correction scheme was utilized to construct a meta-GGA exchange-correlation (XC) functional in which thermal effects are treated at the GGA level. Here, the f TSCAN free-energy XC functional presented here includes thermal effects through the meta-GGA level in the context of the SCAN (strongly constrained and appropriately normed) ground-state functional. The f TSCAN functional provides generality while achieving similar performance to a thermal GGA functional at high temperatures, e.g. pressures within 1% of path integral Monte Carlo simulations of warm dense hydrogen, and a significant improvement over ground-state functionals. At low temperatures, f TSCAN demonstrates improvements in accuracy relative to lower-level and deorbitalized functionals, indicating that calculations using f TSCAN may be expected to perform well across experimentally relevant densities and pressures.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Gyrokinetic simulations of momentum flux parasitic to free-energy transfer

Ion Landau damping interacts with a portion of the E × B drift to cause a nondiffusive outward flux of co-current toroidal angular momentum. Quantitative evaluation of this momentum flux requires nonlinear simulations to determine f L , the fraction of fluctuation free energy that passes through ion Landau damping, in fully developed turbulence. Nonlinear gyrokinetic simulations with the GKW code confirm the presence of the systematic symmetry-breaking momentum flux. For simulations with adiabatic electrons, f L scales inversely with the ion temperature gradient, because only the ion curvature drift can transfer free energy to the electrostatic potential. Although kinetic electrons should, in principle, relax this restriction, the ion Landau damping measured in collisionless kinetic-electron simulations remained at low levels comparable with ion-curvature-drift transfer, except when magnetic shear $\hat{s}$ was strong. A set of simulations scanning the electron pitch-angle scattering rate showed only a weak variation of f L with the electron collisionality. Still, collisional-electron simulations with electron temperature greater than ion temperature unambiguously showed electron-curvature-drift transfer supporting ion Landau damping, leading to a corresponding enhancement of the symmetry-breaking momentum flux.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Gyrokinetic simulations of momentum flux parasitic to free-energy transfer

Ion Landau damping interacts with a portion of the E×B drift to cause a non-diffusive outward flux of co-current toroidal angular momentum. Quantitative evaluation of this momentum flux requires nonlinear simulations to determine fL, the fraction of fluctuation free energy that passes through ion Landau damping, in fully developed turbulence. Nonlinear gyrokinetic simulations with the GKW code confirm the presence of the systematic symmetry-breaking momentum flux. For simulations with adiabatic electrons, fL scales inversely with the ion temperature gradient, because only the ion curvature drift can transfer free energy to the electrostatic potential. Although kinetic electrons should in principle relax this restriction, the ion Landau damping measured in collisionless kinetic-electron simulations remained at low levels comparable with ion-curvature-drift transfer, except when magnetic shear was strong. A set of simulations scanning the electron pitch-angle scattering rate showed only a weak variation of fL with the electron collisionality. However, collisional-electron simulations with electron temperature greater than ion temperature unambiguously showed electron-curvature-drift transfer supporting ion Landau damping, leading to a corresponding enhancement of the symmetry-breaking momentum flux.

intrinsic rotation↗
NASA NTRS1992

Gibbs free energy difference between the undercooled liquid and the beta phase of a Ti-Cr alloy

The heat of fusion and the specific heats of the solid and liquid have been experimentally determined for a Ti60Cr40 alloy. The data are used to evaluate the Gibbs free energy difference, delta-G, between the liquid and the beta phase as a function of temperature to verify a reported spontaneous vitrification (SV) of the beta phase in Ti-Cr alloys. The results show that SV of an undistorted beta phase in the Ti60Cr40 alloy at 873 K is not feasible because delta-G is positive at the temperature. However, delta-G may become negative with additional excess free energy to the beta phase in the form of defects.

Ohsaka, K.↗
DOE OSTI2024

Computing equilibrium free energies through a nonequilibrium quench

Many methods to accelerate sampling of molecular configurations are based on the idea that temperature can be used to accelerate rare transitions. These methods typically compute equilibrium properties at a target temperature using reweighting or through Monte Carlo exchanges between replicas at higher temperatures. A recent paper [G. M. Rotskoff and E. Vanden-Eijnden, Phys. Rev. Lett. 122, 150602 (2019)] demonstrated that accurate equilibrium densities of states can also be computed through a nonequilibrium “quench” process, where sampling is performed at a higher temperature to encourage rapid mixing and then quenched to lower energy states with dissipative dynamics. Here, we provide an implementation of the quench dynamics in LAMMPS and evaluate a new formulation of nonequilibrium estimators for the computation of partition functions or free energy surfaces (FESs) of molecular systems. We show that the method is exact for a minimal model of N-independent harmonic springs and use these analytical results to develop heuristics for the amount of quenching required to obtain accurate sampling. We then test the quench approach on alanine dipeptide, where we show that it gives an FES that is accurate near the most stable configurations using the quench approach but disagrees with a reference umbrella sampling calculation in high FE regions. We then show that combining quenching with umbrella sampling allows the efficient calculation of the free energy in all regions. Moreover, by using this combined scheme, we obtain the FES across a range of temperatures at no additional cost, making it much more efficient than standard umbrella sampling if this information is required. Finally, we discuss how this approach can be extended to solute tempering and demonstrate that it is highly accurate for the case of solvated alanine dipeptide without any additional modifications.

Chemistry↗
DOE OSTI2022

Accurate determination of solvation free energies of neutral organic compounds from first principles

The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various degrees, for an arbitrary system of molecules they have not been achieved simultaneously. For biophysical ensembles that exist at room temperature and pressure, and where the entropic contributions are on par with interaction strengths, it is the free energies that are both most important and most difficult to predict. We compute the free energies of solvation for a diverse set of neutral organic compounds using a polarizable force field fitted entirely to ab initio calculations. The mean absolute errors (MAE) of hydration, cyclohexane solvation, and corresponding partition coefficients are 0.2 kcal/mol, 0.3 kcal/mol and 0.22 log units, i.e. within chemical accuracy. The model (ARROW FF) is multipolar, polarizable, and its accompanying simulation stack includes nuclear quantum effects (NQE). The simulation tools’ computational efficiency is on a par with current state-of-the-art packages. The construction of a wide-coverage molecular modelling toolset from first principles, together with its excellent predictive ability in the liquid phase is a major advance in biomolecular simulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1974

Free energies of formation of WC and WzC and the thermodynamic properties of carbon in solid tungsten

The activity of carbon in the two-phase regions - W + WC and W + W2C was obtained from the carbon content of iron rods equilibrated with mixtures of metal plus carbide powders. From this activity data the standard free energies of formation of WC and W2C were calculated. The temperature of the invariant reaction W2C = W + WC was fixed at 1570 + or - 5K. Using available solubility data for C in solid W, the partial molar free energy of C in the dilute solid solution was also calculated. The heat of solution of C in W, and the excess entropy for the interstitial solid solution, were computed, assuming that the carbon atoms reside in the octahedral interstices of bcc W.

Gupta, D. K.↗
DOE OSTI2024

The Aqueous and Acetonitrile Bond Dissociation Free Energies of N -Hydroxyphthalimide

Widely cited values of 89 and 90.9 kcal/mol for the bond-dissociation free energy of N-hydroxyphthalimide (NHPI) in water and acetonitrile, respectively, are in error. The sources of the errors leading to these values have been explored and corrected. Here, the corrected values are confirmed through new experiments in aqueous and acetonitrile media and are found to be 84.4 ± 0.1 and 80.04 ± 0.06 kcal/mol, respectively.

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

Binding mechanism and binding free energy of amino acids and citrate to hydroxyapatite surfaces as a function of crystallographic facet, pH, and electrolytes

Hydroxyapatite (HAP) is the major mineral phase in bone and teeth. The interaction of individual amino acids and citrate ions with different crystallographic HAP surfaces has remained uncertain for decades, creating a knowledge gap to rationally design interactions with peptides, proteins, and drugs. In this contribution, we quantify the binding mechanisms and binding free energies of the 20 end-capped natural amino acids and citrate ions on the basal (001) and prismatic (010)/(020) planes of hydroxyapatite at pH values of 7 and 5 for the first time at the molecular scale. We utilized over 1500 steered molecular dynamics simulations with highly accurate potentials that reproduce surface and hydration energies of (hkl) hydroxyapatite surfaces at different pH values. Charged residues demonstrate a much higher affinity to HAP than charge-neutral species due to the formation of superficial ion pairs and ease of penetration into layers of water molecules on the mineral surface. Binding free energies range from 0 to -60 kJ/mol and were determined with ~10% uncertainty. The highest affinity was found for citrate, followed by Asp(-) and Glu(-), and followed after a gap by Arg(+), Lys(+), as well as by His(+) at pH 5. The (hkl)-specific area density of calcium ions, the protonation state of phosphate ions, and subsurface directional order of the ions in HAP lead to surface-specific binding patterns. Amino acids without ionic side groups exhibit weak binding, between -3 and 0 kJ/mol, due to difficulties to penetrate the first layer of water molecules on the apatite surfaces. We explain recognition processes that remained elusive in experiments, in prior simulations, discuss agreement with available data, and reconcile conflicting interpretations. In conclusion, the findings can serve as useful input for the design of peptides, proteins, and drug molecules for the modification of bone and teeth-related materials, as well as control of apatite mineralization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1973

Solid/liquid interfacial free energies in binary systems

Description of a semiquantitative technique for predicting the segregation characteristics of smooth interfaces between binary solid and liquid solutions in terms of readily available thermodynamic parameters of the bulk solutions. A lattice-liquid interfacial model and a pair-bonded regular solution model are employed in the treatment with an accommodation for liquid interfacial entropy. The method is used to calculate the interfacial segregation and the free energy of segregation for solid-liquid interfaces between binary solutions for the (111) boundary of fcc crystals. The zone of compositional transition across the interface is shown to be on the order of a few atomic layers in width, being moderately narrower for ideal solutions. The free energy of the segregated interface depends primarily upon the solid composition and the heats of fusion of the component atoms, the composition difference of the solutions, and the difference of the heats of mixing of the solutions.

Nason, D.↗
DOE OSTI2023

Nucleation-mediated reshaping of facetted metallic nanocrystals: Breakdown of the classical free energy picture

Shape stability is key to avoiding degradation of performance for metallic nanocrystals synthesized with facetted non-equilibrium shapes to optimize properties for catalysis, plasmonics, and so on. Reshaping of facetted nanocrystals is controlled by the surface diffusion-mediated nucleation and growth of new outer layers of atoms. Here, Kinetic Monte Carlo (KMC) simulation of a realistic stochastic atomistic-level model is applied to precisely track the reshaping of Pd octahedra and nanocubes. Unexpectedly, separate constrained equilibrium Monte Carlo analysis of the free energy profile during reshaping reveals a fundamental failure of the classical nucleation theory (CNT) prediction for the reshaping barrier and rate. Why? Nucleation barriers can be relatively low for these processes, so the system is not locally equilibrated before crossing the barrier, as assumed in CNT. This claim is supported by an analysis of a first-passage problem for reshaping within a master equation framework for the model that reasonably captures the behavior in KMC simulations.

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

Development of a multiphase equation of state for gallium with experiments and ab initio free-energy calculations

Here, we present a five-phase equation of state (EOS) for elemental gallium (Ga) that is developed using both experimental data and new theoretical predictions. Four experimentally observed solid phases (Ga-I, Ga-II, Ga-III, and Ga-IV) and one liquid phase are included. To improve our understanding of the thermal behavior of Ga and its phase boundaries under compression, we have performed ab initio density functional theory (DFT) free-energy calculations for the Ga-III and liquid phases, which enables us to determine the melt temperature to be 2214 ± 100 K at 110 GPa, extending significantly beyond the existing experimental melt data, which are limited to 25 GPa. In order to best describe the electron-thermal contribution, which dominates the liquid free energy at high temperatures, we have carried out averaged-atom-in-jellium DFT calculations to cover the entire temperature and density range of the EOS. The resulting multiphase Ga EOS is able to accurately reproduce a diverse variety of data, including known phase boundaries, the principal Hugoniot, low-pressure liquid isobars, and diamond-anvil-cell isotherm measurements at high pressures. It agrees more closely with key experimentally measured properties than other Ga EOS models targeted for high-pressure applications.

Wu, Christine J. [Lawrence Livermore National Labo↗
DOE OSTI2024

Metadynamics investigation of lanthanide solvation free energy landscapes and insights into separations energetics

Lanthanide ion solvation chemistry in nonaqueous phases is key to understanding and developing effective separation processes for these critical materials. Due to the complexity and inherent disorder of the solution phase, a comprehensive picture of the solvated metal ion is often difficult to generate solely from conventional spectroscopic approaches and electronic structure calculations, particularly in the extractant phase. In this work, we use classical molecular dynamics (MD) simulation with an advanced sampling technique, metadynamics, supplemented by experimental spectroscopy and speciation analysis, to measure lanthanide solvation free energy landscapes. We define coordination-based collective variables to probe the entire range of solvation configurations in the organic phase of lanthanum (La), europium (Eu), and lutetium (Lu) nitrate salts bound with a commonly used extractant, N,N′-dimethyl, N,N′-dioctylhexylethoxymalonamide (DMDOHEMA). The known lanthanide extraction trend of La ≈ Eu > Lu is readily explained by the measured free energy surfaces, which show consistent DMDOHEMA coordination from La to Eu, followed by loss of DMDOHEMA coordination from Eu to Lu. These simulations suggest how ligand crowding at the metal center can control selectivity, in this case resulting in the opposite extraction trend as observed with other conventional extractants, where the enthalpic contribution from increasing lanthanide charge density across the series dominates the extraction energetics. We also find that the presence of inner-sphere water, verified by time-resolved fluorescence, diversifies the accessible solvation structures. As a result, understanding solvation requires consideration of an entire thermodynamic ensemble, rather than the single dominant lowest-energy structure, as is often considered out of necessity in interpretation of spectroscopic data or in electronic structure-based ligand design approaches. In general, we demonstrate how metadynamics uniquely enables investigation of complex, multidimensional solvation energetic landscapes, and how it can explain selectivity trends where extraction is controlled by more complex mechanisms than simple charge density-based selectivity.

Wang, Xiaoyu↗