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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 OSTI2024

Enhanced Sampling of Crystal Nucleation with Graph Representation Learnt Variables

In this study, we present a graph neural network-based learning approach using an autoencoder setup to derive low-dimensional variables from features observed in experimental crystal structures. These variables are then biased in enhanced sampling to observe state-to-state transitions and reliable thermodynamic weights. Our approach uses simple convolution and pooling methods. To verify the effectiveness of our protocol, we examined the nucleation of various allotropes and polymorphs of iron and glycine from their molten states. Our graph latent variables when biased in well-tempered metadynamics consistently show transitions between states and achieve accurate free energy calculations in agreement with experiments, both of which are indicators of dependable sampling. This underscores the strength and promise of our graph neural net variables for improved sampling. Furthermore, the protocol shown here should be applicable for other systems and with other sampling methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Energetics of high temperature degradation of fentanyl into primary and secondary products

Fentanyl is a synthetic opioid used for managing chronic pain. Due to its higher potency (50–100×) than morphine, fentanyl is also an abused drug. A sensor that could detect illicit fentanyl by identifying its thermally degraded fragments would be helpful to law enforcement. While experimental studies have probed the thermal degradation of fentanyl, little theoretical work has been done to understand the mechanism. Here, we studied the thermal degradation pathways of fentanyl using extensive ab initio molecular dynamics simulations combined with enhanced sampling via multiple-walker metadynamics. We calculated the free energy profile for each bond suggested earlier as a potential degradation point to map the thermodynamic driving forces. In conclusion, we also estimated the forward attempt rate of each bond degradation reaction to gain information about degradation kinetics.

Poudel, Bharat↗
DOE OSTI2022

Single crystal growth of iridates without platinum impurities

Iridates have attracted much interest in the last decade for their novel magnetism emerging in the limit of strong spin-orbit coupling and possible unconventional superconductivity. A standard for growing iridate single crystals has been the flux method using platinum crucibles. Here, in this work, we show that this widely used method compromises the sample quality by inclusion of platinum impurities. We find that Sr 2 ⁢IrO 4 single crystals grown in iridium crucibles show remarkable differences from those grown in platinum crucibles in their sample characterizations using Raman spectroscopy, resistivity, magnetization, optical third harmonic generation, resonant x-ray diffraction, and resonant inelastic x-ray scattering measurements. In particular, we show that several peaks of sizable intensities disappear in the Raman spectra of samples free of platinum impurities, and a significantly larger activation energy is extracted from the resistivity data compared to previously reported values. Furthermore, we find no evidence of the previously reported glide-symmetry-breaking structural distortions and confirm the I⁢ 4 1 / acd space group of the lattice symmetry. Although the platinum impurities are not apparent in the magnetic properties and thus went unnoticed in the stoichiometric insulating phase for a long time, their effects can be much more detrimental to transport properties in chemically doped compounds. Therefore, our result suggests using growth methods that avoid platinum impurities for an investigation of the intrinsic physical properties of iridates, and possible superconducting phases.

36 MATERIALS SCIENCE↗
NASA NTRS2000

Rate Constant and RRKM Product Study for the Reaction Between CH3 and C2H3 at T = 298K

The total rate constant k1 has been determined at P = 1 Torr nominal pressure (He) and at T = 298 K for the vinyl-methyl cross-radical reaction CH3 + C2H3 yields products. The measurements were performed in a discharge flow system coupled with collision-free sampling to a mass spectrometer operated at low electron energies. Vinyl and methyl radicals were generated by the reactions of F with C2H4 and CH4, respectively. The kinetic studies were performed by monitoring the decay of C2H3 with methyl in excess, 6 < |CH3|(sub 0)/|C2H3|(sub 0) < 21. The overall rate coefficient was determined to be k1(298 K) = (1.02 +/- 0.53)x10(exp -10) cubic cm/molecule/s with the quoted uncertainty representing total errors. Numerical modeling was required to correct for secondary vinyl consumption by reactions such as C2H3 + H and C2H3 + C2H3. The present result for k1 at T = 298 K is compared to two previous studies at high pressure (100-300 Torr He) and to a very recent study at low pressure (0.9-3.7 Torr He). Comparison is also made with the rate constant for the similar reaction CH3 + C2H5 and with a value for k1 estimated by the geometric mean rule employing values for k(CH3 + CH3) and k(C2H3 + C2H3). Qualitative product studies at T = 298 K and 200 K indicated formation of C3H6, C2H2, and C2H5 as products of the combination-stabilization, disproportionation, and combination-decomposition channels, respectively, of the CH3 + C2H3 reaction. We also observed the secondary C4H8 product of the subsequent reaction of C3H5 with excess CH3; this observation provides convincing evidence for the combination-decomposition channel yielding C3H5 + H. RRKM calculations with helium as the deactivator support the present and very recent experimental observations that allylic C-H bond rupture is an important path in the combination reaction. The pressure and temperature dependencies of the branching fractions are also predicted.

Thorn, R. Peyton, Jr.↗
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↗
DOE OSTI2023

Systematic modification of functionality in disordered elastic networks through free energy surface tailoring

A combined machine learning–physics–based approach is explored for molecular and materials engineering. Specifically, collective variables, akin to those used in enhanced sampled simulations, are constructed using a machine learning model trained on data gathered from a single system. Through the constructed collective variables, it becomes possible to identify critical molecular interactions in the considered system, the modulation of which enables a systematic tailoring of the system’s free energy landscape. To explore the efficacy of the proposed approach, we use it to engineer allosteric regulation and uniaxial strain fluctuations in a complex disordered elastic network. Its successful application in these two cases provides insights regarding how functionality is governed in systems characterized by extensive connectivity and points to its potential for design of complex molecular systems.

42 ENGINEERING↗
DOE OSTI2021

Ab initio molecular dynamics with enhanced sampling in heterogeneous catalysis

Ab initio molecular dynamics simulations combined with enhanced sampling techniques are becoming widespread methods to investigate chemical phenomena in catalytic systems. These techniques automatically include finite temperature effects, anharmonicity, and collective dynamics in their robust description of enthalpic and entropic contributions, which can have significant impact on reaction free energy landscapes. This contrasts with standard ab initio static approaches that are based on assessing reaction free energies from various coarse-grained descriptions of the reaction potential energy surface. Enhanced sampling ab initio molecular dynamics opens the way to first principles simulations of systems of increasing complexity like solid/liquid catalytic interfaces. Here, we aim at guiding the reader through the basis of these techniques, summarizing their fundamental theoretical and practical aspects, and reviewing the relevant literature in the field. After a brief introduction to the problem, we will illustrate the advantage of using molecular simulations to include finite temperature effects, examine the most common ab initio techniques currently in use, describe their application to solid state heterogeneous catalysts, and finally critically review the most popular enhanced sampling techniques used in computational catalysis.

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

Modeling the Solvation and Acidity of Carboxylic Acids Using an Ab Initio Deep Neural Network Potential

Formic and acetic acid constitute the simplest of carboxylic acids, yet they exhibit fascinating chemistry in the condensed phase such as proton transfer and dimerization. The go-to method of choice for modeling these rare events have been accurate but expensive ab-initio molecular dynamics simulations. Here, we present a deep neural network potential trained using accurate ab-initio data that can be used in tandem with enhanced-sampling methods to perform an efficient exploration of the free-energy surface of aqueous solutions of weak carboxylic acids. In particular, we show that our model captures proton dissociation and provides a good estimate of the pK a , as well as the dimerization of formic and acetic acid. This provides a suitable starting point for applications in different research areas where computational efficiency coupled with the accuracy of ab-initio methods is required.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Monte Carlo Simulations of Crystal Defects in Open Ensembles

Zero- and two-dimensional crystal defects form in open statistical ensembles, such as the grand canonical, that are usually inaccessible with conventional simulation techniques. This longstanding challenge is overcome with a new Hamiltonian Monte Carlo method that samples energy-biased gradual transformations. In conclusion, the method enables free energy calculations for nonideal point defects and the direct prediction of finite-temperature interface structures.

Grain boundaries↗
DOE OSTI2021

Completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: Cosmological implications from two decades of spectroscopic surveys at the Apache Point Observatory

We present the cosmological implications from final measurements of clustering using galaxies, quasars, and Lyα forests from the completed Sloan Digital Sky Survey (SDSS) lineage of experiments in large-scale structure. These experiments, composed of data from SDSS, SDSS-II, BOSS, and eBOSS, offer independent measurements of baryon acoustic oscillation (BAO) measurements of angular-diameter distances and Hubble distances relative to the sound horizon, r d , from eight different samples and six measurements of the growth rate parameter, fσ 8 , from redshift-space distortions (RSD). This composite sample is the most constraining of its kind and allows us to perform a comprehensive assessment of the cosmological model after two decades of dedicated spectroscopic observation. We show that the BAO data alone are able to rule out dark-energy-free models at more than eight standard deviations in an extension to the flat, ΛCDM model that allows for curvature. When combined with Planck Cosmic Microwave Background (CMB) measurements of temperature and polarization, under the same model, the BAO data provide nearly an order of magnitude improvement on curvature constraints relative to primary CMB constraints alone. Independent of distance measurements, the SDSS RSD data complement weak lensing measurements from the Dark Energy Survey (DES) in demonstrating a preference for a flat ΛCDM cosmological model when combined with Planck measurements. The combined BAO and RSD measurements indicate σ 8 =0.85±0.03, implying a growth rate that is consistent with predictions from Planck temperature and polarization data and with General Relativity. When combining the results of SDSS BAO and RSD, Planck, Pantheon Type Ia supernovae (SNe Ia), and DES weak lensing and clustering measurements, all multiple-parameter extensions remain consistent with a ΛCDM model. Regardless of cosmological model, the precision on each of the three parameters, Ω Λ , H 0 , and σ 8 , remains at roughly 1%, showing changes of less than 0.6% in the central values between models. In a model that allows for free curvature and a time-evolving equation of state for dark energy, the combined samples produce a constraint Ω K =-0.0022±0.0022. The dark energy constraints lead to w 0 =-0.909±0.081 and w a =$-0.49_{-0.30}^{+0.35}$, corresponding to an equation of state of w p =-1.018±0.032 at a pivot redshift z p =0.29 and a Dark Energy Task Force Figure of Merit of 94. The inverse distance ladder measurement under this model yields H 0 =68.18±0.79 km s -1 Mpc -1 , remaining in tension with several direct determination methods; the BAO data allow Hubble constant estimates that are robust against the assumption of the cosmological model. In addition, the BAO data allow estimates of H 0 that are independent of the CMB data, with similar central values and precision under a ΛCDM model. Our most constraining combination of data gives the upper limit on the sum of neutrino masses at Σm ν <0.115 eV (95% confidence). Finally, we consider the improvements in cosmology constraints over the last decade by comparing our results to a sample representative of the period 2000-2010. We compute the relative gain across the five dimensions spanned by w, Ω k , Σm ν , H 0 , and σ 8 and find that the SDSS BAO and RSD data reduce the total posterior volume by a factor of 40 relative to the previous generation. Finally, adding again the Planck, DES, and Pantheon SN Ia samples leads to an overall contraction in the five-dimensional posterior volume of 3 orders of magnitude.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

ML-AMD/exa-pd

Exa-pd is a highly parallelizable workflow for constructing multi-element phase diagrams (PDs). It uses standard sampling techniques—molecular dynamics (MD) and Monte Carlo (MC)—as implemented in the LAMMPS package, to simultaneously sample multiple phases on a fine temperature–composition mesh for free-energy calculations. The workflow uses Parsl as a global controller to manage the MD/MC jobs to achieve massive parallelization with almost ideal scalability. The resulting free energies of both liquid and solid phases (including solid solutions) are then fed to CALPHAD modeling using the PYCALPHAD package for the construction of a multi-element PD.

Zhang, Feng [Ames Laboratory (AMES), Ames, IA (Uni↗
DOE OSTI2022

Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols

The accurate and reliable prediction of protein–ligand binding affinities can play a central role in the drug discovery process as well as in personalized medicine. Of considerable importance during lead optimization are the alchemical free energy methods that furnish an estimation of relative binding free energies (RBFE) of similar molecules. Recent advances in these methods have increased their speed, accuracy, and precision. This is evident from the increasing number of retrospective as well as prospective studies employing them. However, such methods still have limited applicability in real-world scenarios due to a number of important yet unresolved issues. Here, we report the findings from a large data set comprising over 500 ligand transformations spanning over 300 ligands binding to a diverse set of 14 different protein targets which furnish statistically robust results on the accuracy, precision, and reproducibility of RBFE calculations. We use ensemble-based methods which are the only way to provide reliable uncertainty quantification given that the underlying molecular dynamics is chaotic. These are implemented using TIES (Thermodynamic Integration with Enhanced Sampling). Results achieve chemical accuracy in all cases. Ensemble simulations also furnish information on the statistical distributions of the free energy calculations which exhibit non-normal behavior. We find that the “enhanced sampling” method known as replica exchange with solute tempering degrades RBFE predictions. We also report definitively on numerous associated alchemical factors including the choice of ligand charge method, flexibility in ligand structure, and the size of the alchemical region including the number of atoms involved in transforming one ligand into another. Our findings provide a key set of recommendations that should be adopted for the reliable application of RBFE methods.

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

A self-referenced in-situ arrival time monitor for X-ray free-electron lasers

We present a novel, highly versatile, and self-referenced arrival time monitor for measuring the femtosecond time delay between a hard X-ray pulse from a free-electron laser and an optical laser pulse, measured directly on the same sample used for pump-probe experiments. Two chirped and picosecond long optical supercontinuum pulses traverse the sample with a mutually fixed time delay of 970 fs, while a femtosecond X-ray pulse arrives at an instant in between both pulses. Behind the sample the supercontinuum pulses are temporally overlapped to yield near-perfect destructive interference in the absence of the X-ray pulse. Stimulation of the sample with an X-ray pulse delivers non-zero contributions at certain optical wavelengths, which serve as a measure of the relative arrival time of the X-ray pulse with an accuracy of better than 25 fs. We find an excellent agreement of our monitor with the existing timing diagnostics at the SACLA XFEL with a Pearson correlation value of 0.98. We demonstrate a high sensitivity to measure X-ray pulses with pulse energies as low as 30 μJ. Using a free-flowing liquid jet as interaction sample ensures the full replacement of the sample volume for each X-ray/optical event, thus enabling its utility even at MHz repetition rate XFEL sources.

47 OTHER INSTRUMENTATION↗
NASA NTRS2013

Good Practices in Free-energy Calculations

As access to computational resources continues to increase, free-energy calculations have emerged as a powerful tool that can play a predictive role in drug design. Yet, in a number of instances, the reliability of these calculations can be improved significantly if a number of precepts, or good practices are followed. For the most part, the theory upon which these good practices rely has been known for many years, but often overlooked, or simply ignored. In other cases, the theoretical developments are too recent for their potential to be fully grasped and merged into popular platforms for the computation of free-energy differences. The current best practices for carrying out free-energy calculations will be reviewed demonstrating that, at little to no additional cost, free-energy estimates could be markedly improved and bounded by meaningful error estimates. In energy perturbation and nonequilibrium work methods, monitoring the probability distributions that underlie the transformation between the states of interest, performing the calculation bidirectionally, stratifying the reaction pathway and choosing the most appropriate paradigms and algorithms for transforming between states offer significant gains in both accuracy and precision. In thermodynamic integration and probability distribution (histogramming) methods, properly designed adaptive techniques yield nearly uniform sampling of the relevant degrees of freedom and, by doing so, could markedly improve efficiency and accuracy of free energy calculations without incurring any additional computational expense.

Pohorille, Andrew↗
DOE OSTI2022

Practical guide to replica exchange transition interface sampling and forward flux sampling

Path sampling approaches have become invaluable tools to explore the mechanisms and dynamics of the so-called rare events that are characterized by transitions between metastable states separated by sizable free energy barriers. Their practical application, in particular to ever more complex molecular systems, is, however, not entirely trivial. Here, focusing on replica exchange transition interface sampling (RETIS) and forward flux sampling (FFS), we discuss a range of analysis tools that can be used to assess the quality and convergence of such simulations, which is crucial to obtain reliable results. The basic ideas of a step-wise evaluation are exemplified for the study of nucleation in several systems with different complexities, providing a general guide for the critical assessment of RETIS and FFS simulations.

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

Demonstration of an x-ray Raman spectroscopy setup to study warm dense carbon at the high energy density instrument of European XFEL

We present a proof-of-principle study demonstrating x-ray Raman Spectroscopy (XRS) from carbon samples at ambient conditions in conjunction with other common diagnostics to study warm dense matter, performed at the high energy density scientific instrument of the European x-ray Free Electron Laser (European XFEL). We obtain sufficient spectral resolution to identify the local structure and chemical bonding of diamond and graphite samples, using highly annealed pyrolytic graphite spectrometers. Due to the high crystal reflectivity and XFEL brightness, we obtain signal strengths that will enable accurate XRS measurements in upcoming pump–probe experiments with a high repetition-rate, where the samples will be pumped with high-power lasers. Molecular dynamics simulations based on density functional theory together with XRS simulations demonstrate the potential of this technique and show predictions for high-energy-density conditions. Our setup allows simultaneous implementation of several different diagnostic methods to reduce ambiguities in the analysis of the experimental results, which, for warm dense matter, often relies on simplifying model assumptions. The promising capabilities demonstrated here provide unprecedented insights into chemical and structural dynamics in warm dense matter states of light elements, including conditions similar to the interiors of planets, low-mass stars, and other celestial bodies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Cr is not an acceptor in 𝛽⁢−G⁢a 2 ⁢O 3

The intensity of red C⁢r 3+ photoluminescence (PL) in monoclinic gallium oxide (𝛽⁢−G⁢a 2 ⁢O 3 ) is suppressed by 𝑛-type conductivity, an effect that has been attributed to a Cr deep acceptor level in the bandgap. In 𝑛-type material, such an acceptor level would be occupied, resulting in the C⁢r 2+ oxidation state and the absence of C⁢r 3+ PL. To test this model, 𝑛-type 𝛽⁢−G⁢a 2 ⁢O 3 crystals co-doped with Cr and Zr (a donor) were grown from the melt. The samples show C⁢r 3+ optical absorption bands and a high free-electron concentration of 4 × 10 18 c⁢m −3 . If Cr were an acceptor, then it would be fully compensated and therefore would not exhibit the C⁢r 3+ optical signature. Hybrid functional calculations indicate that Cr occupies the substitutional octahedral Ga(II) site and that the C⁢r 2+ state is energetically unfavorable, i.e., Cr is not an acceptor. Weak C⁢r 3+ PL was observed in the Cr/Zr co-doped samples. In conclusion, the quenching of PL may be caused by a transfer of energy to free electrons, a nonradiative process that would reduce the emission intensity.

carrier generation & recombination↗
DOE OSTI2026

Deriving effective electrode–ion interactions from free-energy profiles at electrochemical interfaces

Understanding ion adsorption at electrified metal–electrolyte interfaces is essential for accurate modeling of electrochemical systems. Here, in this study, we systematically investigate the free energy profiles of Na + , Cl − , and F − ions at the Au(111)–water interface using enhanced sampling molecular dynamics with both classical force fields and machine-learned interatomic potentials (MLIPs). Our classical metadynamics results reveal a strong dependence of predicted ion adsorption on the Lennard-Jones parameters, highlighting that—without due care—standard mixing rules can lead to qualitatively incorrect descriptions of ion–metal interactions. We present a systematic methodology for tuning the cross term LJ parameters to control adsorption energetics in agreement with more accurate models. As a surrogate for an ab initio model, we employed the recently released Universal Models for Atoms MLIP, which validates classical trends and displays strong specific adsorption for chloride, weak adsorption for fluoride, and no specific adsorption for sodium, in agreement with experimental and theoretical expectations. By integrating molecular-level adsorption free energies into continuum models of the electric double layer, we show that specific ion adsorption substantially alters the interfacial ion population, the potential of zero charge, and the differential capacitance of the system. Our results underscore the critical importance of force field parameterization and advanced interatomic potentials for the predictive modeling of ion-specific effects at electrified interfaces and provide a robust framework for bridging molecular simulations and continuum electrochemical models.

Roncoroni, Fabrice [Lawrence Berkeley National Lab↗