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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

A comparison of probabilistic generative frameworks for molecular simulations

Generative artificial intelligence is now a widely used tool in molecular science. Despite the popularity of probabilistic generative models, numerical experiments benchmarking their performance on molecular data are lacking. Here, in this work, we introduce and explain several classes of generative models, broadly sorted into two categories: flow-based models and diffusion models. We select three representative models: neural spline flows, conditional flow matching, and denoising diffusion probabilistic models, and examine their accuracy, computational cost, and generation speed across datasets with tunable dimensionality, complexity, and modal asymmetry. Our findings are varied, with no one framework being the best for all purposes. In a nutshell, (i) neural spline flows do best at capturing mode asymmetry present in low-dimensional data, (ii) conditional flow matching outperforms other models for high-dimensional data with low complexity, and (iii) denoising diffusion probabilistic models appear the best for low-dimensional data with high complexity. Our datasets include a Gaussian mixture model and the dihedral torsion angle distribution of the Aib9 peptide, generated via a molecular dynamics simulation. We hope our taxonomy of probabilistic generative frameworks and numerical results may guide model selection for a wide range of molecular tasks.

Artificial intelligence↗
DOE OSTI2020

Partitioning of Complex Fluids at Mineral Surfaces

This report summarizes the results obtained during the LDRD project entitled "Partitioning of Complex Fluids at Mineral Interfaces." This research addressed fundamental aspects of such interfaces, which are relevant to energy-water applications in the subsurface, including fossil energy extraction and carbon sequestration. This project directly addresses the problem of selectivity of complex fluid components at mineral-fluid interfaces, where complex fluids are defined as a mixture of hydrophobic and hydrophilic components: e.g., water, aqueous ions, polar/nonpolar organic compounds. Specifically, this project investigates how adsorption selectivity varies with surface properties and fluid composition. Both experimental and molecular modeling techniques were used to better understand trends in surface wettability on mineral surfaces. The experimental techniques spanned the macroscale (contact angle measurements) to the nanoscale (cryogenic electronic microscopy and vibrational spectroscopy). We focused on an anionic surfactant and a well-characterized mineral phase representative of clay phases present in oil- and gas-producing shale deposits. Collectively, the results consistently demonstrate that the presence of surfactant in the aqueous fluid significantly affects the mineral-fluid interfacial structure. Experimental and molecular modeling results reveal details of the surfactant structure at the interface, and how this structure varies with surfactant coverage and fluid composition.

04 OIL SHALES AND TAR SANDS↗
DOE OSTI2021

NENCI-2021. I. A large benchmark database of non-equilibrium non-covalent interactions emphasizing close intermolecular contacts

In this work, we present NENCI-2021, a benchmark database of ~8000 Non-Equilibirum Non-Covalent Interaction energies for a large and diverse selection of intermolecular complexes of biological and chemical relevance. To meet the growing demand for large and high-quality quantum mechanical data in the chemical sciences, NENCI-2021 starts with the 101 molecular dimers in the widely used S66 and S101 databases and extends the scope of these works by (i) including 40 cation–π and anion–π complexes, a fundamentally important class of non-covalent interactions that are found throughout nature and pose a substantial challenge to theory, and (ii) systematically sampling all 141 intermolecular potential energy surfaces (PESs) by simultaneously varying the intermolecular distance and intermolecular angle in each dimer. Designed with an emphasis on close contacts, the complexes in NENCI-2021 were generated by sampling seven intermolecular distances along each PES (ranging from 0.7× to 1.1× the equilibrium separation) and nine intermolecular angles per distance (five for each ion–π complex), yielding an extensive database of 7763 benchmark intermolecular interaction energies (E int ) obtained at the coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory. The E int values in NENCI-2021 span a total of 225.3 kcal/mol, ranging from -38.5 to +186.8 kcal/mol, with a mean (median) E int value of -1.06 kcal/mol (-2.39 kcal/mol). In addition, a wide range of intermolecular atom-pair distances are also present in NENCI-2021, where close intermolecular contacts involving atoms that are located within the so-called van der Waals envelope are prevalent—these interactions, in particular, pose an enormous challenge for molecular modeling and are observed in many important chemical and biological systems. A detailed symmetry-adapted perturbation theory (SAPT)- based energy decomposition analysis also confirms the diverse and comprehensive nature of the intermolecular binding motifs present in NENCI-2021, which now includes a significant number of primarily induction-bound dimers (e.g., cation–π complexes). NENCI-2021 thus spans all regions of the SAPT ternary diagram, thereby warranting a new four-category classification scheme that includes complexes primarily bound by electrostatics (3499), induction (700), dispersion (1372), or mixtures thereof (2192). A critical error analysis performed on a representative set of intermolecular complexes in NENCI-2021 demonstrates that the E int values provided herein have an average error of ±0.1 kcal/mol, even for complexes with strongly repulsive E int values, and maximum errors of ±0.2–0.3 kcal/mol (i.e., ~±1.0 kJ/mol) for the most challenging cases. For these reasons, we expect that NENCI-2021 will play an important role in the testing, training, and development of next-generation classical and polarizable force fields, density functional theory approximations, wavefunction theory methods, and machine learning based intra- and inter-molecular potentials.

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

Enter Gaussian Mixture Modeling Extensions for Improved False Discovery Rate Estimation in GC-MS Metabolomics

Identifying small molecules (e.g., metabolites) is key towards driving scientific advancement in metabolomics, and gas chromatography–mass spectrometry (GC-MS) is an analytic method that may be applied to facilitate this process. The typical GC-MS identification workflow involves quantifying the similarity of an observed sample spectrum and other features (e.g. retention index) to that of several references, noting the compound of the best-matching reference spectrum as the identified metabolite. While a deluge of similarity metrics exists, none characterize the error rate of generated identifications, thereby presenting an unknown risk of false identification or discovery. To quantify this unknown risk, we propose a model-based framework for estimating the false discovery rate (FDR) among a set of identifications. Extending the traditional mixture modeling framework, our method incorporates both similarity score and experimental information in estimating the FDR. We apply these models to identification lists derived from across 548 samples of varying complexity and sample type (e.g., fungal species, standard mixtures, etc.), comparing their performance to that of the traditional Gaussian mixture model (GMM). Through simulation, we additionally assess the impact of reference library size on the accuracy of FDR estimates. In comparing the best performing model extensions to the GMM, our results indicate relative decreases in median absolute estimation error (MAE) ranging from 12% to 70%, based on comparisons of the median MAEs across all hit-lists. Results indicate that these relative performance improvements generally hold despite library size, however FDR estimation error typically worsens as the set of reference compounds diminishes.

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

Coupled heat pulse propagation in two-fluid plasmas

Because of the large mass differences between electrons and ions, the heat diffusion in electron-ion plasmas exhibits more complex behavior than simple heat diffusion found in typical gas mixtures. In particular, heat is diffused in two distinct, but coupled, channels. Conventional single fluid models neglect the resulting complexity, and can often inaccurately interpret the results of heat pulse experiments. However, by recognizing the sensitivity of the electron temperature evolution to the ion diffusivity, not only can previous experiments be interpreted correctly, but informative simultaneous measurements can be made of both ion and electron heat channels.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Systems, methods, and compositions for purifying water

Systems for removing one or more contaminants from water are provided that can include a hydrate formation chamber assembly; a contaminated water diffusion assembly within the hydrate formation chamber assembly; a space between a wall of the hydrate formation chamber assembly and the diffusion assembly; and a guest compound conduit configured to provide a guest compound within the space and form a hydrate comprising water and the guest compound. Methods for removing one or more contaminants from water are provided that can include providing a contaminated water mixture and one or more guest compounds; forming a hydrate complex comprising water and the one or more guest compounds; and separating the water from the guest compounds to provide water with less contaminant. Mixtures are also provided that can include a liquid component comprising water and at least one contaminant, and a solid component comprising a hydrate complex. One embodiment of the system provides methods for production of excess electric power as a byproduct of the desalination process.

McGrail, Bernard P.↗
DOE OSTI2020

Experimental Study of the Fundamental Properties of Warm Dense Mixtures

The aim of the proposed research was to provide a multi-scale study of the properties of warm dense hydrocarbons, by studying the thermodynamic properties through the equation of state and the microscopic properties by x-ray scattering. Understanding the fundamental properties of warm dense mixtures is an intellectual challenge due to the complexity of the system. Unlike liquids or gases, where constituent particle interactions occur through collisions or bonding between valence electrons, in these strongly coupled systems the atoms will be partially ionized and compressed so tightly together that interactions between the inner core electrons can play a role in the systems chemistry. Advances in computational capabilities and development of new theoretical models have been used to predict the properties of mixtures but there is currently no experimental data of the fundamental interaction between the particles in mixtures to test these predictions against. The proposed research was to experimentally investigate the interaction of the different species in hydrocarbons by measuring the compressibility of substances with different carbon and hydrogen ratios and the complexity of the microscopic interactions through elastic and inelastic x-ray scattering. To study the bulk properties of warm dense hydrocarbons we established the Warm Dense Matter Research Laboratory (WDMRL) in the Institute for Shock Physics at Washington State University. The goal was for experiments in the WDMRL to determine shock loading conditions of interest in the hydrocarbon mixtures. We planned on using Hugoniot EOS measurements and a range of carbon and hydrogen concentrations to determine conditions when the EOS of the mixture varied significantly from that of the classical mixing model. Even though shock transit measurements through aluminum foils suggested pressures upto 400GPa, the experiments in the WDMRL were unsuccessful in getting usable shockwave compression data above 100GPa in polystyrene which was below the pressure of interest for hydrocarbon mixtures (>200GPa). To complete the project, we tested a technique using x-ray phase contrast imaging to map the location of tracer layers in a test sample of polycarbonate to record the material motion in dynamically compressed samples. A technique that will be useful for future warm dense matter experiments. These experiments used <200nm gold layers in polycarbonate samples to measure the material velocity and shock speed using x-ray phase contrast imaging. These results were compared to continuum surface measurements performed at ISP and show that the tracer layer technique can measure hydrodynamic properties accurately in dynamically compressed materials.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Harnessing dimethyl ether with ultra-low-grade heat for scaling-resistant brine concentration and fractional crystallization

Solvent-driven separations may enable scalable concentration of hypersaline brines, supporting a circular resource economy from the extraction of lithium and rare earth elements from spent battery and magnet leachates. This work analyses a novel solvent-driven water extraction (SDWE) system employing dimethyl ether (DME) and ultra-low-grade heat for brine concentration and fractional crystallization. SDWE exploits DME’s unique properties: (1) a low dielectric constant that promotes water solubility over charged solutes by a factor of 10 3 , and (2) a high volatility that facilitate efficient DME reconcentration with ultra-low-grade heat. The techno-economic viability of SDWE is assessed with a computational framework that encompasses a liquid–liquid separator and a solvent concentrator. We integrate the extended universal quasichemical model with the virial equation of state to predict the compositions of the complex three-phase DME-water mixture at vapor–liquid and liquid–liquid equilibrium. Subsequently, we optimize the thermodynamic and economic performance of SDWE, by controlling the interstage flash pressure, heat source temperature, and the number of concentrating stages. DME-based SDWE concentrates an input saline feed to 5.5 M and regenerates over 99 % of the DME using ultra-low-grade heat below 50 °C, with a DME/water selectivity ratio of 125. Here our calculations reveal that optimal performance is achieved at interstage flash pressures of 0.4 – 0.5 bar for heat source temperatures between 323–373 K, with improved exergetic efficiencies at lower temperatures. At a heat source temperature of 323 K and an interstage pressure of 0.489 bar, DME-driven SDWE achieves an optimal thermodynamic efficiency of 20.5 % and a projected specific cost of US$ 1.93 m -3 . These specific costs suggest that SDWE is competitive with commercialized thermal distillation technologies, while mitigating the traditional risks associated with scaling in heat and mass exchangers with hypersaline brines.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

A regularized-interface method as a unified formulation for simulations of high-pressure multiphase flows

The injection of multi-species fluids into high-pressure and high-temperature environments beyond the species' critical points is commonly found in engineering applications. At these conditions, for immiscible species, both subcritical interfacial dynamics and supercritical mixing can coexist due to variations in temperature around the mixture critical point. The modeling of these complex transcritical phenomena for large-scale configurations is so far not possible. To address this issue, we propose the Regularized-Interface Method (RIM) as a unified formulation that can describe both sub- and supercritical processes as well as the transition between them. The proposed method is derived via filtering of the nanoscale interface-resolving formulation based on van der Waals' linear gradient theory. Thus, this approach allows for the consistent modeling of interfacial dynamics that vanishes at supercritical conditions, while significantly reducing the temporal and spatial resolution constraints of the original nanoscale formulation. The resulting RIM formulation is examined in interface-capturing simulations of sub-, trans-, and supercritical fuel injection processes, involving droplets and jets. Furthermore, these results highlight the importance of resolving spatio-temporal transitions from subcritical interfacial dynamics to supercritical mixing in high-pressure multiphase simulations, in contrast to commonly employed diffused-interface methods, where interfacial dynamics are often neglected.

Interface capturing↗
DOE OSTI2023

Operando Mechanistic Studies of CO 2 Hydrogenation by Ruthenium Complexes Using High-Pressure NMR Spectroscopy

As a result of increased energy demands, the ability to both reduce carbon dioxide with dihydrogen to formate and conduct the reverse reaction with the same catalyst is of interest as a method for potential fuel generation and use. Ruthenium bis(diphosphine) complexes with and without pendant amines were reacted with mixtures of CO 2 /H 2 gases in the presence of added base to catalytically yield formate; when the base was triethylamine, the reaction was found to be reversible. The reactions were monitored using high-pressure operando 1 H and 31 P{ 1 H} NMR spectroscopy at 18 °C in THF under 40 atm of a 1:1 mixture of H 2 and CO 2 . The rate of production of formate was correlated with the observation of specific organometallic species by NMR spectroscopy under catalytic conditions, including a hydrido–dihydrogen complex. From this operando study, a mechanism is proposed with two competing catalytic cycles for which the predominant cycle is dependent on which base and catalyst are used. Finally, the role of the base is shown to be vital for both catalytic rate and reversibility of the chemical transformation, indicating base selection should be carefully considered.

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

Control of Catalyst Isomers Using an N -Phenyl-Substituted RN(CH 2 CH 2 P i Pr 2 ) 2 Pincer Ligand in CO 2 Hydrogenation and Formic Acid Dehydrogenation

A novel pincer ligand, i Pr PN Ph P [PhN- (CH 2 CH 2 P i Pr 2 ) 2 ], which is an analogue of the versatile MACHO ligand, iPr PN H P [HN(CH 2 CH 2 P i Pr 2 ) 2 ], was synthesized and characterized. The ligand was coordinated to ruthenium, and a series of hydride-containing complexes were isolated and characterized by NMR and IR spectroscopies, as well as X-ray diffraction. Comparisons to previously published analogues ligated by iPr PN H P and iPr PN Me P [CH 3 N(CH 2 CH 2 P i Pr 2 ) 2 ] illustrate that there are large changes in the coordination chemistry that occur when the nitrogen substituent of the pincer ligand is altered. For example, ruthenium hydrides supported by the iPr PN Ph P ligand always form the syn isomer (where syn/anti refer to the relative orientation of the group on nitrogen and the hydride ligand on ruthenium), whereas complexes supported by iPr PN H P form the anti isomer and complexes supported by iPr PN Me P form a mixture of syn and anti isomers. We evaluated the impact of the nitrogen substituent of the pincer ligand in catalysis by comparing a series of iPr PN R P (R = H, Me, Ph)-ligated ruthenium hydride complexes as catalysts for formic acid dehydrogenation and carbon dioxide (CO 2 ) hydrogenation to formate. The iPr PN Ph P-ligated species is the most active for formic acid dehydrogenation, and mechanistic studies suggest that this is likely because there are kinetic advantages for catalysts that operate via the syn isomer. In CO 2 hydrogenation, the iPr PN Ph P-ligated species is again the most active under our optimal conditions, and we report some of the highest turnover frequencies for homogeneous catalysts. Experimental and theoretical insights into the turnover-limiting step of catalysis provide a basis for the observed trends in catalytic activity. Additionally, the stability of our complexes enabled us to detect a previously unobserved autocatalytic effect involving the base that is added to drive the reaction. Overall, by modifying the nitrogen substituent on the MACHO ligand, we have developed highly active catalysts for formic acid dehydrogenation and CO 2 hydrogenation and also provided a framework for future catalyst development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

EF-Hand Battle Royale: Hetero-ion Complexation in Lanmodulin

The lanmodulin (LanM) protein has emerged as an effective means for rare earth element (REE) extraction and separation from complex feedstocks without the use of organic solvents. Whereas the binding of LanM to individual REEs has been well characterized, little is known about the thermodynamics of mixed metal binding complexes (i.e., heterogeneous ion complexes), which limits the ability to accurately predict separation performance for a given metal ion mixture. In this paper, we employ the law of mass action to establish a theory of perfect cooperativity for LanM-REE complexation at the two highest-affinity binding sites. The theory is then used to derive an equation that explains the nonintuitive REE binding behavior of LanM, where separation factors for binary pairs of ions vary widely based on the ratio of ions in the aqueous phase, a phenomenon that is distinct from single-ion-binding chemical chelators. We then experimentally validate this theory and perform the first quantitative characterization of LanM complexation with heterogeneous ion pairs using resin-immobilized LanM. Importantly, the resulting homogeneous and heterogeneous constants enable accurate prediction of the equilibrium state of LanM in the presence of mixtures of up to 10 REEs, confirming that the perfect cooperativity model is an accurate mechanistic description of REE complexation by LanM. We further employ the model to simulate separation performance over a range of homogeneous and heterogeneous binding constants, revealing important insights into how mixed binding differentially impacts REE separations based on the relative positioning of the ion pairs within the lanthanide series. In addition to informing REE separation process optimization, these results provide mathematical and experimental insight into competition dynamics in other ubiquitous and medically relevant, cooperative binding proteins, such as calmodulin.

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

Unraveling design principles of protein landscapes in photosynthetic membranes in plant chloroplasts

The supramolecular organization of proteins within photosynthetic membranes is crucial for energy conversion in plants. Here, we introduce an analytical and computational pipeline that integrates high-resolution cryo–scanning electron microscopy, biochemical quantification, advanced Monte Carlo computer simulations, and statistical methods to elucidate the elusive protein landscapes of grana membranes in intact Arabidopsis leaves. Our integrated analysis challenges the prevailing view that particles on the exoplasmic fracture faces in freeze-fracture samples represent photosystem II exclusively. Instead, these particles also include cytochrome b 6 f complexes. Furthermore, our steric clash analysis demonstrates that stacked membranes contain a mixture of larger PSII supercomplexes (C 2 S 2 M 2 and C 2 S 2 ) in addition to a smaller complex (C 2 ). This suggests that in vivo PSII supercomplexes exist in an equilibrium distribution of differing sizes. Furthermore, we discovered that, although size exclusion effects govern the global protein arrangement, local packing exhibits orientational order indicative of lateral attractive protein-protein interactions.

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

Ion Clusters in Multicomponent Solutions Determined from X-ray PDF and SAXS Analysis: The NaNO 2 –NaOH–H 2 O System

Here, this study explores ion cluster formation in the NaNO 2 –NaOH–H 2 O system to understand how ion cluster formation is influenced by the composition in multicomponent mixtures. X-ray pair distribution function (PDF) and small-angle X-ray scattering (SAXS) identified complex ion clusters in concentrated NaNO 2 and NaOH solutions as well as their mixtures. PDF analysis showed that the Na–O distance depended primarily on total Na + concentrations rather than anion composition, whereas the nitrite-water oxygen distance stayed the same regardless of concentration or composition. This result indicates that the nitrite ion hydration was relatively independent of composition. SAXS confirms local fluctuations and coherent clusters with notable size differences between NaOH and NaNO 2 solutions. SAXS analysis of mixed solutions shows that their clusters are an average of the individual solutions, indicating mixed clusters.

Reynolds, Jacob G. [Central Plateau Cleanup Compan↗
DOE OSTI2021

Effects of non-thermal termolecular chemistry on detonation development in hydrogen (H2) / methane (CH4) - air mixtures

In combustion simulations, it is usually assumed that highly-energized collision complexes (either radical or stable species) formed in exothermic reactions are always under thermal equilibrium as they evolve through competing networks of reactions. However, in practical flames, non-trivial amounts of reactive radicals such as H, O and OH are present apart from O2. As a result, collisions of these reactive species with the energized collision complexes have been shown in recent studies to induce non-thermal reactivity. These studies have also demonstrated that such non-thermal reactions can be suitably represented in macroscopic kinetics models as chemically termolecular reactions. The present work was focused on identifying and quantifying the effects of including such reactions on the evolution of an initial deflagration front to a developing detonation in H2/CH4-air mixtures under boosted internal combustion (IC) engine conditions. Specifically, fully resolved simulations, with and without non-thermal reactivity, were performed for a constant volume reactor containing stoichiometric H2/CH4-air mixture. It was found that inclusion of termolecular chemistry resulted in a delayed onset of end-gas auto-ignition. Concurrently, the developing detonation intensity was observed to be significantly higher. Chemical explosive mode analysis (CEMA) was performed to identify the dominant species/reactions responsible for the observed variation in the results.

Detonation↗
DOE OSTI2023

Well-Defined Iron Sites in Crystalline Carbon Nitride

Carbon nitride materials can be hosts for transition metal sites, but Mössbauer studies on iron complexes in carbon nitrides have always shown a mixture of environments and oxidation states. Here we describe the synthesis and characterization of a crystalline carbon nitride with stoichiometric iron sites that all have the same environment. The material (formula C 6 N 9 H 2 Fe 0.4 Li 1.2 Cl, abbreviated PTI/FeCl 2 ) is derived from reacting poly(triazine imide)·LiCl (PTI/LiCl) with a low-melting FeCl 2 /KCl flux, followed by anaerobic rinsing with methanol. X-ray diffraction, X-ray absorption and Mössbauer spectroscopies, and SQUID magnetometry indicate that there are tetrahedral high-spin iron(II) sites throughout the material, all having the same geometry. As a result, the material is active for electrocatalytic nitrate reduction to ammonia, with a production rate of ca. 0.1 mmol cm –2 h –1 and Faradaic efficiency of ca. 80% at −0.80 V vs RHE.

Anions↗
DOE OSTI2020

Fast and Universal Kohn-Sham Density Functional Theory Algorithm for Warm Dense Matter to Hot Dense Plasma

Understanding many processes, e.g., fusion experiments, planetary interiors, and dwarf stars, depends strongly on microscopic physics modeling of warm dense matter and hot dense plasma. This complex state of matter consists of a transient mixture of degenerate and nearly free electrons, molecules, and ions. This regime challenges both experiment and analytical modeling, necessitating predictive ab initio atomistic computation, typically based on quantum mechanical Kohn-Sham density functional theory (KS-DFT). However, cubic computational scaling with temperature and system size prohibits the use of DFT through much of the warm dense matter regime. A recently developed stochastic approach to KS-DFT can be used at high temperatures, with the exact same accuracy as the deterministic approach, but the stochastic error can converge slowly and it remains expensive for intermediate temperatures (< 50 eV). Here we have developed a universal mixed stochastic-deterministic algorithm for DFT at any temperature. This approach leverages the physics of KS-DFT to seamlessly integrate the best aspects of these different approaches. We demonstrate that this method significantly accelerated self-consistent field calculations for temperatures from 3 to 50 eV, while producing stable molecular dynamics and accurate diffusion coefficients.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗