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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

A model for trapping and re-solution regarding intra-granular bubbles in UO 2 , linked to atomic-scale simulations

In the literature, a clear definition of the irradiation re-solution frequency of gas from bubbles in the UO 2 fuel is absent. Moreover, for intra-granular bubbles, a detailed calculation of the cumulated displaced gas quantities in function of the distance from the radius of the bubble after a re-solution event has never been published. The assessment of these two elements is very useful if we want to increase the adherence of fission gas release codes to our present knowledge of the behavior of fission gases. Hence, we suggest to link the definition of the re-solution frequency to atomic-scale simulations. Furthermore, we present the cumulated displaced gas quantities obtained from Molecular Dynamics calculations, from which we have derived a re-solution profile that can be exploited to better consider the irradiation re-solution phenomenon inside Fission Gas Release codes. On top of that, we have built a new trapping/re-solution model for intra-granular bubbles linked to Molecular Dynamics simulations that can be easily incorporated into Fission Gas Release codes. In conclusion, we also check that the model is properly built through the comparison of the new model against a reference.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Dynamic soil columns simulate Arctic redox biogeochemistry and carbon release during changes in water saturation

Thawing Arctic permafrost can induce hydrologic change and alter redox conditions, shifting the balance of soil organic matter (SOM) decomposition. There remains uncertainty about how soil saturation and redox transitions impact dissolved and gas phase carbon fluxes, and efforts to link hydrobiogeochemical processes to ecosystem-scale models are limited. This study evaluates SOM decomposition of Arctic tundra soils using column experiments, water chemistry measurements, microbial community analysis, and a PFLOTRAN reactive transport model. Soil columns from a thermokarst channel (TC) and an upland tundra (UC) were exposed to cycles of saturation and drainage, which controlled carbon emissions. During saturation, an outflow of dissolved organic carbon from the UC soil correlated with elevated reduced iron and decreased pH; during drainage, UC carbon dioxide fluxes were 70% higher than TC fluxes. Intermittent methane release was observed for TC, consistent with higher methanogen abundance. Slower drainage in the TC soil correlated with more subtle biogeochemical changes. PFLOTRAN simulations captured experimental trends in soil carbon fluxes, oxygen concentrations, and water contents. The model was then used to evaluate additional soil water drainage rates. This study emphasizes the importance of considering hydrologic change when evaluating and simulating SOM decomposition in dynamic Arctic tundra environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Solvent effects on triplet yields in BODIPY-based photosensitizers

Here, we employ molecular dynamics simulations and quantum rate theories to elucidate the complex condensed-phase dynamics underpinning triplet-state formation in organic photosensitizers. Using models informed by first-principles calculations complete with a molecular representation of solvents of different polarities, we elucidate the interplay of the internal and environmental interactions underlying triplet yield. We find that triplet yields depend sensitively on the dielectric stabilization of the charge transfer intermediate that facilitates a transition into the triplet manifold. Our results illustrate the importance of molecularly detailed models in understanding the excited-state internal charge-transfer dynamics of photochemically relevant organic molecules.

Coello Escalante, Leonardo [University of Californ↗
DOE OSTI2026

Free Energy and Flexibility Analysis of Autoinhibited Human BRAF

The RAF serine/threonine protein kinases function as direct effectors of RAS in the intracellular transmission of extracellular growth signals, and they are key targets for drug discovery, given the high incidence of oncogenic mutations in RAF and other components of this signaling pathway. In its inactive state, RAF is held in an autoinhibited conformation in the cytosol through a combination of intramolecular interactions and binding to a regulatory 14−3−3 protein dimer. Activation of RAF is initiated by its interaction with membrane-localized GTP-bound RAS, which induces conformational changes that release RAF from its autoinhibited state. However, the molecular mechanisms governing RAF activation remain incomplete, largely due to the challenges in experimentally capturing the intermediate conformational states in this process. To address this gap, we developed a comprehensive all-atom model of BRAF based on existing cryo-EM structures. Using this model, we performed extensive molecular dynamics simulations to evaluate the stability and free energy landscape of autoinhibited BRAF in solution. Our analysis reveals conformational flexibility within the autoinhibited complex, suggesting that this dynamic behavior may play a role in facilitating BRAF activation upon engagement with the membrane-bound RAS.

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

Selective mass scaling for single-layer thick shell elements in DYNA3D

Hexahedral elements can be adapted to model thin and moderately thick structures by neglecting the coupling of through-thickness stress, resulting in a fully three-dimensional, but simplified, state of stress. These specialized elements, often referred to as “thick” or “solid” shells, are generally employed to model thin-walled structures using continuum mechanics-based material models. In explicit dynamics simulations, where computational speed is important, these elements are integrated with a single quadrature point and a set of anti-hourglassing (stabilizing) forces. Thick shells, by definition, have a thickness dimension smaller than their in-plane dimensions, and this small thickness often determines the stable time step size in simulations, despite the mechanics being approximated. To alleviate this limitation while retaining the relevant dynamics of thin-walled structures, selective mass scaling (SMS), or selective mass “augmentation,” has been proposed in the literature. In this technical report, we explore the application of SMS to single-layer thick shells in the simulation software DYNA3D.

42 ENGINEERING↗
DOE OSTI2026

Learning Latent Representations to Bridge Coarse-Grained and Atomistic Resolutions in Polymer Simulations

We present a machine-learning-based framework for learning reduced-order representations of polymer chain conformations across coarse-grained (CG) and united-atom (UA) fidelities. By employing linear singular value decomposition and nonlinear autoencoders, we compress high-dimensional polymer configurations into latent spaces with minimal loss of structural accuracy. Crucially, we demonstrate a near-perfect linear mapping between CG and UA latent spaces, enabling an efficient super-resolution back-mapping procedure that reconstructs high-fidelity UA configurations from CG simulations. While minor structural inaccuracies occur, they are effectively corrected through a brief molecular dynamics relaxation, forming a practical hybrid machine learning−physics scheme. This approach establishes the key structural prerequisites for accelerated polymer dynamics simulations: a compact and accurate latent encoding of polymer chain conformations and a validated multi-fidelity mapping that permits reconstruction of UA structures from CG configurations. The extension of this framework to explicit time evolution within the latent space, enabling dynamics to be propagated at CG fidelity and decoded to UA resolution only when required, represents a natural and well-motivated direction for future work.

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

Optimization of Solid Oxide Electrolysis Cell Systems Accounting for Long-Term Performance and Health Degradation

This study focuses on optimizing solid oxide electrolysis cell (SOEC) systems for efficient and durable long-term hydrogen (H2) production. While the elevated operating temperatures of SOECs offer advantages in terms of efficiency, they also lead to chemical degradation, which shortens cell lifespan. To address this challenge, dynamic degradation models are coupled with a steady-state, two-dimensional, non-isothermal SOEC model and steady-state auxiliary balance of plant equipment models, within the IDAES modeling and optimization framework. A quasi-steady state approach is presented to reduce model size and computational complexity. Long-term dynamic simulations at constant H2 production rate illustrate the thermal effects of chemical degradation. Dynamic optimization is used to minimize the lifetime cost of H2 production, accounting for SOEC replacement, operating, and energy expenses. Several optimized operating profiles are compared by calculating the Levelized Cost of Hydrogen (LCOH).

Giridhar, Nishant↗
DOE OSTI2024

Optimization of Solid Oxide Electrolysis Cell Systems Accounting for Long-Term Performance and Health Degradation

This study focuses on optimizing solid oxide electrolysis cell (SOEC) systems for efficient and durable long-term hydrogen (H2) production. While the elevated operating temperatures of SOECs offer advantages in terms of efficiency, they also lead to chemical degradation, which shortens cell lifespan. To address this challenge, dynamic degradation models are coupled with a steady-state, two-dimensional, non-isothermal SOEC model and steady-state auxiliary balance of plant equipment models, within the IDAES modeling and optimization framework. A quasi-steady state approach is presented to reduce model size and computational complexity. Long-term dynamic simulations at constant H2 production rate illustrate the thermal effects of chemical degradation. Dynamic optimization is used to minimize the lifetime cost of H2 production, accounting for SOEC replacement, operating, and energy expenses. Several optimized operating profiles are compared by calculating the Levelized Cost of Hydrogen (LCOH).

Giridhar, Nishant↗
DOE OSTI2025

SynopFrame: Multiscale time-dependent visual abstraction framework for analyzing DNA nanotechnology simulations

We present an open-source framework, SynopFrame, that allows DNA nanotechnology (DNA-nano) experts to analyze and understand molecular dynamics simulation trajectories of their designs. We use a multiscale multi-dimensional abstraction space, connect the representations to a projected conformational space plot of the structure’s temporal sequence, and thus enable experts to analyze the dynamics of their structural designs and, specifically, failure cases of the assembly. In addition, our time-dependent abstraction representation allows the biologists, for the first time in a smooth and structurally clear way, to identify and observe temporal transitions of a DNA-nano design from one configuration to another, and to highlight important periods of the simulation for further analysis. We realize SynopFrame as a dashboard of the different synchronized 3D spatial and 2D schematic visual representations, with a color overlay to show essential properties such as the status of hydrogen bonds. The linking of the spatial, schematic, and abstract views ensures that users can effectively analyze the high-frequency motion. We also categorize the status of the hydrogen bonds into a new format to allow us to color-encode it and overlay it on the representations. To demonstrate the utility of SynopFrame, we describe example usage scenarios and report user feedback.

Abstraction space↗
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 OSTI2024

Molecular Dynamics Study of the Effect of Grafting Density on Ion Diffusivity in a MARTINI Coarse-Grained Strong Polyelectrolyte Brush

Because surface-grafted polyelectrolyte brushes (PEBs) are responsive to external stimuli, such as electric fields and ionic strength, PEBs are attractive for applications ranging from drug delivery to separation technologies. Essential to PEB utilization is understanding how critical parameters like grafting density (σ) impact the PEB structure and the dynamics of the PEB and counterions. To study the effect of σ on PEB and the counterion structure and dynamics, we fine-tune a coarse-grained model that retains the chemical specificity of a strong polyelectrolyte, poly[(2-(methacryloyloxy)ethyl) trimethylammonium chloride] (PMETAC), using the MARTINI force field. Using “salt-free” conditions where the counterion concentration balances the charge on the brush, we build coarse-grained (CG) molecular dynamics simulations for MARTINI PMETAC brushes (N = 150 monomers; M W = 31.2 kg/mol) at experimentally relevant values of σ = 0.05, 0.10, 0.20, and 0.40 chains/nm 2 . Using 5 μs simulations, we investigate the effects of grafting density on the PEB structure, ion dissociation dynamics, polymer mobility, and counterion diffusivity. Results show that competition between electrostatic interactions, steric hindrance, and polymer mobility controls counterion diffusivity. Finally, the interplay of these factors leads to diffusivity that depends non-monotonically on σ, with counterion diffusivity peaking at an intermediate σ = 0.10 chains/nm 2 .

36 MATERIALS SCIENCE↗
DOE OSTI2024

Sliceable, Moldable, and Highly Conductive Electrolytes for All-Solid-State Batteries

All-solid-state batteries (ASSBs) require solid electrolytes with high ionic conductivity, stability, and deformability for optimal energy and power density. Here, we developed lithium-deficient lithium yttrium bromide (LYB) solid electrolytes, Li 3–x YBr 6–x (0 ≤ x ≤ 0.50), using a comelting method with controlled lithium deficiency. These electrolytes exhibit favorable mechanical properties such as high moldability and sliceability. The Li 2.65 YBr 5.65 composition has an ionic conductivity of 4.49 mS cm –1 at 25 °C and an activation energy of 0.28 eV. Compared to Li 3 YBr 6 , Li 2.65 YBr 5.65 demonstrates improved rate performance and cycling stability in ASSBs. High-resolution X-ray diffraction confirms the formation of the LYB phase with a C2/m space group. Structural analysis reveals increased cation disorder and larger polyhedral volumes for x > 0 in Li 3–x YBr 6–x , contributing to reduced Li + migration energy barriers. Bond valence site energy calculations and molecular dynamics simulations reveal enhanced 3D lithium-ion transport. NMR spectroscopy further highlights increased Li + dynamics and impurity elimination.

Poudel, Tej P. [Florida State Univ., Tallahassee, ↗
DOE OSTI2025

Ultrafast Events in Electrocyclic Ring-Opening Reactions

Electrocyclic reactions are characterized by the concerted formation and cleavage of multiple σ and π bonds in a molecular system and have been extensively studied since they were introduced by Robert Burns Woodward and Roald Hoffmann in 1965. Recent advances and the integration of time-resolved experiments and nonadiabatic quantum molecular dynamics simulations have transformed the traditional understanding of electrocyclic reactions beyond the Woodward–Hoffmann rules. In this review, we focus on recent studies of 1,3-cyclohexadiene and two of its derivatives, α-phellandrene and α-terpinene, to shed light on the underlying mechanisms of electrocyclic photochemical reactions. We highlight recent progress in ultrafast electron diffraction techniques and the simulation approach of ab initio multiple spawning. Together, these approaches can elucidate molecular structure dynamics from femtosecond to picosecond timescales as well as nuclear and electronic responses at conical intersections.

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

Glovebox Fires Phase 1: Simulations of Open Burner Experiments

Understanding the duration of a fire required to breach a glovebox via glove ports and/or windows within a facility is important in developing mitigation strategies for safety. To facilitate this understanding, both simulation and experiments are utilized. The approach is to first validate the Computation Fluid Dynamics (CFD) code, Fire Dynamics Simulator (FDS), with experimental data collected by New Mexico Tech (NMT) and then perform simulations of full-scale rooms containing gloveboxes to assess numerous scenarios which would otherwise be cost-prohibitive experimentally. This report provides comparison to first-phase experiments involving a fire without a glovebox. A subsequent report will provide comparison to experiments involving a glovebox. The results indicate good agreement with FDS tending to over predict the pre-mixed and diffusion-mode tests by 6% and 10%, respectively.

42 ENGINEERING↗
DOE OSTI2025

Molecular level insight into non-bilayer structure formation in thylakoid membranes: a molecular dynamics study

In oxygenic photosynthetic organisms, the light reactions are performed by protein complexes embedded in the lipid bilayer of thylakoid membranes (TMs). The organization of the bulk lipid molecules into bilayer structures provide optimal conditions for the build-up of the proton motive force (pmf) and its utilization for ATP synthesis. However, the lipid composition of TMs is dominated by the non-bilayer lipid species monogalactosyl diacylglycerol (MGDG), and functional plant TMs, besides the bilayer, contain large amounts of non-bilayer lipid phases. Bulk lipids have been shown to be associated with lumenal, stromal-side and marginal-region proteins and proposed to play roles in the self-assembly and photoprotection of the photosynthetic machinery. Furthermore, it has recently been pointed out that the generation and utilization of pmf for ATP synthesis according to the ‘protet’ or protonic charge transfer model Kell (Biochim Biophys Acta Bioenerg 1865(4):149504, 2024), requires high MGDG content Garab (Physiol Plant 177(2):e70230, 2025). In this study, to gain better insight into the structural and functional roles of MGDG, we employed all atom and coarse-grained molecular dynamics simulations to explore how temperature, hydration levels and varying MGDG concentrations affect the structural and dynamic properties of bilayer membranes constituted of plant thylakoid lipids. Our findings reveal that MGDG promotes increased membrane fluidity and dynamic fluctuations in membrane thickness. MGDG-rich stacked bilayers spontaneously formed inverted hexagonal phases; these transitions were enhanced at low hydration levels and at elevated but physiologically relevant temperatures. It can thus be inferred that MGDG plays important roles in heat and drought stress mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cavity Controlled Upconversion in CdSe Nanoplatelet Polaritons

Exciton-polaritons provide a versatile platform for investigating quantum electrodynamics effects in chemical systems, such as polariton-altered chemical reactivity. However, using polaritons in chemical contexts will require a better understanding of their photophysical properties under ambient conditions, where chemistry is typically performed. Here, we used cavity quality factor to control strong light–matter interactions and in particular the excited state dynamics of colloidal CdSe nanoplatelets (NPLs) coupled to a Fabry– Pérot optical cavity. With increasing cavity quality factor, we observe significant population of the upper polariton (UP) state, exemplified by the rare observation of substantial UP photoluminescence (PL). Excitation of the lower polariton (LP) states results in upconverted PL emission from the UP branch due to efficient exchange of population between the LP, UP and the reservoir of dark states present in collectively coupled polaritonic systems. In addition, we measure time scales for polariton dynamics ~100 ps, implying great potential for NPL based polariton systems to affect photochemical reaction rates. State-of-the-art quantum dynamical simulations show outstanding quantitative agreement with experiments, and thus provide important insight into polariton photophysical dynamics of collectively coupled nanocrystal-based systems. These findings represent a significant step toward the development of practical polariton photochemistry platforms.

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

The Role of Nonequilibrium Solvent Effects in Enhancing Direct CO 2 Capture at the Air–Aqueous Amino Acid Interface

Direct air capture (DAC) technologies are limited by the poor understanding of the dynamic role of interfaces in modulating the chemisorption of CO 2 from air into solutions. While the reactivity of aqueous amine-based solvents in the bulk environment is strongly inhibited by nonequilibrium solvent effects, promoting DAC at interfaces posits a possibility to reduce the coupling with the solvent and significantly accelerate DAC. Building on an experimentally proven concept to bring an anionic glycine absorbent to the interface through ion-pairing interactions with a positively charged surfactant, we establish the fundamental time scales for key elementary steps involved in DAC with rate theory and enhanced-sampling ab initio molecular dynamics simulations. Here, we elucidate the mechanism by which water influences the free energy barriers and dynamical crossing-recrossing of those barriers, affecting the reaction rates. We find that water reorganizes to partially dehydrate [-NH 2 ], facilitating S N 2-based CO 2 conversion to a zwitterion, which then releases a proton via overhydration of [-NH 2 ]. The low-density interfacial water favors dehydration over overhydration, leading to a comparatively higher barrier (slower kinetics) for proton release. The barrier-recrossing events neutralize this effect, letting both steps occur at the same time scale (sub-microseconds) and making the overall DAC process faster at the interface than in the bulk water. Such an understanding of environment-sensitive solvent effects on the reaction kinetics will help design tailored interfaces for enhanced CO 2 capture kinetics via control of solvation and ion paring.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗