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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

A Molecular View of Methane Activation on Ni(111) through Enhanced Sampling and Machine Learning

A combination of machine learned interatomic potentials (MLIPs) and enhanced sampling simulations is used to investigate the activation of methane on a Ni(111) surface. The work entails the development and iterative refinement of MLIPs, initially trained on a dataset constructed via ab initio molecular dynamics (AIMD) simulations, supplemented by adaptive biasing forces, to enrich the sampling of catalytically relevant configurations. Our results reveal that by incorporating collective variables that capture the behavior of the reactant molecule, as well as additional frames that describe the dynamic response of the catalytic surface, it is possible to enhance considerably the accuracy of predicted energies and forces. By employing enhanced sampling schemes in the refinement of the MLIP, we systematically explore the potential energy surface, leading to a refined MLIP capable of predicting DFT-level energies and forces and replicating key geometric characteristics of the catalytic system. The resulting free energy landscapes at several temperatures provide a detailed view of the thermodynamics and dynamics of methane activation. Specifically, as methane approaches and dissociates on the catalytic surface, the process involves the dynamic interplay of CH 4 and the Ni catalyst that includes both enthalpic and entropic contributions. The progression towards the transition state involves an CH 4 moiety that is increasingly restrained in its ability to rotate or translate, while the stage following the transition state is characterized by a notable rise of the Ni atom that interacts with the cleaved C–H bond. Furthermore, this leads to an increase in the mobility of the adsorbed species, a feature that becomes more pronounced at higher temperatures.

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

Computing Reaction Kinetics with MC-PDFT–OPESf: Combining Multireference Electronic Structure Theory and Enhanced Sampling

Accurate rate constants are crucial for understanding and optimizing catalytic reactions mediated by enzymes, metalloproteins, and heterogeneous catalysts. These systems frequently present a dual computational challenge. Multiconfigurational reaction sites require multireference techniques for the accurate treatment of the electronic structure, and high activation barriers prevent efficient sampling of unbiased reactive transitions. In this work, we combine multiconfiguration pair-density functional theory (MC-PDFT) as an accurate and efficient multireference electronic structure method with on-the-fly probability-enhanced sampling flooding (OPESf) as an enhanced sampling method capable of accelerating reactive transitions. We demonstrate the approach on the Diels–Alder [4+2] cycloaddition between cis-butadiene and ethene as a reaction characterized by a large activation barrier and multireference character. MC-PDFT–OPESf provides reaction rates in agreement with experiments at a fraction of the computational cost required by conventional unbiased ab initio calculations. Here, we propose MC-PDFT–OPESf as an efficient approach for computing kinetics in strongly correlated molecular systems.

Chemical calculations↗
DOE OSTI2025

Free-Energy Landscapes and Surface Dynamics in Methane Activation on Ni(511) via Machine Learning and Enhanced Sampling

Methane activation on stepped Ni(511) surfaces involves the rearrangement of surface atoms as the chemical reaction proceeds. This process is particularly sensitive to temperature. Using machine-learned interatomic potentials (MLIPs) coupled with enhanced sampling techniques, we investigate the activation of methane under realistic operando conditions. Our analysis reveals that methane dissociation occurs predominantly at step-edge nickel atoms. As CH x (where x = 3 or 4) species bind to additional surface nickel atoms, their reduced mobility leads to entropic penalties that suppress certain configurations and transition states. This is reflected in the underlying free energy surfaces, where configurations such as methyl binding to hollow sites and activation routes involving two nickel atoms become unfavorable as temperature increases. At elevated temperatures, methane activation extends from step-edge sites to terrace regions because of reduced free-energy barriers and enhanced surface dynamics. By decomposing the free-energy into enthalpic and entropic contributions, we uncover temperature-dependent shifts in the preferences of methane for the relevant active sites and arrive at a detailed molecular picture of methane activation.

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

Simulating Crystallization in a Colloidal System Using State Predictive Information Bottleneck Based Enhanced Sampling

Here, we investigate crystal nucleation in supersaturated colloid suspensions using enhanced molecular dynamics simulations augmented with machine learning techniques. The simulations reveal that crystallization in the model colloidal system studied here, with particles interacting through a repulsive screened Coulomb Yukawa potential, proceeds from vapor to dense liquid droplet to crystalline phases across multiple high barriers. Employing a one-dimensional reaction coordinate derived from the State Predictive Information Bottleneck framework, our simulations capture back-and-forth phase transitions across multiple barriers effectively in biased metadynamics simulations. We obtain relative free energy differences between different phases and also quantify the roles of different molecular level features in driving the phase changes.

Chemistry↗
DOE OSTI2025

Persistent Sampling: Enhancing the Efficiency of Sequential Monte Carlo

Sequential Monte Carlo (SMC) samplers are powerful tools for Bayesian inference but suffer from high computational costs due to their reliance on large particle ensembles for accurate estimates. We introduce persistent sampling (PS), an extension of SMC that systematically retains and reuses particles from all prior iterations to construct a growing, weighted ensemble. By leveraging multiple importance sampling and resampling from a mixture of historical distributions, PS mitigates the need for excessively large particle counts, directly addressing key limitations of SMC such as particle impoverishment and mode collapse. Crucially, PS achieves this without additional likelihood evaluations-weights for persistent particles are computed using cached likelihood values. This framework not only yields more accurate posterior approximations but also produces marginal likelihood estimates with significantly lower variance, enhancing reliability in model comparison. Furthermore, the persistent ensemble enables efficient adaptation of transition kernels by leveraging a larger, decorrelated particle pool. Experiments on high-dimensional Gaussian mixtures, hierarchical models, and non-convex targets demonstrate that PS consistently outperforms standard SMC and related variants, including recycled and waste-free SMC, achieving substantial reductions in mean squared error for posterior expectations and evidence estimates, all at reduced computational cost. PS thus establishes itself as a robust, scalable, and efficient alternative for complex Bayesian inference tasks.

Karamanis, Minas↗
DOE OSTI2026

Custom-trained Machine-learning Interatomic Potentials: ZnCl2 Aqueous Solution

This dataset was generated using an iterative active-learning strategy implemented in the ArcaNN software package (https://github.com/arcann-chem/arcann_training) to train machine-learning interatomic potentials for aqueous ZnCl2 solutions. Each active-learning cycle consisted of three stages: training, exploration, and labeling. The initial training set combined configurations generated in this work from enhanced-sampling ab initio molecular dynamics simulations with configurations from a previously reported neural-network-potential study of aqueous ZnCl2. The enhanced-sampling ab initio molecular dynamics simulations involved Zn–Cl separation and the chloride coordination number around Zn²? as collective variables. These configurations served as the seed dataset. Subsequent active-learning cycles expanded the training set by identifying and labeling configurations that were poorly represented by the current models, thereby improving coverage of ion-association states and changes in local coordination and charge-state environments relevant to the solution free-energy landscape. For all selected configurations, single-point calculations of the total energies and atomic forces were performed within density functional theory using the CP2K Quickstep module. Reference calculations employed the revPBE-D3 and r2SCAN exchange-correlation functionals. Motivated by recent work on aqueous Zn²?, the main revPBE calculations omitted D3 dispersion contributions involving Zn²?, while retaining the D3 correction for water and chloride. For comparison, fully dispersion-corrected revPBE-D3 reference calculations were also performed, with D3 applied to all species, including Zn²?. Valence electrons were treated explicitly, while core electrons were represented using norm-conserving Goedecker–Teter–Hutter pseudopotentials. The wave functions were expanded using the mixed Gaussian-and-plane-wave scheme with TZV2P-MOLOPT basis sets for all elements and a 600 Ry auxiliary plane-wave cutoff for the electron density. Self-consistent-field convergence was accelerated using the orbital-transformation and Direct Inversion in the Iterative Subspace algorithms, with a convergence threshold of 10?6. All single-point calculations were performed in periodic orthorhombic cells. The CELL_REF keyword in CP2K was used to define a fixed reference cell with a box length of 25 Å. This treatment ensured a consistent reference for configurations extracted from NpT trajectories with fluctuating cell dimensions. The resulting DFT energies and atomic forces constitute the ground-truth labels used to train the MLIPs. The resulting MLIP was trained for aqueous ZnCl2 solutions spanning concentrations from 0 to 30 molal and a broad pH range, from strongly acidic to strongly basic conditions. Representative examples of configurations included in the MLIP training dataset are provided below. These include 1) Representative configurations from the dataset labeled at the revPBE-D3 level, with D3 dispersion interactions involving Zn2+ excluded (revPBE-wo-D3). 2) Representative configurations from the dataset labeled at the fully dispersion-corrected revPBE-D3 level, with D3 interactions applied to all species, including Zn2+ (revPBE-D3). 3) Representative configurations from the dataset labeled at the r2SCAN level of theory (r2SCAN).

Dinpajooh, Mohammadhasan [Pacific Northwest Nation↗
DOE OSTI2024

A graph neural network-state predictive information bottleneck (GNN-SPIB) approach for learning molecular thermodynamics and kinetics

Molecular dynamics simulations offer detailed insights into atomic motions but face timescale limitations. Enhanced sampling methods have addressed these challenges but even with machine learning, they often rely on pre-selected expert-based features. Here, in this work, we present a Graph Neural Network-State Predictive Information Bottleneck (GNN-SPIB) framework, which combines graph neural networks and the state predictive information bottleneck to automatically learn low-dimensional representations directly from atomic coordinates. Tested on three benchmark systems, our approach predicts essential structural, thermodynamic and kinetic information for slow processes, demonstrating robustness across diverse systems. The method shows promise for complex systems, enabling effective enhanced sampling without requiring pre-defined reaction coordinates or input features.

Zou, Ziyue↗
DOE OSTI2024

Elucidating and contrasting the mechanisms for Mg and Ca sulfate ion-pair formation with multi-level embedded quantum mechanics/molecular dynamics simulations

Here, solutions and minerals containing sulfate (SO 4 2- ), and Ca 2+ and Mg 2+ cations, are ubiquitous throughout the lithosphere and are significant components of seawater, thus presenting a prototypical system for the study of strong electrolytes and crystal nucleation mechanisms. However, despite their relative abundance, key questions remain unanswered about the most fundamental atomic-level steps of their mineralization pathways and aqueous dynamics. Here, we carry out enhanced sampling multi-level molecular dynamics (MD) embedded correlated wavefunction theory simulations to elucidate ion-pairing mechanisms for Mg–SO 4 and Ca–SO 4 in concentrated aqueous solution, accurately capturing effects arising from both structural dynamics and electron exchange–correlation. We predict contact-ion-pair formation to be barrierless and highly exoergic for Ca–SO 4 , in agreement with its minimal solubility, whereas for Mg–SO 4 , solvent-shared and contact ion pairs have similar free energies, qualitatively consistent with its higher solubility. Finally, we demonstrate that brief high-temperature pre-equilibration may be utilized to accelerate convergence of free energies in blue-moon-ensemble enhanced-sampling MD.

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

Weighted active space protocol for multireference machine-learned potentials

Multireference methods such as multiconfiguration pair-density functional theory accurately capture electronic correlation in systems with strong multiconfigurational character, but their cost precludes direct use in molecular dynamics. Combining these methods with machine-learned interatomic potentials (MLPs) can extend their reach. However, the sensitivity of multireference calculations to the choice of the active space complicates the consistent evaluation of energies and gradients across structurally diverse nuclear configurations. To overcome this limitation, we introduce the weighted active space protocol (WASP), a systematic approach to assign a consistent active space for a given system across uncorrelated configurations. By integrating WASP with MLPs and enhanced sampling techniques, we propose a data-efficient active learning cycle that enables the training of an MLP on multireference data. We demonstrated the approach on the TiC + -catalyzed C–H activation of methane, a reaction that poses challenges for Kohn–Sham density functional theory due to its significant multireference character. This framework enables accurate and efficient modeling of catalytic dynamics, establishing a paradigm for simulating complex reactive processes beyond the limits of conventional electronic-structure methods.

enhanced sampling↗
DOE OSTI2025

Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues

DNA-points accumulation for imaging in nanoscale topography (DNA-PAINT) enables nanoscale imaging with virtually unlimited multiplexing and molecular counting. Here, we address challenges, such as variable imaging performance and target accessibility, that can limit its broader applicability. Specifically, we enhance its capacity for robust single-protein imaging and molecular counting by optimizing the integration of total internal reflection fluorescence microscopy with physical sectioning, in particular, Tokuyasu cryosectioning. Our method, tomographic and kinetically enhanced DNA-PAINT (tkPAINT), achieves 3 nm localization precision across diverse samples, enhanced imager binding, and improved cellular integrity. tkPAINT can facilitate molecular counting with DNA-PAINT inside the nucleus, as demonstrated through its quantification of the in situ abundance of RNA Polymerase II in both HeLa cells as well as mouse tissues. Anticipating that tkPAINT could become a versatile tool for the exploration of biomolecular organization and interactions across cells and tissues, we also demonstrate its capacity to support multiplexing, multimodal targeting of proteins and nucleic acids, and three-dimensional (3D) imaging.

Science & Technology - Other Topics↗
NASA NTRS1994

Performance and durability of high emittance heat receiver surfaces for solar dynamic power systems

Haynes 188, a cobalt-based superalloy, will be used to make thermal energy storage (TES) containment canisters for a 2 kW solar dynamic ground test demonstrator (SD GTD). Haynes 188 containment canisters with a high thermal emittance (epsilon) are desired for radiating heat away from local hot spots, improving the heating distribution, which will in turn improve canister service life. In addition to needing a high emittance, the surface needs to be durable in an elevated temperature, high vacuum environment for an extended time period. Thirty-five Haynes 188 samples were exposed to 14 different types of surface modification techniques for emittance and vacuum heat treatment (VHT) durability enhancement evaluation. Optical properties were obtained for the modified surfaces. Emittance enhanced samples were exposed to VHT for up to 2692 hours at 827 C and less than or equal to 10(exp -6) torr with integral thermal cycling. Optical properties were taken intermittently during exposure, and after final VHT exposure. The various surface modification treatments increased the emittance of pristine Haynes 188 from 0.11 up to 0.86. Seven different surface modification techniques were found to provide surfaces which met the SD GTD receiver VHT durability requirement. Of the 7 surface treatments, 2 were found to display excellent VHT durability: an alumina based (AB) coating and a zirconia based coating. The alumina based coating was chosen for the epsilon enhancement surface modification technique for the SD GTD receiver. Details of the performance and vacuum heat treatment durability of this coating and other Haynes 188 emittance surface modification techniques are discussed. Technology from this program will lead to successful demonstration of solar dynamic power for space applications, and has potential for application in other systems requiring high emittance surfaces.

Degroh, Kim K.↗
DOE OSTI2024

Integrative Multi-PTM Proteomics Reveals Dynamic Global, Redox, Phosphorylation, and Acetylation Regulation in Cytokine-treated Pancreatic Beta Cells

Studying regulation of protein function at a systems level necessitates an understanding of the interplay among diverse post-translational modifications (PTMs). A variety of proteomics sample processing workflows are currently used to study specific PTMs but rarely characterize multiple types of PTMs from the same sample inputs. Method incompatibilities and laborious sample preparation steps complicate large-scale physiological investigations and can lead to variations in results. The single-pot, solid-phase-enhanced sample preparation (SP3) method for sample cleanup is compatible with different lysis buffers and amenable to automation, making it attractive for high-throughput multi-PTM profiling. Herein, we describe an integrative SP3 workflow for multiplexed quantification of protein abundance, cysteine thiol oxidation, phosphorylation, and acetylation. The broad applicability of this approach is demonstrated using cell and tissue samples, and its utility for studying interacting regulatory networks is highlighted in a time-course experiment of cytokine-treated ß-cells. We observed a swift response in global regulation of protein abundances consistent with rapid activation of JAK-STAT and NF-?B signaling pathways. Regulators of these pathways as well as proteins involved in their target processes displayed multi-PTM dynamics indicative of a complex cellular response stages: acute, adaptation, and chronic (prolonged stress). PARP14, a negative regulator of JAK-STAT, had multiple co-localized PTMs that may be involved in intraprotein regulatory crosstalk. Our workflow provides a high-throughput platform that can profile multi-PTMomes from the same sample set, which is valuable in unraveling the functional roles of PTMs and their co-regulation.

proteomics, PTM, automation, SP3, cysteine thiol o↗
NASA NTRS2024

Optimizing Sample Collection and Accessibility through the Biospecimen and Tissue Sharing Collection (BTSC) Program

The Space Radiation Element (SRE) of the Human Research Program (HRP) is dedicated to establishing a robust biospecimen and tissue sharing collection (BTSC) program that enhances sample collection, tracking, access, distribution, and usability, with the goal of maximizing scientific return. By leveraging biospecimens and tissues from previous experiments, HRP effectively achieves its scientific objectives in characterizing and mitigating the human health impacts of spaceflight while optimizing resource utilization. To further improve the usability and accessibility of the current biospecimen archive, the project aims to expand upon NASA's existing resources and institutional knowledge, ensuring ongoing modernization. To facilitate seamless navigation of the program's workflow, an educational series on the BTSC program is provided to Principal Investigators (PIs). This comprehensive series equips PIs with crucial information on submitting their inventory via the BTSC Metadata Intake Form, ultimately leading to the public availability of their data on NASA's Life Science Portal (NLSP). Covering various aspects such as metadata submission instructions and backend processes for transferring metadata to the Laboratory Information Management System (LIMS), the series incorporates guidance from NASA's Biological Institutional Scientific Collection (NBISC) and Ames Life Sciences Data Archive (ALSDA). The BTSC program represents a significant stride towards enhancing the usability and accessibility of biospecimens for space research. By enabling NASA to deepen its understanding of the health implications of long-term spaceflight, this initiative plays a pivotal role in ensuring the safety and well-being of astronauts.

Shelita Renee Augustus↗
DOE OSTI2026

Neural network potentials with effective charge separation for non-equilibrium dynamics of ionic solids: a ZnO case study

Developing neural network potentials (NNPs) accurate under non-equilibrium dynamics is challenging, as such systems require extensive sampling beyond equilibrium phases. Here we construct high-fidelity NNPs for zinc oxide (ZnO), a polymorphic ionic solid, using density functional theory (DFT) reference data. To efficiently capture transitional configurations, we combine enhanced-sampling molecular dynamics with empirical potentials, data distillation, and pretraining on short-range atomic energies (A-Train), followed by transfer learning with DFT-relabeled datasets. This hierarchical approach improves transferability across polymorphs and stress states. We further introduce effective charge separation, treating long-range Coulombic terms analytically while short-range residual interactions are learned by the NNP. The optimal effective charges fall in the range 0.5–1.0 q e , consistent with dielectric-screened values derived from formal charges but distinct from Bader estimates. Motivated by this observation, we propose a simple data-driven protocol in which effective charges are optimized by comparing DFT reference energies with explicit Coulomb calculations, without additional NNP training. This strategy improves accuracy and transferability in DFT-level predictions of energies, forces, and stress. Together, these results provide a practical charge-selection framework for robust NNP development in ionic solids, enabling reliable simulation of polymorphic phase transformations and non-equilibrium dynamics.

Chemistry↗