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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

Heracles: Predictive Tools for Opioid Crisis Intervention - m/q Initiative Project Report

The opioid crisis in the United States is being fueled primarily by fentanyl and its molecular analogs, which can be anywhere from 50 to 1,000 times more potent than morphine. Fentanyl itself is straightforward to synthesize; furthermore, the structure is such that fentanyl’s flexible, rotatable side chains are easy to modify to create new analogs. Reference-free computational techniques to predict and identify new fentanyls have the potential to provide a desperately needed preemptive advantage to regulatory stakeholders and toxicologists. The computational pipeline Heracles was developed with this preemptive advantage in mind. Heracles has two primary components: 1) the creation of an in silico library of putative fentanyl analogs, and 2) a downselection pipeline to prioritize generated fentanyl analogs predicted to be potent and easy to synthesize. Experimental observables were also predicted for prioritized analogs, with validation of the observables begun. Heracles has demonstrated potential to aid in the advancement of reference-free paradigms while providing new tools to first responders and other stakeholders attempting to mitigate the opioid crisis.

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

Nontrivial nanostructure, stress relaxation mechanisms, and crystallography for pressure-induced Si-I → Si-II phase transformation

Crystallographic theory based on energy minimization suggests austenite-twinned martensite interfaces with specific orientation, which are confirmed experimentally for various materials. Pressure-induced phase transformation (PT) from semiconducting Si-I to metallic Si-II, due to very large and anisotropic transformation strain, may challenge this theory. Here, unexpected nanostructure evolution during Si-I → Si-II PT is revealed by combining molecular dynamics (MD), crystallographic theory, generalized for strained crystals, and in situ real-time Laue X-ray diffraction (XRD). Twinned Si-II, consisting of two martensitic variants, and unexpected nanobands, consisting of alternating strongly deformed and rotated residual Si-I and third variant of Si-II, form {111} interface with Si-I and produce almost self-accommodated nanostructure despite the large transformation volumetric strain of -0.237. The interfacial bands arrest the {111} interfaces, leading to repeating nucleation-growth-arrest process and to growth by propagating {110} interface, which (as well as {111} interface) do not appear in traditional crystallographic theory.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation

Effective gene regulation by the tetrahydrofolate riboswitch depends not only on ligand affinity but also on the kinetics of ligand association, which involves two cooperative binding sites. Here, we have determined a 1.9-Å resolution crystal structure of the ligand-free THF riboswitch aptamer. The pseudoknot binding site ‘unwinds’ in the absence of ligand, whereby the adjacent helical domains (P1, P2, and P3) become disjointed, resulting in rotation and misalignment of the gene-regulatory P1 helix with respect to P3. In contrast, the second binding site at the three-way junction, which is the first to fold, is structurally conserved between apo and holo forms. This suggests a kinetic role for this site, in which binding of the first ligand molecule to the stably folded three-way junction promotes formation of the regulatory pseudoknot site and subsequent binding of the second molecule. As such, these findings provide a molecular basis for both conformational switching and kinetic control.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Dataset for manuscript "Consequences of the failure of equipartition for the p-V behavior of liquid water and the hydration free energy components of a small protein"

Previously, we showed that in the molecular dynamics simulation of a rigid model of water it is necessary to use an integration time-step dt that is less than or equal to 0.5 fs to ensure equipartition between translational and rotational modes. We extended that study in the NVT ensemble to NpT conditions and to an aqueous protein. We study neat liquid water with the rigid, SPC/E model and the protein BBA (PDB ID: 1FME) solvated in the rigid, TIP3P model. We examined integration time-steps ranging from 0.5 fs to 4.0 fs for various thermostat plus barostat combinations. We find that a small time-step, dt, is necessary to ensure consistent prediction of the simulation volume. Hydrogen mass repartitioning alleviates the problem somewhat, but is ineffective for the typical time-step used with this approach. The compressibility, a measure of volume fluctuations, is seen to be sensitive to dt. Using the mean volume estimated from the NpT simulation, we examined the electrostatic and van der Waals contribution to the hydration free energy of the protein in the NVT ensemble. These contributions are also sensitive to dt. In going from a time-step of 2 fs to a time-step of 0.5 fs, the change in the net electrostatic plus van der Waals contribution to the hydration of BBA is already in excess of the folding free energy reported for this protein. The data-set contains the simulation metadata and log files that support the claims noted above.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Restoring Symmetry and Enhancing Exchange via Chiral Molecular-Magnetic Hexagons

Modified behaviors of molecules, designed for device or energy applications, can occur due to lattice-molecule incompatibilities in point-group symmetries (PGS), long-range interactions between neighboring molecules, or latticemolecule charge transfer. Such sensitivities are prerequisite for the use of quantum molecules as devices, but removing certain broken symmetries is desirable from the standpoint of simplifying their behaviors. Here, we demonstrate symmetry restoration to molecular-magnetic lattices and show that it leads to strengthened exchange-coupling due to dipolar electrostatic interactions between neighboring molecules and due to manifestations of an earlier identification of a spin-sensitive slightly mobile electron by Hooshmand et al. Starting with a broken symmetry molecular magnet of current interest, we demonstrate a more robust structure composed of six molecular magnets on a h-BN-like surface. The broken point-group symmetry is healed by constructing interpenetrating equilateral triangular structures that are appropriately ratcheted to preserve three-fold rotational symmetry and inversion symmetry.

Pederson, Mark R.↗
DOE OSTI2026

Microscopic Mechanisms of Superionic Na-ion Conductivity in Crystalline and Amorphous NaMOCl 4 (M = Nb, Ta) Solid Electrolytes

Sodium-ion solid electrolytes offer a sustainable route toward next-generation batteries, but few match the performance of their lithium counterparts. Halide-based NaMOCl 4 (M = Nb, Ta) has recently emerged as a promising analogue to LiMOCl 4 , yet its structure–transport relationships remain unclear due to poor crystallinity in experiments. Here, we combine density functional theory and machine-learned molecular dynamics to reveal that crystalline NaMOCl 4 exhibits negligible room-temperature conductivity with high activation barriers arising from vacancy-mediated diffusion below an order–disorder transition. Above this transition, rotational and translational motion of the [MO 2/2 Cl 4 – ] ∞ chains create new Na sites and enhances transport. In contrast, the amorphous phase inherently supports facile, three-dimensional Na diffusion through dynamic framework flexibility. These results show that ordered crystalline phases hinder ionic transport, while disorder – either thermally induced or structural – facilitates it, revising prior assumptions from the Li system and providing design principles for high-conductivity Na halide electrolytes.

Wei, Grace [University of California, Berkeley, CA↗
DOE OSTI2026

Dataset_for_Molecular_Motion_Below_the_Glass_Transition_A_Solid-State_NMR_Study_of_Siloxane_Polymer_Dynamics Study

This dataset contains solid-state 1H and 13C NMR relaxometry data, differential scanning calorimetry (DSC) data, and size exclusion chromatography (SEC/GPC) data supporting the study of sub-glass-transition (sub-Tg) molecular dynamics in a composition- and sequence-controlled series of diphenyl-substituted polysiloxanes (PDMS, 14Ph, 33Ph, 50Ph, 67Ph, and 100Ph; 0–100% diphenylsiloxane content by mole).All solid-state NMR data were acquired on a 200 MHz Bruker Avance III HD spectrometer using a static 7 mm HX probe or a 4 mm HX probe under 4 kHz magic-angle spinning. Raw Bruker TopSpin experiment folders are included for: (1) variable-temperature 1H lineshape measurements used to determine linewidth (FWHM) as a function of temperature across the glass transition; (2) 1H T1 (saturation recovery with solid-echo detection), probing nanosecond-scale dynamics near the 1H Larmor frequency; (3) 1H T1rho (direct spin-lock, 62.5 kHz), probing microsecond-scale segmental dynamics; (4) 13C-detected Lee–Goldburg cross-polarization 1H T1rho (LGCPH T1rho) for 33Ph and 50Ph, resolving aromatic and aliphatic proton environments; and (5) 13C T1 relaxation for 33Ph and 50Ph. Differential scanning calorimetry data (TA Instruments DSC 25, −150 to +120 °C, up to +300 °C for 100Ph, 10 °C/min) are included for all six compositions and support the glass-transition temperatures in Table 1 and Figure 1. Size exclusion chromatography data (Agilent 1200 Series, PL-Gel 300 mixed-C column, THF mobile phase, polystyrene calibration standards) are included for the three synthesized copolymers (33Ph, 50Ph, 67Ph) and support the number-average molecular weights in Table 1. Processed data include per-composition relaxation-time summaries (Excel), curve-fitting and Bloembergen-Purcell-Pound (BPP) model analysis notebooks (Jupyter/Python), and Igor Pro (.pxp) master files used to generate the manuscript's figures.

Bloembergen-Purcell-Pound theory↗
DOE OSTI2022

Semi-empirical quantum optics for mid-infrared molecular nanophotonics

Nanoscale infrared (IR) resonators with sub-diffraction limited mode volumes and open geometries have emerged as new platforms for implementing cavity quantum electrodynamics at room temperature. The use of IR nanoantennas and tip nanoprobes to study strong light–matter coupling of molecular vibrations with the vacuum field can be exploited for IR quantum control with nanometer spatial and femtosecond temporal resolution. In order to advance the development of molecule-based quantum nanophotonics in the mid-IR, we propose a generally applicable semi-empirical methodology based on quantum optics to describe light–matter interaction in systems driven by mid-IR femtosecond laser pulses. The theory is shown to reproduce recent experiments on the acceleration of the vibrational relaxation rate in infrared nanostructures. It also provides physical insights on the implementation of coherent phase rotations of the near-field using broadband nanotips. We then apply the quantum framework to develop general tip-design rules for the experimental manipulation of vibrational strong coupling and Fano interference effects in open infrared resonators. We finally propose the possibility of transferring the natural anharmonicity of molecular vibrational levels to the resonator near-field in the weak coupling regime to implement intensity-dependent phase shifts of the coupled system response with strong pulses and develop a vibrational chirping model to understand the effect. The semi-empirical quantum theory is equivalent to first-principles techniques based on Maxwell’s equations, but its lower computational cost suggests its use as a rapid design tool for the development of strongly coupled infrared nanophotonic hardware for applications ranging from quantum control of materials to quantum information processing.

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

Development of a machine-learning-based ionic-force correction model for quantum molecular dynamic simulations of warm dense matter

In this work Δ learning is used to map orbital-free density functional theory (OF-DFT) ionic forces to the corresponding Kohn-Sham (KS) DFT ionic forces. The development of the approximate force difference in terms of the ion positions is constructed and serves as a stand in for the ground truth force difference. Descriptor vectors for ion configurations are constructed using all distance between ions in conjunction with an indexing based on a nearest neighbor ranking. It is demonstrated that such a scheme of descriptors can uniquely describe an ionic configuration up to a rotation and reflection when no ambiguity in the nearest neighbor ranking exists. How to handle the case when an ambiguity exists in the nearest neighbor ranking is discussed. As a proof of principle, the model is trained and tested on warm dense hydrogen at temperatures between 1 and 15 eV. Once tested, the model was used to perform molecular dynamic simulations of warm dense hydrogen. Furthermore, the resulting energies and pressures are within 1% and 2% of their respective target KS values.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Third-body stabilization of supercritical CO 2 in CO oxidation: development and application of a ReaxFF force field for the CO/O/CO 2 system

Supercritical CO 2 (scCO 2 ) plays a crucial role as a solvent in separation processes, advanced power cycles, and materials processing. Nonetheless, the atomistic comprehension of how the dense scCO 2 matrix influences the fundamental reaction of carbon monoxide (CO) is still insufficiently explored. Experimental studies and molecular dynamics (MD) simulations frequently fail to detect the highly reactive, transient intermediates, such as atomic oxygen (O), that drive these reactions. Here, to address this issue, we have developed a novel ReaxFF reactive force field for the CO 2 /CO/O system. The force field parameters were calibrated using density functional theory and second-order Møller-Plesset calculations to model CO 2 crystal properties, intermolecular interactions, bond dissociation curves, and reaction energy barriers. The force field reproduces the cohesive energy of the CO 2 crystal, the pressure characteristics of bulk scCO 2 , the equation-of-state behavior over a wide pressure–density range, the pressure dependence of the C–O bond length under compression, and the structural properties of liquid and scCO 2 , as documented by experiments, ab-initio MD, and prominent non-reactive models. The force field was subsequently applied to study the CO + O → CO 2 reaction. In a dilute environment, the reaction is inefficient as the newly formed CO 2 rapidly dissociates due to excess kinetic and potential energy acquired from the exothermic reaction. Conversely, in a dense scCO 2 environment, the surrounding matrix acts as an efficient third body, stabilizing the emerging CO2 product via molecular collisions. Statistical analysis confirms an average excess energy dissipation of 133.9 ± 3.6 kcal/mol over 112.4 ± 17.9 ps. Kinetic energy decomposition reveals that ∼ 92% of the excess kinetic energy is stored in internal (rotational and vibrational) degrees of freedom. This ReaxFF force field establishes a mechanistic foundation for third-body stabilization in dense reactive environments.

Chowdhury, Emdadul Haque [Pennsylvania State Univ.↗
DOE OSTI2024

Stochastic modeling of x-ray superfluorescence

An approach to modeling the dynamics of x-ray amplified spontaneous emission and superfluorescence, the phenomenon of collective x-ray emission initiated by intense pulses of x-ray free-electron lasers, is developed based on stochastic partial differential equations. The equations are derived from first principles, and the relevant approximations, derivation steps, and extensions specific to stimulated x-ray emission are presented. The resulting equations take the form of three-dimensional generalized Maxwell-Bloch equations augmented with noise terms for both field and atomic variables. The derived noise terms possess specific correlation properties that enable the correct reconstruction of spontaneous emission. Consequently, the developed theoretical formalism is universally suitable for describing all stages of stimulated x-ray emission: spontaneous emission, amplified spontaneous emission, and superfluorescence. Here, we present numerical examples that illustrate various properties of the emitted field, including spatiotemporal coherence and spectral-angular and polarization characteristics. We anticipate that the proposed theoretical framework will establish a robust foundation for interpreting measurements in stimulated x-ray emission spectroscopy, modeling x-ray laser oscillators, and describing other experiments leveraging x-ray superfluorescence.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

A Measurement of Atmospheric Circular Polarization with POLARBEAR

At millimeter wavelengths, the atmospheric emission is circularly polarized owing to the Zeeman splitting of molecular oxygen by the Earth's magnetic field. We report a measurement of the signal in the 150 GHz band using 3 yr of observational data with the POLARBEAR project. Nonidealities of a continuously rotating half-wave plate (HWP) partially convert circularly polarized light to linearly polarized light. While POLARBEAR detectors are sensitive to linear polarization, this effect makes them sensitive to circular polarization. Although this was not the intended use, we utilized this conversion to measure circular polarization. We reconstruct the azimuthal gradient of the circular polarization signal and measure its dependency from the scanning direction and the detector bandpass. We compare the signal with a simulation based on atmospheric emission theory, the detector bandpass, and the HWP leakage spectrum model. We find the ratio of the observed azimuthal slope to the simulated slope is 0.92 ± 0.01(stat) ± 0.07(sys). This ratio corresponds to a brightness temperature of 3.8 mK at the effective band center of 121.8 GHz and bandwidth of 3.5 GHz estimated from representative detector bandpass and the spectrum of Zeeman emission. This result validates our understanding of the instrument and reinforces the feasibility of measuring the circular polarization using the imperfection of continuously rotating HWP. Continuously rotating HWP is popular in ongoing and future cosmic microwave background experiments to modulate the polarized signal. This work shows a method for signal extraction and leakage subtraction that can help measure circular polarization in such experiments.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Ethylene Polymerizations Catalyzed by Fluorinated “Sandwich” Diimine-Nickel and Palladium Complexes

Nickel and palladium complexes bearing “sandwich” diimine ligands with perfluorinated aryl caps have been synthesized, characterized, and explored in ethylene polymerization reactions. The X-ray crystallographic analysis of the precatalysts 16 and 6b show differences from their non-fluorinated analogues 17 and 19, with the perfluorinated aryl caps centered precisely over the nickel and palladium centers which results in higher buried volumes of the metal centers relative to the non-fluorinated analogs. The sandwich diimine palladium complexes 5a and 5b containing perfluorinated aryl caps polymerize ethylene in a controlled fashion with activities that are substantially increased compared with their non-fluorinated analogues. Migratory insertion rates in relevant methyl ethylene complexes agree with activities exhibited in bulk polymerization experiments. DFT studies suggest that facility of ethylene rotation from its preferred orientation perpendicular to the Pd-alkyl bond into a parallel in-plane conformation contributes to the higher polymerization activity for 5b relative to 18a. For these palladium systems polymer molecular weights can be controlled via hydrogen addition (hydrogenolysis) which is unusual for late transition metal-catalyzed olefin polymerizations with no catalyst deactivation occurring. Sandwich diimine nickel complexes 6a and 6b with perfluorinated aryl caps show ethylene polymerization activities that are about half that of classical tetraisopropyl-substituted catalyst 2 but again are more active than the analogous nonfluorinated sandwich complexes. Ethylene polymerizations exhibit living behavior and branched ultra-high molecular weight polyethylenes (UHMWPEs) with very low molecular weight distributions (less than 1.1) are obtained. The activated nickel catalysts are stable in the absence of monomer and show good long-term stability at 25 °C.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Wave packet dynamics and control in excited states of molecular nitrogen

Wave packet interferometry with vacuum ultraviolet light has been used to probe a complex region of the electronic spectrum of molecular nitrogen, N 2 . Wave packets of Rydberg and valence states were excited by using double pulses of vacuum ultraviolet (VUV), free-electron-laser (FEL) light. These wave packets were composed of contributions from multiple electronic states with a moderate principal quantum number (n ~ 4-9) and a range of vibrational and rotational quantum numbers. The phase relationship of the two FEL pulses varied in time, but as demonstrated previously, a shot-by-shot analysis allows the spectra to be sorted according to the phase between the two pulses. The wave packets were probed by angle-resolved photoionization using an infrared pulse with a variable delay after the pair of excitation pulses. The photoelectron branching fractions and angular distributions display oscillations that depend on both the time delays and the relative phases of the VUV pulses. The combination of frequency, time delay, and phase selection provides significant control over the ionization process and ultimately improves the ability to analyze and assign complex molecular spectra.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

The Role of Surface Hydroxyls in the Mobility of Carboxylates on Surfaces: Dynamics of Acetate on Anatase TiO 2 (101)

The dynamics of reactive intermediates are important in catalysis for understanding transient species, which can drive reactivity and the transport of species to reaction centers. In particular, the interplay between surface-bound carboxylic acids and carboxylates is important for numerous chemical transformations, including CO 2 hydrogenation and ketonization. Here, we investigate the dynamics of acetic acid on anatase TiO 2 (101) using scanning tunneling microscopy experiments and density functional theory calculations. We demonstrate the concomitant diffusion of bidentate acetate and a bridging hydroxyl and provide evidence for the transient formation of molecular monodentate acetic acid. The diffusion rate is strongly dependent on the position of hydroxyl and adjacent acetate(s). A facile three-step diffusion process is proposed consisting of acetate and hydroxyl recombination, acetic acid rotation, and acetic acid dissociation. Here this study clearly demonstrates that the dynamics of bidentate acetate could be important in forming monodentate species, which are proposed to drive selective ketonization.

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

Formation of a single quasicrystal upon collision of multiple grains

Abstract Quasicrystals exhibit long-range order but lack translational symmetry. When grown as single crystals, they possess distinctive and unusual properties owing to the absence of grain boundaries. Unfortunately, conventional methods such as bulk crystal growth or thin film deposition only allow us to synthesize either polycrystalline quasicrystals or quasicrystals that are at most a few centimeters in size. Here, we reveal through real-time and 3D imaging the formation of a single decagonal quasicrystal arising from a hard collision between multiple growing quasicrystals in an Al-Co-Ni liquid. Through corresponding molecular dynamics simulations, we examine the underlying kinetics of quasicrystal coalescence and investigate the effects of initial misorientation between the growing quasicrystalline grains on the formation of grain boundaries. At small misorientation, coalescence occurs following rigid rotation that is facilitated by phasons. Our joint experimental-computational discovery paves the way toward fabrication of single, large-scale quasicrystals for novel applications.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Ground and excited state gradients with end-to-end differentiable semiempirical quantum chemistry

Accurate and efficient gradients of molecular energy with respect to nuclear degrees of freedom are essential for geometry optimization and molecular dynamics, including simulations that go beyond the Born–Oppenheimer regime. A common approach involves deriving analytical formulas for new electronic structure methods, which is often conceptually difficult and requires tedious coding. Here, we implement analytical, semi-numerical, and automatic differentiation (AD)-based gradient pathways for semiempirical Hamiltonian models in the PYSEQM software package, leveraging both graphics processing unit (GPU) and central processing unit (CPU) architectures. We further extend these capabilities to excited states calculated using the configuration interaction singles and time-dependent Hartree–Fock ansätze. We benchmark wall time, peak memory usage, and accuracy across three molecular families of varying chemical complexity, including systems of up to a thousand atoms. For ground-state simulations, analytical and AD gradients achieve near-identical GPU runtimes, while semi-numerical gradients are slower on GPU but remain competitive on CPU. For excited states, both analytical and custom AD approaches using implicit differentiation show similar performance and low memory requirements, whereas gradients with full AD are memory-limited. AD gradients match analytical ones in accuracy across all tested systems, aided by a quaternion-based diatomic frame rotation for two-center quantities that ensures smooth energy surfaces. Overall, automatic differentiation emerges as a practical alternative to analytical gradients in semiempirical quantum chemistry, offering high accuracy while allowing seamless integration in AI-driven workflows and popular packages, such as PyTorch and JAX. Our results provide actionable guidance for selecting optimal gradient strategies in large-scale ground- and excited-state molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗