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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Molecular mechanism of secreted amyloid-β precursor protein in binding and modulating GABABR1a

A recent phenomenal study discovered that the extension domain of secreted amyloid-β precursor protein (sAPP) can bind to the intrinsically disordered sushi 1 domain of the γ-aminobutyric acid type B receptor subunit 1a (GABA B R1a) and modulate its synaptic transmission. The work provided an important structural foundation for the modulation of GABA B R1a; however, the detailed molecular interaction mechanism, crucial for future drug design, remains elusive. Here, we further investigated the dynamical interactions between sAPP peptides and the natively unstructured sushi 1 domain using all-atom molecular dynamics simulations, for both the 17-residue sAPP peptide (APP 17-mer) and its minimally active 9 residue segment (APP 9-mer). We then explored mutations of the APP 9-mer with rigorous free energy perturbation (FEP) calculations. Our in silico mutagenesis studies revealed key residues (D4, W6, and W7) responsible for the binding with the sushi 1 domain. More importantly, one double mutation based on different vertebrate APP sequences from evolution exhibited a stronger binding (ΔΔG = -1.91 ± 0.66 kcal mol -1 ), indicating a potentially enhanced GABA B R1a modulator. These large-scale simulations may provide new insights into the binding mechanism between sAPP and the sushi 1 domain, which could open new avenues in the development of future GABA B R1a-specific therapeutics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1996

The Quantum Phase-Dynamical Properties of the Squeezed Vacuum State Intensity-Couple Interacting with the Atom

The Phase-dynamical properties of the squeezed vacuum state intensity-couple interacting with the two-level atom in an ideal cavity are studied using the Hermitian phase operator formalism. Exact general expressions for the phase distribution and the associated expectation value and variance of the phase operator have been derived. we have also obtained the analytic results of the phase variance for two special cases-weakly and strongly squeezed vacuum. The results calculated numerically show that squeezing has a significant effect on the phase properties of squeezed vacuum.

Fan, An-Fu↗
DOE OSTI2025

Cross-scale covariance for material property prediction

A simulation can stand its ground against an experiment only if its prediction uncertainty is known. The unknown accuracy of interatomic potentials (IPs) is a major source of prediction uncertainty, severely limiting the use of large-scale classical atomistic simulations in a wide range of scientific and engineering applications. Here we explore covariance between predictions of metal plasticity, from 178 large-scale (~10 8 atoms) molecular dynamics (MD) simulations, and a variety of indicator properties computed at small-scales (≤10 2 atoms). All simulations use the same 178 IPs. In a manner similar to statistical studies in public health, we analyze correlations of strength with indicators, identify the best predictor properties, and build a cross-scale “strength-on-predictors” regression model. This model is then used to estimate regression error over the statistical pool of IPs. Small-scale predictors found to be highly covariant with strength are computed using expensive quantum-accurate calculations and used to predict flow strength, within the statistical error bounds established in our study.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Electron Quantum Dynamics in Strong-Field Irradiation

The major goal of the project was to investigate the nonsequential ionization dynamics of atomic systems with two active electrons under intense laser irradiation. In order to gain insights into such nonlinear dynamical systems, one must resort to clever numerical methods due to the poor scaling of computational memory and time. Accordingly, we have extended the virtual detector method of Feuerstein and Thumm by incorporating quasi-classical “virtual” particles that evolve alongside the Schrödinger wavefunction. A major and recent part of this research effort was to further extend the virtual-detector method to model a two-active-electron atomic system.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Dynamic Excitonic Beam Switching with Atomically‐Thin Binary Blazed Gratings

Abstract Beam steering metasurfaces are ultra‐compact optical coatings that offer on‐demand redirection of optical power to specific diffraction orders. To achieve this, spatial gradients are commonly introduced in the phase of light scattered by plasmon or Mie resonant nanoparticles within the metasurface grating's unit cell. However, these phase gradients are oftentimes difficult to tune post‐fabrication. Recently, excitons in monolayer 2D semiconductors have emerged as a new metasurface building block, due to their strong and electrically‐tunable resonant light‐matter interaction. These 2D excitonic metasurfaces offer the tantalizing prospect of beam switching within a single monolayer. Here, it is demonstrated how the 2D analog of binary blazed gratings enables such beam switching by mere nanopatterning of a large monolayer WS 2 , even though nanoscale ribbons of WS 2 do not support geometrical resonances. By introducing a gradient in the nanoribbon width within the metasurface unit cell, an amplitude gradient combined with a small phase gradient in the scattered fields results in asymmetric diffraction efficiencies. Using a scattered‐field analysis, it is shown that these gradients can be further engineered via interference effects with the substrate reflection. Finally, the electrical tunability of the exciton resonance is leveraged to achieve selective and dynamic beam switching with an atomically‐thin metasurface.

Guarneri, Ludovica [Van der Waals‐Zeeman Institute↗
DOE OSTI2023

Effect of Solvent on the Interaction of Lignin with a Zeolite Nanosheet in the Condensed Phase

Lignin is the essential building block of lignocellulosic biomass, an excellent renewable source of different aromatic monomers for the polymer and biofuel industry. The depolymerization of lignin into value-added chemicals and fuels through the catalytic process poses a significant challenge due to the complex structure of lignin. Understanding lignin’s conformational diversity and dynamics in the liquid phase is crucial to designing an effective depolymerization process. Here, we conducted all-atom molecular dynamics simulations to understand the conformation and dynamics of softwood lignin on the all-silica zeolite nanosheet based on the MFI topology in a binary mixture of water–methanol at three different molar compositions (0%, 50%, and 100% methanol). We observed that the methanol–surface interaction is stronger than the water–surface interaction, and methanol readily diffused into the MFI core. Lignin surface contacts decrease with increasing methanol composition due to higher solubility and dynamics. Lignin dynamics on the surface in neat water is an order of magnitude smaller than methanol. Here, we also found that lignin adopts a slightly extended conformation when it stays on the surface than in the bulk solution phase for the pure water case, whereas for pure methanol and the binary solution structures are statistically similar.

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

Scale Invariance of Hot Spot Formation in TATB High Explosives

Shock-induced detonation of insensitive high explosives based on 1,3,5-triamino-2,4,6-trinitrobenzene starts with formation of hot spots at microstructural defects but has eluded atomistic modeling treatment at micron length scales. To this end, we performed multimicron scale all-atom molecular dynamics (MD) simulations of hot spots that form during the collapse of cylindrical pores with diameters between 10 and 300 nm. Our MD simulations show that hot spots formed at pores larger than 20 nm exhibit temperature fields with scale-invariant features for sizes up to at least 300 nm. Through a continuum-based grain-scale modeling framework, we span and extend beyond the size scales currently accessible to MD and find that hot spot scale invariance is a general feature that arises when the mechanical strength is insensitive to strain rate. Finally, our results demonstrate the applicability of all-atom MD to simulate the complicated dynamical evolution of micron-sized systems and bolster confidence in insights from MD simulations of materials that exhibit strength with negligible rate dependence over the relevant intervals.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Unravelling the dynamics of the maturation protein in MS2 bacteriophage via molecular simulations

The MS2 bacteriophage capsid serves as a model system for studying viral structure and function. Mature MS2 virus consists of 178 capsid proteins and a single maturation protein (MP), which is essential for host receptor binding and infection initiation. Despite its critical role, the dynamic behavior of the capsid with the MP remains poorly understood. To address this, we conducted 0.5 µs all-atom molecular dynamics (MD) simulations of the MS2 capsid with and without the MP, revealing key insights into its structural dynamics. Our simulations showed that MP exhibits high flexibility, particularly in the “tip” and “side-loop” regions, which undergo significant motions that likely enhance its ability to engage with the F-pilus receptor. Detailed analysis of MP conformational states revealed that loop rearrangements around H357 enable transient switching between “semi-closed” and “open” conformations, suggesting a conformational selection mechanism for pilus binding. Additionally, ion interaction analyses revealed distinct sodium and chloride binding patterns, where sodium ions were mostly found at the outer capsid shell, while chloride ions interacted with the basic residues on the RNA-facing side. We also found that the presence of the MP enhances salt-bridge interactions, contributing to increased capsid stability, yet it does not significantly alter the pore sizes of pentameric and hexameric units. Together, these findings provide new insights into the functional role of the MP, highlighting its contribution to capsid stability and host receptor engagement. This study offers a foundation for understanding capsid dynamics relevant to viral infectivity and may guide future rational strategies aimed at disrupting host-virus interactions.

Capsid stability↗
DOE OSTI2022

Barkas effect in strongly magnetized plasmas

Strongly magnetized plasmas, which are characterized by the particle gyrofrequency exceeding the plasma frequency, exhibit novel transport properties. For example, recent work showed that the friction force on a test charge moving through a strongly magnetized plasma not only consists of the typical stopping power component but also includes components perpendicular to the test charge's velocity. However, these studies only considered test charges that have the same sign as the charge of the plasma particles. Here, we extend these calculations to the case of charges with opposite signs (such as an ion interacting with strongly magnetized electrons). This is done with both a novel generalized Boltzmann kinetic theory and molecular dynamics simulations. It is found that the friction force changes dramatically depending on the sign of the interacting charges. Likewise, the stopping power component for oppositely charged particles decreases in magnitude compared with like-charged particles, and the perpendicular components increase in magnitude. Moreover, the difference between the two cases increases as the gyrofrequency becomes larger compared with the plasma frequency. Finally, the electrical resistivity is calculated from the friction force, where it is found that strong magnetization in conjunction with oppositely charged interactions significantly decreases the parallel resistivity and increases the perpendicular resistivity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Alpha-relaxation by scattering and medium-range atomic correlation in simple liquids

The relaxation dynamics of liquid and glass can be studied by inelastic x-ray or neutron scattering through the intermediate scattering function F(Q, t), where Q is the momentum transfer of scattering. Because of the time-consuming nature of these measurements, F(Q, t) is usually measured only at the first peak of the structure function S(Q), and its principal decay time is referred to as the α-relaxation time τ α . τ α is generally considered to describe the relaxation time of the bulk, which is related to viscosity and is controlled by the atomic cage around an atom. Here, through simulations on metallic liquids, we show that the α-relaxation time determined by scattering experiments does not purely reflect viscosity but is influenced by changes in spatial cooperativity. We also demonstrate that atomic caging is not exerted by the nearest neighbors but involves more cooperative atomic dynamics of the atomic medium-range order.

Glass transitions↗
DOE OSTI2023

Structure, Dynamics, and Hydrogen Transport in Amorphous Polymers: An Analysis of the Interplay between Free Volume Element Distribution and Local Segmental Dynamics from Molecular Dynamics Simulations

Polymers are attractive membrane materials owing to their mechanical robustness and relatively inexpensive fabrication. An important indicator of membrane performance are free volume elements (FVE): microporous void spaces created by the inefficient packing of bulky groups along the polymer chain. FVEs tend to degrade over time, as polymer chains reorganize irreversibly. While it is widely accepted that polymer flexibility has an impact on membrane transport properties, the molecular nature of this impact is still not well understood. By the establishment of a correlation between local chain dynamics and the distribution of free volume elements (FVEs), penetrant transport can be regulated more efficiently in amorphous polymer membranes. In this work, we implement all-atom molecular dynamics (MD) simulations to explore the relationship between chain dynamics and free volume in three polymers with different levels of backbone flexibility: polymethylpentene (PMP), polystyrene (PS), and HAB-6FDA thermally rearranged polymer (TRP). We construct these polymers at different temperatures and examine how temperature impacts the FVE distribution and segmental mobility. Our analysis shows that chain segments near FVEs have higher mobility compared with the atoms in the bulk; the extent of this difference increases with chain flexibility. Increasing the chain flexibility by increasing the temperature results in a broader FVE distribution. Rigid polymers such as TRP show the most robust FVE distribution and are not significantly affected by the temperature change. To capture penetrant diffusion through the polymer matrix, hydrogen is inserted and the diffusion is measured at different temperatures; hydrogen mobility is influenced by the FVE structure and overall mobility of polymer chains. Lastly, at low temperatures, hydrogen mobility is influenced by void distribution, while at high temperatures, polymer dynamics dictate hydrogen transport.

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

Non-reactive facet specific adsorption as a route to remediation of chlorinated organic contaminants

The present work quantifies metal-contaminant interactions between palladium substrates and three salient chlorinated organic contaminants, namely trichloroethylene 1,3,5-trichlorobenzene (TCB), and 3,3′,4,4′-tetrachlorobiphenyl (PCB77). Given that Pd is one of the conventional catalytically active materials known for contaminant removal, maximizing catalytic efficiency through optimal adsorption dynamics reduces the cost of remediation of contaminants that are persistent water pollutants chronically affecting public health. Adsorption efficiency analyses from all-atom molecular dynamics (MD) simulations advance the understanding of reaction mechanisms available from density functional theory (DFT) calculations to an extractable feature scale that can fit the parametric design of supported metal catalytic systems and feed into high throughput catalyst selection. Data on residence time, site-specific adsorption, binding energies, packing geometries, orientation profiles, and the effect of adsorbate size show the anomalous behaviour of organic contaminant adsorption on the undercoordinated {110} surface as compared to the {111} and {100} surfaces. The intermolecular interaction within contaminants from molecular dynamics simulation exhibits refreshing results than ordinary single molecule density functional theory calculation. Since complete adsorption and dechlorination is an essential step for chlorinated organic contaminant remediation pathways, the presented profiles provide essential information for designing efficient remediation systems through facet-controlled palladium nanoparticles.

Guo, Hao↗
DOE OSTI2025

Atomically Revealing Bulk Point Defect Dynamics in Hydrogen‐Driven γ‐Fe 2 O 3 → Fe 3 O 4 → FeO Transformation

Understanding how point defects in the bulk govern redox transformations is essential for advancing hydrogen-based metal production and designing high-performance oxide materials. This study reveals the atomic-scale mechanisms driving hydrogen-induced reduction of γ-Fe 2 O 3 to Fe 3 O 4 , focusing on how bulk vacancy dynamics dictate structural evolution and reaction kinetics. A key finding is the pronounced contrast in defect behavior between the two oxides: in γ-Fe 2 O 3 , intrinsic Fe vacancies promote oxygen vacancy clustering, destabilizing the local lattice and driving nanopore formation. In contrast, Fe 3 O 4 exhibits a higher oxygen vacancy formation energy and lacks intrinsic Fe vacancies, suppressing vacancy aggregation and maintaining a dense, pore-free structure. This divergence governs distinct reduction pathways—γ-Fe 2 O 3 undergoes an interface-reaction-limited transformation confined to the γ-Fe 2 O 3 /Fe 3 O 4 boundary, while Fe 3 O 4 supports a uniform increase in oxygen vacancy concentration, enabling bulk-phase reduction to lower-oxide FeO. Integrated in situ electron microscopy and density functional theory modeling uncover a vacancy-mediated mechanism, where synergistic cation-anion vacancy dynamics steer microstructure evolution and phase progression. These insights highlight the critical role of vacancy dynamics in controlling oxide reactivity and offer a pathway toward vacancy engineering to enhance reduction kinetics in hydrogen metallurgy and to tailor porosity, reactivity, and structural resilience in oxide-based catalysts and energy materials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Mimicking Natural Photosynthesis: Designing Ultrafast Photosensitized Electron Transfer into Multiheme Cytochrome Protein Nanowires

Efficient nanomaterials for artificial photosynthesis require fast and robust unidirectional electron transfer (ET) from photosensitizers through charge-separation and accumulation units to redox-active catalytic sites. We explored the ultrafast time-scale limits of photo-induced charge transfer between a Ru(II)tris(bipyridine) derivative photosensitizer and PpcA, a 3-heme c-type cytochrome serving as a nanoscale biological wire. Four covalent attachment sites (K28C, K29C, K52C, and G53C) were engineered in PpcA enabling site-specific covalent labeling with expected donor-acceptor (DA) distances of 4–8 Å. X-ray scattering results demonstrated that mutations and chemical labeling did not disrupt the structure of the proteins. Time-resolved spectroscopy revealed three orders of magnitude difference in charge transfer rates for the systems with otherwise similar DA distances and the same number of covalent bonds separating donors and acceptors. All-atom molecular dynamics simulations provided additional insight into the structure-function requirements for ultrafast charge transfer and the requirement of van der Waals contact between aromatic atoms of photosensitizers and hemes in order to observe sub-nanosecond ET. This work demonstrates opportunities to utilize multi-heme c-cytochromes as frameworks for designing ultrafast light-driven ET into charge-accumulating biohybrid model systems, and ultimately for mimicking the photosynthetic paradigm of efficiently coupling ultrafast, light-driven electron transfer chemistry to multi-step catalysis within small, experimentally versatile photosynthetic biohybrid assemblies.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Dynamic Activation of Single-Atom Catalysts by Reaction Intermediates: Conversion of Formic Acid on Rh/Fe 3 O 4 (001)

The stability and activity of supported single-atom catalysts (SACs) represent critical yet opposing factors limiting our ability to explore and exploit their unique properties. Here, this study demonstrates the operation of a switchable catalyst that is activated in the presence of surface intermediates and reverts back to a stable but inactive form when the reaction is completed. We employ atomically defined Rh-Fe 3 O 4 (001) catalysts to demonstrate how structurally stable Rh, bound in surface octahedral Fe sites, gets destabilized to form highly active Rh adatoms and small clusters. Conversion of formic acid, leading initially to surface formate and hydroxyl species, is employed as a model reaction to probe the dynamics of such processes. We find that surface hydroxyl recombination to water through the Mars van Krevelen mechanism reduces Rh coordination, triggering its conversion to active Rh adatoms. Since such lattice oxygen exchange is observed in many acid-base and redox chemistries, the process can be broadly applicable to controlling the activation of the range of SACs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Reconstruction of effective potential from statistical analysis of dynamic trajectories

The broad incorporation of microscopic methods is yielding a wealth of information on the atomic and mesoscale dynamics of individual atoms, molecules, and particles on surfaces and in open volumes. Analysis of such data necessitates statistical frameworks to convert observed dynamic behaviors to effective properties of materials. Here, we develop a method for the stochastic reconstruction of effective local potentials solely from observed structural data collected from molecular dynamics simulations (i.e., data analogous to those obtained via atomically resolved microscopies). Using the silicon vacancy defect in graphene as a model, we apply the statistical framework presented herein to reconstruct the free energy landscape from the calculated atomic displacements. Evidence of consistency between the reconstructed local potential and the trajectory data from which it was produced is presented, along with a quantitative assessment of the uncertainty in the inferred parameters.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Complete spectroscopy in the attosecond regime

Harnessing light waveforms at attosecond time scales provides information of the structure and dynamics of matter on it's natural time scales. For this reason attosecond metrology has been at the forefront of the optical sciences for more than a decade, and it represents the latest time-domain frontier of the quantum world. Attosecond light pulses are commonly generated using higher-order harmonic generation (HHG) , a process capable of generating XUV coherent pulses. In addition to generate attosecond pulses, HHG can be used to study the structure and dynamics of atoms and molecules by analyzing the spectral content of the XUV pulses. This approach is known as HHG spectroscopy and it provides a coherent, time-dependent approach to study structure and dynamics in the quantum world. In this proposal we will generate harmonics from two optical foci produced by a system of a two-dimensional spatial light modulator (SLM) and a lens. In the far eld the train of attosecond pulses will interfere creating harmonic-dependent fringes. The position of such fringes is a direct measurement of the relative phase between the two foci and they also carry information about the quantum state of the target atom or molecule. Therefore, by measuring the amplitude and relative phase of the emitted harmonics we will have access to both, the amplitude and phase of the dipole moments of the studied target. Because the two beams are completely indistinguishable from each other up to a few millimeters from the focus, both driving pulses share the exact beam path. So far we have measured a jitter of 700 zeptoseconds with a 12.5 attosecond resolution in the delay control of the two foci. These two time scales represent some of the best time controls ever achieved to date.

74 ATOMIC AND MOLECULAR PHYSICS↗