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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Structural characterization of an intrinsically disordered protein complex using integrated small-angle neutron scattering and computing

Characterizing structural ensembles of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins is essential for studying structure–function relationships. Due to the different neutron scattering lengths of hydrogen and deuterium, selective labeling and contrast matching in small-angle neutron scattering (SANS) becomes an effective tool to study dynamic structures of disordered systems. However, experimental timescales typically capture measurements averaged over multiple conformations, leaving complex SANS data for disentanglement. We hereby demonstrate an integrated method to elucidate the structural ensemble of a complex formed by two IDRs. We use data from both full contrast and contrast matching with residue-specific deuterium labeling SANS experiments, microsecond all-atom molecular dynamics (MD) simulations with four molecular mechanics force fields, and an autoencoder-based deep learning (DL) algorithm. From our combined approach, we show that selective deuteration provides additional information that helps characterize structural ensembles. We find that among the four force fields, a99SB-disp and CHARMM36m show the strongest agreement with SANS and NMR experiments. In addition, our DL algorithm not only complements conventional structural analysis methods but also successfully differentiates NMR and MD structures which are indistinguishable on the free energy surface. Finally, we present an ensemble that describes experimental SANS and NMR data better than MD ensembles generated by one single force field and reveal three clusters of distinct conformations. Our results demonstrate a new integrated approach for characterizing structural ensembles of IDPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Grain Growth and Coarsening Dynamics in a Compositionally Asymmetric Block Copolymer Revealed by X-ray Photon Correlation Spectroscopy

The dynamics of nanostructured soft materials crucially impact their associated macroscopic material properties, yet they are often difficult to measure due to spatiotemporal limitations of conventional instrumentation. Herein, we use X-ray photon correlation spectroscopy (XPCS) to directly observe particle-scale dynamics during grain growth and coarsening in a BCC- forming diblock polymer melt, with specific attention to the distribution of structural relaxation times associated with the interplanar (110) distance. Following sample quenching from the disordered state, these dynamical phenomena surprisingly exhibit little dependence on time and thermal quench depth. We posit that these relaxations stem from collective particle motions during grain rotation. We also observe unusual internally-referenced heterodyne correlations, which enable measurements of speed distributions within the sample. In this work, these speeds are significantly slower and appear at much longer annealing times than those previously reported during grain nucleation and growth in microphase separated block polymer melts. Drawing on analogies between polycrystalline hard and soft materials, we ascribe these speed distributions to misorientation-dependent grain boundary migration during ordered domain coarsening and anomalously fast, cooperative string-like particle motion along the grain boundaries. Thus, these coherent X-ray measurements provide new opportunities to interrogate grain boundary structure and dynamics in polycrystalline soft materials.

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

Bridging length scales in organic mixed ionic–electronic conductors through internal strain and mesoscale dynamics

Understanding the structural and dynamic properties of disordered systems at the mesoscale is crucial. This is particularly important in organic mixed ionic-electronic conductors (OMIECs), which undergo significant and complex structural changes when operated in an electrolyte. Here, in this study, we investigate the mesoscale strain, reversibility and dynamics of a model OMIEC material under external electrochemical potential using operando X-ray photon correlation spectroscopy. Our results reveal that strain and structural hysteresis depend on the sample's cycling history, establishing a comprehensive kinetic sequence bridging the macroscopic and microscopic behaviours of OMIECs. Furthermore, we uncover the equilibrium and non-equilibrium dynamics of charge carriers and material-doping states, highlighting the unexpected coupling between charge carrier dynamics and mesoscale order. These findings advance our understanding of the structure-dynamics-function relationships in OMIECs, opening pathways for designing and engineering materials with improved performance and functionality in non-equilibrium states during device operation. Understanding mesoscale structure and dynamics in organic mixed ionic-electronic conductors is crucial. Mesoscale strain kinetics and structural hysteresis have been studied, and they uncover the coupling between charge carrier dynamics and mesoscale order in organic mixed ionic-electronic conductors.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures

Proteins have been found to inhabit a diverse set of three-dimensional structures. The dynamics that govern protein interconversion between structures happen over a wide range of time scales-picoseconds to seconds. Our understanding of protein functions and dynamics is largely reliant upon our ability to elucidate physically populated structures. From an experimental structural characterization perspective, we are often limited to measuring the ensemble-averaged structure both in the steady-state and time-resolved regimes. Generating kinetic models and understanding protein structure–function relationships require atomistic knowledge of the populated states in the ensemble. Here, we present ensemble refinement methodologies that integrate time-resolved experimental signals with molecular dynamics models. We first discuss integration of experimental structural restraints to molecular models in disordered protein systems that adhere to the principle of maximum entropy for creating a complete set of ensemble structures. We then propose strategies to find kinetic pathways between the refined structures, using time-resolved inputs to guide molecular dynamics trajectories and the use of inference to generate tailored stimuli to prepare a desired ensemble of protein states.

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

Solvent-mediated carboxylic acid diammonium spacer for synthesizing FA-based 2D Dion–Jacobson perovskites toward efficient solar cells

Two-dimensional (2D) perovskites are promising for photovoltaic applications due to their outstanding optical properties and better environmental stability compared to three-dimensional (3D) perovskites. Unlike 2D Ruddlesden–Popper (RP) perovskites, which use monovalent ammonium spacers, Dion–Jacobson (DJ) perovskites employ divalent organic spacers that enhance structural stability by mitigating weak van der Waals interactions. However, the random phase distribution and disorder crystal orientation in 2D DJ perovskites create deep quantum wells, hindering charge transfer and reducing short-circuit current density (J SC ) and overall photovoltaic performance. This study introduces an organic diammonium, 1,4-butanediamine diacetate (BDAAc 2 ), to replace the traditional halide spacer 1,4-butanediamine iodide (BDADI 2 ). This substitution regulates perovskites crystallization dynamics, reducing compositional disorder and random phase distribution, thus improving the quality of the perovskite films. The robust coordination interactions between BDAAc 2 and the perovskite inorganic framework lead to an ordered [PbX 6 ] 4− arrangement, suppressing the formation of complex intermediate phases and significantly enhancing δ phase crystallinity in the intermediate film. This results in a high yield of high-quality α phase. Consequently, the resulting 2D DJ perovskite solar cells based on BDAFA 3 Pb 4 (I 0.9 Br 0.1 ) 13 achieve a higher power conversion efficiency of 16.41% and an elevated J SC of 20.46 mA cm −2 .

14 SOLAR ENERGY↗
DOE OSTI2025

Structure refinement and anisotropic atomic displacement parameters of 1M Illite: Rietveld and pair distribution function analysis using synchrotron X-ray radiation

Illite, a widespread clay mineral, plays a pivotal role in geological processes, notably as an indicator in diagenetic and hydrothermal alteration environments, and possesses significant industrial relevance in applications including ceramics, construction and catalysis. However, challenges including its nanoscale crystallinity, structural disorder and frequent interstratification with other clay minerals have hindered detailed structural characterization using conventional X-ray diffraction (XRD) techniques. This study employs integrated synchrotron XRD and pair distribution function (PDF) analysis to elucidate the crystal structure of the 1M illite polytype, yielding the first determination of its anisotropic atomic displacement parameters (U aniso ). TheseU aniso parameters provide critical insights into atomic dynamics and static disorder within the structure, enabling a more refined understanding of structure–property relationships. This integrated approach, combining synchrotron XRD, Rietveld refinement and PDF analysis, yields a comprehensive structural characterization, capturing both average crystallographic and local atomic arrangements. Considering illite's widespread geological occurrence and industrial importance, this high-precision structural dataset, especially the determinedU aniso values, provides a crucial benchmark for future modeling and simulation efforts targeting accurate prediction of its physicochemical behavior.

Chemistry↗
DOE OSTI2025

Anomalous lattice relaxation dynamics in optimally doped La 2−𝑥⁢ Sr 𝑥 ⁢CuO 4

The atomic lattice plays a critical role in the emergence of high-𝑇 𝑐 superconductivity in cuprates. While the dynamics associated with electron-lattice coupling typically unfold on picosecond-to-femtosecond timescales, we present an x-ray photon correlation spectroscopy investigation on an optimally doped La-based cuprate that reveals a strong response of kilosecond-scale lattice relaxation dynamics to the superconducting state. Notably, an anomaly emerges around 𝑇 𝑐 : upon cooling into the superconducting state, the average atomic relaxation lifetime decreases, i.e., dynamics accelerate. This indicates a significant change in the local disorder-induced strain field dynamics at the superconducting transition, highlighting a remarkable coupling between superconductivity and the lattice on quasistatic timescales.

Petsch, A. N. [SLAC National Accelerator Laborator↗
DOE OSTI2020

Radiative and Nonradiative Recombinations in Organic Radical Emitters: The Effect of Guest–Host Interactions

Radical-carrying organic molecules have received significant attention to bypass the issue related to harvesting triplet excitons in current light-emitting materials. While the computational efforts conducted so far have treated these radical emitters as isolated entities, in actual devices, they are embedded in a host matrix and subject to emitter–host interactions. In this study, by combining molecular dynamics simulations and density functional theory calculations, the impact of the host matrix on the optoelectronic performance of radical emitters is evaluated, taking as a representative example the (4-ncarbazolyl-2,6-dichlorophenyl)bis(2,4,6-trichlorophenyl)-methyl (TTM-3NCz) radical emitter dispersed in a 4,4-bis(carbazol-9-yl)biphenyl (CBP) host. A morphological analysis shows that steric effects around the radical centers, carried by the TTM electron-poor moieties of the emitters, disfavor π–π interactions with the host molecules, which leads to random intermolecular orientations around the TTM moieties. The 3NCz electron-rich moieties of the emitters, however, have much lesser spatial hindrance for intermolecular π–π stacking, which modulates the structural and electronic properties of the emitters in the host matrix. The influence of dynamic and static disorders on the radiative and nonradiative recombination processes is also investigated and it is found that the rates of nonradiative recombination are small, which opens the way to 100% internal quantum efficiency for the doublet-based emission process.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Dissecting the structural heterogeneity of proteins by native mass spectrometry

Abstract A single gene yields many forms of proteins via combinations of posttranscriptional/posttranslational modifications. Proteins also fold into higher‐order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the “bottom‐up” approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher‐order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the “top‐down” approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in‐depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero‐complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near‐native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding the molecular heterogeneity of proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The curious case of the structural phase transition in SnSe insights from neutron total scattering

Abstract At elevated temperatures SnSe is reported to undergo a structural transition from the low symmetry orthorhombic GeS-type to a higher symmetry orthorhombic TlI-type. Although increasing symmetry should likewise increase lattice thermal conductivity, many experiments on single crystals and polycrystalline materials indicate that this is not the case. Here we present temperature dependent analysis of time-of-flight (TOF) neutron total scattering data in combination with theoretical modeling to probe the local to long-range evolution of the structure. We report that while SnSe is well characterized on average within the high symmetry space group above the transition, over length scales of a few unit cells SnSe remains better characterized in the low symmetry GeS-type space group. Our finding from robust modeling provides further insight into the curious case of a dynamic order-disorder phase transition in SnSe, a model consistent with the soft-phonon picture of the high thermoelectric power above the phase transition.

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

Antifungal symbiotic peptide NCR044 exhibits unique structure and multifaceted mechanisms of action that confer plant protection

In the indeterminate nodules of a model legume Medicago truncatula, ~700 nodule-specific cysteine-rich (NCR) peptides with conserved cysteine signature are expressed. NCR peptides are highly diverse in sequence, and some of these cationic peptides exhibit antimicrobial activity in vitro and in vivo. However, there is a lack of knowledge regarding their structural architecture, antifungal activity, and modes of action against plant fungal pathogens. Here, the three-dimensional NMR structure of the 36-amino acid NCR044 peptide was solved. This unique structure was largely disordered and highly dynamic with one four-residue α-helix and one three-residue antiparallel β-sheet stabilized by two disulfide bonds. NCR044 peptide also exhibited potent fungicidal activity against multiple plant fungal pathogens, including Botrytis cinerea and three Fusarium spp. It inhibited germination in quiescent spores of B. cinerea. In germlings, it breached the fungal plasma membrane and induced reactive oxygen species. It bound to multiple bioactive phosphoinositides in vitro. Time-lapse confocal and superresolution microscopy revealed strong fungal cell wall binding, penetration of the cell membrane at discrete foci, followed by gradual loss of turgor, subsequent accumulation in the cytoplasm, and elevated levels in nucleoli of germlings. Spray-applied NCR044 significantly reduced gray mold disease symptoms caused by the fungal pathogen B. cinerea in tomato and tobacco plants, and postharvest products. Our work illustrates the antifungal activity of a structurally unique NCR peptide against plant fungal pathogens and paves the way for future development of this class of peptides as a spray-on fungistat/fungicide.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Developments in SRW Code and Sirepo Framework Supporting Simulation of Time-Dependent Coherent X-ray Scattering Experiments

Physical optics simulations for beamlines and experiments are essential for the effective use of synchrotron light source facilities such as NSLS-II at BNL. The SRW software package supports such source-to-detector simulations for coherent X-ray scattering and imaging experiments through its Python interface and Sirepo browser-based graphical user interface. This allows one to define custom sample models, assess the feasibility of an experiment, and estimate most appropriate beamline settings before using valuable beamtime. We discuss the recent use of general-purpose GPU resources and coherent mode decomposition algorithms in SRW to accelerate physical optics simulations with partially coherent X-rays. To illustrate these new capabilities, we describe simulations of typical time series of partially coherent scattering images used in X-ray Photon Correlation Spectroscopy (XPCS) experiments; aiming to characterize the nanoscale dynamics of a disordered sample, representing a solution of nanoparticles undergoing Brownian diffusion.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Design of an amplitude-splitting hard x-ray delay line with subnanoradian stability

We propose the design and analysis of a hard x-ray split-delay optical arrangement that combines diffractive and crystal optics. Transmission gratings are employed to achieve the much-desired amplitude splitting and recombination of the beam. Asymmetric channel-cut crystals are utilized to tune the relative delay time. The use of a dispersion-compensation arrangement of the crystals allows the system to achieve subnanoradian pointing stability during a delay scan. It further minimizes wavefront distortion and preserves the pulse front and pulse duration. We analyze the performance of a prototype design that can cover a delay time range of 15 ps with a sub-20 fs time resolution at 10 keV. We anticipate that this system can fully satisfy the very demanding stability requirements for performing split-pulse x-ray photon correlation spectroscopy measurements for the investigation of fast atomic scale dynamics in complex disordered matter.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

A Holistic Approach for Elucidating Local Structure, Dynamics, and Speciation in Molten Salts with High Structural Disorder

To examine ion solvation, exchange, and speciation for minority components in molten salts (MS) typically found as corrosion products, we propose a multimodal approach combining extended X-ray absorption fine structure (EXAFS) spectroscopy, optical spectroscopy, ab initio molecular dynamics (AIMD) simulations, and rate theory of ion exchange. Going beyond conventional EXAFS analysis, our method can accurately quantify populations of different coordination states of ions with highly disordered coordination environments via linear combination fitting of the EXAFS spectra of these coordination states computed from AIMD to the experimental EXAFS spectrum. In a case study of dilute Ni(II) dissolved in the ZnCl 2 +KCl melts, our method reveals heterogeneous distributions of coordination states of Ni(II) that are sensitive to variations in temperature and melt composition. These results are fully explained by the difference in the chloride exchange dynamics at varied temperatures and melt compositions. Finally, this insight will enable a better understanding and control of ion solubility and transport in MS.

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

Reducing opioid use disorder and overdose deaths in the United States: A dynamic modeling analysis

Opioid overdose deaths remain a major public health crisis. We used a system dynamics simulation model of the U.S. opioid-using population age 12 and older to explore the impacts of 11 strategies on the prevalence of opioid use disorder (OUD) and fatal opioid overdoses from 2022 to 2032. These strategies spanned opioid misuse and OUD prevention, buprenorphine capacity, recovery support, and overdose harm reduction. By 2032, three strategies saved the most lives: (i) reducing the risk of opioid overdose involving fentanyl use, which may be achieved through fentanyl-focused harm reduction services; (ii) increasing naloxone distribution to people who use opioids; and (iii) recovery support for people in remission, which reduced deaths by reducing OUD. Increasing buprenorphine providers’ capacity to treat more people decreased fatal overdose, but only in the short term. Our analysis provides insight into the kinds of multifaceted approaches needed to save lives.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Disorder Enhanced Thermalization in Interacting Many-Particle System

We introduce an extension of the non-equilibrium dynamical mean field theory to incorporate the effects of static random disorder in the dynamics of a many-particle system by integrating out different disorder configurations resulting in an effective time-dependent density-density interaction. We use this method to study the non-equilibrium transient dynamics of a system described by the Fermi Anderson-Hubbard model following an interaction and disorder quench. The method recovers the solution of the disorder-free case for which the system exhibits qualitatively distinct dynamical behaviors in the weak-coupling (prethermalization) and strong-coupling regimes (collapse-and-revival oscillations). However, we find that weak random disorder promotes thermalization. In the weak coupling regime, the jump in the quasiparticle weight in the prethermal regime is suppressed by random disorder while in the strong-coupling regime, random disorder reduces the amplitude of the quasiparticle weight oscillations. These results highlight the importance of disorder in the dynamics of realistic many-particle systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Real-Space Local Dynamics of Molten Inorganic Salts Using Van Hove Correlation Function

Molten inorganic salts are attracting resurgent attention because of their unique physicochemical properties, making them promising media for next-generation concentrating solar power systems and molten salt reactors. The dynamics of these highly disordered ionic media is largely studied by theoretical simulations, while the robust experimental techniques capable of observing local dynamics are not well-developed. To provide fundamental insights into the atomic-scale transport properties of molten salts, we report the real-space dynamics of molten magnesium chloride at high temperatures employing the Van Hove correlation function obtained by inelastic neutron scattering. Overall, our results directly depict the distance-dependent dynamics of a molten salt on the picosecond time scale. This study demonstrates the capability of the developed approach to describe the locally correlated- and self-dynamics in molten salts, significantly improving our understanding of the interplay between microscopic structural parameters and their dynamics that ultimately control physical properties of condensed matter in extreme environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗