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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules

A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods—UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Advanced Interactive 3D Visualization Tool for Customizable Analyses of Tomography Datasets in Material Science

Current methods for visualizing and analyzing 3D tomography datasets in materials science often lack the interactivity and depth required for detailed structural insights. This limitation restricts a researchers' ability to accurately interpret complex data, which is critical for advancing material innovations and understanding structural properties. To address this issue, we have developed a novel, web-based interactive 3D visualization and analysis tool from the Trame framework that offers customizable features to enhance data interpretability. The tool allows users to adjust parameters such as visible range, slice planes, data rotation, and layering, providing a more detailed and dynamic view of complex structures. Its user-friendly web interface increases the accessibility and ease of use for both novice and experienced researchers, to visualize large volumetric datasets. The tool supports a diverse range of data formats, making it versatile for various research applications. Unique capabilities include real-time data manipulation, automated feature detection, context-sensitive feedback, and real-time volume calculations and distributions per sliced region or layer, alongside the ability to quickly generate high-quality screenshots and videos for presentations and reports. These advancements offer a comprehensive solution for enhanced 3D data exploration, significantly improving the analysis process and communication of results in materials science.

36 - MATERIALS SCIENCE↗
DOE OSTI2024

Adaptive Narrowband Damping for Improving Harmonic Stability of Modular Multilevel Converter

Harmonic instability events between modular multilevel converter (MMC) and ac systems have been widely reported in recent years. To damp harmonic resonance, this paper proposes an adaptive narrowband damping control that automatically programs, adds, and adjusts the damping around the oscillation frequency when an oscillation is detected. First, the paper presents a low-pass filter design for MMC control loops that pushes all negative damping of the MMC impedance down to the medium-frequency range (< ~ 1000 Hz). Then, an adaptive damping control that uses online oscillation detection is proposed, which can automatically configure the narrowband damper to provide positive damping to the MMC around the detected oscillation frequency. In contrast to existing narrowband damping methods, the proposed adaptive narrowband damper dynamically adjusts the damping gain and the width of the damping range based on continuous monitoring of system resonance conditions (e.g., adjust damping gain to zero when the system resonance disappears). Electromagnetic transient simulation results validate the efficacy of the proposed method in two typical MMC-based power systems.

active damping↗
DOE OSTI2021

Orbitally selective resonant photodoping to enhance superconductivity

Signatures of superconductivity at elevated temperatures above T c in high-temperature superconductors have been observed near 1/8 hole doping for photoexcitation with infrared or optical light polarized either in the CuO 2 plane or along the c axis. While the use of in-plane polarization has been effective for incident energies aligned to specific phonons, c-axis laser excitation in a broad range between 5 μm and 400 nm was found to affect the superconducting dynamics in striped La 1.88 5Ba 0.115 CuO 4 , with a maximum enhancement in the 1/ω dependence to the conductivity observed at 800 nm. This broad energy range, specifically 800 nm, is not resonant with any phonon modes, yet induced electronic excitations appear to be connected to superconductivity at energy scales well above the typical gap energies in the cuprates. A critical question is, What can be responsible for such an effect at 800 nm? Using time-dependent exact diagonalization, we demonstrate that the holes in the CuO 2 plane can be photoexcited into the charge reservoir layers at resonant wavelengths within a multiband Hubbard model. This orbitally selective photoinduced charge transfer effectively changes the in-plane doping level, which can lead to an enhancement of T c near the 1/8 anomaly.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Concentration-Dependent Solvation Structure and Dynamics of Aqueous Sulfuric Acid Using Multinuclear NMR and DFT

Sulfuric acid is a ubiquitous compound for industrial processes and aqueous sulfate solutions also play a critical role in electrolytes for many prominent battery chemistries. While the thermodynamic literature for it is quite well-developed, comprehensive studies of the solvation structure, and particularly molecular-scale dynamical and transport properties, are less available. This study applies a multinuclear NMR approach to the elucidation of the solvation structure and dynamics over a wide temperature (-10 – 50?C) and concentration (0 – 18 M) range, combining 17O shift, linewidth, and T1 relaxation measurements, 33S shift and linewidth measurements, and 1H PFG-NMR measurements of the proton self-diffusivity. In conjunction, these results indicate a crossover between two regimes of solvation structure and dynamics, occurring above the concentration associated with the deep eutectic point (~ 4.5 M), with the high-concentration regime dominated by strong water-sulfate correlation. This description was borne out in detail by the activation energy trends with increasing concentration derived from the relaxation of both the H2O/H3O+ and H2SO4/HSO4-/SO42- 17O resonances and the 1H self-diffusivity. However, the 17O chemical shift difference between the H2O/H3O+ and H2SO4/HSO4-/SO42- resonances across the entire temperature range is nevertheless strikingly linear. A computational approach coupling MD simulations and DFT NMR shift calculations to reproduce this trend is presented, which will be the subject of further development. This combination of multinuclear, dynamical NMR and computational methods, and the results furnished by this study, will provide a platform for future studies on battery electrolytes where aqueous sulfate chemistry plays a central role in the solution structure.

Bazak, Jonathan D.↗
DOE OSTI2023

Manipulating Growth and Propagation of Correlations in Dipolar Multilayers: From Pair Production to Bosonic Kitaev Models

Here, we study the nonequilibrium dynamics of dipoles confined in multiple stacked two-dimensional layers realizing a long-range interacting quantum spin 1/2 XXX model. We demonstrate that strong in-plane interactions can protect a manifold of collective layer dynamics. This then allows us to map the many-body spin dynamics to bosonic models. In a bilayer configuration we show how to engineer the paradigmatic two-mode squeezing Hamiltonian known from quantum optics, resulting in exponential production of entangled pairs and generation of metrologically useful entanglement from initially prepared product states. In multilayer configurations we engineer a bosonic variant of the Kitaev model displaying chiral propagation along the layer direction. Our study illustrates how the control over interactions, lattice geometry, and state preparation in interacting dipolar systems uniquely afforded by AMO platforms such as Rydberg and magnetic atoms, polar molecules, or trapped ions allows for the control over the temporal and spatial propagation of correlations for applications in quantum sensing and quantum simulation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Short- and medium-range orders in Al90Tb10 glass and their relation to the structures of competing crystalline phases

Molecular dynamics simulations using an interatomic potential developed by artificial neural network deep machine learning are performed to study the local structural order in Al90Tb10 metallic glass. We show that more than 80% of the Tb-centered clusters in Al90Tb10 glass have short-range order (SRO) with their 17 first coordination shell atoms stacked in a ‘3661’ or ‘15551’ sequence. Medium-range order (MRO) in Bergman-type packing extended out to the second and third coordination shells is also clearly observed. Analysis of the network formed by the ‘3661’ and ‘15551’ clusters show that ~82% of such SRO units share their faces or vertexes, while only ~6% of neighboring SRO pairs are interpenetrating. Such a network topology is consistent with the Bergman-type MRO around the Tb-centers. Moreover, crystal structure searches using genetic algorithm and the neural network interatomic potential reveal several low-energy metastable crystalline structures in the composition range close to Al 90 Tb 10 . Some of these crystalline structures have the ‘3661’ SRO while others have the ‘15551’ SRO. While the crystalline structures with the ‘3661’ SRO also exhibit the MRO very similar to that observed in the glass, the ones with the ‘15551’ SRO have very different atomic packing in the second and third shells around the Tb centers from that of the Bergman-type MRO observed in the glassy phase.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Observation of Collective Molecular Dynamics in a Chalcogenide Glass: Results from X-ray Photon Correlation Spectroscopy

The structural relaxation processes in a Ge 3 As 52 S 45 molecular chalcogenide glass sample were directly studied by X-ray photon correlation spectroscopy (XPCS). XPCS was conducted at the first sharp diffraction peak at q = 1.16 Å -1 at temperatures ranging from 123 K to above the glass transition at 328 K, and the results showed two different dynamical regimes. At a low temperature, the observed glass dynamics are slow and dominated by X-ray-photon-induced effects, which are temperature independent. At a higher temperature, we observed a dramatic decrease in the fluctuation timescales, indicating that the dynamics were mainly due to the intermolecular correlation of the As 4 S 3 molecule in the glass. The timescales in this high-temperature range agree well with those determined from measurements of the Newtonian viscosity. Here our XPCS studies suggest an extended length scale of the relaxation process in glassy Ge 3 As 52 S 45 from the single molecule to the intermolecular range across the glass transition, providing a unique direct probe of the dynamics beyond the length scales of the individual molecule.

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

Shadow Molecular Dynamics and Atomic Cluster Expansions for Flexible Charge Models

Here, a shadow molecular dynamics scheme for flexible charge models is presented where the shadow Born–Oppenheimer potential is derived from a coarse-grained approximation of range-separated density functional theory. The interatomic potential, including the atomic electronegativities and the charge-independent short-range part of the potential and force terms, is modeled by the linear atomic cluster expansion (ACE), which provides a computationally efficient alternative to many machine learning methods. The shadow molecular dynamics scheme is based on extended Lagrangian (XL) Born–Oppenheimer molecular dynamics (BOMD). XL-BOMD provides stable dynamics while avoiding the costly computational overhead associated with solving an all-to-all system of equations, which normally is required to determine the relaxed electronic ground state prior to each force evaluation. To demonstrate the proposed shadow molecular dynamics scheme for flexible charge models using atomic cluster expansion, we emulate the dynamics generated from self-consistent charge density functional tight-binding (SCC-DFTB) theory using a second-order charge equilibration (QEq) model. The charge-independent potentials and electronegativities of the QEq model are trained for a supercell of uranium oxide (UO 2 ) and a molecular system of liquid water. The combined ACE+XL-QEq molecular dynamics simulations are stable over a wide range of temperatures both for the oxide and for the molecular systems and provide a precise sampling of the Born–Oppenheimer potential energy surfaces. Accurate ground Coulomb energies are produced by the ACE-based electronegativity model during an NVE simulation of UO 2 , predicted to be within 1 meV of those from SCC-DFTB on average during comparable simulations.

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

Hidden quantum criticality and entanglement in quench dynamics

Entanglement exhibits universal behavior near the ground-state critical point where correlations are long ranged and the thermodynamic entropy is vanishing. On the other hand, a quantum quench imparts extensive energy and results in a build up of entropy, hence no critical behavior is expected at long times. In this work, we present a new paradigm in the quench dynamics of integrable spin chains which exhibit a ground-state order-disorder phase transition at a critical line. Specifically, we consider a quench along the critical line which displays a volume-law behavior of the entropy and exponentially decaying correlations; however, we show that quantum criticality is hidden in higher-order correlations and becomes manifest via measures such as the mutual information and logarithmic negativity. Furthermore, we showcase the scale invariance of the Rényi mutual information between disjoint regions as further evidence for genuine critical behavior. We attribute the emergent quantum criticality to the soft mode not getting excited in spite of the quench. Moreover, the results presented here are universal to models whose low-energy or long-wavelength dynamics are well described by a free-fermionic field theory. Our results are amenable to an experimental realization on different quantum simulator platforms, particularly the Rydberg simulators. Published by the American Physical Society 2024

Paul, Sanku↗
DOE OSTI2023

Topology induced crossover between Langevin, subdiffusion, and Brownian diffusion regimes in supercooled water

Despite extensive studies of supercooled water, it remains challenging to understand its peculiar dynamic anomalous properties. In this work, we integrated full atomistic simulations of supercooled water over the temperature range of room temperature to 200 K using a quantum-mechanics-based polarizable force field with the dressed dynamics method that couples fast collision events and slow reorganization dynamics of hydrogen-bond networks. Our analysis unveils the salient multiscale features in the transient relaxation dynamics of supercooled water. A classical Langevin behavior dominates at fast timescales, while long-time relaxations unveil two different activation barriers in two temperature regions: below and above 230 K. The modulation of the entropy spectrum by temperature is elucidated in terms of a three-state model underlined by the complexity of the water dynamics associated with a topological transition of a strong hydrogen-bond network. This state-dependent network topology is quantitatively characterized by power-law exponents of inverse network connectivity from 200 to 298 K. Finally, this work provides valuable guidance for further studies on the transient relaxation dynamics of supercooled water.

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

Farmer characteristics and decision-making: A model for bioenergy crop adoption

We report the commercial development of biofuels and bioproducts depends on whether renewable biomass feedstock is available while not directly competing with the production of food. Farmers are one of the most important stakeholders in the biofuel supply chain and confront a range of uncertainties while entering the bioenergy market. Their decision-making process is extremely complex and rarely purely rational. Modeling farmer behavior requires considering a wide range of individual-level factors, socio-temporal dynamics, institutional settings, and their interactions. These characteristics make agent-based modeling a suitable framework for evaluating such systems. We developed a model to simulate farmer bioenergy crop adoption behavior across a 50-county study region in Nebraska, Kansas, and Colorado. The analysis considers adoption decisions for two bioenergy feedstocks, crop residues and energy crops. We examine the influence of individual and farm characteristics, market structure, social networks, and media influence on farmer adoption decisions. Our results indicate that different factors can have varied impacts on the speed of adoption for the crop residues and energy crops. Identifying levers that have the most impact on grower adoption can inform the design of interventions both from policy and private sector standpoints with important implications for the future the bioenergy industry.

09 BIOMASS FUELS↗
DOE OSTI2022

In-situ thermal analysis of intermetallic and thermite projectiles in high velocity impact experiments

Particle fragmentation influences thermochemical energy conversion processes in different ways and is of significance in energy generation technologies. Different reactive material formulations trigger varied thermal response in extreme environments such as high velocity impact. Here we investigated optical thermal response of powder gun launched intermetallic (Al:Zr) and thermite (Al:MoO 3 ) projectiles using pyrometry and thermography. Projectiles were launched at 1250 m/s into an air-filled chamber and impacted a steel witness plate to create a dust explosion. The pyrometer was configured to measure temperatures directly at the point of impact, while the thermographic system measured temperatures throughout the explosion chamber. Results show that impact temperatures ranged between 3500 and 4000 K, but that the dynamics of energy conversion were different for the intermetallic and thermite projectiles. The intermetallic exhibited secondary reactions due to fragmented debris impacting the walls of the chamber. The thermite exhibited greater gas generation, propelling the debris field, and producing a more stochastic response with faster spreading and dissipation of thermal energy. Unique features such as microexplosions within fragmented particles were also analyzed. While both reactive materials produce similar temperatures, their mechanisms of energy conversion and release are different, indicating the potential of these materials for different ballistic applications.

42 ENGINEERING↗
DOE OSTI2024

Effects of boundary hydraulics, dissolved oxygen, and dissolved organic carbon on growth and death dynamics of aerobic microbes in riverbed dune-induced hyporheic zones

Surface and groundwater interact in the hyporheic zone beneath and adjacent to rivers in the presence of a diverse microbial community. Heterotrophic bacteria mediate a range of environmentally important reactions, yet few studies have quantified bacterial growth and death dynamics in the hyporheic zone, and none have systematically analyzed their response to variations in hydraulic or chemical conditions. Here we used MODFLOW and SEAM3D to simulate hydraulics; dissolved oxygen (DO) and dissolved organic carbon (DOC) transport; and aerobic microbial metabolism, growth, and death in hyporheic zones induced by riverbed dunes. We ran simulations both with and without growth/death processes, and varied hydraulic parameters and DO/DOC boundary concentrations. Microbial biomass reached steady state (t = 3 days) in every simulation, at which time there was greater biomass and DOC biodegradation rates in the hyporheic flowcell (300% and 85% higher for the base case, respectively) when accounting for microbial growth dynamics. This occurred as microbial biomass tailored its spatial distribution to the availability of DO and DOC, demonstrating the importance of simulating growth/death processes. Biomass generally increased with hyporheic flow cell area as upwelling groundwater decreased. When varying surface water DO and DOC source concentrations relative to the base case, the greatest effect on biomass occurred when increasing DOC and decreasing DO. We determined minimum DO and DOC steady-state concentrations required for microbial growth, but the minimums were not absolute or related by stoichiometry. Increasing DOC created a smaller area of microbes with higher concentrations relative to the base case. Increasing DO slightly increased the area occupied by microbes while keeping the total biomass nearly constant. Overall, microbial growth and death dynamics depend on DO and DOC availability in the hyporheic zone, which is dependent on DOC/DO boundary concentrations and hyporheic flow paths, and in turn the hydraulic interaction between surface water and groundwater.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

The exit-wave power-cepstrum transform for scanning nanobeam electron diffraction: robust strain mapping at subnanometer resolution and subpicometer precision

Scanning nanobeam electron diffraction (NBED) with fast pixelated detectors is a valuable technique for rapid, spatially resolved mapping of lattice structure over a wide range of length scales. However, intensity variations caused by dynamical diffraction and sample mistilts can hinder the measurement of diffracted disk centers as necessary for quantification. Robust data processing techniques are needed to provide accurate and precise measurements for complex samples and non-ideal conditions. Here we present an approach to address these challenges using a transform, called the exit wave power cepstrum (EWPC), inspired by cepstral analysis in audio signal processing. The EWPC transforms NBED patterns into real-space patterns with sharp peaks corresponding to inter-atomic spacings. We describe a simple analytical model for interpretation of these patterns that cleanly decouples lattice information from the intensity variations in NBED patterns caused by tilt and thickness. With tracking the inter-atomic spacing peaks in EWPC patterns, strain mapping is demonstrated for two practical applications: mapping of ferroelectric domains in epitaxially strained PbTiO 3 films and mapping of strain profiles in arbitrarily oriented core-shell Pt-Co nanoparticle fuel-cell catalysts. The EWPC transform enables lattice structure measurement at sub-pm precision and sub-nm resolution that is robust to small sample mistilts and random orientations.

42 ENGINEERING↗
DOE OSTI2024

Structural Properties of [N1888][TFSI] Ionic Liquid: A Small Angle Neutron Scattering and Polarizable Molecular Dynamics Study

In this study, we investigate the quaternary ammonium-based ionic liquid (QAIL), methyltrioctylammonium bis(trifluoromethylsulfonyl)imide, [N 1888 ][TFSI], utilizing small angle neutron scattering (SANS) measurements and polarizable molecular dynamics (MD) simulations to characterize the shortand long-range liquid structure. Scattering structure factors show signatures of three length scales in reciprocal space indicative of alternating polarity (k ~ 0.44 Å –1 ), charge (k ~ 0.75 Å –1 ), and neighboring or adjacent (k ~ 1.46 Å –1 ) domains. Excellent agreement between simulation and experimental scattering structure factors validates various simulation analyses that provide detailed atomistic characterization of the different length scale correlations. The first solvation shell structure is illustrated by obtaining radial, angular, dihedral, and combined distribution functions, where two dominant spatial motifs, N + ···N – and N + ···O – , compete for optimal packing around the polar head of the [N 1888 ] + cation. Intermediate and long-range structures are governed by the balance between local electroneutrality and octyl chain networking, respectively. By computing the charge-correlation structure factor, S ZZ , and the spatial extent of the octyl chain network using graph theory, the bulk-phase structure of [N 1888 ][TFSI] is characterized in terms of electrostatic screening and apolar domain formation length scales.

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

Scaling Analysis of Two–Phase Flow in Fractal Permeability Fields

Fluid mixing in permeable media is essential in many practical applications. The mixing process is a consequence of velocity fluctuations owing to geological heterogeneities and mobility contrast of fluids. Heterogeneities in natural rocks are often spatially correlated, and their properties, such as permeability, may be described using fractal distributions. This work models the fractal characteristics of such permeability fields in which the covariance function is expressed as a power-law function. A generalized scaling relation is derived relating various fractal permeability fields using the magnitude of their fluctuations. Here, this relation reveals the self-similar behavior of two-phase flow in such permeable media. To that end, a recently developed, high-resolution numerical simulator is employed to validate the analytically derived scaling relations. Two flow problems are considered in which flow is governed by 1) a linear, and 2) a nonlinear transport equation. Due to the probabilistic representation of the fractal permeability fields, a sensitivity study is conducted for each flow scenario to determine the number of realizations required for statistical convergence. Scaling analysis is performed using ensemble averages of simulated saturation profiles and their mixing lengths. Results support the validity of the developed scaling relation across the range of investigated flow conditions at intermediate times. The dynamics of linear flow in the asymptotic regime is affected by the correlation structure of heterogeneity. In nonlinear flow, scaling behavior appears to be dominated by the degree of nonlinearity.

58 GEOSCIENCES↗
DOE OSTI2022

Representing Socio‐Economic Uncertainty in Human System Models

Abstract Socio‐economic development pathways and their implications for the environment are highly uncertain, and energy transitions will involve complex interactions among sectors. Here, traditional Monte Carlo analysis is paired with scenario discovery techniques to provide a richer portrait of these complexities. Modeled uncertain input variables include costs of advanced energy technologies, energy efficiency trends, fossil fuel resource availability, elasticities of substitution for labor, capital, and energy across economic sectors, population growth, and labor and capital productivity. The sampled values are simulated through a multi‐sector, multi‐region, recursively dynamic model of the world economy to explore a range of possible future outcomes. We find that many patterns of energy and technology development are possible for various long‐term environmental pathways and that sectoral output for most sectors is little affected through 2050 by the long‐term temperature target, but with tight constraints on emissions, emission intensities must fall much more rapidly. Scenario discovery techniques are applied to the large uncertainty ensembles to explore if there are prevailing storylines behind outcomes of interest. An illustrative investigation focused on different levels of economic growth shows many combinations of pathways and no single storyline emerging for a given economic outcome. This method can be extended to other outcomes of interest, exploring the nature of scenarios with both tail and median outcomes. Sampling from a Monte Carlo generated ensemble provides a rich set of scenarios to investigate, and potentially aids in avoiding heuristic biases in less structured scenario approaches.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗