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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

SDynPy: A Structural Dynamics Python Library

SAND2023-11957O SDynPy software can be used in digital signal processing, modal analysis, and geometry algorithms that are available in open literature, specifically the Synthesize Modes and Correlate and polynomial-based multiple reference modal fitters. This software can be used to perform structural dynamic testing and analysis. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Rohe, Daniel↗
DOE OSTI2022

Cooperative allostery and structural dynamics of streptavidin at cryogenic- and ambient-temperature

Multimeric protein assemblies are abundant in nature. Streptavidin is an attractive protein that provides a paradigm system to investigate the intra- and intermolecular interactions of multimeric protein complexes. Also, it offers a versatile tool for biotechnological applications. Here, we present two apo-streptavidin structures, the first one is an ambient temperature Serial Femtosecond X-ray crystal (Apo-SFX) structure at 1.7 Å resolution and the second one is a cryogenic crystal structure (Apo-Cryo) at 1.1 Å resolution. These structures are mostly in agreement with previous structural data. Combined with computational analysis, these structures provide invaluable information about structural dynamics of apo streptavidin. Collectively, these data further reveal a novel cooperative allostery of streptavidin which binds to substrate via water molecules that provide a polar interaction network and mimics the substrate biotin which displays one of the strongest affinities found in nature.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling

Soft condensed matter is challenging to study due to the vast time and length scales that are necessary to accurately represent complex systems and capture their underlying physics. Multiscale simulations are necessary to study processes that have disparate time and/or length scales, which abound throughout biology and other complex systems. Herein we present ezAlign, an open-source software for converting coarse-grained molecular dynamics structures to atomistic representation, allowing multiscale modeling of biomolecular systems. The ezAlign v1.1 software package is publicly available for download at github.com/LLNL/ezAlign. Its underlying methodology is based on a simple alignment of an atomistic template molecule, followed by position-restraint energy minimization, which forces the atomistic molecule to adopt a conformation consistent with the coarse-grained molecule. The molecules are then combined, solvated, minimized, and equilibrated with position restraints. Validation of the process was conducted on a pure POPC membrane and compared with other popular methods to construct atomistic membranes. Additional examples, including surfactant self-assembly, membrane proteins, and more complex bacterial and human plasma membrane models, are also presented. By providing these examples, parameter files, code, and an easy-to-follow recipe to add new molecules, this work will aid future multiscale modeling efforts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Nanosecond Structural Dynamics during Electrical Melting of Charge Density Waves in 1⁢T-TaS 2

Electrical control of charge density waves has been of immense interest, as the strong underlying electron-lattice interactions potentially open new, efficient pathways for manipulating their ordering and, consequently, their electronic properties. However, the transition mechanisms are often unclear as electric field, current, carrier injection, heat, and strain can all contribute and play varying roles across length scales and timescales. Here, we provide insight on how electrical stimulation melts the room temperature charge density wave order in 1T-TaS 2 by visualizing the atomic and mesoscopic structural dynamics from quasistatic to nanosecond pulsed melting. Using a newly developed ultrafast electron microscope setup with electrical stimulation, we reveal the order and strain dynamics during voltage pulses as short as 20 ns. The order parameter dynamics across a range of pulse amplitudes and durations support a thermally driven mechanism even for fields as high as 19 kV cm -1 . In addition, time-resolved imaging reveals a heterogeneous, mesoscopic strain response across the flake, including MHz-scale acoustic resonances that emerge during sufficiently short pulsed excitation which may modulate the order. In conclusion, these results suggest that metallic charge density wave phases like studied here may be more robust to electronic switching pathways than insulating ones, motivating further investigations at higher fields and currents in this and other related systems.

36 MATERIALS SCIENCE↗
DOE OSTI2023

LANL Test Engineering’s Structural Dynamics Research and Development Efforts [Slides]

LANL's priority roles are serving as a nuclear weapons design agency and a nuclear weapons production agency; addressing nuclear threats; and performing national security science, technology, and engineering. LANL’s Test Engineering organization serves the national mission of maintaining a strategic nuclear deterrent by providing high-quality, empirical evidence through the execution and assessment of weapons system and component testing. Shock and vibration environmental testing provides one key piece of evidence for evaluation and qualification of these systems and components in the service environments incurred during a lifetime in the stockpile. LANL’s Test Engineering group continuously pursues research and development in structural dynamics to improve shock and vibration testing capabilities, processes, and analysis techniques to increase the fidelity of service environment recreations in laboratory testing settings. This talk will highlight several ongoing projects to represent these R&D efforts.

42 ENGINEERING↗
DOE OSTI2025

Acetylcholinesterase: Structure, dynamics, and interactions with organophosphorus compounds

Acetylcholinesterase (AChE) is an enzyme that hydrolyzes the neurotransmitter acetylcholine (ACh), removing it from the synaptic cleft after the transmission of an electrical signal, making it an essential component of chemical neurotransmission. AChE is a serine hydrolase, containing a catalytic triad of Ser/His/Glu. AChE is a prime target for pharmaceuticals treating a variety of neurological disorders. It is also the target of synthetic organophosphorus (OP) compounds that have been used as pesticides and chemical warfare agents. OP compounds contain a potent leaving group, such as fluorine, and act by forming a covalent adduct with the catalytic serine of the AChE active site. A wealth of structural information is available for AChE, including over 300 structures, including a subset of structures in complex with drugs as well as OP compounds. This review will highlight the interactions between OP compounds and AChE from a structural and computational perspective, with a discussion of access to the active site, as well as side reactions that lead to dealkylation of the OP-catalytic serine adduct, a process known as aging. We conclude that while the majority of the conformational changes needed to accommodate the OP compounds are localized to the acyl loop in the crystal structures, molecular dynamics simulations highlight the potential for a far more dynamic enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Simulating Extreme Precipitation in the United States in the Energy Exascale Earth System Model: Investigating the Importance of Representing Convective Intensity versus Dynamic Structure (Final Report)

Weather events that produce extreme precipitation are associated with severe flooding and winds that result in thousands of deaths and billions of dollars in damages annually in the United States (U.S.). This project aims to improve understanding of the small- and large-scale processes that govern these events and improve our ability to project changes in these extreme events under the influences of natural variability and human activities. We focus on two promising directions in the development of the U.S. Department of Energy’s Energy Exascale Earth System Model (E3SM) to investigate the tradeoffs between resolving the convective-scale processes that control the intensity versus the intermediate-scale processes that control the dynamic structure of the most prominent extreme precipitation events that impact the U.S. throughout the year (i.e., mesoscale convective systems, tropical cyclones, and extratropical cyclone).

58 GEOSCIENCES↗
DOE OSTI2026

The effect of hydroxyl spacing in diols on the solvation structure, dynamics, and transport properties of choline chloride-based deep eutectic solvents

Deep eutectic solvents (DESs) are a class of liquids that offer great potential in alleviating some of the challenges present in today's long-term energy storage methods because they have physical properties that are favorable for storable electrolyte solutions. In this work, a series of glycols (ethylene glycol, 1,3-propanediol, 1,4-butanediol, and 1,5-pentanediol) were studied as potential hydrogen bond donors (HBD) with a common choline chloride (ChCl) as the hydrogen bond acceptor (HBA). The solvation dynamics of the prepared systems were studied by measuring the solvent reorganization response using femtosecond transient absorption spectroscopy (fs-TA). Conductivity, viscosity, density, ET(30) polarity, and dynamics of the prepared DESs were analyzed, with a particular interest in determining the effect of HBD chain length on these parameters. Here, classical molecular dynamics simulations were employed to investigate how the local liquid structure, solvent dynamics, and bulk solvent properties vary with changes in glycol chain length.

Conductivity↗
DOE OSTI2022

Characterizing Dynamic Structure in Battery Electrodes by Time-Resolved Cryo-TEM

In recent years, cryogenic transmission electron microscopy (cryo-TEM) has enabled high-resolution characterization of sensitive battery materials by minimizing electron beam-induced artifacts and damage. Success of this technique relies on the preparation of thin, rapidly frozen samples, generally by disassembling batteries under inert atmosphere, transferring materials of interest to a TEM grid, and finally plunge freezing into a cryogen. In material degradation studies, this extensive time between electrochemical cycling and cryo-TEM characterization leaves room for structural relaxation, diffusion, and other dynamic processes that make it difficult to precisely correlate the imaged structure with the native structure that evolves during battery cycling or aging. Here, we present a method to integrate battery cycling with fast preparation of electrode samples for cryo-TEM. This enables higher fidelity between the structures characterized and the electrochemical state of interest, which we use to study deformation in silicon nanoparticle anodes for lithium-ion batteries.

CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS↗
DOE OSTI2022

Kuramoto synchronization of quantum tunneling polarons for describing the dynamic structure in cuprate superconductors

A major open topic in cuprates is the interplay between the lattice and electronic dynamics and the importance of their coupling to the mechanism of high-temperature superconductivity (HTSC). As evidenced by extended x-ray absorption fine structure (EXAFS) experiments, anharmonic structural effects are correlated with the charge dynamics and the transition to a superconducting phase in different HTSC compounds. Here, in this paper, we describe how structural anharmonic effects can be coupled to electronic and lattice dynamics in cuprate systems by performing the exact diagonalization of a prototype anharmonic many-body Hamiltonian on a relevant 6-atom cluster and show that the EXAFS results can be understood as a Kuramoto synchronization transition between coupled internal quantum tunneling of polarons associated with the two-site distribution of the copper–apical oxygen (Cu-O ap ) pair in the dynamic structure. The transition is driven by the anharmonicity of the lattice vibrations and promotes the pumping of charge, initially stored at the apical oxygen reservoirs, into the copper-oxide plane. Simultaneously, a finite projection of the internal quantum tunneling polaron extends to the copper–planar oxygen (Cu-O pl ) pair. All these findings allow an interpretation based on an effective quantum-mechanical triple-well potential associated with the oxygen sites of the 6-atom cluster, which accurately represents the phase synchronization of apical oxygens and lattice-assisted charge transfer to the CuO 2 plane.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Structure, dynamics, and redox reactivity of an all-purpose flavodoxin

The flavodoxin of Rhodopseudomonas palustris CGA009 (Rp9Fld) supplies highly reducing equivalents to crucial en- zymes such as hydrogenase, especially when the organism is iron-restricted. By acquiring those electrons from photodriven electron flow via the bifurcating electron transfer flavoprotein, Rp9Fld provides solar power to vital metabolic processes. To understand Rp9Fld’s ability to work with diverse partners, we solved its crystal structure. We observed the canonical fla- vodoxin (Fld) fold and features common to other long-chain Flds but not all the surface loops thought to recognize part- ner proteins. Moreover, some of the loops display alternative structures and dynamics. To advance studies of protein– protein associations and conformational consequences, we assigned the 19F NMR signals of all five tyrosines (Tyrs). Our electrochemical measurements show that incorporation of 3- 19 F-Tyr in place of Tyr has only a modest effect on Rp9Fld’s redox properties even though Tyrs flank the flavin on both sides. Meanwhile, the 19 F probes demonstrate the expected paramagnetic effect, with signals from nearby Tyrs becoming broadened beyond detection when the flavin semiquinone is formed. However, the temperature dependencies of chemical shifts and linewidths reveal dynamics affecting loops close to the flavin and regions that bind to partners in a variety of systems. These coincide with patterns of amino acid type conservation but not retention of specific residues, arguing against detailed specificity with respect to partners. We pro- pose that the loops surrounding the flavin adopt altered con- formations upon binding to partners and may even participate actively in electron transfer.

19F NMR↗
DOE OSTI2023

Effective sensor location for detection of change in structural dynamic response

This paper investigates the sensitivity of structural system response to the sensor location by investigating consequences of small changes in the location to the structural system response. The paper discusses how maximum observability (based on mode shape and the participation of that mode in the input provided) drives optimal location. The structural responses were investigated in terms of the g-rms response for various low-frequency inputs (pure sinusoids and real-life inputs such as an earthquake and trains). Results were then analyzed in the context of Modal Contributions Factors (MCF) and changes to the Force-to-response Transfer Functions (TRFs). A modal-matching process is first presented using a Matlab TM -based Finite Element Method (FEM) model of a cantilever beam and instrumentation to determine the location of a small mass based on three different criteria. Subsequently, the structural response is investigated using experiments and the FEM model. The accelerometer of small mass (at 1/3 height) was moved up or down to obtain changes in the structural response (TRF) to various realistic low-frequency inputs. Modal Contribution Factor (MCF) and derivative (slope) of the associated mode-shapes were correlated to the observed changes in TRFs. Results show how optimal sensor locations for detecting change in structural response can be based on the MCFs and the associated mode-shapes.

Woodall, J.↗
DOE OSTI2024

Influence of pump laser fluence on ultrafast myoglobin structural dynamics

High-intensity femtosecond pulses from an X-ray free-electron laser enable pump–probe experiments for the investigation of electronic and nuclear changes during light-induced reactions. On timescales ranging from femtoseconds to milliseconds and for a variety of biological systems, time-resolved serial femtosecond crystallography (TR-SFX) has provided detailed structural data for light-induced isomerization, breakage or formation of chemical bonds and electron transfer. However, all ultrafast TR-SFX studies to date have employed such high pump laser energies that nominally several photons were absorbed per chromophore. As multiphoton absorption may force the protein response into non-physiological pathways, it is of great concern whether this experimental approach allows valid conclusions to be drawn vis-à-vis biologically relevant single-photon-induced reactions. Here we describe ultrafast pump–probe SFX experiments on the photodissociation of carboxymyoglobin, showing that different pump laser fluences yield markedly different results. In particular, the dynamics of structural changes and observed indicators of the mechanistically important coherent oscillations of the Fe–CO bond distance (predicted by recent quantum wavepacket dynamics) are seen to depend strongly on pump laser energy, in line with quantum chemical analysis. Our results confirm both the feasibility and necessity of performing ultrafast TR-SFX pump–probe experiments in the linear photoexcitation regime. We consider this to be a starting point for reassessing both the design and the interpretation of ultrafast TR-SFX pump–probe experiments such that mechanistically relevant insight emerges.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structure, dynamics, and electrochemistry of choline chloride/ethylene glycol eutectic solvents at an electrode surface explored by molecular dynamics simulations

Choline chloride and ethylene glycol mixtures with 1:2, 1:4, and 1:6 molar ratios on the surfaces of graphite and gold electrodes were studied using classical molecular dynamics simulations. Both neutral and charged electrodes were considered. The liquid composition, solvation structure, molecular orientation, and dynamics at the electrode surface are significantly different from those of the bulk liquid. These properties strongly depend on the electrode material and charge density, whereas they are less sensitive to the overall solvent composition. The effect of the electrode on the composition, structure, and orientation of the liquid fades beyond ∼10 Å from the surface of the electrode. This distance corresponds to about two layers of the structured solvent, despite the fact that the layered structure extends to at least five layers or about 25 Å. However, the electrode influences solvent dynamics over a longer distance. The electrochemical properties of the eutectic solvent at both electrode surfaces were also studied. The simulations captured the experimental differential capacitance shapes for both electrode systems, although the magnitudes and exact shapes differ. The simulations further revealed that the solvent in the first solvation layer can both overscreen and underscreen the electrode charges depending on the electrode material and electrode potential.

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

Dynamic structural determinants in bacterial microcompartment shells

Bacterial microcompartments (BMCs) are polyhedral structures that segregate enzymatic cargo from the cytosol via encapsulation within a protein shell. Unlike other biological polyhedra, such as viral capsids and encapsulins, BMC shells can exhibit a highly advantageous structural and functional plasticity, conforming to a variety of anabolic (CO 2 fixation in carboxysomes) and catabolic (nutrient assimilation in metabolosomes) roles. Consequently, understanding the subunit properties and associated protein–protein interaction processes that guide shell assembly and function is a necessary step to fully harness BMCs as modular, biotechnological nanomachines. Here, we describe the recent insights into the dynamics of structural features of the key BMC domain (Pfam00936)-containing proteins, which serve as a structural template for BMC-H and BMC-T shell building blocks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Sensitive detection of structural dynamics using a statistical framework for comparative crystallography

Chemical and conformational changes are crucial to protein function and its pharmacological control. X-ray crystallography can reveal these changes in atomic detail, but standard analysis methods, which refine separate datasets, often overlook differences that are subtle or arise in only a subset of molecules. Direct comparison of crystallographic datasets is, in principle, more powerful, but systematic errors (“scales”) often mask changes in the crystallographic observables (“structure factors”). Machine learning algorithms that jointly estimate scales and structure factors can address this limitation. Here, we augment this approach with multivariate, structured priors derived from crystallographic theory, implemented in the variational deep learning framework Careless. Doing so strongly improves the detection of protein dynamics, element-specific anomalous signals, and the binding of drug candidates, offering a robust approach to comparative crystallography and, potentially, to detection of protein dynamics by other structure determination methods.

Hekstra, Doeke R. [Harvard Univ., Cambridge, MA (U↗
DOE OSTI2025

Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF‐Trap

The constant fragment (Fc) of the immunoglobulin G1 (IgG1) subtype is increasingly recognized as a crucial scaffold in the development of advanced therapeutics due to its enhanced specificity, efficacy, and extended half‐life. A prime example is VEGF‐Trap (Aflibercept), a recombinant fusion protein that merges the Fc region of the IgG1 subtype with the binding domains of vascular endothelial growth factor receptors (VEGFR)‐1 and VEGFR‐2. The Fc region's role in N‐glycosylation is particularly important, as it significantly influences protein stability. Herein, the first near‐physiological temperature structures of the N‐glycan‐bound Fc fragment of IgG1 subtype from a biosimilar VEGF‐Trap are presented, determined using the SPring‐8 Angstrom Compact free electron LAser (SACLA) and the Turkish Light Source (Turkish DeLight). Comparative analysis with cryogenic structures, including existing data, reveals alternate conformations within the glycan‐binding pocket. Furthermore, molecular dynamics simulations indicate the presence of a high degree of structural plasticity, explaining how the protein adapts its structure through conformational changes. The observed structural fluctuations/conformational changes demonstrate the effect of N‐glycans on protein stability. These findings offer new insights into the molecular basis of Fc‐mediated functions and provide valuable information for the design of next‐generation therapeutics.

60 APPLIED LIFE SCIENCES↗