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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structural Insights into the Dynamics of Water in SOD1 Catalysis and Drug Interactions

Superoxide dismutase 1 (SOD1) is a crucial enzyme that protects cells from oxidative damage by converting superoxide radicals into H 2 O 2 and O 2 . This detoxification process, essential for cellular homeostasis, relies on a precisely orchestrated catalytic mechanism involving the copper cation, while the zinc cation contributes to the structural integrity of the enzyme. This study presents the 2.3 Å crystal structure of human SOD1 (PDB ID: 9IYK), revealing an assembly of six homodimers and twelve distinct active sites. The water molecules form a complex hydrogen-bonding network that drives proton transfer and sustains active site dynamics. Our structure also uncovers subtle conformational changes that highlight the intrinsic flexibility of SOD1, which is essential for its function. Additionally, we observe how these dynamic structural features may be linked to pathological mutations associated with amyotrophic lateral sclerosis (ALS). By advancing our understanding of hSOD1’s mechanistic intricacies and the influence of water coordination, this study offers valuable insights for developing therapeutic strategies targeting ALS. Our structure’s unique conformations and active site interactions illuminate new facets of hSOD1 function, underscoring the critical role of structural dynamics in enzyme catalysis. Moreover, we conducted a molecular docking analysis using SOD1 for potential radical scavengers and Abelson non-receptor tyrosine kinase (c-Abl, Abl1) inhibitors targeting misfolded SOD1 aggregation along with oxidative stress and apoptosis, respectively. The results showed that CHEMBL1075867, a free radical scavenger derivative, showed the most promising docking results and interactions at the binding site of hSOD1, highlighting its promising role for further studies against SOD1-mediated ALS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Polymer Conformations and Diffusion Through a Monolayer of Confining Nanoparticles

We present coarse-grained molecular dynamics simulations to probe chain-scale polymer conformations and diffusion between confining nanoparticles (NPs). By constructing a monolayer of hexagonally-packed NPs in a polymer melt with athermal interactions, we observe the magnitude and length-scale over which homogeneously confining NPs impact the polymer behavior, which provides fundamental insights into more complex polymer nanocomposites. We show that polymer conformations are more perturbed under strong confinement (i.e. when the interparticle distance, ID, is less than twice the polymer radius of gyration, 2R g ) as compared to around an isolated NP, and the effect depends on the ratio of R NP /R g rather than either independently. In fact, these conformations can be quantitatively replicated by executing a simple random walk in a similarly confining environment. We also show that polymer diffusion is slowed by the presence of NPs and the slowing persists far beyond the length-scale over which polymer conformations are perturbed. Although the slowing is strongest ~R g from the NPs, the diffusion coefficient is slower even beyond ~5R g from the NPs. Furthermore, by analyzing the directional van Hove distributions, we show polymer diffusion away from the NP monolayer is bulk-like while diffusion through the monolayer is slower with increasing NP confinement. Furthermore, these molecular dynamics simulations provide fundamental insights into the temporal and spatial effect of confining, athermal NPs on chain-scale polymer conformations and diffusion.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structural mechanism of Escherichia coli cyanase

Cyanase plays a vital role in the detoxification of cyanate and supplies a continuous nitrogen source for soil microbes by converting cyanate to ammonia and carbon dioxide in a bicarbonate-dependent reaction. The structures of cyanase complexed with dianion inhibitors, in conjunction with biochemical studies, suggest putative binding sites for substrates. However, the substrate-recognition and reaction mechanisms of cyanase remain unclear. Here, crystal structures of cyanase from Escherichia coli were determined in the native form and in complexes with cyanate, bicarbonate and intermediates at 1.5–1.9 Å resolution using synchrotron X-rays and an X-ray free-electron laser. Cyanate and bicarbonate interact with the highly conserved Arg96, Ser122 and Ala123 in the active site. Further, in the presence of a mixture of cyanate and bicarbonate, three different electron densities for intermediates were observed in the cyanase structures. Moreover, the observed electron density could explain the dynamics of the substrate or product. In addition to conformational changes in the substrate-binding pocket, dynamic movement of Leu151 was observed, which functions as a gate for the passage of substrates or products. These findings provide a structural mechanism for the substrate-binding and reaction process of cyanase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Towards Provable Security in Industrial Control Systems Via Dynamic Protocol Attestation

Industrial control systems (ICSs) increasingly rely on digital technologies vulnerable to cyber attacks. Cyber attackers can infiltrate ICSs and execute malicious actions. Individually, each action seems innocuous. But taken together, they cause the system to enter an unsafe state. These attacks have resulted in dramatic consequences such as physical damage, economic loss, and environmental catastrophes. This paper introduces a methodology that restricts actions using protocols. These protocols only allow safe actions to execute. Protocols are written in a domain specific language we have embedded in an interactive theorem prover (ITP). The ITP enables formal, machine-checked proofs to ensure protocols maintain safety properties. We use dynamic attestation to ensure ICSs conform to their protocol even if an adversary compromises a component. Since protocol conformance prevents unsafe actions, the previously mentioned cyber attacks become impossible. We demonstrate the effectiveness of our methodology using an example from the Fischertechnik Industry 4.0 platform. We measure dynamic attestation's impact on latency and throughput. Our approach is a starting point for studying how to combine formal methods and protocol design to thwart attacks intended to cripple ICSs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A bistable and reconfigurable molecular system with encodable bonds

Molecular systems with ability to controllably transform between different conformations play pivotal roles in regulating biochemical functions. Here, we report the design of a bistable DNA origami four-way junction (DOJ) molecular system that adopts two distinct stable conformations with controllable reconfigurability by using conformation-controlled base stacking. Exquisite control over DOJ’s conformation and transformation is realized by programming the stacking bonds (quasi–blunt-ends) within the junction to induce prescribed coaxial stacking of neighboring junction arms. A specific DOJ conformation may be achieved by encoding the stacking bonds with binary stacking sequences based on thermodynamic calculations. Dynamic transformations of DOJ between various conformations are achieved by using specific environmental and molecular stimulations to reprogram the stacking codes. This work provides a useful platform for constructing self-assembled DNA nanostructures and nanomachines and insights for future design of artificial molecular systems with increasing complexity and reconfigurability.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Engineering Structural Transitions in a Multilevel Molecular Switch via Intermolecular Coupling

Controlling molecular conformations with atomic precision is essential for advancing molecular functional electronics, as well as our understanding of molecular dynamics. While switching between bistable molecular conformers is common in nature, creating systems with multiple, addressable states remains synthetically challenging. Here, we demonstrate a bottom-up strategy in which intermolecular interactions give rise to multilevel functionality within a simple two-molecule assembly. Using low-temperature scanning tunneling microscopy, we show that a pyrrolidine dimer on Cu(100) exhibits six distinct adsorption conformations, exceeding the four expected from two independent bistable units. This unusual complexity arises from the interplay between intermolecular van der Waals attraction and steric repulsion, which reshapes the potential energy landscape and changes a single high-energy transition into a sequential two-step pathway. Each step is driven by low-energy inelastic electron excitations, achieving a switching efficiency an order of magnitude higher than that of the monomer. Here, by tuning the bias voltage and tip–molecule distance, we achieve deterministic control over multiple stable states, establishing a general design principle for on-demand engineering of collective molecular behavior and energy-efficient multilevel molecular devices.

Molecular interactions↗
NASA NTRS2000

Development of a Enhanced Thermal Barrier for RSRM Nozzle Joints

A carbon fiber rope is being considered as replacement for the RTV thermal barrier that is currently used to protect o-rings in RSRM nozzle joints, Performance requirements include its ability to cool propellant gases filter slag and particulates, and conform to various joint assembly conditions as well as dynamic flight motion. Testing has shown its superior heat resistance, even in oxidative and corrosive environments. Testing has also demonstrated excellent performance of this system in sub-scale motors. Cold flow testing, has demonstrated its ability to conform to motor dynamics. Manufacture and assembly testing have demonstrated the ease of gland machining as well as assembly in a full-scale nozzle.

Bauer, P. H.↗
DOE OSTI2025

Influence of Steric and Electronic Properties of P2 Groups on Covalent Inhibitor Binding to SARS-CoV-2 Main Protease

The main protease (MPro) of SARS-CoV-2 is a critical enzyme required for viral replication, making it a prime target for antiviral drug development. Covalent inhibitors, which form a stable interaction with the catalytic C145, have demonstrated strong inhibition of MPro, but the influence of steric and electronic properties of P2 substituents, designed to engage the S2 substrate-binding subsite within the MPro active site, on inhibitor binding affinity remains underexplored. Here, in this study, we design and characterize two hybrid covalent inhibitors, BBH-3 and BBH-4, and present their X-ray crystallographic structures in complex with MPro, providing molecular insights into how their distinct P2 groups, a dichlorobenzyl moiety in BBH-3 and an adamantyl substituent in BBH-4, affect binding conformation and active site adaptability. Comparative structural analyses with previously characterized inhibitors, including BBH-2 and Mcule-5948770040, reveal how the P2 bulkiness and electronic properties influence active site dynamics, particularly through interactions with the S2 and S5 subsites. The P2 group of BBH-3 induces conformational shifts in the S2 helix and the S5 loop, while BBH-4 displaces M49, stabilizing its binding through hydrophobic interactions. Isothermal titration calorimetry further elucidates the impact of P2 modifications on inhibitor affinity, revealing a delicate balance between enthalpic and entropic contributions. The data demonstrate that BBH-3 exhibits less favorable binding, affirming that dichlorobenzyl substitution at the P2 position has a more negative impact on the affinity for MPro than bulky saturated cyclic groups. This underscores the feature that MPro active site malleability may be accompanied by a conformational strain.

SARS-CoV-2↗
DOE OSTI2022

Towards the Accurate Thermodynamic Characterization of Enzyme Reaction Mechanisms

We employed QM/MM molecular dynamics (MD) simulations to characterize the rate-limiting step of the glycosylation reaction of pancreatic α-amylase with combined DFT/molecular dynamics methods (PBE/def2-SVP : AMBER). Upon careful choice of four starting active site conformations based on thorough reactivity criteria, Gibbs energy profiles were calculated with umbrella sampling simulations within a statistical convergence of 1 -2 kcal · mol -1 . Nevertheless, Gibbs activation barriers and reaction energies still varied from 11.0 to 16.8 kcal · mol -1 and -6.3 to +3.8 kcal · mol -1 depending on the starting conformations, showing that despite significant state-of-the-art QM/MM MD sampling (0.5 ns/profile) the result still depends on the starting structure. In conclusion, the results supported the one step dissociative mechanism of Asp197 glycosylation preceded by an acid-base reaction by the Glu233, which are qualitatively similar to those from multi-PES QM/MM studies, and thus support the use of the latter to determine enzyme reaction mechanisms.

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

Improving Ionic Conformality Across Polymer Electrolyte|Electrode Interfaces

Maintaining uniform ionic transport at electrode|electrolyte interfaces, i.e., ionic conformality, remains challenging in polymer electrolyte (PE)-based solid-state batteries. Morphological conformality does not necessarily imply ionic conformality. In PEs, which typically consist of a mechanically supporting component and distinct ionically conductive components, the rearrangement or depletion of mobile ion-conductive domains at interfaces can disrupt ionic transport pathways. Such localized ionic depletion contributes to interfacial instability and capacity degradation in high-voltage lithium-metal batteries. Herein, an electrolyte design approach aimed at minimizing interfacial heterogeneities is demonstrated through compositional adjustments, characterized by spatially resolved structural and chemical X-ray techniques and NMR diffusometry to elucidate ion transport dynamics. This approach improves ionic conformality at electrode interfaces, enhancing cycling stability in Li||LiNi 0.8 Co 0.1 Mn 0.1 O 2 (NMC811) coin and pouch cells cycled at high voltages. These results contribute to understanding interfacial behaviors in multiphase PEs and inform strategies for improving stability across solid-state battery interfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Nonextensive hydrodynamics of boost-invariant plasmas

We use quasiparticle anisotropic hydrodynamics to study the non-conformal and non-extensive dynamics of a system undergoing boost-invariant Bjorken expansion. To introduce nonextensivity, we use an underlying Tsallis distribution with a time-dependent nonextensivity parameter q. By taking moments of the quasiparticle Boltzmann equation in the relaxation-time approximation, we obtain dynamical equations which allow us to determine the time evolution of all microscopic parameters including q. We compare numerical solutions for bulk observables obtained using the nonextensive evolution with results obtained using quasiparticle anisotropic hydrodynamics with a Boltzmann distribution function (q → 1). We show that the evolution of the temperature, pressure ratio, and scaled energy density, are quite insensitive to which distribution function is assumed. However, we find significant differences in the early-time evolution of the bulk pressure which are observed for even small deviations from the Boltzmann distribution function. Finally, we discuss the existence of non-conformal hydrodynamic attractors for the longitudinal and transverse pressures, the bulk and shear viscous corrections, and the nonextensivity parameter q.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Molecular Dynamics Simulations of a Catalytic Multivalent Peptide–Nanoparticle Complex

Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide–nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure–function relationship, for technological and nanomedical applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

LoTToR: An Algorithm for Missing-Wedge Correction of the Low-Tilt Tomographic 3D Reconstruction of a Single-Molecule Structure

A single-molecule three-dimensional (3D) structure is essential for understanding the thermal vibrations and dynamics as well as the conformational changes during the chemical reaction of macromolecules. Individual-particle electron tomography (IPET) is an approach for obtaining a snap-shot 3D structure of an individual macromolecule particle by aligning the tilt series of electron tomographic (ET) images of a targeted particle through a focused iterative 3D reconstruction method. The method can reduce the influence on the 3D reconstruction from large-scale image distortion and deformation. Due to the mechanical tilt limitation, 3D reconstruction often contains missing-wedge artifacts, presented as elongation and an anisotropic resolution. Here, we report a post-processing method to correct the missing-wedge artifact. This low-tilt tomographic reconstruction (LoTToR) method contains a model-free iteration process under a set of constraints in real and reciprocal spaces. A proof of concept is conducted by using the LoTToR on a phantom, i.e., a simulated 3D reconstruction from a low-tilt series of images, including that within a tilt range of ±15°. The method is validated by using both negative-staining (NS) and cryo-electron tomography (cryo-ET) experimental data. A significantly reduced missing-wedge artifact verifies the capability of LoTToR, suggesting a new tool to support the future study of macromolecular dynamics, fluctuation and chemical activity from the viewpoint of single-molecule 3D structure determination.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data

In the past few decades, prediction of macromolecular structures beyond the native conformation has been aided by the development of molecular dynamics (MD) protocols aimed at exploration of the energetic landscape of proteins. Yet, the computed structures do not always agree with experimental observables, calling for further development of the MD strategies to bring the computations and experiments closer together. Here, we report a scalable, efficient MD simulation approach that incorporates an x-ray solution scattering signal as a driving force for the conformational search of stable structural configurations outside of the native basin. We further demonstrate the importance of inclusion of the hydration layer effect for a precise description of the processes involving large changes in the solvent exposed area, such as unfolding. Utilization of the graphics processing unit allows for an efficient all-atom calculation of scattering patterns on-the-fly, even for large biomolecules, resulting in a speed-up of the calculation of the associated driving force. The utility of the methodology is demonstrated on two model protein systems, the structural transition of lysine-, arginine-, ornithine-binding protein and the folding of deca-alanine. We discuss how the present approach will aid in the interpretation of dynamical scattering experiments on protein folding and association.

Hsu, Darren J.↗
DOE OSTI2025

Structural switching dynamically controls the doubly pseudoknotted Rous sarcoma virus–programmed ribosomal frameshifting element

A hallmark of retrovirus replication is the translation of two different polyproteins from one RNA through programmed –1 frameshifting. This is a mechanism in which the actively translating ribosome is induced to slip in the 5′ direction at a defined codon and then continues translating in the new reading frame. Programmed frameshifting controls the stoichiometry of viral proteins and is therefore under stringent evolutionary selection. Forty years ago, the first frameshifting stimulatory element was discovered in the Rous sarcoma virus. The ~120 nt RNA segment was predicted to contain a pseudoknot, but its 3D structure has remained elusive. Now, we have determined cryoEM and X-ray crystallographic structures of this classic retroviral element, finding that it adopts a butterfly-like double-pseudoknot fold. One “wing” contains a dynamic pyrimidine-rich helix, observed crystallographically in two conformations and in a third conformation via cryoEM. The other wing encompasses the predicted pseudoknot, which interacts with a second unexpected pseudoknot through a toggle residue, A2546. This key purine switches conformations between structural states and tunes the stability of interacting residues in the two wings. We find that its mutation can modulate frameshifting by as much as 50-fold, likely by altering the relative abundance of different structural states in the conformational ensemble of the RNA. Taken together, our structure–function analyses reveal how a dynamic double pseudoknot junction stimulates frameshifting by taking advantage of conformational heterogeneity, supporting a multistate model in which high Shannon entropy enhances frameshifting efficiency.

Science & Technology - Other Topics↗
DOE OSTI2024

Dissecting neurofilament tail sequence-phosphorylation-structure relationships with multicomponent reconstituted protein brushes

Neurofilaments (NFs) are multisubunit, bottlebrush-shaped intermediate filaments abundant in the axonal cytoskeleton. Each NF subunit contains a long intrinsically disordered tail domain, which protrudes from the NF core to form a “brush” surrounding each NF. Precisely how the tails’ variable charge patterns and repetitive phosphorylation sites mediate their conformation within the brush remains an open question in axonal biology. We address this problem by grafting recombinant NF tail protein constructs NF-Light, -Medium, and -Heavy (NFL, NFM, and NFH) to surfaces, yielding protein brushes of defined stoichiometry that can be phosphorylated in vitro. Atomic force microscopy measurements reveal that brush height depends on composition monotonically but not always linearly for binary NFL:NFM or NFL:NFH systems, and that NFM-based brushes are highly extended, while brushes incorporating the much larger NFH are surprisingly compact even after multisite phosphorylation. Complementary self-consistent field theory (SCFT) predicts multilayer brush morphologies for NFM and phosphorylated NFH brushes. Further experiments and SCFT analysis with designed mutants reveal that N-terminal negative charges in the NFH tail repel phosphorylated residues to generate the multilayer morphology, while the C-terminal charge-neutral region contributes to multilayer brush morphology but not total brush height. Charge-shuffled NFM variants show that charge segregation promotes brush collapse near physiological ionic strengths. Collectively, this study supports a role for NFM in establishing a dynamic range for NF brush conformation, lending insight into previous in vitro and in vivo findings. More broadly, this work establishes a platform for dissecting contributions of disordered protein sequence to conformation at interfaces.

Science & Technology - Other Topics↗
DOE OSTI2021

Computational Approach for Rapidly Predicting Temperature–Dependent Polymer Solubilities Using Molecular–Scale Models

One promising approach to recycle multicomponent plastic waste (e. g., multilayer plastic films) is selective dissolution. Selective dissolution is a solvent-mediated process in which differences in polymer solubility in a carefully chosen solvent system are exploited to recover a target polymer. Here, a computational approach was developed that rapidly predicts temperature-dependent polymer solubilities to guide the design of solvent systems for solvent-mediated polymer recycling. Polymer conformations were obtained from molecular dynamics simulations by modeling the polymer as a short oligomer and then used as input to the conductor-like screening model for real solvents (COSMO-RS) for solubility predictions. Using polyethylene (PE) and ethylene vinyl alcohol (EVOH) as representative polymers, the effect of simulation parameters was systematically studied, and predicted solubilities were found to be in good agreement with experimental measurements. Furthermore, the applicability of the approach was demonstrated by identifying selective solvents for PE and EVOH dissolution from a library of 524 solvents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗