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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations

Peptoids are a class of sequence-defined biomimetic polymers with peptide-like backbones and side chains located on backbone nitrogens rather than alpha carbons. These materials demonstrate a strong ability for precise control of single-chain structure, multiunit self-assembly, and macromolecular assembly through careful tuning of sequence due to the diversity of available side chains, although the driving forces behind these assemblies are often not understood. Prior experimental work has shown that linked 15mer peptoids can mimic the protein helical hairpin structure by leveraging the chirality-inducing nature of bulky side chains and hydrophobicity, but there are still gaps in our understanding of the relationship between sequence, stability, and particular secondary or tertiary structure. Here, we present a molecular dynamics (MD) study on the folding behavior of these polymers into hairpins, discussing the differences in structure from sequences with various characteristics in water and acetonitrile, and then compare the handedness preference of common helical motifs between solvents.

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

Probing pH-Dependent Dehydration Dynamics of Mg and Ca Cations in Aqueous Solutions with Multi-Level Quantum Mechanics/Molecular Dynamics Simulations

The dehydration of aqueous calcium and magnesium cations is the most fundamental process controlling their reactivity in chemical and biological phenomena, such as the formation of ionic solids or passing through ion channels. It holds particular relevance in light of recent advancements in the development of carbon capture techniques that rely on mineralization for long-term carbon storage. Specifically, dehydration of Ca 2+ and Mg 2+ is a key step in proposed carbon capture processes aiming to exploit the relatively high concentration of dissolved carbon dioxide in seawater via the formation of carbonate minerals from solvated Ca 2+ and Mg 2+ cations for sequestration and storage. Nevertheless, atomic-scale understanding of the dehydration of aqueous Ca 2+ and Mg 2+ cations remains limited. Here, we utilize rare event sampling via density functional theory molecular dynamics and embedded wavefunction theory calculations to elucidate the dehydration dynamics of aqueous Ca 2+ and Mg 2+ . Emphasis is placed on the investigation of the effect pH has on the stability of the different coordination environments. Here, our results reveal significant differences in the dehydration dynamics of the two cations and provide insight into how they may be modulated by pH changes.

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

Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation

The conformational ensemble of intrinsically disordered proteins, such as α-synuclein, are responsible for their function and malfunction. Misfolding of α-synuclein can lead to neurodegenerative diseases, and the ability to study their conformations and those of other intrinsically disordered proteins under varying physiological conditions can be crucial to understanding and preventing pathologies. In contrast to well-folded peptides, a consensus feature of IDPs is their low hydropathy and high charge, which makes their conformations sensitive to pH perturbation. We examine a prominent member of this subset of IDPs, α-synuclein, using a divide-and-conquer scheme that provides enhanced sampling of IDP structural ensembles. We constructed conformational ensembles of α-synuclein under neutral (pH ~ 7) and low (pH ~ 3) pH conditions and compared our results with available information obtained from smFRET, SAXS, and NMR studies. Specifically, α-synuclein has been found to in a more compact state at low pH conditions and the structural changes observed are consistent with those from experiments. We also characterize the conformational and dynamic differences between these ensembles and discussed the implication on promoting pathogenic fibril formation. We find that under low pH conditions, neutralization of negatively charged residues leads to compaction of the C-terminal portion of α-synuclein while internal reorganization allows α-synuclein to maintain its overall end-to-end distance. Here, we also observe different levels of intra-protein interaction between three regions of α-synuclein at varying pH and a shift towards more hydrophilic interactions with decreasing pH.

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

Confinement Effects on Proton Transfer in TiO 2 Nanopores from Machine Learning Potential Molecular Dynamics Simulations

Improved understanding of proton transfer in nanopores is critical for a wide range of emerging applications, yet experimentally probing mechanisms and energetics of this process remains a significant challenge. To help reveal details of this process, we developed and applied a machine learning potential derived from first-principles calculations to examine water reactivity and proton transfer in TiO 2 slit-pores. Here, we find that confinement of water within pores smaller than 0.5 nm imposes strong and complex effects on water reactivity and proton transfer. Although the proton transfer mechanism is similar to that at a TiO 2 interface with bulk water, confinement reduces the activation energy of this process, leading to more frequent proton transfer events. This enhanced proton transfer stems from the contraction of oxygen–oxygen distances dictated by the interplay between confinement and hydrophilic interactions. Our simulations also highlight the importance of the surface topology, where faster proton transport is found in the direction where a unique arrangement of surface oxygens enables the formation of an ordered water chain. In a broader context, our study demonstrates that proton transfer in hydrophilic nanopores can be enhanced by controlling pore size, surface chemistry, and topology.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Mechanism of Solid Electrolyte Interphase Formation on Lithium Anodes Studied by Molecular Dynamics Simulations

We investigated the initial formation of the SEI on lithium-metal anodes in presence of several electrolyte compositions using ReaxFF, in absence of a bias potential. We observed the formation of well-defined regions with different density and oxidation states of Li. Dissolution of Li metal atoms results in an uneven distribution of Li in the liquid phase. The electrolyte decomposition mechanism was studied for various electrolyte mixtures. Overall, the reaction mechanisms observed with ReaxFF are in good agreement with previous reports using DFT. However, we found some discrepancies in specific predictions by the ReaxFF that should be addressed in future work.

25 ENERGY STORAGE↗
DOE OSTI2026

3D probabilistic fracture mechanics / computational fluid dynamics simulation of a reactor pressure vessel under transient conditions

Reactor pressure vessels (RPVs) are safety-critical light-water-reactor components that, under irradiation, experience long-term material degradation in the form of embrittlement. This can increase their susceptibility to fracture under thermal-shock conditions, which could occur during off-normal transients such as loss-of-coolant accidents (LOCAs). During a LOCA, the most severe conditions for the RPV occur when emergency core cooling water is injected through the cold legs into the water-and-steam-filled RPV. The rapid cooling of the downcomer and internal RPV surface causes decreased temperature and elevated thermally driven tensile stresses in the RPV wall. This, combined with long-term material embrittlement, may cause fracture initiation at pre-existing flaws, challenging the integrity of the RPV. Assessing RPV integrity during transients with a large spatial variation in the coolant temperature requires a modeling approach that considers the effects of spatially varying coolant temperature on the fracture probability of a population of flaws distributed throughout the RPV, accounting for spatially varying embrittlement. Here, the present study addresses this need by demonstrating first-of-its-kind coupling of a high-fidelity 3D computational fluid dynamics code with 3D probabilistic fracture mechanics This was accomplished using representative models of a pressurized-water reactor subjected to small- and medium-break LOCA conditions, both of which can result in large spatial temperature variations. While the observed impact of accounting for 3D effects was minimal under the small-break LOCA this study indicates a significant increase in the probability of fracture initiation under the medium-break LOCA when 3D effects are considered, relative to a spatially uniform cooling scenario.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2020

Corrigendum and Addendum: Helium flux effects on bubble growth and surface morphology in plasma-facing tungsten from large-scale molecular dynamics simulations (2019 Nucl. Fusion 59 066035)

Two of the simulations discussed in a prior article (Hammond et al 2019 Nucl. Fusion 59 066035) were affected by a simulation glitch. We repeated the affected calculations and discuss them here. Here, the overall conclusions are essentially unchanged, though the details are different. In particular, observations that we referred to as ‘concerted bursting’ were caused primarily by non-physical heating and cooling applied by the thermostat after most atoms’ velocities were deleted (for reasons that are not known for certain). The phenomenon of one bubble bursting and causing another nearby bubble to burst does exist, though its effects are much less spectacular in the absence of non-physical driving forces. The observation of an interconnected network of sub-surface cavities formed by burst bubbles is real, and the observation of holes on the surface 1–2 nm in diameter is also confirmed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Polymorphism and phase transitions in layered uranium(VI) hydroxides: Ab initio lattice dynamics simulations of UO 2 (OH) 2

The phase transitions and thermodynamics of stoichiometric α-, β-, and γ-UO 2 (OH) 2 polymorphs are investigated using density functional perturbation theory. The pressure-induced β(Pbca) → α(Cmca) phase transition is reproduced by calculations, with a volume reduction of ΔV/V = -14.7% similar to experiment. Consistent with observation, a temperature-driven γ(P2 1 /c) → β(Pbca) phase transition is predicted near 533 K. At 298.15K, the computed standard molar heat capacity of α-UO 2 (OH) 2 is C p 0 = 112.1 J mol -1 K -1 , only 1.6% smaller than the value of C p 0 = 113.96 ± 0.12 J mol -1 K -1 measured by calorimetry. C p 0 = 112.4 and 104.8 J mol -1 K -1 are predicted for the β- and γ-UO 2 (OH) 2 polymorphs, respectively. The calculated molar enthalpy and Gibbs energy functions of the α-, β-, and γ-UO 2 (OH) 2 polymorphs are also reported.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Carbon fiber synthesis from pitch: Insights from ReaxFF based molecular dynamics simulations

Despite the potential to lowering fabrication costs of pitch-based carbon fiber (CF) compared to polyacrylonitrile-based CF, large scale utilization is currently limited by the complexity in manufacturing. This is mainly due to the lack of consistency between the pitch structure/chemistry and CF properties under different processing conditions. Here, we employed full atomistic simulations based on reactive force fields to investigate the conversion of pitch precursors to CFs. Additionally, it was found that at the carbonization stage, the consumption rates of precursors, gas formations, and solid yields (carbonized CFs) are all dependent on the composition and arrangement of molecular moieties in the precursor. Specifically, precursors with sp 3 carbons in the cata-condensed core area have limited decomposition pathways (i.e., limited reaction sites), which leads to the formation of carbonized CFs with similar compositions. Furthermore, carbonized CFs possess distinct structural characteristics, and finally lead to the formation of CFs with different moduli. By analyzing CF crystallinity and elemental composition, general rationales are proposed for the selection of optimal precursors and processing conditions, and thus shed lights on parameter screening during industrial CF synthesis. For instance, inclusion of sp 3 carbons in cata- condensed rings can be preferred over the presence of sp 3 carbons on side chains.

01 COAL, LIGNITE, AND PEAT↗