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Multiphase Computational Fluid Dynamics Simulation of Ignition Overpressure and Plume-Water Interaction in the SLS Scale Model Acoustics Test

The solid rocket boosters (SRBs) on the Space Launch System (SLS) generate powerful ignition overpressure (IOP) waves that can potentially damage the vehicle and surrounding ground structures. Based on historical Shuttle experience, the IOP will be mitigated by utilizing an IOP/Sound Suppression (SS) water system which sprays water in and around the SRB and RS-25 engine plumes. However, the complex multiphase physics of the resulting plume-water interaction can lead to undesirable effects, such as high velocity water spray onto the engine nozzles and SRB nozzle side loads. Prior to launch, insight into this environment can be achieved through scale model testing and predictive computational fluid dynamics (CFD) modeling. The Scale Model Acoustic Test (SMAT) was conducted at Marshall Space Flight Center to provide the data necessary to develop the SLS liftoff acoustic environments by using a 5% scale SLS vehicle, fully integrated with a scaled IOP/SS water system, mobile launcher (ML), and tower. NASA engineers have put forth significant effort in validating the Loci/CHEM-Real Fluids multiphase CFD solver on a wet hold down test from the SMAT series. In this paper, the IOP acoustics and plume-water interactions predicted by the CFD model are compared and validated against the experiment, enabling relatively inexpensive, rapid turnaround for multiphase launch environment analyses to support future flights and design evolutions of SLS and other launch vehicles.

John E. Soto↗
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 OSTI2019

DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

Background Genome-scale models of metabolism and macromolecular expression (ME models) enable systems-level computation of proteome allocation coupled to metabolic phenotype. Results We develop DynamicME, an algorithm enabling time-course simulation of cell metabolism and protein expression. DynamicME correctly predicted the substrate utilization hierarchy on a mixed carbon substrate medium. We also found good agreement between predicted and measured time-course expression profiles. ME models involve considerably more parameters than metabolic models (M models). We thus generate an ensemble of models (each model having its rate constants perturbed), and then analyze the models by identifying archetypal time-course metabolite concentration profiles. Furthermore, we use a metaheuristic optimization method to calibrate ME model parameters using time-course measurements such as from a (fed-) batch culture. Finally, we show that constraints on protein concentration dynamics (“inertia”) alter the metabolic response to environmental fluctuations, including increased substrate-level phosphorylation and lowered oxidative phosphorylation. Conclusions Overall, DynamicME provides a novel method for understanding proteome allocation and metabolism under complex and transient environments, and to utilize time-course cell culture data for model-based interpretation or model refinement.

Mathematical & Computational Biology↗
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 OSTI2016

Neutron scattering of residual hydrogen in 1,4-dioxane d 8 liquid: Understanding measurements with molecular dynamics simulations

That incoherent scattering from protiated molecular liquids adds a constant background to the measured scattering intensity is well-known, but less appreciated is the fact that coherent scattering is also induced by the presence of hydrogen in a deuterated liquid. In fact, the scattering intensity can be very sensitive, in the small-q region, with respect to the amounts and distribution of residual H in the system. We used 1,4-dioxane liquid to demonstrate that the partial structure factors of the HD and DD atom pairs contribute significantly to intermolecular scattering and that uncertainty in the extent of deuteration account for discrepancies between simulations and measurements. Both contributions to uncertainty have similar magnitudes: scattering interference of the hydrogen–deuterium pair, and complementary interference from the deuterium–deuterium pair by virtue of chemical inhomogeneity. This situation arises in practice since deuteration of liquids is often 99% or less. A combined experimental and extensive computational study of static thermal neutron scattering of 1,4-dioxane demonstrates the foregoing. We show, through simulations, that the reason for the differences is the content of protiated dioxane (vendors quote 1%). We estimate that up to 5% (at 298 K and at 343 K) protiated molar fraction may be involved in generating the scattering differences. Finally, we find that the particular distribution of hydrogen in the protiated molecules affects the results significantly; here, we considered molecules to be either fully protiated or fully deuterated. This scenario best reconciles the computational and experimental results, and leads us to speculate that the deuteration synthesis process tends to leave a molecule either fully deuterated or fully protiated. As a result, we have used 1,4-dioxane as a model liquid, the effects described in this study extend to similar liquids, and similar systematic experimental/computational studies can be performed to either understand measurements or calibrate/validate molecular dynamics models.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
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 OSTI2016

Diffusion of biomass pyrolysis products in H-ZSM-5 by molecular dynamics simulations

Diffusion of biomass pyrolysis vapors and their upgraded products is an essential catalytic property of zeolites during catalytic fast pyrolysis and likely plays a critical role in the selectivity of these catalysts. Characterizing the diffusivities of representative biofuel molecules is critical to understand shape selectivity and interpret product distribution. Yet, experimental measurements on the diffusivities of oxygenated biofuel molecules at pyrolysis temperatures are very limited in the literature. As an alternative approach, we conducted MD simulations to measure the diffusion coefficients of several selected molecules that are representative of biomass pyrolysis vapors, namely water, methanol, glycolaldehyde, and toluene in H-ZSM-5 zeolite. The results show the diffusion coefficients calculated via MD simulations are consistent with available NMR measurements at room temperature. The effect of molecular weight and molecular critical diameter on the diffusivity among the chosen model compounds is also examined. Furthermore, we have characterized the diffusivities of representative biofuel molecules, namely xylene isomers, in H-ZSM-5. Our calculations determined that the ratio of the diffusion coefficients for xylene isomers is p -xylene: o -xylene: m -xylene ≈ 83:3:1 at 700 K. Furthermore, our results also demonstrate the different diffusivity between p-xylene and toluene is due to the molecular orientations when the molecules diffuse along the channels in H-ZSM-5 and provide deep insight into the effect of molecular orientation on its diffusivity.

09 BIOMASS FUELS↗
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↗
DOE OSTI2016

Accurate and efficient prediction of fine-resolution hydrologic and carbon dynamic simulations from coarse-resolution models

The topography, and the biotic and abiotic parameters are typically upscaled to make watershed-scale hydrologic-biogeochemical models computationally tractable. However, upscaling procedure can produce biases when nonlinear interactions between different processes are not fully captured at coarse resolutions. Here, we applied the Proper Orthogonal Decomposition Mapping Method (PODMM) to downscale the field solutions from a coarse (7 km) resolution grid to a fine (220 m) resolution grid. PODMM trains a reduced-order model (ROM) with coarse-resolution and fine-resolution solutions, here obtained using PAWS+CLM, a quasi-3-D watershed processes model that has been validated for many temperate watersheds. Subsequent fine-resolution solutions were approximated based only on coarse-resolution solutions and the ROM. The approximation errors were efficiently quantified using an error estimator. By jointly estimating correlated variables and temporally varying the ROM parameters, we further reduced the approximation errors by up to 20%. We also improved the method's robustness by constructing multiple ROMs using different set of variables, and selecting the best approximation based on the error estimator. The ROMs produced accurate downscaling of soil moisture, latent heat flux, and net primary production with O(1000) reduction in computational cost. The subgrid distributions were also nearly indistinguishable from the ones obtained using the fine-resolution model. Compared to coarse-resolution solutions, biases in upscaled ROM solutions were reduced by up to 80%. This method has the potential to help address the long-standing spatial scaling problem in hydrology and enable long-time integration, parameter estimation, and stochastic uncertainty analysis while accurately representing the heterogeneities.

58 GEOSCIENCES↗