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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Ionic transport in electrostatic Janus Membranes. An explicit solvent molecular dynamic simulation.

Janus –or two-sided, charged membranes offer promise as ionic current rectifiers. In such systems, pores consisting of two regions of opposite charge can be used to generate a current from a gradient in salinity. The efficiency of nanoscale Janus pores increases dramatically as their diameter becomes smaller. However, little is known about the underlying transport processes, particularly under experimentally accessible conditions. In this work, we examine the molecular basis for rectification in Janus nanopores using an applied electric field. Molecular simulations with explicit water and ions are used to examine the structure and dynamics of all molecular species in aqueous electrolyte solutions. For several macroscopic observables, the results of such simulations are consistent with experimental observations on asymmetric membranes. Our analysis reveals a number of previously unknown features, including a pronounced local re-orientation of water molecules in the pores, and a segregation of ionic species that has not been anticipated by previously reported continuum analyses of Janus pores. Using these insights, a model is proposed for ionic current rectification in which electric leakage at pore entrance controls net transport.

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

Imaging phonon dynamics with ultrafast electron microscopy: Kinematical and dynamical simulations

Ultrafast x-ray and electron scattering techniques have proven to be useful for probing the transient elastic lattice deformations associated with photoexcited coherent acoustic phonons. Indeed, femtosecond electron imaging using an ultrafast electron microscope (UEM) has been used to directly image the influence of nanoscale structural and morphological discontinuities on the emergence, propagation, dispersion, and decay behaviors in a variety of materials. Here, we describe our progress toward the development of methods ultimately aimed at quantifying acoustic-phonon properties from real-space UEM images via conventional image simulation methods extended to the associated strain-wave lattice deformation symmetries and extents. Using a model system consisting of pristine single-crystal Ge and a single, symmetric Lamb-type guided-wave mode, we calculate the transient strain profiles excited in a wedge specimen and then apply both kinematical- and dynamical-scattering methods to simulate the resulting UEM bright-field images. While measurable contrast strengths arising from the phonon wavetrains are found for optimally oriented specimens using both approaches, incorporation of dynamical scattering effects via a multi-slice method returns better qualitative agreement with experimental observations. Contrast strengths arising solely from phonon-induced local lattice deformations are increased by nearly an order of magnitude when incorporating multiple electron scattering effects. We also explicitly demonstrate the effects of changes in global specimen orientation on the observed contrast strength, and we discuss the implications for increasing the sophistication of the model with respect to quantification of phonon properties from UEM images.

36 MATERIALS SCIENCE↗
DOE OSTI2023

$\mathrm{DRAGON}$: A multi-GPU orbital-free density functional theory molecular dynamics simulation package for modeling of warm dense matter

As progress in electronic structure theoretical methods is made, ab initio molecular dynamics (MD) based on orbital-free density functional theory (OF-DFT) is becoming increasingly more successful at substituting the traditional, very accurate but computationally costly Kohn–Sham (KS) approach for simulations of matter at the challenging warm dense matter (WDM) regime. However, despite the significant cost alleviation of eliminating the dependence on the KS orbitals, OF-DFT MD runs require ~10 2 to 10 3 CPU cores running for days, or even weeks, for simulations of systems comprised of 10 2 to 10 3 atoms, depending on thermodynamic conditions. Here we present DRAGON, a multi-GPU OF-DFT MD code for fast and efficient simulations of WDM. With a relatively small allocation of resources (4 to 8 GPU devices) it can provide an order of magnitude speedup for simulations containing $\mathscr{O}$(10 4 ) atoms and target systems composed of $\mathscr{O}$(10 5 ) atoms at conditions within the WDM regime, which is currently outside the capabilities of CPU codes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Protein Molecular Dynamics Simulations with Approximate QM: What Can We Learn?

Classical force fields are essential for computer simulations of proteins and are typically parameterized to reproduce secondary and tertiary structure of isolated proteins. However, while protein-protein interactions are ubiquitous in nature, they are not considered in parameterization efforts and are far less understood than isolated proteins. A better characterization of intermolecular interactions is widely recognized as a key to revolutionizing drug and therapeutic developments with high-throughput computational screening. Urgently needed is a critical assessment of the performance of modern protein force fields against first-principles electronic structure methods and experiments. In a daring step toward this goal, we here describe a comparison of peptide folding dynamics as predicted by a molecular mechanics force field on the one hand and by an approximate electronic structure quantum mechanical (QM) method based on density-functional tight-binding (DFTB) on the other. We further compare the dynamics from straightforward DFTB simulations with a near-linear scaling version of DFTB for massively parallel computation based on the fragment molecular orbital (FMO-DFTB) method. We illustrate differences between the phenomenology of the folding dynamics from these three methods for a small model peptide, as well as charge polarization and dynamic fluctuations, point out possible correlations and implications for force field developers, and discuss the lessons learned that might become applicable to future predictive high-throughput computer screening for personalized neoantigen cancer therapy.

Irle, Stephan↗
DOE OSTI2021

Anisotropic fluid dynamical simulations of heavy-ion collisions

We present VAH, a (3+1)–dimensional simulation that evolves the far-from-equilibrium quark-gluon plasma produced in ultrarelativistic heavy-ion collisions with anisotropic fluid dynamics. We solve the hydrodynamic equations on an Eulerian grid using the Kurganov–Tadmor algorithm in combination with a new adaptive Runge–Kutta method. Our numerical scheme allows us to start the simulation soon after the nuclear collision, largely avoiding the need to integrate it with a separate pre-equilibrium dynamics module. We test the code's performance by simulating on the Eulerian grid conformal and non-conformal Bjorken flow as well as conformal Gubser flow, whose (0+1)–dimensional solutions are precisely known. Finally, we compare non-conformal anisotropic hydrodynamics to second-order viscous hydrodynamics in central Pb+Pb collisions and find that the former's longitudinal flow profile responds more consistently to the fluid's gradients along the spacetime rapidity direction.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Elucidating and contrasting the mechanisms for Mg and Ca sulfate ion-pair formation with multi-level embedded quantum mechanics/molecular dynamics simulations

Here, solutions and minerals containing sulfate (SO 4 2- ), and Ca 2+ and Mg 2+ cations, are ubiquitous throughout the lithosphere and are significant components of seawater, thus presenting a prototypical system for the study of strong electrolytes and crystal nucleation mechanisms. However, despite their relative abundance, key questions remain unanswered about the most fundamental atomic-level steps of their mineralization pathways and aqueous dynamics. Here, we carry out enhanced sampling multi-level molecular dynamics (MD) embedded correlated wavefunction theory simulations to elucidate ion-pairing mechanisms for Mg–SO 4 and Ca–SO 4 in concentrated aqueous solution, accurately capturing effects arising from both structural dynamics and electron exchange–correlation. We predict contact-ion-pair formation to be barrierless and highly exoergic for Ca–SO 4 , in agreement with its minimal solubility, whereas for Mg–SO 4 , solvent-shared and contact ion pairs have similar free energies, qualitatively consistent with its higher solubility. Finally, we demonstrate that brief high-temperature pre-equilibration may be utilized to accelerate convergence of free energies in blue-moon-ensemble enhanced-sampling MD.

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

Particlization in fluid dynamical simulations of heavy-ion collisions: The IS3D module

The IS3D particlization module simulates the emission of hadrons from heavy-ion collisions via Monte-Carlo sampling of the Cooper–Frye formula which converts fluid dynamical information into local phase-space distributions for hadrons. The code package includes multiple choices for the non-equilibrium correction to these distribution functions: the 14-moment approximation, first-order Chapman–Enskog expansion, and two types of modified equilibrium distributions. This makes it possible to explore to what extent heavy-ion experimental data are sensitive to different choices for δf n , presently the main source of theoretical uncertainty in the particlization stage. Here, we validate our particle sampler with a high degree of precision by generating several million hadron emission events from a longitudinally boost-invariant hypersurface and comparing the event-averaged particle spectra and space–time distributions to the Cooper–Frye formula.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Effect of Mg and Ni impurities on tritium diffusion in lithium ceramics through cluster dynamics simulations

This study investigates the impact of Mg and Ni doping on tritium diffusion in LiAlO 2 and LiAl 5 O 8 ceramics, that are used in tritium-producing burnable absorber rods (TPBARs). Utilizing Centipede simulations across a broad temperature range (500 K to 1250 K), we explore the interplay between defect dynamics, cluster formation, and tritium mobility. In LiAlO 2 , Mg doping significantly enhances tritium diffusivity by increasing tritium interstitial concentrations and diffusion coefficients of key species, thereby doubling the overall tritium diffusivity. Ni doping, while shifting the dominant defect to Li vacancies, maintains high tritium mobility due to the low binding energy of Li vacancy-tritium complexes, which ensures effective tritium migration. In LiAl 5 O 8 , Mg and Ni doping results in a slight reduction in the diffusion coefficients of key species, yet the dramatic increase in tritium interstitial concentrations compensates, leading to a net small increase in tritium diffusivity. In conclusion, the findings highlight the critical role of defects in tritium transport and the effect of Mg and Ni defects on the performance of these ceramics in demanding nuclear environments.

Cluster dynamics↗
DOE OSTI2020

Exploring non-adiabaticity to CO reduction reaction through ab initio molecular dynamics simulation

Non-adiabatic chemical reaction refers to the electronic excitation during reactions. This effect cannot be modeled by the ground-state Born-Oppenheimer molecular dynamics (BO-MD), where the electronic structure is at the ground state for every step of ions' movement. Although the non-adiabatic effect has been explored extensively in gas phase reactions, its role in electrochemical reactions, such as water splitting and CO 2 reduction, in electrolyte has been rarely explored. On the other hand, electrochemical reactions usually involve electron transport; thus, a non-adiabatic process can naturally play a significant role. In this work, using one-step CO 2 reduction as an example, we investigated the role of the non-adiabatic effect in the reaction. The reaction barriers were computed by adiabatic BO-MD and non-adiabatic real-time time dependent density functional theory (rt-TDDFT). We found that by including the non-adiabatic effect, rt-TDDFT could increase the reaction barrier up to 6% compared to the BO-MD calculated barrier when the solvent model is used to represent water. Simulations were carried out using explicit water molecules around the reaction site under different overpotentials, and similar non-adiabatic effects were found.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry

Targeted protein degradation (TPD) is a promising approach in drug discovery for degrading proteins implicated in diseases. A key step in this process is the formation of a ternary complex where a heterobifunctional molecule induces proximity of an E3 ligase to a protein of interest (POI), thus facilitating ubiquitin transfer to the POI. In this work, we characterize 3 steps in the TPD process. (1) We simulate the ternary complex formation of SMARCA2 bromodomain and VHL E3 ligase by combining hydrogen-deuterium exchange mass spectrometry with weighted ensemble molecular dynamics (MD). (2) We characterize the conformational heterogeneity of the ternary complex using Hamiltonian replica exchange simulations and small-angle X-ray scattering. (3) We assess the ubiquitination of the POI in the context of the full Cullin-RING Ligase, confirming experimental ubiquitinomics results. Differences in degradation efficiency can be explained by the proximity of lysine residues on the POI relative to ubiquitin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Insights into the Reactivity of Brookite TiO 2 Nanorods in Liquid Water from Ab Initio Molecular Dynamics Simulations

Brookite TiO 2 , a rare natural polymorph of TiO 2 , has been reported to be an excellent photocatalyst for the production of hydrogen from water and aqueous alcohol solutions, especially when it is reduced and synthesized in the form of nanorods. Here, we investigate the reactivity of stoichiometric and reduced brookite nanorods in liquid water using ab initio molecular dynamics and hybrid density functional theory calculations. Our simulations show a much higher water dissociation fraction on reduced nanorods than on stoichiometric ones, with an accumulation of the resulting bridging hydroxyls (O br H) and terminal hydroxyls (Ti –OH) on different facets of the nanorod. ObrH groups accumulate preferentially on low-energy (210) facets, where they are stabilized by adjacent reduced Ti (Ti 3+ ) sites, while Ti –OH groups prefer to form at the four-fold coordinated Ti atoms on high-energy (010) facets. This hydroxylation pattern also favors the spatial localization of excited holes on the (010) facets. This coupling between water-induced surface chemistry and charge separation underpins the enhanced photocatalytic activity of brookite nanorods, providing useful information for the design of more efficient TiO2-based nanostructures for solar-driven hydrogen evolution.

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

Dynamic Simulation of a Sub-Critical Coal Fired Power Plant

In order to address the demanding operating conditions for remaining coal-fired power plants, a dynamic model and a suite of tools have been developed for studying load cycling and to find optimization opportunities. A sub-critical steam cycle power plant was modeled in a flow-sheet modeling tool, APROS™. The model represented the firing system, economizer, evaporator, superheat, and reheat systems. Four loads from 100% TMCR to 25% TMCR were calibrated and tested such that low-to-high cycling could be studied. The model was run through various load cycles; one of which is presented here. This modeling is a prototype for general use in developing cutting edge controls products and for maximizing economic, low-emissions, and efficient operation of the existing coal power fleet.

Braun, Timothy↗
DOE OSTI2024

Accelerating structural dynamics simulations with localised phenomena through matrix compression and projection‐based model order reduction

In this work, a novel approach is introduced for accelerating the solution of structural dynamics problems in the presence of localised phenomena, such as cracks. For this category of problems, conventional projection-based Model Order Reduction (MOR) methods are either limited with respect to the range of system configurations that can be represented or require frequent solutions of the Full Order Model (FOM) to update the low-dimensional spaces, in which solutions are represented. In the proposed approach, low-dimensional spaces, constructed for the healthy structure, are enriched with appropriately selected columns of the flexibility matrix of the system. It can be shown that these spaces contain the solution to the original problem for the static case, while their dimension is much smaller. In order to allow their online construction for arbitrary localised features, the full flexibility matrix of the system should be available. To this end, a hierarchical representation is used for the matrices involved, allowing to compute the flexibility matrix efficiently and with reduced memory requirements. The resulting method offers significant speedups, without sacrificing the flexibility and accuracy of the full order model. The performance and limitations of the approach are studied through a series of examples in structural dynamics.

fracture mechanics↗
DOE OSTI2024

Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package

Simulating chemically reactive phenomena such as proton transport on nanosecond to microsecond and beyond time scales is a challenging task. Ab initio methods are unable to currently access these time scales routinely, and traditional molecular dynamics methods feature fixed bonding arrangements that cannot account for changes in the system’s bonding topology. The Multiscale Reactive Molecular Dynamics (MS-RMD) method, as implemented in the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) software package for the LAMMPS molecular dynamics code, offers a method to routinely sample longer time scale reactive simulation data with statistical precision. RAPTOR may also be interfaced with enhanced sampling methods to drive simulations toward the analysis of reactive rare events, and a number of collective variables (CVs) have been developed to facilitate this. Key advances to this methodology, including GPU acceleration efforts and novel CVs to model water wire formation are reviewed, along with recent applications of the method which demonstrate its versatility and robustness.

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

Molecular Dynamics Simulations of Helium Bubble Formation in Palladium Tritides [Slides]

Pd readily absorbs hydrogen and its isotopes, and can be used to purify gas mixtures involving tritium. Tritium decays to He, forming He bubbles. Bubbles causes possible PCT effects swelling, He release, all leading to failures. Radioactive decay experiments take many years. Molecular dynamics (MD) studies can be quickly done. No previous MD methods can simulate He bubble nucleation and growth.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Molecular Dynamics Simulations of Helium Bubble Formation in Palladium Tritides [Slides]

Pd readily absorbs hydrogen and its isotopes, and can be used to purify gas mixtures involving tritium. Tritium decays to He, forming He bubbles. Bubbles causes possible PCT effects swelling, He release, all leading to failures. Radioactive decay experiments take many years. Molecular dynamics (MD) studies can be quickly done. No previous MD methods can simulate He bubble nucleation and growth.

74 ATOMIC AND MOLECULAR PHYSICS↗