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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
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 OSTI2020

Active Learning A Neural Network Model For Gold Clusters & Bulk From Sparse First Principles Training Data

Small metal clusters are of fundamental scientific interest and of tremendous significance in catalysis. These nanoscale clusters display diverse geometries and structural motifs depending on the cluster size; a knowledge of this size-dependent structural motifs and their dynamical evolution has been of longstanding interest. Given the high computational cost of first-principles calculations, molecular modeling and atomistic simulations such as molecular dynamics (MD) has proven to be an important complementary tool to aid this understanding. Classical MD typically employ predefined functional forms which limits their ability to capture such complex size-dependent structural and dynamical transformation. Neural Network (NN) based potentials represent flexible alternatives and in principle, well-trained NN potentials can provide high level of flexibility, transferability and accuracy on-par with the reference model used for training. A major challenge, however, is that NN models are interpolative and requires large quantities (similar to 10 4 or greater) of training data to ensure that the model adequately samples the energy landscape both near and far-from-equilibrium. A highly desirable goal is minimize the number of training data, especially if the underlying reference model is first-principles based and hence expensive. In this work, we introduce an active learning (AL) scheme that trains a NN model on-the-fly with minimal amount of first-principles based training data. Our AL workflow is initiated with a sparse training dataset (similar to 1 to 5 data points) and is updated on-the-fly via a Nested Ensemble Monte Carlo scheme that iteratively queries the energy landscape in regions of failure and updates the training pool to improve the network performance. Using a representative system of gold clusters, we demonstrate that our AL workflow can train a NN with similar to 500 total reference calculations. Using an extensive DFT test set of similar to 1100 configurations, we show that our AL-NN is able to accurately predict both the DFT energies and the forces for clusters of a myriad of different sizes. Our NN predictions are within 30 meV/atom and 40 meV/angstrom of the reference DFT calculations. Moreover, our AL-NN model also adequately captures the various size-dependent structural and dynamical properties of gold clusters in excellent agreement with DFT calculations and available experiments. We finally show that our AL-NN model also captures bulk properties reasonably well, even though they were not included in the training data.

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

Selective mass scaling for single-layer thick shell elements in DYNA3D

Hexahedral elements can be adapted to model thin and moderately thick structures by neglecting the coupling of through-thickness stress, resulting in a fully three-dimensional, but simplified, state of stress. These specialized elements, often referred to as “thick” or “solid” shells, are generally employed to model thin-walled structures using continuum mechanics-based material models. In explicit dynamics simulations, where computational speed is important, these elements are integrated with a single quadrature point and a set of anti-hourglassing (stabilizing) forces. Thick shells, by definition, have a thickness dimension smaller than their in-plane dimensions, and this small thickness often determines the stable time step size in simulations, despite the mechanics being approximated. To alleviate this limitation while retaining the relevant dynamics of thin-walled structures, selective mass scaling (SMS), or selective mass “augmentation,” has been proposed in the literature. In this technical report, we explore the application of SMS to single-layer thick shells in the simulation software DYNA3D.

42 ENGINEERING↗
DOE OSTI2021

Exceptional Radiation Absorption in a Pentagon-Based Si Allotrope

Excellent photovoltaic performance is predicted in a pentagonal covalent network of Si in a hollow structure exhibiting both thermal and dynamical stability. Consisting of a combination of sp 2 and sp 3 hybridized Si atomic orbitals, the GW0 computed band structure shows an indirect band gap near the zone edge and also a manifold of directly absorbing transitions at frequencies in the window of visible light, in distinction with conventional Si. Hydrogenation of a single sp 2 site is predicted to lead to a robust local magnetic moment. In this study, we find a low formation energy at low pressure that is compatible with other experimentally known phases, suggesting that a stable phase might be obtained.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Computational insights into the lattice dynamics of Pu(IV) oxalates

Despite its use in PuO 2 production, the structure of anhydrous Pu(C 2 O 4 ) 2 is still not completely understood. Recently, two candidate structures for Pu(C 2 O 4 ) 2 were proposed via density functional theory (DFT), after which the first experimental optical vibrational spectra were reported. Here, in this study, we calculated the lattice dynamics of the candidate structures using DFT and found that the primary difference between them is the presence of a vibrational mode near 1380 cm -1 in one structure. The frequency and optical activity of this mode agree well with the published experimental results, providing strong support for this calculated structure as that of anhydrous Pu(C 2 O 4 ) 2 .

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2021

Structural and Dynamical Design Principles for Iron-Sulfur Clusters in Sequence Defined Polymers

This integrated synthetic and computational effort uses sequence defined polymers such as peptoids, and triazines, capable of mimicking a flexible protein environment to control the positioning of side chains around redox cofactors. This strategy will allow modulation of redox properties through both direct and indirect mechanisms. To this end the aim is defined to test the underlying hypothesis: that principles and critical functionalities governing the binding and tuning of naturally occurring electron carrier co-factors can be identified and used to predictably design and synthesize maquettes based on non-natural polymers resulting in new modular biomimetic scaffolds for Electron Transfer Materials. This will be achieved through design and synthesis of ligands that can stabilize iron-sulfur clusters and tune the redox potential based on sequence.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Elastic Properties of Plasma-Exposed Tungsten Predicted by Molecular-Dynamics Simulations

We report results of systematic molecular-dynamics computations of the elastic properties of single-crystalline tungsten containing structural defects, voids and overpressurized He nanobubbles, related to plasma exposure of tungsten serving as a plasma- facing component (PFC) in nuclear fusion devices. Our computations reveal that the empty voids are centers of dilatation resulting in development of tensile stress in the tungsten matrix, whereas He-filled voids (nanobubbles) introduce compressive stress in the plasma-exposed tungsten. We find that the dependence of the elastic moduli of plasma-exposed tungsten, namely, the bulk, Young, and shear modulus, on its void fraction follows a universal exponential scaling relation. We also find that the elastic moduli of plasma-exposed tungsten soften substantially as a function of He content in the tungsten matrix, following an exponential scaling relation; this He-induced exponential softening is in addition to the softening caused in the matrix with increasing temperature. A systematic characterization of the dependence of the elastic moduli on the He bubble size reveals that He bubble growth affects significantly both the bulk modulus and the Poisson ratio of plasma-exposed tungsten, while its effect on the Young and shear moduli of the plasma-exposed material is weak. Our findings contribute directly to the development of a structure-properties database that is required for the predictive modeling of the dynamical response of PFCs in nuclear fusion devices.

36 MATERIALS SCIENCE↗
DOE OSTI2025

AMR-Wind: A Performance-Portable, High-Fidelity Flow Solver for Wind Farm Simulations

We present AMR-Wind, a verified and validated high-fidelity computational-fluid-dynamics code for wind farm flows. AMR-Wind is a block-structured, adaptive-mesh, incompressible-flow solver that enables predictive simulations of the atmospheric boundary layer and wind plants. It is a highly scalable code designed for parallel high-performance computing with a specific focus on performance portability for current and future computing architectures, including graphical processing units (GPUs). In this paper, we detail the governing equations, the numerical methods, and the turbine models. Establishing a foundation for the correctness of the code, we present the results of formal verification and validation. The verification studies, which include a novel actuator line test case, indicate that AMR-Wind is spatially and temporally second-order accurate. The validation studies demonstrate that the key physics capabilities implemented in the code, including actuator disk models, actuator line models, turbulence models, and large eddy simulation (LES) models for atmospheric boundary layers, perform well in comparison to reference data from established computational tools and theory. We conclude with a demonstration simulation of a 12-turbine wind farm operating in a turbulent atmospheric boundary layer, detailing computational performance and realistic wake interactions.

17 WIND ENERGY↗
DOE OSTI2020

Computationally Directed Discovery of MoBi 2

Incorporating bismuth, the heaviest element stable to radioactive decay, into new materials enables the creation of emergent properties such as permanent magnetism, superconductivity, and nontrivial topology. Understanding the factors that drive Bi reactivity is critical for the realization of these properties. Using pressure as a tunable synthetic vector, we can access unexplored regions of phase space to foster reactivity between elements that do not react under ambient conditions. Furthermore, combining computational and experimental methods for materials discovery at high-pressures provides broader insight into the thermodynamic landscape than can be achieved through experiment alone, informing our understanding of the dominant chemical factors governing structure formation. Herein, we report our combined computational and experimental exploration of the Mo–Bi system, for which no binary intermetallic structures were previously known. Using the ab initio random structure searching (AIRSS) approach, we identified multiple synthetic targets between 0–50 GPa. Highpressure in situ powder X-ray diffraction experiments performed in diamond anvil cells confirmed that Mo–Bi mixtures exhibit rich chemistry upon the application of pressure, including experimental realization of the computationally predicted CuAl 2 -type MoBi 2 structure at 35.8(5) GPa. Electronic structure and phonon dispersion calculations on MoBi 2 revealed a correlation between valence electron count and bonding in high-pressure transition metal–Bi structures as well as identified two dynamically stable ambient pressure polymorphs. Our study demonstrates the power of the combined computational–experimental approach in capturing highpressure reactivity for efficient materials discovery.

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

LDRD 226360 Final Project Report: Simulated X-ray Diffraction and Machine Learning for Optimizing Dynamic Experiment Analysis

This report is the final documentation for the one-year LDRD project 226360: Simulated X-ray Diffraction and Machine Learning for Optimizing Dynamic Experiment Analysis. As Sandia has successfully developed in-house X-ray diffraction tools for study of atomic structure in experiments, it has become increasingly important to develop computational analysis methods to support these experiments. When dynamically compressed lattices and orientations are not known a priori, the identification requires a cumbersome and sometimes intractable search of possible final states. These final states can include phase transition, deformation and mixed/evolving states. Our work consists of three parts: (1) development of an XRD simulation tool and use of traditional data science methods to match XRD patterns to experiments; (2) development of ML-based models capable of decomposing and identifying the lattice and orientation components of multicomponent experimental diffraction patterns; and (3) conducting experiments which showcase these new analysis tools in the study of phase transition mechanisms. Our target material has been cadmium sulfide, which exhibits complex orientation-dependent phase transformation mechanisms. In our current one-year LDRD, we have begun the analysis of high-quality c-axis CdS diffraction data from DCS and Thor experiments, which had until recently eluded orientation identification.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Systematic input scheme for many-boson Hamiltonians with applications to the two-dimensional 𝜙 4 theory

We develop a novel, systematic input scheme for many-boson Hamiltonians in order to solve field theory problems within the light-front Hamiltonian formalism via quantum computing. We present our discussion of this input scheme based on the light-front Hamiltonian of the two-dimensional ϕ 4 theory. In our input scheme, we employ a set of quantum registers, where each register encodes the occupation of a distinct boson mode as binaries. We squeeze the boson operators of each mode and present the Hamiltonian in terms of unique combinations of the squeezed-boson operators. We design the circuit modules for these unique combinations. Based on these circuit modules, we block encode the many-boson Hamiltonian utilizing the idea of quantum walk. For demonstration purposes, we present the spectral calculations of the Hamiltonian utilizing the hybrid quantum-classical symmetry-adapted quantum Krylov subspace diagonalization algorithm based on our input scheme, where the quantum computations are performed with the IBM Qiskit quantum simulator. The results of the hybrid calculations agree with exact results. Here, we can incorporate the input scheme in this work with the input scheme for many-fermion Hamiltonians; they jointly offer new pathways to solving the structure and dynamics of more general field theory problems on future fault-tolerant quantum computers.

Ab initio calculations↗
DOE OSTI2022

kynema-fmb [SWR-23-07]

Kynema-FMB (FKA: Kynema) is an open-source performance portable flexible multibody (FMB) dynamics solver designed for time-domain simulations. While originally tailored for wind turbine structural dynamics, the formulation and implementation are those of a general flexible-multidbody dynamics solver that can readily be applied to a wide range of systems. Kynema was designed with a narrow focus, namely to provide a lightweight, fast, accurate FMD solver for coupling to computational-fluid-dynamics (CFD) codes, especially the CFD codes in the Kynema suite, for fluid-structure-interaction (FSI) simulations. Kynema-FMB is equipped to model systems that can be represented as a collection of beams and rigid bodies that are connected through constraints. Degrees of freedom are defined in the inertial/global frame of reference and include displacements and rotations (formally as rotation matrices, but stored as quaternions). The underlying formulation is built on a Lie-group time integrator designed for index-3 differential-algebraic equations, which is second-order accurate in time (Bruls et al., 2012). Beam models are based on geometrically exact beam theory and are discretized as high-order spectral finite elements similar to those in BeamDyn (Wang et al., 2017). The governing equations for a FMD system like a wind turbine constitute a highly nonlinear system of constrained partial-differential equations. Kynema-FMB uses analytical Jacobians in the nonlinear-system solves in each time step. Linear systems use sparse storage and several third-party sparse-linear-system solvers are enabled. Ill conditioning of linear systems is mitigated with preconditioning described in Bottasso et al, 2008. Kynema-FMB is integrated with a simple open-source controller (ROSCO). There is an application programming interface (API) for coupling to geometry-resolved CFD (like that in Sharma et al., 2023) and actuator-force CFD (like that in Kuhn et al., 2025). In the latter, for actuator-line models, Kynema-FMB includes an internal blade-element solver that depends on user-provided lookup tables for coefficients of lift and drag, i.e., aerodynamic polars. Kynema-FMB is written in C++ and leverages Kokkos and Kokkos-Kernels (KokkosEcosystem) as its performance portability layer enabling simulations on both CPU and GPU systems. The repository is equipped with extensive automated testing at the unit and regression/system levels. The following describes the high-level development objectives conceived for Kynema: *Kynema will follow modern software development best practices, including test-driven development (TDD), version control, hierarchical automated testing, and continuous integration (CI) for a robust development environment. *The core data structures are memory efficient and enable vectorization and parallelization at multiple levels. *Data structures are data-oriented to exploit methods for accelerated computing including high utilization of chip resources (e.g., single instruction multiple data (SIMD) instruction sets) and parallelization using GP-GPUs. *The computational algorithms incorporate robust open-source libraries for mathematical operations, resource allocation, and data management. *The API design considers multiple stakeholder needs and ensure integration with existing and future ecosystems for data science, machine learning, and AI. *Kynema-FMB is written in modern C++ and leverages Kokkos as its performance-portability library with inspiration from the kynema stack.

Sprague, MichaelA.↗
DOE OSTI2024

phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids

Phosphorylated amino acids are involved in many cell regulatory networks; proteins containing these post-translational modifications are widely studied both experimentally and computationally. Simulations are used to investigate a wide range of structural and dynamic properties of biomolecules, such as ligand binding, enzyme-reaction mechanisms, and protein folding. However, the development of force field parameters for the simulation of proteins containing phosphorylated amino acids using the Amber program has not kept pace with the development of parameters for standard amino acids, and it is challenging to model these modified amino acids with accuracy comparable to proteins containing only standard amino acids. In particular, the popular ff14SB and ff19SB models do not contain parameters for phosphorylated amino acids. Here, the dihedral parameters for the side chains of the most common phosphorylated amino acids are trained against reference data from QM calculations adopting the ff14SB approach, followed by validation against experimental data. Finally, library files and corresponding parameter files are provided, with versions that are compatible with both ff14SB and ff19SB.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Validation of simulated wave energy converter responses to focused waves

Focused waves are increasingly used as a design method to predict extreme loads for offshore structures, such as wave energy converters (WECs). However, the ability of computational methods to accurately simulate the prescribed focused waves and resulting wave structure interactions is not well validated. This study uses two computational fluid dynamic methods, WEC-Sim and STAR-CCM+, to evaluate the responses of two taut-moored WEC-like buoys to three different focused waves. WEC-Sim is a computationally efficient, mid-fidelity model, based on linearised potential flow theory. In contrast, STAR-CCM+ is a high-fidelity, three-dimensional, unsteady, Reynolds-averaged Navier–Stokes-based model. The two buoy geometries considered are a hemispherical-bottom cylinder and a truncated cylinder with a cylindrical moon pool. Three prescribed focused waves are generated in both codes, and the simulated displacements and mooring loads are obtained for each of the hydrodynamic bodies. The resulting STAR-CCM+ generated focused waves have approximately the same accuracy, in comparison with the analytic solution, as experimentally generated focused waves. The WEC-Sim simulated responses, when using viscous coefficients tuned to the measured displacements, are, on average, within 11.5% of experimentally measured values, whereas the STAR-CCM+ simulated responses are, on average, within 14.2% of the experimental values.

16 TIDAL AND WAVE POWER↗
DOE OSTI2022

Multiplexed Anodic Stripping Voltammetry Detection of Heavy Metals in Water Using Nanocomposites Modified Screen-Printed Electrodes Integrated With a 3D-Printed Flow Cell

In this study, we present multiplexed anodic stripping voltammetry (ASV) detection of heavy metal ions (HMIs)—As(III), Cd(II), and Pb(II)—using a homemade electrochemical cell consisting of dual working, reference and counter screen-printed electrodes (SPE) on polyimide substrate integrated with a 3D-printed flow cell. Working and counter electrodes were fabricated by the screen-printing of graphite paste while the Ag/AgCl paste was screen-printed as a reference electrode (Ag/AgCl quasi-reference electrode). The working electrodes were modified with (BiO) 2 CO 3 -reduced graphene oxide (rGO)-Nafion [(BiO) 2 CO 3 -rGO-Nafion] and Fe 3 O 4 magnetic nanoparticles (Fe 3 O 4 MNPs) decorated Au nanoparticles (AuNPs)-ionic liquid (IL) (Fe 3 O 4 -Au-IL) nanocomposites separately to enhance HMIs sensing. Electrochemical detection was achieved using square wave ASV technique. The desired structure of the flow electrochemical cell was optimized by the computational fluid dynamic (CFD). Different experimental parameters for stripping analysis of HMIs were optimized including deposition time, deposition potential and flow rate. The linear range of calibration curves with the sensing nanocomposites modified SPE for the three metal ions was from 0–50 μg/L. The limits of detection (S/N = 3) were estimated to be 2.4 μg/L for As(III), 1.2 μg/L for Pb(II) and 0.8 μg/L for Cd(II). Furthermore, the homemade flow anodic stripping sensor platform was used to detect HMIs in simulated river water with a 95–101% recovery, indicating high selectivity and accuracy and great potential for applicability even in complex matrices.

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

Phase Diagram of Nuclear Pastas in Neutron Star Crusts

Two neural networks were trained to predict, respectively, the Euler characteristic and the curvature of nuclear pastas in neutron star crust conditions generated by molecular dynamics simulations of neutron star matter with 0.1 < x < 0.5, 0.040 fm−3 < ρ < 0.085 fm−3 (0.68 × 1014 g/cm3 < ρ < 1.43 × 1014 g/cm3), and 0.2 MeV < T < 4.0 MeV, where x is proton content, the density is ρ, and the temperature is T. The predictions of the two networks were combined to determine the nuclear pasta phase that is thermodynamically stable at a given x, ρ, and T, and a three-dimensional phase diagram that extrapolated slightly the regions of existing molecular dynamics data was computed. The jungle gym and anti-jungle gym structures are prevalent at high temperature and low density, while the anti-jungle gym and anti-gnocchi structures dominate at high temperature and high density. A diversity of structures exist at low temperatures and intermediate density and proton content. The trained models used in this work are open access and available at a public repository to promote comparison to pastas obtained with other models.

Muñoz, Jorge A. (ORCID:0000000294870079)↗
DOE OSTI2021

Nonadiabatic Molecular Dynamics Study of the Relaxation Pathways of Photoexcited Cyclooctatetraene

In the current study, we present nonadiabatic (NAMD) and adiabatic molecular dynamics simulations of the transition-state dynamics of photoexcited cyclooctatetraene (COT). The equilibrium-state structure and absorption spectra are analyzed using the semiempirical Austin Model 1 potential. The NAMD simulations are obtained by a surface-hopping algorithm. We analyzed in detail an active excited to ground state relaxation pathway accompanied by an S 2 /S 3 (D 2d ) → S 1 (D 8h ) → S o (D 4h ) → S o (D 2d ) double-bond shifting mechanism. The simulated excitation lifetime is in good agreement with experiment. The first excited singlet state S1 plays a crucial role in the photochemistry. Here, the obtained critical molecular conformations, energy barrier, and transition-state lifetime results will provide a basis for further investigations of the bond-order inversion and photoswitching process of COT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗