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Results for “computational structural dynamics”

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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Analytical nonadiabatic coupling and state-specific energy gradient for the crystal field Hamiltonian describing lanthanide single-ion magnets

Paramagnetic molecules with a metal ion as an electron spin center are promising building blocks for molecular qubits and high-density memory arrays. However, fast spin relaxation and decoherence in these molecules lead to a rapid loss of magnetization and quantum information. Nonadiabatic coupling (NAC), closely related to spin-vibrational coupling, is the main source of spin relaxation and decoherence in paramagnetic molecules at higher temperatures. Predicting these couplings using numerical differentiation requires a large number of computationally intensive ab initio or crystal field electronic structure calculations. To reduce computational cost and improve accuracy, we derive and implement analytical NAC and state-specific energy gradient for the ab initio parametrized crystal field Hamiltonian describing single-ion molecular magnets. Our implementation requires only a single crystal field calculation. In addition, the accurate NACs and state-specific energy gradients can be used to model spin relaxation using sophisticated nonadiabatic molecular dynamics, which avoids the harmonic approximation for molecular vibrations. To test our implementation, we calculate the NAC values for three lanthanide complexes. Finally, the predicted values support the relaxation mechanisms reported in previous studies.

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

Nonlinear Interface Reduction for Time-Domain Analysis of Hurty/Craig-Bampton Superelements with Frictional Contact

Virtual prototyping in engineering design relies today on modern numerical models of contacting structures with accurate resolution of interface mechanics, which strongly affect the system-level stiffness and energy dissipation due to frictional losses. High-fidelity modeling within the localized interfaces is required to resolve local quantities of interest that may drive design decisions. The high-resolution finite element meshes necessary to resolve inter-component stresses tend to be computationally expensive, particularly when the analyst is interested in response time histories. The Hurty/Craig-Bampton (HCB) transformation is a widely used method in structural dynamics for reducing the interior portion of a finite element model while having the ability to retain all nonlinear contact degrees of freedom (DOF) in physical coordinates. These models may still require many DOF to adequately resolve the kinematics of the interface, leading to inadequate reduction and computational savings. This study proposes a novel interface reduction method to overcome these challenges by means of system-level characteristic constraint (SCC) modes and properly orthogonal interface modal derivatives (POIMDs) for transient dynamic analyses. Both SCC modes and POIMDs are computed using the reduced HCB mass and stiffness matrices, which can be directly computed from many commercial finite element analysis software. Comparison of time history responses to an impulse-type load in a mechanical beam assembly indicate that the interface-reduced model correlates well with the HCB truth model. Localized features like slip and contact area are well-represented in the time domain when the beam assembly is loaded with a broadband excitation. The proposed method also yields reduced-order models with greater critical timestep lengths for explicit integration schemes.

42 ENGINEERING↗
DOE OSTI2025

Pseudoatom molecular dynamics plasma microfields

Spectral lines are powerful diagnostic tools for both laboratory and astrophysical plasmas, as their shape is sensitive to the plasma environment. The low-frequency component of the electric microfield is an important input for semi-analytic line broadening codes. Here, in this paper, we detail a new method of calculating plasma microfields using configuration-resolved pseudoatom molecular dynamics. This approach accounts for both quantum atomic structure and N-body effects, similar to density functional theory molecular dynamics, but with less computational cost. We present pseudoatom microfields at plasma conditions relevant for recent high energy density laboratory astrophysics experiments conducted at the Sandia Z-Machine, National Ignition Facility, and Linac Coherent Light Source. Compared to established microfield codes we find moderate deviations at solid density conditions and strong agreement at lower plasma densities.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Evaluating the Chemical Reactivity of DFT-Simulated Liquid Water with Hydrated Electrons via the Dual Descriptor

Modeling the various properties of liquid water, particularly its reactivity, has been a longstanding challenge for simulation methods. Recently, ab initio simulations based on density functional theory (DFT) have come to the fore as tenable methods for calculating the properties and reactivity of water, with varying degrees of success for different exchange-correlation functionals. In particular, hybrid-GGA and meta-GGA functionals have been shown to reproduce many of the structural, dynamical, and energetic properties of water to a high degree of accuracy relative to their computational cost. Here, we show that the dual descriptor (DD) measure of nucleophilicity and electrophilicity, which is sometimes used to elucidate organic chemistry reaction mechanisms, can also be used to characterize the reactivity of DFTsimulated liquid water. The DD is especially apt for understanding the reactivity of excess electrons with water as its calculation explicitly involves adding and removing an excess electron from a reference system. We use the DD to explore the reactivity of water simulated using three different DFT functionals: the LDA functional (LDA), a hybrid-GGA functional (PBE0), and a hybrid meta- GGA functional (SCAN0). Using the DD, we show that the SCAN0 functional with the standard 25% Hartree–Fock exchange produces simulated liquid water with many regions that are far more reactive than either PBE0 or LDA. To understand the implications of these highly reactive regions, we then add a strong nucleophile in the form of an excess electron and find that although PBE0 and LDA predict stable hydrated electrons, the excess electron reacts nearly instantaneously with SCAN0 water via proton abstraction to form a hydrogen atom and hydroxide ion. We show that the DD provides the ability to not only predict whether or not liquid water will react with a hydrated electron but also which particular waters will be involved solely from analyzing pure water configurations generated with each functional. We rationalize this result in terms of the known trap-seeking behavior of injected hydrated electrons, which are able to find the most electronegative region in bulk water. These results highlight the utility of the dual descriptor as a fast and interpretable method for investigating condensed-phase reactivity with excess electrons.

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

Predictive Rules of Efflux Inhibition and Avoidance in Pseudomonas aeruginosa

Antibiotic-resistant bacteria rapidly spread in clinical and natural environments and challenge our modern lifestyle. A major component of defense against antibiotics in Gram-negative bacteria is a drug permeation barrier created by active efflux across the outer membrane. We identified molecular determinants defining the propensity of small peptidomimetic molecules to avoid and inhibit efflux pumps in Pseudomonas aeruginosa, a human pathogen notorious for its antibiotic resistance. Combining experimental and computational protocols, we mapped the fate of the compounds from structure-activity relationships through their dynamic behavior in solution, permeation across both the inner and outer membranes, and interaction with MexB, the major efflux transporter of P. aeruginosa. We identified predictors of efflux avoidance and inhibition and demonstrated their power by using a library of traditional antibiotics and compound series and by generating new inhibitors of MexB. The identified predictors will enable the discovery and optimization of antibacterial agents suitable for treatment of P. aeruginosa infections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

MULTISTEP AND CONTINUOUS PHYSICS-INFORMED NEURAL NETWORK METHODS FOR LEARNING GOVERNING EQUATIONS AND CONSTITUTIVE RELATIONS

In this work, we investigate the applicability and relative merit of discrete and continuous versions of physics-informed neural network (PINN) methods for learning unknown governing equations or constitutive relations in a nonlinear dynamical system. In the case of unknown dynamics, entire right-hand-side (RHS) equations of the ordinary differential equations are unknown. In the case of unknown constitutive relations, however, the RHS equations are known up to the specification of constitutive relations (that may depend on the state of the system). We use a deep neural network to model unknown governing equations or constitutive relations. The discrete PINN approach combines classical multistep discretization methods for dynamical systems with neural-network-based machine learning methods. On the other hand, the continuous versions utilize deep neural networks to minimize the residual function for the continuous governing equations. We use the case of a fedbatch bioreactor system to study the effectiveness of these approaches and discuss conditions for their applicability. Our results indicate that the accuracy of the trained neural network models is much higher for the cases where we only have to learn a constitutive relation instead of all dynamics. This finding corroborates the well-known fact from scientific computing that building as much structural information as is available into an algorithm can enhance its efficiency and/or accuracy.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

On the Response of a Herschel–Bulkley Fluid Due to a Moving Plate

In this paper, we study the boundary-layer flow of a Herschel–Bulkley fluid due to a moving plate; this problem has been experimentally investigated by others, where the fluid was assumed to be Carbopol, which has similar properties to cement. The computational fluid dynamics finite volume method from the open-source toolbox/library OpenFOAM is used on structured quad grids to solve the mass and the linear momentum conservation equations using the solver “overInterDyMFoam” customized with non-Newtonian viscosity libraries. The governing equations are solved numerically by using regularization methods in the context of the overset meshing technique. The results indicate that there is a good comparison between the experimental data and the simulations. The boundary layer thicknesses are predicted within the uncertainties of the measurements. The simulations indicate strong sensitivities to the rheological properties of the fluid.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Data‐Driven Engineering of Thermostable Collagen‐Mimetic Peptoid Triple Helices

Collagen-mimetic peptides (CMPs) are engineered molecules designed to replicate the triple-helical structure of natural collagen. A repeating x–y-Gly sequence is the defining motif of CMPs and is critical to their triple-helical structure and stability. Substitutions to the residues occupying the x and y positions present a means to modulate the CMP structure and properties. Peptoid residues—N-substituted glycine derivatives—present an attractive potential substitution due to their thermal stability, proteolytic resistance, biocompatibility, and diverse palette of non-natural side chains, but also tend to introduce a high degree of backbone flexibility that can diminish the stability of the triple helix. In this work, we report a computational active learning cycle comprising molecular dynamics simulation, Gaussian process regression, and Bayesian optimization to computationally identify a number of promising peptoid substitutions predicted to stabilize the desired quaternary structure through side chain interactions and produce stable peptoid-based collagen-like triple helices. To experimentally test the computational predictions, a top candidate identified by the screen was synthesized and imaged using scanning electron microscopy to resolve fibril-like bundles consistent with collagen-like triple helices. This work predicts a number of CMP peptoid substitutions capable of forming stable triple-helical structures, presents a generalizable design strategy for engineering desired peptoid structures, and opens new avenues for the design of peptoid-based biomimetic materials.

active learning↗
DOE OSTI2020

3D diffractive imaging of nanoparticle ensembles using an x-ray laser

Single particle imaging at x-ray free electron lasers (XFELs) has the potential to determine the structure and dynamics of single biomolecules at room temperature. Two major hurdles have prevented this potential from being reached, namely, the collection of sufficient high-quality diffraction patterns and robust computational purification to overcome structural heterogeneity. We report the breaking of both of these barriers using gold nanoparticle test samples, recording around 10 million diffraction patterns at the European XFEL and structurally and orientationally sorting the patterns to obtain better than 3-nm-resolution 3D reconstructions for each of four samples. With these new developments, integrating advancements in x-ray sources, fast-framing detectors, efficient sample delivery, and data analysis algorithms, we illuminate the path towards sub-nanometer biomolecular imaging. The methods developed here can also be extended to characterize ensembles that are inherently diverse to obtain their full structural landscape.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Gaussian integral method for void fraction

Here, a novel method, the Gaussian Integral Method (GIM), is presented for calculating void fractions in Computational Fluid Dynamics–Discrete Element Method (CFD-DEM) simulations. GIM is versatile and applicable to various grid types, including structured and unstructured polyhedral meshes, without requiring special boundary treatments. An optimization technique is introduced to make GIM independent of grid resolution and type. The method is validated against experimental data from a fluidized bed, demonstrating that GIM produces realistic simulations closely resembling experimental observations. Additionally, unstructured polyhedral grids using GIM outperform structured grids of equivalent resolution, yielding results more aligned with experimental data. The gradient of the void fraction is computed in the CFD solver and utilized in the DEM solver for precise estimation at particle locations. Overall, GIM provides an effective solution for void fraction calculations in particulate media simulations with complex geometries, enhancing the accuracy and applicability of CFD-DEM simulations for industrial processes.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

PyCCE: A python package for custer correlation expansion simulations of spin qubit dynamics.

PyCCE, an open-source Python library for simulating the dynamics of spin qubits in a spin bath, is presented using the cluster-correlation expansion (CCE) method. PyCCE includes modules to generate realistic spin baths, employing coupling parameters computed from first principles with electronic structure codes, and enables the user to run simulations with either the conventional or generalized CCE method. Three use cases of the Python library are illustrated: the calculation of the Hahn-echo coherence time of the nitrogen-vacancy in diamond; the calculation of the coherence time of the basal divacancy in silicon carbide at avoided crossings; and the calculation for magnetic field orientation-dependent dynamics of a shallow donor in silicon. The complete documentation, downloadable tutorials, and installation instructions are available at https://pycce.readthedocs.io/en/latest/.

coherence↗
DOE OSTI2022

A low-rank power iteration scheme for neutron transport criticality problems

Computing effective eigenvalues for neutron transport often requires a fine numerical resolution. Here, the main challenge of such computations is the high memory effort of classical solvers, which limits the accuracy of chosen discretizations. In this work, we derive a method for the computation of effective eigenvalues when the underlying solution has a low-rank structure. This is accomplished by utilizing dynamical low-rank approximation (DLRA), which is an efficient strategy to derive time evolution equations for low-rank solution representations. The main idea is to interpret the iterates of the classical inverse power iteration as pseudo-time steps and apply the DLRA concepts in this framework. In our numerical experiment, we demonstrate that our method significantly reduces memory requirements while achieving the desired accuracy. Analytic investigations show that the proposed iteration scheme inherits the convergence speed of the inverse power iteration, at least for a simplified setting.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Generalized representative structures for atomistic systems

A new method is presented to generate atomic structures that reproduce the essential characteristics of arbitrary material systems, phases, or ensembles. Previous methods allow one to reproduce the essential characteristics (e.g. the chemical disorder) of a large random alloy within a small crystal structure. The ability to generate small representations of random alloys, along with the restriction to crystal systems, results from using the fixed-lattice cluster correlations to describe structural characteristics. A more general description of the structural characteristics of atomic systems is obtained using complete sets of atomic environment descriptors. These are used within for generating representative atomic structures without restriction to fixed lattices. A general data-driven approach is provided here utilizing the atomic cluster expansion (ACE) basis. The N-body ACE descriptors are a complete set of atomic environment descriptors that span both chemical and spatial degrees of freedom and are used within for describing atomic structures. The generalized representative structure (GRS) method presented within generates small atomic structures that reproduce ACE descriptor distributions corresponding to arbitrary structural and chemical complexity. It is shown that systematically improvable representations of crystalline systems on fixed parent lattices, amorphous materials, liquids, and ensembles of atomic structures may be produced efficiently through optimization algorithms. With the GRS method, we highlight reduced representations of atomistic machine-learning training datasets that contain similar amounts of information and small 40–72 atom representations of liquid phases. The ability to use GRS methodology as a driver for informed novel structure generation is also demonstrated. The advantages over other data-driven methods and state-of-the-art methods restricted to high-symmetry systems are highlighted.

atomic cluster expansion↗
DOE OSTI2024

Nuclear Fuel and Pu Redox Studies from The Glenn T. Seaborg Institute at Idaho National Laboratory

The Glenn T. Seaborg Institute at Idaho National Laboratory (INL-GTSI) focuses on advancing fundamental research in the actinide sciences by providing unique opportunities to early career scientists and engineers to gain experience studying the actinide elements and their associated systems. The INL-GTSI is built from three focus areas that are based on the expertise and supporting infrastructure at INL and include solid state chemistry and physics, solution phase chemistry and physics, and forensic and isotope science. INL is the lead Laboratory for nuclear energy research and development in the U. S. and the research on nuclear fuels performed under the INL-GTSI gives good examples of solid state studies. Uranium-Molybdenum (U-Mo) alloys are leading fuel candidates for conversion of high performance research and test reactors to low-enriched fuels. During irradiation, generated fission gas accumulates into bubbles and self-organizes into a gas bubble superlattice (GBS) that effectively stores fission gases and inhibits fuel swelling. A study on the early self- organizing behavior of the GBS shows that not only grain boundaries but the interfaces between the U-Mo matrix and uranium carbide (UC) impurities are important to GBS formation.[1] In solution, understanding the complex redox behavior of plutonium in aqueous environments is critical for establishing optimized nuclear waste reprocessing solvent systems and storage tank environments. INL-GTSI researchers have produced an experimentally validated multi-scale model of the gamma radiation induced behavior of plutonium ions in concentrated aqueous HNO3 solutions.[2] Here, gamma radiation effected only minimal steady state changes in the redox distribution of the plutonium oxidation states. The redox cycling between Pu(IV) and Pu(III) is demonstrated to be mediated by the •OH/NO3• radical oxidation of Pu(III) and the H2O2/HNO3 driven reduction of Pu(IV). The INL-GTSI offers young researchers the unique chance to work directly with actinide bearing materials in a U. S. National Laboratory environment. Further topical areas of interest to the INL-GTSI include, but are not limited to, fundamental actinide properties, structure/property (electronic, magnetic, thermal) relations, actinide quantum criticality, f- electron interactions, electron correlations, computational studies, new phases, defect effects, interface interactions, isotope production and separation, forensic analytical chemistry, structure and dynamic properties of actinides in non-aqueous media, separations chemistry and kinetics for advanced nuclear fuel cycles, radiation effects, and innovative and advanced ligand design for complexation of the actinides.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics

SARS-CoV-2 depends on -1 programmed ribosomal frameshifting (-1 PRF) to express proteins essential for its replication. The RNA pseudoknot stimulating -1 PRF is thus an attractive drug target. However, the structural models of this pseudoknot obtained from cryo-EM and crystallography differ in some important features, leaving the pseudoknot structure unclear. We measured the solution structure of the pseudoknot using small-angle X-ray scattering (SAXS). The measured profile did not agree with profiles computed from the previously solved structures. Beginning with each of these solved structures, we used the SAXS data to direct all atom molecular dynamics (MD) simulations to improve the agreement in profiles. In all cases, this refinement resulted in a bent conformation that more closely resembled the cryo-EM structures than the crystal structure. Applying the same approach to a point mutant abolishing -1 PRF revealed a notably more bent structure with reoriented helices. This work clarifies the dynamic structures of the SARS-CoV-2 pseudoknot in solution.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

How Atomic Bonding Plays the Hardness Behavior in the Al–Co–Cr–Cu–Fe–Ni High Entropy Family

A systematic study on a face-centered cubic-based compositionally complex alloy system Al–Co–Cr–Cu–Fe–Ni in its single-phase state is carried out, where a mother senary compound Al 8 Co 17 Cr 17 Cu 8 Fe 17 Ni 33 and five of its suballoys, obtained by removing one element at a time, are investigated and exhaustively analyzed determining the contribution of each alloying element in the solid solution. The senary and the quinaries are compared using experimental techniques including X-ray absorption spectroscopy, X-ray diffraction, transmission electron microscopy, and first principles hybrid Monte Carlo/molecular dynamics simulations. Chemical short-range order and bond length distances have been determined both at the experimental and computational level. Electronic structure and local atomic distortions up to 5.2 Å have been correlated to the microhardness values. A linear regression model connecting hardness with local lattice distortions is presented.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Computing inelastic neutron scattering spectra from molecular dynamics trajectories

Abstract Inelastic neutron scattering (INS) provides a weighted density of phonon modes. Currently, INS spectra can only be interpreted for perfectly crystalline materials because of high computational cost for electronic simulations. INS has the potential to provide detailed morphological information if sufficiently large volumes and appropriate structural variety are simulated. Here, we propose a method that allows direct comparison between INS data with molecular dynamics simulations, a simulation method that is frequently used to simulate semicrystalline/amorphous materials. We illustrate the technique by analyzing spectra of a well-studied conjugated polymer, poly(3-hexylthiophene-2,5-diyl) (P3HT) and conclude that our technique provides improved volume and structural variety, but that the classical force field requires improvement before the morphology can be accurately interpreted.

36 MATERIALS SCIENCE↗