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At least 145 records · Page 8

Roadmap on methods and software for electronic structure based simulations in chemistry and materials

This Roadmap article provides a succinct, comprehensive overview of the state of electronic structure methods and software for molecular and materials simulations. Seventeen distinct sections collect insights by 51 leading scientists in the field. Each contribution addresses the status of a particular area, as well as current challenges and anticipated future advances, with a particular eye towards software related aspects and providing key references for further reading. Foundational sections cover density functional theory and its implementation in real-world simulation frameworks, Green's function based many-body perturbation theory, wave-function based and stochastic electronic structure approaches, relativistic effects and semiempirical electronic structure theory approaches. Subsequent sections cover nuclear quantum effects, real-time propagation of the electronic structure, challenges for computational spectroscopy simulations, and exploration of complex potential energy surfaces. The final sections summarize practical aspects, including computational workflows for complex simulation tasks, the impact of current and future high-performance computing architectures, software engineering practices, education and training to maintain and broaden the community, as well as the status of and needs for electronic structure based modeling from the vantage point of industry environments. Overall, the field of electronic structure software and method development continues to unlock immense opportunities for future scientific discovery, based on the growing ability of computations to reveal complex phenomena, processes and properties that are determined by the make-up of matter at the atomic scale, with high precision.

36 MATERIALS SCIENCE↗

Molecular-Resolution Electron Imaging of Defects and Dynamics at the Ice-Water Interface

Water crystallization into hexagonal ice (type I h ) is one of the most critical processes relevant to the Earth’s environment and human activities. However, despite recent breakthroughs in imaging non-equilibrium condensed ice structures, the ice-water interface has never been imaged at a molecular resolution. This is primarily due to the low stability of the hydrogen bonds in ice under high-resolution microscopy conditions and a lack of methods to prepare compatible samples. Here, this presentation describes the first molecular-resolution imaging of ice crystallized from liquid water and the ice-water interface using high-resolution transmission electron microscopy (HRTEM). By encapsulating deionized (DI) water between two amorphous carbon (a-C) TEM grids and subsequently freezing it with liquid N 2 on a cryo sample stage, we generated two types of ice: non-equilibrium, condensed ice from the atmosphere and encapsulated ice from the DI water (Fig. 1A). Condensed ice usually shows irregular, spherulitic shapes (Fig. 1B). Selected area electron diffraction (SAED) shows that they are a mixture of cubic and hexagonal crystals (Fig. 1C). On the contrary, encapsulated ice forms thin films that contain large-area single-crystalline regions of hexagonal ice oriented along the [0001] zone axis (Fig. 1D). Differential electron energy-loss spectroscopy (EELS) confirmed the high purity of the encapsulated ice free from organic contaminations that are common in other encapsulation methods for HRTEM such as graphene liquid cells. These single-crystalline areas are robust under the electron beam up to ~100 e/Å 2 s. Aberration-corrected HRTEM imaging in these areas achieved a line resolution of ~1.3 Å (Fig. 1E and F). This platform allows us to study near-equilibrium ice structures and dynamics at an unprecedented spatial resolution (Fig. 2). For example, we discovered subdomain-rich regions near the defective crystal edges despite the structure appearing single-crystalline according to diffraction criteria. These subdomains connect via low-angle grain boundaries with flat energy landscapes as a function of tilt angles (according to simulations), showing the high tolerance of ice to defect structures. When we tuned the sample temperature and electron flux rate, we observed radiolysis-controlled bubble generation and dissolution in ice single crystals near a steady state of bubble dynamics. Furthermore, rich beam-induced melting and recrystallization dynamics were observed at the ice-water interface with lattice resolution. These data represent the first observation of the ice-water phase transformation at the sub-nanometer level. In summary, the methods developed in this work enabled molecular-resolution observations of ice and the ice-water interface and shed light on the microstructures and phase transformation pathways. Finer control on the temperature, electron irradiation profile, and imaging detector could eventually lead to real-time observation of ice nucleation in water and address long-standing questions in the nucleation pathways.

74 ATOMIC AND MOLECULAR PHYSICS↗

BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

Abstract BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models and computational chemistry methods development. This update reports significant growth and enhancements since our last review in 2016. Of note, the database now contains 2.9 million binding measurements spanning 1.3 million compounds and thousands of protein targets. This growth is largely attributable to our unique focus on curating data from US patents, which has yielded a substantial influx of novel binding data. Recent improvements include a remake of the website following responsive web design principles, enhanced search and filtering capabilities, new data download options and webservices and establishment of a long-term data archive replicated across dispersed sites. We also discuss BindingDB’s positioning relative to related resources, its open data sharing policies, insights gleaned from the dataset and plans for future growth and development.

Liu, Tiqing↗

Continuous-variable quantum computation of the O(3) model in 1+1 dimensions

We formulate the $O(3)$ non-linear sigma model in $1+1$ dimensions as a limit of a three-component scalar field theory restricted to the unit sphere in the large squeezing limit. This allows us to describe the model in terms of the continuous variable (CV) approach to quantum computing. Here we construct the ground state and excited states using the coupled cluster ansatz and find excellent agreement with the exact diagonalization results for a small number of lattice sites. We then present the simulation protocol for the time evolution of the model using CV gates, estimate the discretization error, and present numerical results obtained from a photonic quantum simulator. We expect that the methods developed in this work will be useful for exploring interesting dynamics for a wide class of sigma models and gauge theories, as well as for simulating scattering events on quantum hardware in the coming decade.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Direct statistical simulation of the Lorenz96 system in model reduction approaches

Direct statistical simulation (DSS) of nonlinear dynamical systems bypasses the traditional route of accumulating statistics by lengthy direct numerical simulations by solving the equations that govern the statistics themselves. DSS suffers, however, from the curse of dimensionality as the statistics (such as correlations) generally have higher dimensions than the underlying dynamical variables. Here we investigate two approaches to reduce the dimensionality of DSS, illustrating each method with numerical experiments with the Lorenz96 dynamical system. The forms of DSS chosen here involve approximate closures at second and third order in the equal-time cumulants. We demonstrate significant reduction in computational effort that can be achieved without sacrificing the accuracy of DSS. The methods developed here can be applied to turbulent fluid and magnetohydrodynamical systems. Published by the American Physical Society 2025

Li, Kuan↗

Real-Time Operator Evolution in Two and Three Dimensions via Sparse Pauli Dynamics

We study real-time operator evolution using sparse Pauli dynamics, a recently developed method for simulating expectation values of quantum circuits. On the examples of energy and charge diffusion in one-dimensional (1D) spin chains and sudden quench dynamics in the 2D transverse-field Ising model, it is shown that this approach can compete with state-of-the-art tensor network methods. We further demonstrate the flexibility of the approach by studying quench dynamics in the 3D transverse-field Ising model that is highly challenging for tensor network methods. For the simulation of expectation value dynamics starting in a computational basis state, we introduce an extension of sparse Pauli dynamics that truncates the growing sum of Pauli operators by discarding terms with a large number of X and Y matrices. This is validated by our 2D and 3D simulations. Finally, we argue that sparse Pauli dynamics is not only capable of converging challenging observables to high accuracy, but can also serve as a reliable approximate approach even when given only limited computational resources. Published by the American Physical Society 2025

Begušić, Tomislav (ORCID:0000000279424134)↗

Energy filtering–induced ultrahigh thermoelectric power factors in Ni 3 Ge

Traditional thermoelectric materials rely on low thermal conductivity to enhance their efficiency but suffer from inherently limited power factors. Innovative pathways to optimize electronic transport are thus crucial. Here, we achieve ultrahigh power factors in Ni 3 Ge-based systems through an unconventional thermoelectric materials design principle. When overlapping flat and dispersive bands are engineered to the Fermi level, charge carriers can undergo intense interband scattering, yielding an energy filtering effect similar to what has long been predicted in certain nanostructured materials. Via a multistep DFT-based screening method developed here, we find a family of L1 2 -ordered binary compounds with ultrahigh power factors up to 11 mW m −1 K −2 near room temperature, which are driven by an intrinsic phonon-mediated energy filtering mechanism. Our comprehensive experimental and theoretical study of these intriguing materials paves the way for understanding and designing high-performance scattering-tuned metallic thermoelectrics.

Science & Technology - Other Topics↗

Mitigation of Pitting on Nitrogen-Doped Niobium Surfaces through Two-Step Electropolishing

Surface processing of niobium superconducting RF cavities used in particle accelerators is crucial for determining their performance. The nitrogen (N)-doping method, developed at Fermilab, enhances the cavities’ quality factor by doping the cavity’s interior surface with N atoms at 800 °C. After N-doping, electropolishing (EP) is employed to remove the niobium nitride phases and attain the desired concentration of interstitial N atoms. This study explores the effects of EP conditions on N-doped niobium samples. The samples were electropolished at 5 to 40 °C and voltages between 3 and 22 V. Different EP voltage ranges produced two types of pits, classified based on their sizes. Larger pits, linked to higher voltages, are also affected by the reaction rate. Pitting could be reduced at a lower temperature and adequate EP voltage. However, to effectively minimize gas evolution forming large-sized pitting, peeling off the top nitride layer before EP might be beneficial. This was achieved through precise low-voltage etching, forming a two-step EP process. The process involves removing the top 100–200 nm layer at a low voltage, followed by standard EP to remove the required material. This two-step EP process effectively mitigated the pitting risk associated with gas evolution on N-doped surfaces.

43 PARTICLE ACCELERATORS↗

Progress and Perspectives: Zirconium Electrodeposition from Different Electrolytes

Zirconium (Zr) possesses outstanding properties, including exceptional chemical resistance and a high melting point, and is therefore desirable for use in a wide variety of challenging environments, such as in nuclear reactors and the chemical processing industry. To minimize the amount of Zr required for any given application, developing methods for generating metallic Zr coatings is highly advantageous. Owing to Zr’s highly negative reduction potential, electrodeposition in traditional solvents at near ambient temperatures remains challenging and thus not well understood. Due to the extreme conditions required to deposit this metal, extensive work has been conducted in molten salt electrolytes, however the broad applicability of this methodology is limited due to its corrosivity. The primary focus of this article is to present an overview of Zr’s electrochemical behavior and to consolidate the efforts of researchers in exploring electrodeposition techniques for Zr involving aqueous, organic, ionic liquid, deep eutectic, and molten salt solvents. With this information, we highlight trends across solvent systems and opportunities for future research.

42 ENGINEERING↗

ATcT — Active Thermochemical Tables Python Interface

SF-25-140 atct is a lightweight, Python client for the ATcT v1 API that enables programmatic access to high-accuracy thermochemical data and turnkey reaction-enthalpy analysis. The package implements full v1 endpoint coverage (species lookup by ATcT ID, name, formula, SMILES, InChI, CAS RN; covariance queries; health checks) with robust error handling, retries, and environment-based configuration for local/production endpoints. Beyond data retrieval, atct provides rigorously implemented reaction calculators that propagate uncertainties via either (i) a conventional independent-errors method (0 K or 298.15 K) or (ii) covariance-aware propagation using provided covariances at 298.15 K. Typed data classes ensure transparent, reproducible data structures and carry ATcT Thermochemical Network (TN) version identifiers for provenance. Dual import paths and comprehensive examples facilitate integration into research pipelines, enabling reproducible thermochemical calculations, automated validation, and downstream method development.

Bross, DavidHamilton [Argonne National Laboratory ↗

Pooled PPIseq: Screening the SARS-CoV-2 and human interface with a scalable multiplexed protein-protein interaction assay platform

Protein-Protein Interactions (PPIs) are a key interface between virus and host, and these interactions are important to both viral reprogramming of the host and to host restriction of viral infection. In particular, viral-host PPI networks can be used to further our understanding of the molecular mechanisms of tissue specificity, host range, and virulence. At higher scales, viral-host PPI screening could also be used to screen for small-molecule antivirals that interfere with essential viral-host interactions, or to explore how the PPI networks between interacting viral and host genomes co-evolve. Current high-throughput PPI assays have screened entire viral-host PPI networks. However, these studies are time consuming, often require specialized equipment, and are difficult to further scale. Here, we develop methods that make larger-scale viral-host PPI screening more accessible. This approach combines the mDHFR split-tag reporter with the iSeq2 interaction-barcoding system to permit massively-multiplexed PPI quantification by simple pooled engineering of barcoded constructs, integration of these constructs into budding yeast, and fitness measurements by pooled cell competitions and barcode-sequencing. We applied this method to screen for PPIs between SARS-CoV-2 proteins and human proteins, screening in triplicate >180,000 ORF-ORF combinations represented by >1,000,000 barcoded lineages. Our results complement previous screens by identifying 74 putative PPIs, including interactions between ORF7A with the taste receptors TAS2R41 and TAS2R7, and between NSP4 with the transmembrane KDELR2 and KDELR3. We show that this PPI screening method is highly scalable, enabling larger studies aimed at generating a broad understanding of how viral effector proteins converge on cellular targets to effect replication.

60 APPLIED LIFE SCIENCES↗

Transverse orbital angular momentum and polarization entangled spatiotemporal structured light

Intra-system entanglement occurs between non-separable modes within the same system. For optical systems, the various degrees of freedom of light represent different modes, and the potential use of light to create higher dimensional classical entangle states offers a promising potential to drive new technological developments. In this work, we present experimental results demonstrating the orthogonality between transverse orbital angular momentum (t-OAM) of different spatiotemporal topological charges, a previously unverified property of t-OAM. Based on those results, we developed methods to create and characterize a novel family of t-OAM and polarization entangled spatiotemporal structured light. We further provide theoretical analysis to support our study of the entanglement between those modes. By demonstrating the feasibility of leveraging t-OAM as a new family of modes for classical entanglement, our work represents a new advancement towards higher dimensional classical entanglement strategies.

42 ENGINEERING↗

Machine Learned Force Field Modeling of Metal Organic Frameworks for CO2 Direct Air Capture

Metal organic frameworks (MOFs) are a large class of porous materials and have garnered significant interest due to their large surface areas and their tunable physical and chemical properties. Numerous prior studies have been performed to screen large databases of this material class for promising DAC sorbent materials. These studies have often relied on classical model potentials. While density functional theory (DFT) calculations have been shown to be very accurate for modeling the interaction of CO2 with MOFs, such calculations are too computationally demanding for statistically significant adsorption predictions. To overcome this barrier, we developed methods for training models to achieve DFT-level accuracy for the forces and energies associated with MOF flexibility and CO2 adsorption using machine learned force fields (MLFFs). These methods were parametrized based on DFT calculations of CO2 in a flexible MOF and used to predict MOF structural properties as well as CO2 adsorption in several MOFs.

Findley, John↗

Large-x partons from Jefferson Lab to the LHC

This project addressed the longitudinal quark and gluon structure of hadrons, a key topic in the 2015 and 2023 NSAC long range plans for nuclear science. The research encompassed and combined theoretical studies with advanced Quantum Chromo Dynamics (QCD) analysis of experimental data, from Jefferson Lab to the Large Hadron Collider. The results have pushed the boundaries in both aspects, and capitalized on the results and methods developed in previous grant renewals.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Mechanisms of Mobility of Grain Boundaries in Tungsten

The objective of this study is to assess the mechanical robustness of tungsten in first-wall applications for tokamaks. These applications unavoidably involve the challenges of high temperature and radiation damage. Here we report progress on determining the mechanisms governing the mobility of tungsten grain boundaries at high temperature, a key property in the process of recrystallization. The determination of mechanisms enables predictive analytic models of grain boundary response to driving forces like the energy stored in the damaged metal lattice that is released as a grain boundary sweeps through it. In prior work we studied tungsten grain boundary properties such as the energies of boundaries with various orientations and misorientations, including energies of grain boundaries whose high-temperature structure differs from the structure at ambient conditions. We have calculated properties associated with the grain boundary mobility including the response of grain boundaries to applied shear stress. We have also developed methods for direct calculation of the motion of curved grain boundaries at high temperature using molecular dynamics. Here we again utilize molecular dynamics simulation of grain boundary motion and go further to analyze how the defect content in a grain boundary evolves as the boundary moves under the action of a driving force.

36 MATERIALS SCIENCE↗

Using Infrasound to Inform Avalanche Hazard Forecasts

Avalanches are natural hazards that occur when an unstable mass of snow breaks away from a mountain slope. It is expected that climate change will lead to increased avalanche activity, which can cause interruptions to water and power infrastructure, transportation blockages, higher risk for loss of life, and changes to ecosystems. Avalanche forecasts are key to mitigating hazards, and observations of recent avalanches comprise one of the key observations for deciding danger level. It is well understood that infrasound can be used to detect and locate snow avalanches in transitional snowpacks, even during snowstorms, but similar studies are lacking for maritime snowpacks. Here we show results from an infrasound field experiment in Tutl’uh (Turnagain Arm), Alaska, USA between January 31 – April 30 field deployment campaign. We show that (1) methods developed for transitional snowpacks can be applied to maritime snowpacks in Alaska, (2) background noise may be higher in this region due to natural and anthropogenic influences, and (3) low-cost infrasound sensors can withstand the harsh Alaskan winter and successfully collect data. We also discuss the impact of this work and a path forward.

58 GEOSCIENCES↗

Modeling of Seismic Waves Through Geologic Metamaterials

This project conducted a modeling study on seismic invisibility cloaks that render geologic targets invisible to seismic waves, using the concept of seismic metamaterials. We present a parametric numerical study on the behaviors of seismic waves through cloaks with different design parameters as well as degrees of geologic heterogeneity. In addition, a seismic cloaking strategy is proposed for a future field-scale experiment at a real-world test bed. This feasibility study will guide future field experiment designs and ultimately allow us to conduct systematic field-scale tests employing Sandia’s existing resources and field expertise. The ultimate goal is to develop methods and design parameters of seismic invisibility cloaks to protect against natural and man-made seismic waves. Seismic cloaking has potential applications in several areas of national security, energy, and natural hazard reduction.

58 GEOSCIENCES↗

Preliminary Design of Engineering-Scale Salt Accident Analysis Facility to Support Molten Salt Reactor Licensing

Systems-level nuclear accident analysis codes for reactor licensing must be validated using experimental data that represent behaviors expected during actual full-scale accidents. Some behaviors may arise from coupled processes and only manifest at large scales. This report presents the preliminary design of the Salt Accident Analysis Facility (SAAF, pronounced “safe”), which is an experimental test facility to be constructed at Argonne that can be used to conduct integrated salt accident tests at an engineering scale. The measurement capabilities of the SAAF are based on previously developed methods and will provide the representative datasets that are needed to support molten salt reactor (MSR) licensing. Details of the design, the processes to be quantified, the measurement techniques for quantifying the processes, the variables that can be adjusted to simulate different accident scenarios, and operational considerations are presented herein. This report provides stakeholders the opportunity to give feedback on the test facility capabilities and planned analyses before it is constructed.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗