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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A high order Cartesian grid, finite volume method for elliptic interface problems

We present a higher-order finite volume method for solving elliptic PDEs with jump conditions on interfaces embedded in a 2D Cartesian grid. Second, fourth, and sixth order accuracy is demonstrated on a variety of tests including problems with high-contrast and spatially varying coefficients, large discontinuities in the source term, and complex interface geometries. We include a generalized truncation error analysis based on cell-centered Taylor series expansions, which then define stencils in terms of local discrete solution data and geometric information. In the process, we develop a simple method based on Green's theorem for computing exact geometric moments directly from an implicit function definition of the embedded interface. This approach produces stencils with a simple bilinear representation, where spatially-varying coefficients and jump conditions can be easily included and finite volume conservation can be enforced.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

High-order dimensionally-split Cartesian embedded boundary method for non-dissipative schemes

Centered finite-difference schemes are commonly used for high-fidelity turbulent flow simulations in canonical configurations because of their non-dissipative property and computational efficiency. However, their use in flow simulations over complex geometries is limited by the requirements of a structured grid and a stable boundary treatment in the absence of artificial (numerical) dissipation. Cartesian embedded boundary (EB) approaches provide an efficient structured-grid framework to apply difference schemes over complex domains. However, they are often restricted to low orders of accuracy because of numerical instabilities at the embedded boundaries and the issues of small-cell problem that are difficult to address with high-order accuracy. The present work discusses a systematic approach to obtain high-order EB methods with non-dissipative centered schemes in the interior. This approach, based on satisfying the primary and secondary conservation conditions, is employed to derive EB schemes that are up to sixth-order accurate in the interior and fourth-order accurate globally for hyperbolic, parabolic as well as incompletely parabolic problems. The proposed finite-difference discretization is, by construction, dimensionally split and addresses the small-cell problem without any cell/geometry transformations, thus, highly simplifying implementation in a flow solver. Various linear and non-linear numerical tests are performed to evaluate the stability and the accuracy of the proposed EB schemes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Comparing three generations of D-Wave quantum annealers for minor embedded combinatorial optimization problems

Abstract Quantum annealing (QA) is a novel type of analog computation that aims to use quantum mechanical fluctuations to search for optimal solutions of Ising problems. QA in the transverse Ising model, implemented on D-Wave quantum processing units, are available as cloud computing resources. In this study we report concise benchmarks across three generations of D-Wave quantum annealers, consisting of four different devices, for the NP-hard discrete combinatorial optimization problems unweighted maximum clique and unweighted maximum cut on random graphs. The Ising, or equivalently quadratic unconstrained binary optimization, formulation of these problems do not require auxiliary variables for order reduction, and their overall structure and weights are not highly variable, which makes these problems simple test cases to understand the sampling capability of current D-Wave quantum annealers. All-to-all minor embeddings of size 52, with relatively uniform chain lengths, are used for a direct comparison across the Chimera, Pegasus, and Zephyr device topologies. A grid-search over annealing times and the minor embedding chain strengths is performed in order to determine the level of reasonable performance for each device and problem type. Experiment metrics that are reported are approximation ratios for non-broken chain samples, chain break proportions, and time-to-solution for the maximum clique problem instances. How fairly the quantum annealers sample optimal maximum cliques, for instances which contain multiple maximum cliques, is quantified using entropy of the measured ground state distributions. The newest generation of quantum annealing hardware, which has a Zephyr hardware connectivity, performed the best overall with respect to approximation ratios and chain break frequencies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Carbon aerogels with integrated engineered macroporous architectures for improved mass transport

Carbon aerogels (CAs) combine unique properties including ultra-high surface area, high electrical conductivity, corrosion resistance, and robust mechanical properties making them ideal materials for electrochemical applications. Traditional CA synthesis results in isotropic, random nanoporous networks that work well for applications relying on diffusional mass transport. However, many applications would benefit from integration of engineered macroporous network structures that enable directed pressure-gradient-driven mass transport. In this study, we report on using 3D-printed sacrificial polymeric templates to generate templated CAs (t-CAs) with integrated engineered nonrandom macroporous network structures. Specifically, we used projection micro-stereo-lithography (PμSL) and two-photon polymerization direct laser writing (2PP-DLW) to fabricate millimeter-to-centimeter-sized 3D sacrificial polymeric templates with features ranging from tens of microns (PμSL) to 100s of nanometers (2PP-DLW). T-CAs were fabricated by infiltrating the templates with resorcinol-formaldehyde (RF) precursor solution, followed by carbonization at 1050 °C to simultaneously convert the RF gel to a CA and decompose the 3D-printed template, leaving an embedded templated macroporous network structure behind. X-ray computer tomography confirms integration of the macroporous architecture defined by the template. The templated macroporous architecture improves mass transport in t-CAs compared to traditional bulk CA as demonstrated by more uniform activation and their response in electrochemical cyclic voltammetry and galvanostatic charge-discharge tests.

36 MATERIALS SCIENCE↗
DOE OSTI2024

PigmentHunter: A point-and-click application for automated chlorophyll-protein simulations

Chlorophyll proteins (CPs) are the workhorses of biological photosynthesis, working together to absorb solar energy, transfer it to chemically active reaction centers, and control the charge-separation process that drives its storage as chemical energy. Yet predicting CP optical and electronic properties remains a serious challenge, driven by the computational difficulty of treating large, electronically coupled molecular pigments embedded in a dynamically structured protein environment. To address this challenge, we introduce here an analysis tool called PigmentHunter, which automates the process of preparing CP structures for molecular dynamics (MD), running short MD simulations on the nanoHUB.org science gateway, and then using electrostatic and steric analysis routines to predict optical absorption, fluorescence, and circular dichroism spectra within a Frenkel exciton model. Inter-pigment couplings are evaluated using point-dipole or transition-charge coupling models, while site energies can be estimated using both electrostatic and ring-deformation approaches. The package is built in a Jupyter Notebook environment, with a point-and-click interface that can be used either to manually prepare individual structures or to batch-process many structures at once. Here, we illustrate PigmentHunter’s capabilities with example simulations on spectral line shapes in the light harvesting 2 complex, site energies in the Fenna–Matthews–Olson protein, and ring deformation in photosystems I and II.

14 SOLAR ENERGY↗
DOE OSTI2025

FluxRETAP: a REaction TArget Prioritization genome-scale modeling technique for selecting genetic targets

MOTIVATION: Metabolic engineering is rapidly evolving as a result of new advances in synthetic biology tools and automation platforms that enable high throughput strain construction, as well as the development of machine learning tools (ML) for biology. However, selecting genetic engineering targets that effectively guide the metabolic engineering process is still challenging. ML can provide predictive power for synthetic biology, but current technical limitations prevent the independent use of ML approaches without previous biological knowledge. RESULTS: Here, we present FluxRETAP, a simple and computationally inexpensive method that leverages the prior mechanistic knowledge embedded in genome-scale models for suggesting targets for genetic overexpression, downregulation or deletion, with the final goal of increasing the production of a desired metabolite. This method can provide a list of desirable engineering targets that can be combined with current ML pipelines. FluxRETAP captured 100% of reaction targets experimentally verified to improve Escherichia coli isoprenol production, 50% of targets that experimentally improved taxadiene production in E. coli and ∼60% of genetic targets from a verified minimal constrained cut-set in Pseudomonas putida, while providing additional high priority targets that could be tested. Overall, FluxRETAP is an efficient algorithm for identifying a prioritized list of testable genetic and reaction targets. AVAILABILITY AND IMPLEMENTATION: FluxRETAP is implemented in python and released under the creative commons license. The implementation and code are freely available at: https://github.com/JBEI/FluxRETAP.

Czajka, Jeffrey J↗
DOE OSTI2022

AbBERT: Learning Antibody Humanness via Masked Language Modeling

Understanding the degree of humanness of antibody sequences is critical to the therapeutic antibody development process to reduce the risk of failure modes like immunogenicity or poor manufacturability. We introduce AbBERT, a transformer-based language model trained on up to 20 million unpaired heavy/light chain sequences from the Observed Antibody Space database. We first validate AbBERT using a novel “multi-mask” scoring procedure to demonstrate high accuracy in predicting complementary determining regions—including the challenging hypervariable H3 region. We then demonstrate several uses of AbBERT at various points along the antibody design process. AbBERT enhances in silico antibody optimization via deep reinforcement learning by utilizing its learned embeddings as additional observations during optimization. Within a larger computational antibody design platform, AbBERT has been successfully applied as an additional design objective, where it displays strong correlations with computational tools predicting antibody structural stability. Finally, mutant antibody sequences that have been scored as unfavorable by AbBERT have shown corresponding low yields when expressed in cells. These use cases demonstrate the power of language modeling within computational antibody design.

Bioinformatics↗
DOE OSTI2022

ML-PSA

The computer code uses a parallel simulated annealing framework with embedded machine learning components to solve multi-constrained optimization problems. The software automatically balances the execution of low and high fidelity physics models within the optimization procedure. The low fidelity model is used to rapidly explore the design space while the high fidelity physics model is executed sparingly to account for complex design constraints that are not resolved by the quickly executing low fidelity model.

Gurecky, William↗
DOE OSTI2024

Flux REaction TArget Prioritization (Flux RETAP) v1

Metabolic engineering is evolving rapidly as a result of new advances in synthetic biology and automation, as well as the irruption of machine learning (ML). ML has been shown to provide the predictive power synthetic biology lacked and needed, and to be able to effectively guide the metabolic engineering process. However, current technical limitations prevent the independent application of ML approaches to metabolic engineering without the use of previous biological knowledge in the form of a prioritized list of desirable engineering targets. Here, we present FluxRETAP, a simple and computationally inexpensive method that leverages the prior mechanistic knowledge embedded in genome-scale metabolic models (GSMs) for suggesting targets for genetic overexpression, downregulation or deletion, with the final goal of increasing metabolite production. FluxRETAP captured 100% of reaction targets experimentally verified to improve Escherichia coli isoprenol production in the literature accessible to us, 50% of targets that experimentally improved taxadiene production in E. coli and ~60% of genetic targets from a verified minimal constrained cut-set in Pseudomonas putida while providing additional high priority targets that could be tested. Overall, FluxRETAP is an efficient algorithm for identifying a prioritized list of testable genetic and reaction targets which can also be utilized in ML pipelines.

Czajka, Jeffrey [Battelle Memorial Institute, Paci↗
DOE OSTI2023

G 0 W 0 Ionization Potentials of First-Row Transition Metal Aqua Ions

Here, we report computations of the vertical ionization potentials within the GW approximation of the near-complete series of first-row transition metal (V–Cu) aqua ions in their most common oxidation states, i.e., V 3+ , Cr 3+ , Cr 2+ , Mn 2+ , Fe 3+ , Fe 2+ , Co 2+ , Ni 2+ , and Cu 2+ . The d-orbital occupancy of these systems spans a broad range from d 2 to d 9 . All of the structures were first optimized at the density functional theory level using a large cluster of explicit water molecules that are embedded in a continuum solvation model. Vertical ionization potentials were computed with the one-shot G 0 W 0 approach on a range of transition metal ion clusters (6, 18, 40, and 60 explicit water molecules), wherein the convergence with respect to the basis set size was evaluated using the systems with 40 water molecules. We assess the results using three different density functional approximations as starting points for the vertical ionization potential calculations, namely, G 0 W 0 @PBE, G 0 W 0 @PBE0, and G 0 W 0 @r 2 SCAN. While the predicted ground-state structures are similar to all three exchange-correlation functionals, the vertical ionization potentials were in closer agreement with experiment when using the G 0 W 0 @PBE0 and G 0 W 0 @r 2 SCAN approaches, with the r 2 SCAN-based calculations being significantly less expensive. Computed bond distances and vertical ionization potentials for all structures are in good agreement with available experimental data.

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

Embedding Methods for Quantum Chemistry: Applications from Materials to Life Sciences

Quantum mechanical embedding methods hold the promise to transform not just the way calculations are performed, but to significantly reduce computational costs and improve scaling for macro molecular systems containing hundreds if not thousands of atoms. The field of embedding has grown increasingly broad with many approaches of different intersecting flavors. Here, we lay out the methods into two streams: QM:MM and QM:QM, showcasing the advantages and disadvantages of both. We provide a review of the literature, the underpinning theories including our contributions, and we highlight current applications with select examples spanning both materials and life sciences. Lastly, we conclude with prospects and future outlook on embedding, and our view on the use of universal test case scenarios for cross comparisons of the many available (and future) embedding theories.

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

Enhancing the Q-Factor of a Practical Qubit Niobium Three-Dimensional λ/4-Resonator Through Surface Treatment

Quantum computing stands as a revolutionary frontier in information technology, with the potential to solve complex problems far beyond the capacity of classical computers. At the heart of this disruptive innovation are qubits, forming the fundamental backbone of quantum computing. A leading-edge solution for constructing robust, enduring qubits involves embedding a Josephson junction within a high Q-factor, superconducting three-dimensional cavity. Further, our recent innovation lies in developing a uniquely optimized, quarter-wave resonator-based superconducting cavity, functioning at 6 GHz, specifically tailored for quantum computers. In this work, we elucidate our advancement towards elevating the Q-factor tenfold, an achievement made possible through the enhancement of machining precision, the application of rigorous postprocessing techniques—including mechanical, chemical, and surface treatments—as well as the refinement of our testing methods.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

CAFE AU LAIT: Compute-Aware Federated Augmented Low-Rank AI Training

Federated finetuning is crucial for unlocking the knowledge embedded in pretrained Large Language Models (LLMs) when data are geographically distributed across clients. Unlike finetuning with data from a single institution, federated finetuning allows collaboration across multiple institutions, enabling the utilization of diverse and decentralized datasets while preserving data privacy. Given the high computing costs of LLM training and the emphasis on energy efficiency in Federated Learning (FL), Low-Rank Adaptation (LoRA) has emerged as a widely adopted algorithm due to its significantly reduced number of trainable parameters. However, this assumes that all data silos have the necessary computing resources to compute local updates of LLMs. Nevertheless, in practice, the computing resources across clients are highly heterogeneous: while some may have access to hundreds of GPUs, others might have limited or no GPU access. Recently, federated finetuning using synthetic data has been proposed, allowing clients to participate in a collaborative training run without training LLMs locally. However, our experimental results reveal a performance gap between models trained using synthetic data and those trained using local updates. Motivated by the observed heterogeneity in computing resources and the performance gap, we propose a novel two-stage algorithm that leverages the storage and computing capabilities of a strong server. In the first stage, under the coordination of the strong server, clients with limited computing resources collaborate to generate synthetic data, which is transferred to and stored on the strong server. In the second stage, the strong server uses this synthetic data on behalf of the resource-constrained clients to perform federated LoRA finetuning alongside clients with sufficient computing resources. This approach ensures that all clients can participate in the finetuning process. Experimental results demonstrate that incorporating local updates from even a small fraction of clients improves performance compared to using synthetic data for all clients. Furthermore, we incorporate the Gaussian mechanism in both stages to guarantee client-level differential privacy.

Wang, Jiayi [ORNL]↗
DOE OSTI2023

Modbus RTU for Embedded Cyber Secure Inverter Controller

The Modbus communication protocol is a widely adopted communication standard in industrial control systems. This communication protocol is known for being reliable and straightforward to implement while being versatile in terms of its operating parameters while supporting multiple formats over various hardware infrastructures and architectures. Many intelligent devices such as Programmable Logic Controllers (PLCs), Human-Machine Interfaces (HMIs), Internet-of-Things (IoT), and various Operational Technologies (OT) utilize Modbus for their communication systems. These types of systems must communicate with each other through a standardized and central communication process. To support the integration of these modular systems, a Field-Programmable Gate Array (FPGA) can act as an embedded central routing fabric for this communication to take place. Embedded systems are versatile enough to interface with various devices and systems to accomplish various goals. Additionally, embedded systems require relatively small physical designs to minimize the required resources to facilitate the intended application by providing low-level system access. This minimization of system resources goes hand in hand with reducing the financial cost of a proposed solution or system. As remotely collaborating researchers often use FPGAs to prototype designs that are required to have a method for data transmission among systems, it is imperative to provide a baseline standard for communications among devices and systems. A typical method of implementing the Modbus RTU communication protocol in an embedded environment is using integrated logic architectures within the FPGA called “Intellectual Property (IP) cores.” IP cores can be designed using integrated logic or circuit designs to function as an embedded processor. These IP cores can then perform the required computational actions to support the Modbus RTU communication protocol by utilizing high-level programming languages such as the C programming language. The hardware description language of Very High-Speed Integrated Circuit Hardware Description Language (VHDL) allows for the control of real hardware at the logic gate and signal level. These logic gates and signals can be designed and controlled to perform desired actions based on the system design. Programming an FPGA using VHDL allows an individual to access the lowest abstraction level of the system during FPGA development. This level of abstraction is referred to as the register-transfer level (RTL), which gives access to manipulating values and variables at the register level. This register-level manipulation provides precision over creating the logical circuit within the FPGA, thus minimizing the required code to perform desired operations. The Modbus RTU communication protocol can be implemented within an FPGA using VHDL programming to establish a standardized and embedded serial communication pathway. This implementation provides a standardized communication protocol to streamline research efforts among researchers, thus increasing the efficiency of research efforts. Additionally, this Modbus RTU implementation requires fewer resources when compared to typical communication protocol implementations that utilize an IP core, reducing the hardware requirement for effective research efforts.

communication↗
DOE OSTI2025

Embedded random phase approximation for magnetic systems: H 2 dissociative adsorption on Fe(110)

The random phase approximation (RPA), a method for treating electron correlation, has been shown to be superior to standard density functional theory (DFT) approximations in numerous cases. However, the RPA’s computational cost is substantially higher than that of DFT, particularly restricting its application to extended surfaces. The recently introduced embedded RPA (emb-RPA) approach [Wei et al., J. Chem. Phys. 159(19), 194108 (2023)] reduces this computational cost by approximately two orders of magnitude. While previous applications of emb-RPA focused on non-spin-polarized systems, here we extend the approach to ferromagnetic ones. Unlike other embedded correlated wavefunction methods, such as embedded complete active space self-consistent field theory, emb-RPA is advantageous for spin-polarized systems because the RPA is compatible with unrestricted DFT solutions, which are eigenfunctions of the spin angular momentum operator S z but not the total spin-squared operator S 2 . By applying emb-RPA with specific magnetization constraints, we achieved a speedup of two to three orders of magnitude (one order when accounting for the one-time embedding potential optimization cost) with only small errors (∼50 meV) compared to full periodic RPA. Moreover, emb-RPA significantly reduces the over-binding errors of DFT approximations. In conclusion, we anticipate that the acceleration enabled by the spin-polarized emb-RPA approach will broaden the applicability of RPA to magnetic materials.

Density functional theory↗
DOE OSTI2021

Application of the locally self-consistent embedding approach to the Anderson model with non-uniform random distributions

Highlights: • Typical Medium Theory (TMT) for the Anderson Localization. • Locally Self-Consistent Multiple Scattering Method (LSMS) for Random Disordered Systems. • Linear Scaling Computational Method for Random Disordered Systems. We apply the recently developed embedding scheme for the locally self-consistent method to random disorder electrons systems. The method is based on the locally self-consistent multiple scattering theory and the typical medium theory. The locally self-consistent multiple scattering theory divides a system into many small designated local interaction zones. The subsystem within each local interaction zone is embedded in a self-consistent field from the typical medium theory. This approximation allows the study of random systems with large numbers of sites. We present results for the three dimensional Anderson model with different random disorder potential distributions. Using the typical density of states as an indicator of Anderson localization, we find that the method can capture the localization for commonly studied disorder potentials. These include the uniform distribution, the Gaussian distribution, and even the unbounded Cauchy distribution.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Privacy-Preserving Control of Partitioned Energy Resources

Distributed energy resources are an increasingly important part of the electric grid. We examine the problem of partitioning a distributed energy resource among many users while providing privacy to them. In this model, clients can send requests to a server, the server can verify that the requests are valid and aggregate them, but it cannot see the actual values in the requests. Without privacy, each user is forced to reveal their daily schedule or energy use. Energy resources add a novel challenge that prior systems do not address: they require verifying limits on private power (a rate over time) and energy (a sum) values. Furthermore, the cryptographic mechanisms must run on embedded energy control systems. We describe Weft, a novel cryptographic system that verifies both power (rate) and energy (integral) constraints on private client values and aggregates them. The key insight behind the approach is to rely on additively homomorphic secret shares, which allows servers to compute sums from rates. We present 3 cryptographic proof systems with different system trade-off for embedded systems: bit-splitting proofs minimize memory use, sorting proofs minimize computation, and commitment proofs minimize network communication. Using bit-splitting proofs, it takes an IoT client using a CortexM microcontroller 4 minutes of compute time to privately control its share of an energy resource for a day at 20s granularity.

Laufer, Evan↗