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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Synergism of anisotropic and computational NMR methods reveals the likely configuration of phormidolide A

Characterization of the complex molecular scaffold of the marine polyketide natural product phormidolide A represents a challenge that has persisted for nearly two decades. In light of discordant results arising from recent synthetic and biosynthetic reports, a rigorous study of the configuration of phormidolide A was necessary. This report outlines a synergistic effort employing computational and anisotropic NMR investigation, that provided orthogonal confirmation of the reassigned side chain, as well as supporting a further correction of the C7 stereocenter.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Brochure for the DOE Office of Science Workshop on Envisioning Frontiers in AI and Computing for Biological Research

In February of 2025 a joint ASCR/BER workshop was held to identify key transformational research directions for understanding biology using artificial intelligence (AI), digital twins and high-performance (HPC) computational methods to facilitate scientific discovery and innovation in support of the Department of Energy mission. AI technologies offer exciting new groundbreaking methods to analyze large volumes of complex biological data, thereby greatly accelerating the ability to understand, predict, and design biological processes for beneficial purposes. In the laboratory, the bridging of AI-enabled automated experimental technologies, HPC and digital twins will provide potent tools for researchers to explore the fundamental nature of biology and harness its inherent metabolic potential for a variety of beneficial purposes. The focus of this workshop was on how high-performance computational methods can impact this objective by exploring digital twins, foundational models, and data-driven approaches with applications to advance automated laboratory experiments, modeling of complex living systems and engineering new functions into plants and microbial systems relevant to DOE mission. Workshop attendees with expertise in plant science, microbiology, mathematics, computer science, and AI assessed the current state of the science, trends, and AI challenges at the interface of plant and microbial systems biology and computational science to identify opportunities for high-impact research. This collaborative effort capitalized on ASCR's advancements in applied mathematics, computer science, and Exascale systems, and BER's expertise in basic genomics-enabled research on DOE relevant plant and microbial systems. The workshop culminated in four key priority research directions to guide future research and development within DOE Office of Science programs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

An eigenvalue-based method for computing the relaxed pressure in compressible multiphase flow with N phases

The modeling of compressible multiphase flows is a decades-old area of study with many applications across various fields. Many of these application areas use stiff pressure relaxation. This process involves the solution of a nonlinear system with N + 1 equations and N + 1 unknowns, where N is the number of phases. The resolution of this system with general equations of state (EOSs) is difficult. Furthermore, nonlinear systems can admit multiple solutions, and current solution methods do not address this possibility. Very recently, a thermodynamic relaxation method was introduced, which effectively maps a relatively simple predictor equation of state onto a more complex target equation of state. In this context, the target EOSs are the chosen EOSs for the thermodynamic model. Furthermore, this thermodynamic relaxation has the benefit of simplifying the stiff pressure relaxation system of equations. In this article, we show this system reduces to a polynomial of degree N, which can be recast as an eigenvalue problem through the use of the associated companion matrix. We show that although this eigenvalue method is generally less efficient than Newton–Raphson iteration, it does not suffer from convergence issues and finds all N roots of the polynomial. Hence, the method provides a fail-safe for root-finding iterative methods and a way to address the issue of multiple solutions to the nonlinear system of equations in stiff pressure relaxation.

Eigenvalue algorithm↗
DOE OSTI2022

The Dynamics of Ions on Phased Radio-frequency Carpets in High Pressure Gases and Application for Barium Tagging in Xenon Gas Time Projection Chambers

Radio-frequency (RF) carpets with ultra-fine pitches are examined for ion transport in gases at atmospheric pressures and above. We develop new analytic and computational methods for modeling RF ion transport at densities where dynamics are strongly influenced by buffer gas collisions. An analytic description of levitating and sweeping forces from phased arrays is obtained, then thermodynamic and kinetic principles are used to calculate ion loss rates in the presence of collisions. This methodology is validated against detailed microscopic SIMION simulations. We then explore a parameter space of special interest for neutrinoless double beta decay experiments: transport of barium ions in xenon at pressures from 1 to 10 bar. Our computations account for molecular ion formation and pressure dependent mobility as well as finite temperature effects. We discuss the challenges associated with achieving suitable operating conditions, which lie beyond the capabilities of existing devices, using presently available or near-future manufacturing techniques.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Summary Report of the FY24 DOE Contributions to the GIF VHTR CMVB

The Generation-IV Forum (GIF) Very-High-Temperature Reactor-Computational Methods Validation and Benchmark (VHTR-CMVB) initiative, involving organizations from Korea Atomic Energy Research Institute (KAERI) (South Korea), Institute of Nuclear and New Energy Technology of Tsinghua University (INET) (China), U.S. Department of Energy (DOE) (U.S.), Joint Research Centre (JRC) (Europe), and Japan Atomic Energy Agency (JAEA) (Japan), is dedicated to the verification and validation of tools for High-Temperature Gas-Cooled Reactors (HTGRs) analysis, using data shared by Computational Methods Validation and Benchmark (CMVB) signatories. For FY24, the US DOE CMVB has committed to several critical activities. Under WP1, led by the US, the integration of the High Temperature Gas Cooled Reactor - Pebble-Bed Module (HTR-PM) Phenomena Identification and Ranking Table (PIRT) into the comparative PIRT is progressing, with a new draft of the comparison tables issued earlier this year and currently being utilized by INET for their contribution. Neutronic validation efforts under WP3 include the preparation of the burnup analysis benchmark, preliminary calculations, and the development of reference models and results. In WP2, a validation exercise for hot gas mixing in the lower plenum of HTR-PM is in progress, using experimental data from INET (China) to validate modeling approaches. A model of the experimental facility has been developed using StarCCM+, with initial calculations slated for presentation at the GIF CMVB meeting this fall. Another WP2 activity focuses on validating numerical models for air-cooled Reactor Cavity Cooling System (RCCS) with experimental data from the Wisconsin Madison RCCS facility. A high-fidelity model, developed using NEK-RS, is currently being validated with available data from a low power forced convection test. These efforts are aimed at enhancing and confirming the accuracy of HTGR analysis tools, ensuring their alignment with experimental data and regulatory requirements.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures

Structures of many large biomolecular assemblies are now being determined using integrative approaches. In these approaches, information derived from multiple experimental and computational methods is combined to compute three-dimensional structures of multi-protein complexes and other macromolecular machines. A standalone prototype data resource for integrative structures called PDB-Dev was built, based on recommendations of the Integrative and Hybrid Methods (IHM) Task Force of the Worldwide Protein Data Bank (wwPDB). This effort included developing data standards and software tools for collecting, curating, validating, visualizing, archiving, and disseminating integrative structures that span diverse spatiotemporal scales and conformational states. Mechanisms have been created to validate integrative structures based on the experimental data underpinning them. Building upon this foundational framework, PDB-Dev has been further expanded to handle large dynamic macromolecular systems and integrative structures that combine, for example, experimental restraints with atomic coordinates computed by machine learning algorithms. Data standards and supporting tools have also been extended to capture information about biomolecular dynamics, such as conformational transitions and related kinetic data derived from biophysical methods. Recently, PDB-Dev was unified with the PDB archive and rebranded as PDB-IHM (pdb-ihm.org), further promoting FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data stewardship for integrative structural biology.

IHMCIF↗
DOE OSTI2023

EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment

Abstract Background Adding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with new data, adding sequences into a constraint alignment constructed using biological knowledge, or computing alignments in the presence of sequence length heterogeneity. Although this is a natural problem, only a few tools have been developed to use this information with high fidelity. Results We present EMMA (Extending Multiple alignments using MAFFT--add) for the problem of adding a set of unaligned sequences into a multiple sequence alignment (i.e., a constraint alignment). EMMA builds on MAFFT--add, which is also designed to add sequences into a given constraint alignment. EMMA improves on MAFFT--add methods by using a divide-and-conquer framework to scale its most accurate version, MAFFT-linsi--add, to constraint alignments with many sequences. We show that EMMA has an accuracy advantage over other techniques for adding sequences into alignments under many realistic conditions and can scale to large datasets with high accuracy (hundreds of thousands of sequences). EMMA is available at https://github.com/c5shen/EMMA . Conclusions EMMA is a new tool that provides high accuracy and scalability for adding sequences into an existing alignment.

Shen, Chengze↗
DOE OSTI2020

Three-dimensional traction microscopy accounting for cell-induced matrix degradation

Tractions exerted by cells on the extracellular matrix (ECM) are critical in many important physiological and pathological processes such as embryonic morphogenesis, wound healing, and cancer metastasis. Three-dimensional Traction Microscopy (3DTM) is a tool to quantify cellular tractions by first measuring the displacement field in the ECM in response to these tractions, and then using this measurement to infer tractions. Most applications of 3DTM have assumed that the ECM has spatially-uniform mechanical properties, but cells secrete enzymes that can locally degrade the ECM. In this work, a novel computational method is developed to quantify both cellular tractions and ECM degradation. In particular, the ECM is modeled as a hyperelastic, Neo-Hookean solid, whose material parameters are corrupted by a single degradation parameter. The feasibility of determining both the traction and the degradation parameter is first demonstrated by showing the existence and uniqueness of the solution. An inverse problem is then formulated to determine the nodal values of the traction vector and the degradation parameter, with the objective of minimizing the difference between a predicted and measured displacement field, under the constraint that the predicted displacement field satisfies the equation of equilibrium. The inverse problem is solved by means of a gradient-based optimization approach, and the gradient is computed efficiently using appropriately derived adjoint fields. The computational method is validated in-silico using a geometrically realistic neuronal cell model and synthetic traction and degradation fields. It is found that the method accurately recovers both the traction and degradation fields. Moreover, it is found that neglecting ECM degradation can yield significant errors in traction measurements. Finally, our method can extend the range of context where tractions can be appropriately measured.

42 ENGINEERING↗
DOE OSTI2025

An Investigation of Thermal Properties of 2D Materials [Dissertation]

Studying the thermal conductivity of 2D materials is important due to the applications of 2D materials in fields such as thermal management, thermoelectricity, renewable energy, and sensors. As such, measurements of the thermal conductivity of these 2D materials become important to measure. Thermal conductivity is often difficult to measure for 2D materials due to their atomically thin nature and many experimental methods for doing so requiring contact with the sample, which can alter the thermal properties. A non-contact method for calculating the thermal conductivity of 2D materials supported on substrates in order to model the thermal conductivity of 2D materials for devices, is proposed and experimentally performed in this dissertation. The optothermal Raman technique is a useful non-contact diagnostic technique useful in determining the thermal conductivity of 2D materials. The optothermal Raman typically does not account for heat losses due to convection or radiation or substrate resistance, which are shown to be important factors to consider when developing an optothermal Raman model. Additionally, the calculation of the interfacial thermal conductance between the bottom surface of the sample and the top surface of the substrate, plays an important role in determining the final value of the thermal conductivity of a supported sample, and will yield differing results based on whether or not the conductance is calculated using an approach such as the Diffuse Mismatch Model (DMM) or calculated directly by varying the laser heating profile (usually done by changing the laser objective). This is shown to be the case for both graphene on Ni, graphene on Cu, and SnSe 2 on Cu. In addition to experimentally calculating the thermal conductivity of a 2D material with the optothermal Raman technique, the thermal conductivity of 2D materials can also be calculated using computational methods. The three-phonon method is a method which can be used to simulate phonon scattering processes and determine the thermal conductivity of semiconductors, wherein phonon scattering is the dominant mechanism which determines the thermal conductivity. The three-phonon method uses relaxation times for phonon scattering with other phonons, electrons, and other material system elements, such as isotopes or material defects, in order to create a single-mode relaxation time approximation (SMRTA), which is used to calculate the final value of the thermal conductivity. An important consideration when determining the thermal conductivity of a 2D material using this method is the device geometry, which is reflected in this work as the phonon-boundary scattering relaxation time. This inclusion is important along with the inclusion of phonon-electron scattering in accurately determining the thermal conductivity of a 2D material. In both the optothermal Raman experiments and the three-phonon method computations, strain is shown to have a demonstrable effect on the thermal conductivity of 2D materials. When a 1.1% strain was applied to the mechanical properties of SnSe, the three-phonon processes yielded a lower thermal conductivity than the no-strain case. For the optothermal Raman experiments, the strain induced in the Cu substrate and transferred to a single-layer graphene (SLG) sample yields a trend where the thermal conductivity of the SLG decreases with respect to strain applied. In the case where the interfacial thermal conductance was calculated directly, the conductance increased with respect to strain applied. This presents strain as a reliable and viable method for tuning the thermal properties of 2D materials for device applications.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Alternating Direction Decomposition with Strong Bounding and Convexification (ADDSBC) for Solving Security Constrained AC Unit Commitment Problems

This project aims to develop efficient and robust computational methods for solving the security-constrained unit commitment and alternating current optimal power flow problem (SC-UC-ACOPF). The SC-UC-ACOPF problem is at the center of the short-term operation of the U.S. Power Grid. It is solved every week, every day, and every 10 minutes to plan for the optimal action of electricity generation and consumption by minimizing the generation cost and maintaining power system reliability against potential disruptions of equipment failures. In mathematical terms, SC-UC-ACOPF is a challenging large-scale mixed-integer nonlinear optimization model. This means that the decisions involve both discrete variables, e.g. the turning on and off of generators and switching of transmission lines and transformers, and continuous decisions, e.g. the amount of energy generated by each generator and the power flows in the power grid. The physics of the power flow is described by nonlinear equations involving real and reactive power and bus voltages. Another key feature is the large number of contingencies, i.e. the system needs to stay reliable in face of failure of any one equipment, such as transmission lines and generators. The U.S. power grids are extremely complicated and large scale with more than 5,000 generators, 50,000 buses, and 100,000 high-voltage transmission lines, making the SC-UC-ACOPF a very large-scale computation challenge. The research developed in this project aims to solve the SC-UC-ACOPF problems in the three timescales, i.e. weekly, daily, and every 10-min. The proposed computational methods are built on a principled algorithmic approach of decomposition and penalization. More specifically, the algorithm develops spatial and temporal decomposition by exploiting the strong temporal coupling and weak spatial coupling of the UC problem and the complementary feature, i.e. weak temporal coupling and strong spatial coupling of the ACOPF problem. The algorithm also leverages recent progresses in strong convex relaxation of ACOPF. A unique feature of the proposed approach is that it generates a valid, global upper bound on the optimal maximum profit. In this way, a global optimality gap is available to measure the quality of the solution. To further speed up computation, the research team has developed a plethora of effective heuristics to strengthen the iterative penalty-based decomposition framework. For instance, a heuristic is developed to construct inner approximations of the time coupling constraints within the time decoupled problems. Contingencies are pre-screened and low-rank matrix computation is exploited to find the almost unique solution to each contingency. A novel heuristic for line switching is proposed and tested with positive impacts on instances where line switching is beneficial. Taking a systematic approach and carefully handling every detail of the problem pays off. The TIM-GO’s performance throughout the trials and the final event was stellar. TIM-GO garnered the second highest total prize money and is ranked in the top three positions across all categories of comparison.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Simulations of nonradiative processes in semiconductor nanocrystals

The description of carrier dynamics in spatially confined semiconductor nanocrystals (NCs), which have enhanced electron–hole and exciton–phonon interactions, is a great challenge for modern computational science. These NCs typically contain thousands of atoms and tens of thousands of valence electrons with discrete spectra at low excitation energies, similar to atoms and molecules, that converge to the continuum bulk limit at higher energies. Computational methods developed for molecules are limited to very small nanoclusters, and methods for bulk systems with periodic boundary conditions are not suitable due to the lack of translational symmetry in NCs. This perspective focuses on our recent efforts in developing a unified atomistic model based on the semiempirical pseudopotential approach, which is parameterized by first-principle calculations and validated against experimental measurements, to describe two of the main nonradiative relaxation processes of quantum confined excitons: exciton cooling and Auger recombination. Here, we focus on the description of both electron–hole and exciton–phonon interactions in our approach and discuss the role of size, shape, and interfacing on the electronic properties and dynamics for II–VI and III–V semiconductor NCs.

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

Modern quantum chemistry with [Open]Molcas

MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree–Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

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

Modeling Pb(II) Adsorption on Mineral Surfaces: Bridging Density Functional Theory and Experiment with Thermodynamic Insights

Despite decades of work on aqueous lead (Pb) adsorption on a-Fe2O3 (hematite) and a-Al2O3 (alumina), gaps between measurements and modeling obscure molecular-level understanding. Achieving well-matched geometries between theory and experimental for mineral-water interfaces is a hurdle, as surface functional group type and distribution must be accounted for in determining mechanisms. Additionally, computational methods that can describe the substrate are often not appropriate to capture aqueous effects. Progress requires focusing on well-studied and relevant systems, such as key facets (001),(012), and (110) of hematite and alumina, and ubiquitous contaminants such as aqueous Pb. In the past, bulk-parametrized bond-valence principles were used to rationalize Pb(II) adsorption trends. These approaches can break down at surfaces, where flexible bonding environments and adsorption-induced surface relaxations play a critical role. Here, we adapt and apply a density functional theory (DFT) and thermodynamics framework, integrating DFT-calculated energies with experimental data and electrochemical principles, to predict Pb(II) adsorption. Our model results capture trends across the full set of surfaces and predict that inner-sphere Pb(II) sorption on (001) alumina varies from unfavorable to weakly favorable across a range of pH conditions. This aligns with experiment insights that Pb(II) interacts at that surface through outer-sphere interactions. Extending to Fe(II) adsorption, we demonstrate a coverage-dependent site preference, potentially explaining disorder in overlayers grown by the oxidative adsorption of Fe(II) on hematite (001).

lead contamination↗
DOE OSTI2022

Bringing Trimmed Serendipity Methods to Computational Practice in Firedrake

We present an implementation of the trimmed serendipity finite element family, using the open-source finite element package Firedrake. The new elements can be used seamlessly within the software suite for problems requiring H 1 , H (curl), or H (div)-conforming elements on meshes of squares or cubes. To test how well trimmed serendipity elements perform in comparison to traditional tensor product elements, we perform a sequence of numerical experiments including the primal Poisson, mixed Poisson, and Maxwell cavity eigenvalue problems. Overall, we find that the trimmed serendipity elements converge, as expected, at the same rate as the respective tensor product elements, while being able to offer significant savings in the time or memory required to solve certain problems.

97 MATHEMATICS AND COMPUTING↗