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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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661 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Scalable molecular dynamics on CPU and GPU architectures with NAMD

NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temperature, pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mechanical/molecular-mechanical descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.

high-performance computing↗
DOE OSTI2022

Mechanisms of Retention and Transport of Fission Products in Virgin and Irradiated Nuclear Graphite

To fulfill the design and licensing requirements for advanced reactors, the U.S. Department of Energy (DOE) is specifically interested in targeted research to quantify the mechanisms of fission product transport and retention in graphitic grades that will likely be used in next-generation very/high temperature reactors, fluoride salt-cooled high temperature reactors and molten salt reactors. We have examined an integrated experimental-computational approach to determine the diffusivities of selected fission products – ruthenium (Ru) and silver (Ag) in five nuclear graphite grades – POCO AXF-5Q, POCO ZXF-5Q, PCEA, IG110, and NBG-18. Experimental investigation for diffusion of other fission products (iodine, cesium, and krypton) in graphite could not be carried out due to extreme evaporation due to high vapor pressure, despite several attempts incorporating various experimental schemes. Experimental investigation with irradiated graphite could not be carried out because necessary approval to transport irradiated graphite could not be obtained due to procedural reasons at ORNL and national policy change in UK. An effort was made to “produce” by ion sputtering, but it was discontinued because the outcome did not adequately represent irradiated graphite. Thin film and “cup-and-cap” methods were employed to deposit fission products, diffusion annealed were carried out in an argon atmosphere, and concentration profiles were determined by dynamic secondary ion mass spectroscopy depth profiling technique. Regardless of graphite type, anomalous diffusion behavior of Ru (i.e., lower than expected based on Arrhenius temperature dependence) at an intermediate temperature, around 600 to 700 °C, was observed. Diffusion behavior of silver on the other hand agreed well to the Arrhenius temperature dependence although the excessive evaporation of silver hampered the accurate determination of diffusivities at temperature higher than 900 °C. In general, silver was observed to diffuse faster than Ru in the temperature range compared from 500 to 900 °C, had consistently had higher pre-exponential factor corresponding to higher jump frequency. To understand the abnormal diffusional behavior of Ru in graphite in intermediate temperature range, a detailed microstructural analysis was carried out. Clustering of Ru into particles on the surface of graphite was observed around 700 °C corresponding to de-wetting and spheroidization. This change would influence the boundary condition of diffusion, although features of clustering was much smaller (<1 mm) than the SIMS raster size (120 x 120 mm). Raman spectroscopy also demonstrated that Raman peak intensity for Ru decreased significantly for samples annealed higher than 700 °C and presence of Ru in graphite altered the crystallinity of graphite. To further elucidate the abnormal diffusion behavior observed in intermediate temperature investigated, the vibrational properties of graphene, bilayer graphene and Kr atoms in bilayer graphene were investigated with molecular dynamics. Krypton, which is a fission product, was introduced between a bilayer graphene system to evaluate (i) whether the phonon dispersion curves change with high temperature in bilayer graphene (ii) whether the addition of Kr atoms between the bilayer introduces any significant change in the vibrational properties, and (iii) whether any change in the vibrational properties can be correlated to the diffusive behavior of Kr atoms. The results show that the Kr atoms indeed exhibit an anomalous diffusive behavior at 550°C. Phonon analysis shows that a few phonon frequencies are enhanced as much as 20 to 30 % with the addition of just 0.2 at.% Kr. So, this may explain the unexpected self-diffusivity of fission products.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Learning in continuous action space for developing high dimensional potential energy models

Reinforcement learning (RL) approaches that combine a tree search with deep learning have found remarkable success in searching exorbitantly large, albeit discrete action spaces, as in chess, Shogi and Go. Many real-world materials discovery and design applications, however, involve multi-dimensional search problems and learning domains that have continuous action spaces. Exploring high-dimensional potential energy models of materials is an example. Traditionally, these searches are time consuming (often several years for a single bulk system) and driven by human intuition and/or expertise and more recently by global/local optimization searches that have issues with convergence and/or do not scale well with the search dimensionality. Here, in a departure from discrete action and other gradient-based approaches, we introduce a RL strategy based on decision trees that incorporates modified rewards for improved exploration, efficient sampling during playouts and a “window scaling scheme" for enhanced exploitation, to enable efficient and scalable search for continuous action space problems. Using high-dimensional artificial landscapes and control RL problems, we successfully benchmark our approach against popular global optimization schemes and state of the art policy gradient methods, respectively. We demonstrate its efficacy to parameterize potential models (physics based and high-dimensional neural networks) for 54 different elemental systems across the periodic table as well as alloys. We analyze error trends across different elements in the latent space and trace their origin to elemental structural diversity and the smoothness of the element energy surface. Broadly, our RL strategy will be applicable to many other physical science problems involving search over continuous action spaces.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Optimal Bayesian supervised domain adaptation for RNA sequencing data

Abstract Motivation When learning to subtype complex disease based on next-generation sequencing data, the amount of available data is often limited. Recent works have tried to leverage data from other domains to design better predictors in the target domain of interest with varying degrees of success. But they are either limited to the cases requiring the outcome label correspondence across domains or cannot leverage the label information at all. Moreover, the existing methods cannot usually benefit from other information available a priori such as gene interaction networks. Results In this article, we develop a generative optimal Bayesian supervised domain adaptation (OBSDA) model that can integrate RNA sequencing (RNA-Seq) data from different domains along with their labels for improving prediction accuracy in the target domain. Our model can be applied in cases where different domains share the same labels or have different ones. OBSDA is based on a hierarchical Bayesian negative binomial model with parameter factorization, for which the optimal predictor can be derived by marginalization of likelihood over the posterior of the parameters. We first provide an efficient Gibbs sampler for parameter inference in OBSDA. Then, we leverage the gene-gene network prior information and construct an informed and flexible variational family to infer the posterior distributions of model parameters. Comprehensive experiments on real-world RNA-Seq data demonstrate the superior performance of OBSDA, in terms of accuracy in identifying cancer subtypes by utilizing data from different domains. Moreover, we show that by taking advantage of the prior network information we can further improve the performance. Availability and implementation The source code for implementations of OBSDA and SI-OBSDA are available at the following link. https://github.com/SHBLK/BSDA. Supplementary information Supplementary data are available at Bioinformatics online.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Quantitative metrics for evaluating thermonuclear design codes and physics models applied to the National Ignition Campaign

In this study, physics models and design codes for hot dense plasmas undergoing thermonuclear burn are evaluated objectively using statistical metrics that compare the difference between calculations and data relative to the experimental uncertainties. The analysis is applied to the National Ignition Campaign (NIC) because it is relevant, comprehensive, and well documented. The statistics confirm that a key process afflicting NIC performance is mix driven by hydrodynamic instabilities as approximated here using the KL model [G. Dimonte and R. Tipton, Phys. Fluids 18, 085101 (2006)]. New physics models are also presented for instability-driven magnetic fields [B. Srinivasan et al., Phys. Rev. Lett. 108, 165002 (2012)] and the Coulomb logarithm for electron–ion thermal relaxation [G. Dimonte and J. Daligault, Phys. Rev. Lett. 101, 135001 (2008)]. The plasma-generated magnetic fields improve the agreement between code and data in a statistically significant manner by reducing the electron thermal conduction in the hot-spot via the Hall term. The Coulomb logarithm is presented in a numerically practical form that incorporates recent theoretical advances. However, it does not improve the agreement between the code and data because the thermal relaxation is so fast in non-ignited NIC plasmas that the typical 20% error does not change the tight coupling between electrons and ions. Even with these improved physics models, the one-dimensional simulations presented here are not able to describe the high-convergence NIC implosions in a statistically acceptable manner. Of the heroic multi-dimensional simulations of Clark et al. [Phys. Plasmas 23, 056302 (2016)], only those in three-dimensions satisfy the statistical acceptance criterion.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

The Influence of Alkyl Spacers and Molecular Weight on the Charge Transport and Storage Properties of Oxy‐Bithiophene‐Based Conjugated Polymers

Abstract Conjugated polymers (CPs) with polar side chains can conduct electronic and ionic charges simultaneously, making them promising for bioelectronics, electrocatalysis and energy storage. Recent work showed that adding alkyl spacers between CP backbones and polar side chains improved electronic charge carrier mobility, reduced swelling and enhanced stability, without compromising ion transport. However, how alkyl spacers impact polymer backbone conformation and, subsequently, electronic properties remain unclear. In this work, we design two oxy‐bithiophene‐based CP series, each featuring progressively extended alkyl spacer lengths and two distinct molecular weight (MW) distributions. Using operando characterisations, we evaluate the (spectro)electrochemical and swelling properties of the polymer thin films, and their performance in organic field‐effect transistors and organic electrochemical transistors. Surprisingly, alkyl spacers negatively impact the hole mobility of our polymers, with higher MW amplifying this effect. Using molecular dynamics simulations, we show that it is thermodynamically favourable for adjacent non‐polar alkyl spacers to aggregate in polar electrolytes, leading to backbone twisting. Further spectroscopic measurements corroborate this prediction. Our findings demonstrate the active interactions between side chain structure, MW and electrolyte/solvent polarity in influencing polymer performance, underscoring the importance of considering solvation environment effects on polymer conformation when designing new mixed conducting CPs for electrochemical applications.

Yu, Hang [Department of Physics and Centre for Pro↗
DOE OSTI2025

Toward Computation-Guided Design of Tunable Organic-Inorganic CdS Quantum Dot Binary Superlattices

Combining the advantages of structural programmability in sequence-defined biomimetic molecules and the controllable packing geometry in nanoparticle superlattices, we demonstrate a self-assembled organic-inorganic superlattice whose structure can be altered with the slightest change in the sequence of the organic counterpart. Here, oleate-coated CdS quantum dots (QDs) form a square-packed superlattice with a 1:1 molar equivalence of a di-block amphiphilic peptoid (Nbrpe6Dig) in chloroform. In contrast, no apparent structure is observed in the organic solvent alone. Based on theoretical evidence, we show that the assembly is a binary superlattice where both the CdS QDs and the peptoids serve as building blocks and further predict a correlation between the superlattice structure and the peptoid sequence. The computationally guided prediction is validated by experiments where superlattice transformation is observed with modified peptoids. The mechanism identified in our work inspires new ways to control and tune organic-inorganic hybrid nanomaterial self-assembly.

Qi, Xin↗
DOE OSTI2025

An Overview of the Molten Salt Thermal Properties Database–Thermophysical, Version 4.0 (MSTDB-TP V.4.0)

A central repository of thermophysical and thermochemical properties of molten salt compositions of relevance to molten salt reactors (MSRs) is vital in supporting the broad community of MSR developers, who are at various stages of developing and deploying their reactor designs. In general, these MSR designs differ significantly from developer to developer (e.g., with respect to the hardness of the neutron spectra, level of fissile loading, target multicomponent temperatures and power levels, and moderating capabilities). Therefore, the fuel and coolant salts being considered vary greatly: they may be chlorides or fluorides, they utilize different actinides at different ratios, and the cations in the melt are selected based on perceived advantages and disadvantages. Considering the general need for thermal properties, and the vastness of the array of potential candidate salt mixtures, the Molten Salt Thermal Properties Database (MSTDB) was initiated in 2018 with the goal of providing thermophysical and thermochemical characterization of key molten salt compounds and mixtures across their temperature and compositional domains. The MSTDB is thus divided into the thermophysical arm (MSTDB-TP) and the thermochemical arm (MSTDB-TC). The MSTDB is an effort funded by the Department of Energy, Office of Nuclear Energy (DOE-NE) Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, and the MSR Campaign. This report provides an overview of the MSTDB-TP v4.0 in terms of the data contained within, the state of the tools used to access the data, the availability of predictive models that leverage the raw data in the database, the preliminary status of developmental efforts that are currently underway, and an account of future goals for MSTDB-TP. The primary goal for the update from MSTDB-TP v.3.1 to v4.0 was the incorporation of surface tension data into the database; this property is important for thermal hydraulics modeling and species transport in other tools that have been developed under the NEAMS program. A breakdown of the surface tension data that have been added into MSTDB-TP v4.0 is provided herein, and the manner in which the quality of the data has been assessed is also documented. For MSTDB-TP v4.0, newly published thermophysical property data—primarily from collaborative experimental efforts under the MSR Campaign—have been incorporated into the database, and the resulting expansion is documented here. Because of the size to which MSTDB-TP has grown, the raw data format has now been recast into JavaScript Object Notation (JSON) format for easier connection with the MSTDB-TP application programming interface (API). Saline; the pre-existing comma-separated value (CSV) format has been deprecated but is still maintained, accessible, and up to date. As a final effort in packaging the MSTDB-TP v4.0 update, the graphical user interface (GUI) for MSTDB has been updated to allow full accessibility to the density and viscosity predictive models, which are based on Redlich-Kister expansions of MSTDB-TP raw data. Some other major aspects of this report, in terms of preliminary and future work, include: (1) documentation of the formalism and preliminary testing of a kinetic theory model that may act as a predictive model for thermal conductivity; (2) documentation of the candidate predictive models that may be considered in the future for surface tension, making use of the surface tension data now in MSTDB-TP v4.0; (3) a preliminary account of a data collection process that will enable the filling of additional gaps within MSTDB-TP, namely with data which have been collected computationally (e.g., through ab initio molecular dynamics).

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

ADEPT: A Pedagogical Framework for Integrating Agentic AI with Deterministic Scientific Workflows

The integration of Large Language Models (LLMs) into scientific research promises to accelerate discovery, yet a significant gap remains between the dynamic reasoning of Artificial Intelligence (AI) agents and the static, deterministic nature of canonical scientific workflows. This paper introduces ADEPT (Agentic Discovery and Exploration Platform for Tools), a reference architecture and pedagogical framework explicitly designed to bridge this gap. ADEPT's primary mission is to provide a transparent, "glass-box" environment where researchers and engineers can learn to effectively wrap established scientific software (e.g., BLAST, Nextflow pipelines) and compose it into reliable, agent-driven workflows. We describe its modular, multi-server architecture, which leverages the Model Context Protocol (MCP) for tool serving, LangGraph for robust agentic orchestration, and a secure nsjail-based sandbox for safe code execution. By prioritizing architectural clarity, safety, and modularity, ADEPT serves as an extensible blueprint for building trustworthy AI-augmented systems and fosters the collaborative development necessary to responsibly employ agentic AI for science. We provide practical examples of how to adapt and extend this framework, highlighting its utility in workforce development and AI-readiness capabilities across research and development projects.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

A fault-tolerant neutral-atom architecture for universal quantum computation

Quantum error correction (QEC) is essential for the realization of large-scale quantum computers. However, owing to the complexity of operating on the encoded ‘logical’ qubits, understanding the physical principles for building fault-tolerant quantum devices and combining them into efficient architectures is an outstanding scientific challenge. Here we use reconfigurable arrays of up to 448 neutral atoms to implement the key elements of a universal, fault-tolerant quantum processing architecture and experimentally explore their underlying working mechanisms. We first use surface codes to study how repeated QEC suppresses errors, demonstrating 2.14(13)x below-threshold performance in a four-round characterization circuit by leveraging atom loss detection and machine learning decoding. We then investigate logical entanglement using transversal gates and lattice surgery and extend it to universal logic through transversal teleportation with three-dimensional [[15,1,3]] codes, enabling arbitrary-angle synthesis with polylogarithmic overhead. Finally, we develop mid-circuit qubit reuse16, increasing experimental cycle rates by two orders of magnitude and enabling deep-circuit protocols with dozens of logical qubits and hundreds of logical teleportations with [[7,1,3]] and high-rate [[16,6,4]] codes while maintaining constant internal entropy. Our experiments show key principles for efficient architecture design, involving the interplay between quantum logic and entropy removal, judiciously using physical entanglement in logic gates and magic state generation, and leveraging teleportations for universality and physical qubit reset. These results establish foundations for scalable, universal error-corrected processing and its practical implementation in neutral atom systems.

atomic and molecular physics↗
DOE OSTI2025

Recent Developments in DFTB+, a Software Package for Efficient Atomistic Quantum Mechanical Simulations

DFTB+ is a flexible, open-source software package developed by its community, designed for fast and efficient atomistic quantum mechanical simulations. It employs various methods that approximate density functional theory (DFT), such as density functional-based tight binding (DFTB) and the extended tight binding (xTB) approach allowing simulations of large systems over extended time scales with reasonable accuracy, while being significantly faster than traditional ab initio methods. In recent years, several new extensions of the DFTB method have been developed and implemented in the DFTB+ program package in order to improve the accuracy and generality of the available simulation results. In this paper, we review those enhancements, show several use case examples and discuss the strengths and limitations of its features.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Atomate2: modular workflows for materials science

High-throughput density functional theory (DFT) calculations have become a vital element of computational materials science, enabling materials screening, property database generation, and training of “universal” machine learning models. While several software frameworks have emerged to support these computational efforts, new developments such as machine learned force fields have increased demands for more flexible and programmable workflow solutions. This manuscript introduces atomate2, a comprehensive evolution of our original atomate framework, designed to address existing limitations in computational materials research infrastructure. Key features include the support for multiple electronic structure packages and interoperability between them, along with generalizable workflows that can be written in an abstract form irrespective of the DFT package or machine learning force field used within them. Our hope is that atomate2's improved usability and extensibility can reduce technical barriers for high-throughput research workflows and facilitate the rapid adoption of emerging methods in computational material science.

97 MATHEMATICS AND COMPUTING↗