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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Creation of the VADER Code in SCALE [Abstract]

The VADER (Validation Analysis Data Evaluation Resource) is a new module in SCALE 6.3 that has been derived from the legacy USLSTATS program. VADER is a tool that allows the determination of bias and bias uncertainty for criticality safety computational methods. The older USLSTATS program, written in Java, existed outside of SCALE and provided tools to calculate only the confidence band with administrative margin (sometimes called USL-1) and the single-sided uniform width closed interval (USL-2). For normality testing it only offered a crude chi- squared normality test that had no user-configurable options and presented a simple pass/no-pass functionality.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Hybrid finite element and Brownian dynamics method for charged particles

Diffusion is often the rate-determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. A previous study introduced a new hybrid diffusion method that couples the strengths of each of these two methods, but was limited by the lack of interactions among the particles; the force on each particle had to be from an external field. This study further develops the method to allow charged particles. The method is derived for a general multidimensional system and is presented using a basic test case for a one-dimensional linear system with one charged species and a radially symmetric system with three charged species.

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

Evolving language of pediatric anxiety in electronic health records

Objectives This study aimed to identify and quantify semantic drift (ie, the change in semantic meaning over time) within expert-defined anxiety-related (AR) terminology and compare it to common electronic health record (EHR) vocabulary across longitudinal pediatric clinical notes. Materials and Methods A corpus of pediatric clinical notes from 2009 to 2022 was analyzed using computational methods. Semantic drift for each term was quantified using cosine similarity between annual temporal word embeddings. Contextual meaning was examined through changes in nearest neighbors across years. The Laws of Semantic Change were applied to assess the influence of word frequency and polysemy. Vocabulary terms were categorized as AR or common EHR. Results 98% of AR terminology maintained a cosine similarity between 0.00 and 0.50, indicating moderate semantic stability, whereas 90% of common EHR terms remained between 0.00 and 0.25, showing greater contextual stability overall. Frequent terms exhibited minimal change (Frequency Coefficient = 0.04), whereas highly polysemous or abbreviated terms showed less stability (Polysemy Coefficient = 0.630). AR terminology drifted more slowly than general EHR vocabulary (Type Coefficient = −0.179), further supported by significant year–type interactions (Coef = −0.09 to −0.523). Discussion Although anxiety-related terminology demonstrates slower semantic drift than general EHR vocabulary, subtle contextual shifts still occur that may affect downstream interpretability and retrieval in automated systems. Conclusion Continuous linguistic monitoring and adaptive modeling are essential to maintain semantic fidelity and ensure the long-term reliability of clinical decision support systems as healthcare documentation evolves.

Pediatric anxiety disorders↗
DOE OSTI2018

Investigation of protein quaternary structure via stoichiometry and symmetry information

The Protein Data Bank (PDB) is the single worldwide archive of experimentally-determined three-dimensional (3D) structures of proteins and nucleic acids. As of January 2017, the PDB housed more than 125,000 structures and was growing by more than 11,000 structures annually. Since the 3D structure of a protein is vital to understand the mechanisms of biological processes, diseases, and drug design, correct oligomeric assembly information is of critical importance. Unfortunately, the biologically relevant oligomeric form of a 3D structure is not directly obtainable by X-ray crystallography, whilst in solution methods (NMR or single particle EM) it is known from the experiment. Instead, this information may be provided by the PDB Depositor as metadata coming from additional experiments, be inferred by sequence-sequence comparisons with similar proteins of known oligomeric state, or predicted using software, such as PISA (Proteins, Interfaces, Structures and Assemblies) or EPPIC (Evolutionary Protein Protein Interface Classifier). Despite significant efforts by professional PDB Biocurators during data deposition, there remain a number of structures in the archive with incorrect quaternary structure descriptions (or annotations). Further investigation is, therefore, needed to evaluate the correctness of quaternary structure annotations. In this study, we aim to identify the most probable oligomeric states for proteins represented in the PDB. Our approach evaluated the performance of four independent prediction methods, including text mining of primary publications, inference from homologous protein structures, and two computational methods (PISA and EPPIC). Aggregating predictions to give consensus results outperformed all four of the independent prediction methods, yielding 83% correct, 9% wrong, and 8% inconclusive predictions, when tested with a well-curated benchmark dataset. We have developed a freely-available web-based tool to make this approach accessible to researchers and PDB Biocurators.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Modelling Charged Defects in Non-Cubic Semiconductors for Radiation Effects Studies in Next Generation Materials

This final report summarizes the results of the Laboratory Directed Research and Development (LDRD) Project Number 212587 entitled "Modeling Charged Defects in Non-Cubic Semiconductors for Radiation Effects Studies in Next Generation Electronic Materials" . The goal of this project was to extend a predictive capability for modeling defect level energies using first principle density functional theory methods (e.g., for radiation effects assessments) to semiconductors with non-cubic crystal structures. Computational methods that proved accurate for predicting defect levels in standard cubic semiconductors, were found to have shortcomings when applied to the lowered symmetry structures prevalent in next generation electronic materials such as SiC, GaN, and Ga 2 0 3 , stemming from an error in the treatment of the electrostatic boundary conditions. I describe methods to generalized the local moment countercharge (LMCC) scheme to position a charge in bulk supercell calculations of charged defects, circumventing the problem of measuring a dipole in a periodically replicated bulk calculation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

DYFLOW: A flexible framework for orchestrating scientific workflows on supercomputers

Modern scientific workflows are increasing in complexity with growth in computation power, incorporation of non-traditional computation methods, and advances in technologies enabling data streaming to support on-the-fly computation. These workflows have unpredictable runtime behaviors, and a fixed, predetermined resource assignment on supercomputers can be inefficient for overall performance and throughput. Inability to change resource assignments further limits the scientists to avail of science-driven opportunities or respond to failures.We introduce DYFLOW, a flexible framework that orchestrates scientific workflows on supercomputers based on user-designed policies. DYFLOW compartmentalizes orchestration stages into simplified constructs, and end-users can program and reuse them according to their workflow requirements through an easy-to-use interface. These constructs hide the intricacies involved in runtime management from end-users, for instance, procurement of information to understand the workflow state, assessment, and supervision of the runtime changes. DYFLOW is designed to work alongside existing workflow management systems and reuse the available (static) support for workflow management. We have integrated DYFLOW with an existing workflow management tool as a demonstration. With experiments performed on use cases from three types of scientific workflows and two different parallel architectures, we show that DYFLOW achieves the desired orchestration incurring a small cost to carry out the runtime changes.

Singhal, Swati↗
DOE OSTI2021

Mesoscopic Modeling and Rapid Simulation of Incremental Changes in Epidemic Scenarios on GPUs

In simulation-based studies and analyses of epidemics, a major challenge lies in resolving the conflict between fidelity of models and the speed of their simulation. Another related challenge arises in dealing with the large number of what–if scenarios that need to be explored. Here, we describe new computational methods that together provide an approach to dealing with both challenges. A mesoscopic modeling approach is described that strikes a middle ground between macroscopic models based on coupled differential equations and microscopic models built on fine-grained behaviors at the individual entity level. The mesoscopic approach offers the ability to incorporate complex compositions of multiple layers of dynamics even while retaining the potential for aggregate behaviors at varying levels. It also is an excellent match to the accelerator-based architectures of modern computing platforms in which graphical processing units (GPUs) can be exploited for fast simulation via the parallel execution mode of single instruction multiple thread (SIMT). The challenge of simulating a large number of scenarios is addressed via a method of sharing model state and computation across a tree of what–if scenarios that are localized, incremental changes to a large base simulation. A combination of the mesoscopic modeling approach and the incremental what–if scenario tree evaluation has been implemented in the software on modern GPUs. Synthetic simulation scenarios are presented to demonstrate the computational characteristics of our approach. Results from the experiments with large population data, including USA, UK, and India, illustrate the modeling methodology and computational performance on thousands of synthetically generated what–if scenarios. Execution of our implementation scaled to 8192 GPUs of supercomputing platforms demonstrates the ability to rapidly evaluate what–if scenarios several orders of magnitude faster than the conventional methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Time-dependent-bases with local CUR decomposition method for accelerating turbulent combustion simulations

Here, this study presents a novel reduced-order modeling framework, Time-Dependent Bases with Local CUR decomposition (TDB-L-CUR), designed to efficiently and accurately approximate the species transport equations in reacting flow simulations. The method extends the existing TDB-CUR approach for chemically reacting flows (Jung et al. Comput. Methods Appl. Mech. Engrg. 437 (2025) 117758), which leverages matrix decomposition techniques to form a global-in-space, time-dependent low-dimensional manifold. While TDB-CUR performs well in homogeneous systems, it may be less well-suited to spatially heterogeneous systems such as turbulent flames, where higher-rank approximations are typically required. The proposed TDB-L-CUR framework introduces two methodological extensions to the baseline approach. First, it applies unsupervised clustering to partition the physical domain into distinct regions, enabling spatially localized manifold construction, thereby reducing the rank required for the reduced-order representation. Second, it incorporates a computational singular perturbation (CSP)-based scheme for identifying and penalizing fast species, allowing for spatio-temporally adaptive mitigation of chemical stiffness. The proposed framework is validated on a hierarchy of test cases, including a one-dimensional premixed flame, a two-dimensional nonpremixed ignition case with vortex interaction, and a three-dimensional turbulent premixed flame. TDB-L-CUR significantly improves accuracy over TDB-CUR while further reducing computational cost. The fully on-the-fly formulation of TDB-L-CUR (i.e., requiring no offline training or prior knowledge) makes it a robust and scalable tool for reduced-order modeling of reactive flows.

Local manifold↗
DOE OSTI2022

Decoding the protein–ligand interactions using parallel graph neural networks

Abstract Protein–ligand interactions (PLIs) are essential for biochemical functionality and their identification is crucial for estimating biophysical properties for rational therapeutic design. Currently, experimental characterization of these properties is the most accurate method, however, this is very time-consuming and labor-intensive. A number of computational methods have been developed in this context but most of the existing PLI prediction heavily depends on 2D protein sequence data. Here, we present a novel parallel graph neural network (GNN) to integrate knowledge representation and reasoning for PLI prediction to perform deep learning guided by expert knowledge and informed by 3D structural data. We develop two distinct GNN architectures: $$\hbox {GNN}_{\mathrm{F}}$$ GNN F is the base implementation that employs distinct featurization to enhance domain-awareness, while $$\hbox {GNN}_{\mathrm{P}}$$ GNN P is a novel implementation that can predict with no prior knowledge of the intermolecular interactions. The comprehensive evaluation demonstrated that GNN can successfully capture the binary interactions between ligand and protein’s 3D structure with 0.979 test accuracy for $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and 0.958 for $$\hbox {GNN}_{\mathrm{P}}$$ GNN P for predicting activity of a protein–ligand complex. These models are further adapted for regression tasks to predict experimental binding affinities and $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 crucial for compound’s potency and efficacy. We achieve a Pearson correlation coefficient of 0.66 and 0.65 on experimental affinity and 0.50 and 0.51 on $$\hbox {pIC}_{\mathrm{50}}$$ pIC 50 with $$\hbox {GNN}_{\mathrm{F}}$$ GNN F and $$\hbox {GNN}_{\mathrm{P}}$$ GNN P , respectively, outperforming similar 2D sequence based models. Our method can serve as an interpretable and explainable artificial intelligence (AI) tool for predicted activity, potency, and biophysical properties of lead candidates. To this end, we show the utility of $$\hbox {GNN}_{\mathrm{P}}$$ GNN P on SARS-Cov-2 protein targets by screening a large compound library and comparing the prediction with the experimentally measured data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Multiscale method based on coupled lattice‐Boltzmann and Langevin‐dynamics for direct simulation of nanoscale particle/polymer suspensions in complex flows

Summary A hybrid computational method coupling the lattice‐Boltzmann (LB) method and a Langevin‐dynamics (LD) method is developed to simulate nanoscale particle and polymer (NPP) suspensions in the presence of both thermal fluctuation and long‐range many‐body hydrodynamic interactions (HIs). Brownian motion of the NPP is explicitly captured by a stochastic forcing term in the LD method. The LD method is two‐way coupled to the nonfluctuating LB fluid through a discrete LB forcing source distribution to capture the long‐range HI. To ensure intrinsically linear scalability with respect to the number of particles, a Eulerian‐host algorithm for short‐distance particle neighbor search and interaction is developed and embedded to LB‐LD framework. The validity and accuracy of the LB‐LD approach are demonstrated through several sample problems. The simulation results show good agreements with theory and experiment. The LB‐LD approach can be favorably incorporated into complex multiscale computational frameworks for efficiently simulating multiscale multicomponent particulate suspension systems such as complex blood suspensions.

Liu, Zixiang↗
DOE OSTI2019

Interface-Resolved Simulations of Reactor Flows

The presented review paper outlines the recent progress of the high-resolution single- and two-phase flow simulations of reactor-relevant flows. Rapid development of high-performance computing capabilities is creating exciting opportunities to study complex reactor thermal hydraulic phenomena. Today’s advances in thermal hydraulic analysis, machine learning techniques and interface resolved simulations will help pave the way to the next level of understanding of two-phase flow behavior in complex geometries. This paper consists of two major parts: (i) history and review of interface tracking simulations for nuclear thermal hydraulics in recent years and (ii) several opportunities to apply those advanced tools in the future. First part will discuss typical computational methods used for those simulations, provide some examples of the past work, as well as computational cost estimates and affordability of such simulations for research and industrial applications. In the second part some specific examples are discussed which could be analyzed using exascale supercomputers being designed and projected to be online in the early 2020s. New generation methodologies are required in order to take full advantage of those capabilities to greatly enhance the scientific understanding of complex two-phase flow phenomena in nuclear reactors under normal operation and postulated accident conditions.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2014

Mining Building Energy Management System Data Using Fuzzy Anomaly Detection and Linguistic Descriptions

Building Energy Management Systems (BEMSs) are essential components of modern buildings that utilize digital control technologies to minimize energy consumption while maintaining high levels of occupant comfort. However, BEMSs can only achieve these energy savings when properly tuned and controlled. Since indoor environment is dependent on uncertain criteria such as weather, occupancy, and thermal state, performance of BEMS can be sub-optimal at times. Unfortunately, the complexity of BEMS control mechanism, the large amount of data available and inter-relations between the data can make identifying these sub-optimal behaviors difficult. This paper proposes a novel Fuzzy Anomaly Detection and Linguistic Description (Fuzzy-ADLD) based method for improving the understandability of BEMS behavior for improved state-awareness. The presented method is composed of two main parts: 1) detection of anomalous BEMS behavior and 2) linguistic representation of BEMS behavior. The first part utilizes modified nearest neighbor clustering algorithm and fuzzy logic rule extraction technique to build a model of normal BEMS behavior. The second part of the presented method computes the most relevant linguistic description of the identified anomalies. The presented Fuzzy-ADLD method was applied to real-world BEMS system and compared against a traditional alarm based BEMS. In six different scenarios, the Fuzzy-ADLD method identified anomalous behavior either as fast as or faster (an hour or more), that the alarm based BEMS. In addition, the Fuzzy-ADLD method identified cases that were missed by the alarm based system, demonstrating potential for increased state-awareness of abnormal building behavior.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2017

4th Penn State Bioinorganic Workshop

The research area of biological inorganic chemistry encompasses a wide variety of subfields, including molecular biology, biochemistry, biophysics, inorganic chemistry, analytical chemistry, physical chemistry, and theoretical chemistry, as well as many different methods, such as biochemical characterization of enzymes, reaction kinetics, a plethora of spectroscopic techniques, and computational methods. The above methods are combined to understand the formation, function, and regulation of the many metallo-cofactors found in Nature as well as to identify novel metallo-cofactors. Many metalloenzyme-catalyzed reactions are extremely complex, but are of fundamental importance to science and society. Examples include (i) the reduction of the chemically inert molecule, dinitrogen, to ammonia by the enzyme nitrogenase (this reaction is fundamental for the production of nitrogen fertilizers); (ii) the oxidation of water to dioxygen by the Mn4Ca cluster found in photosystem II; and (iii) myriad reactions in which aliphatic, inert C-H bonds are cleaved for subsequent functionalization of the carbon atoms (the latter reactions are important in the biosynthesis of many natural products). Because of the broad range of areas and techniques employed in this field, research in bioinorganic chemistry is typically carried out collaboratively between two or more research groups. It is of paramount importance that researchers working in this field have a good, basic, working knowledge of many methods and approaches employed in the field, in order to design and discuss experiments with collaborators. Therefore, the training of students working in bioinorganic chemistry is an important aspect of this field. Hugely successful “bioinorganic workshops” were offered in the 1990s at The University of Georgia. These workshops laid the foundation for many of the extant collaborative research efforts in this area today. The large and diverse group of bioinorganic chemists at The Pennsylvania State University and our unique laboratory space are well suited for the continuation of such training workshops. The co-principal investigators of this award lead these efforts. After a smaller “trial workshop” in 2010, the Penn State bioinorganic group, led by the co-PIs, offers these workshops biennially. The 2012, 2014, and 2016 workshops provided training to 123, 162, and 153 participants, respectively, by offering (i) a series of lectures given by faculty experts on the given topic, (ii) hands-on training in small groups by experts in the various methods, and (iii) sharing research results of the participants by oral and poster presentations. The centerpiece of the workshops is the hands-on training, in which approximately half of the participants from all ranks (undergraduate students to faculty) served as teachers. In this section, the traditional roles of teachers and students were sometimes reversed to the extent that undergraduate students taught faculty in the students' areas of specialty. We anticipate that these workshops will facilitate research in bioinorganic chemistry and will help establish future collaborations among “workshop alumni” to carry out cutting-edge research in bioinorganic chemistry that will address many important topics relevant to our society.

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

FY21 Status report on the CMVB and CNWG International Collaborations

The ART-GCR Methods area includes an international collaboration work package that covers the tasks defined for the Computational Methods Validation and Benchmark (CMVB)and Civil Nuclear Energy Research and Development Working Group (CNWG) projects. This report summarizes the status of the FY21 tasks and planned FY22 DOE contributions. The CMVB Project Arrangement (PA) is not yet formally approved by all signatories, and no work has therefore been performed in FY21 at INL related to this activity. The CNWG activities inFY21 consisted of the simulation of the High Temperature Test Reactor (HTTR) Loss Of Forced Cooling (LOFC) experimental with the Idaho National Laboratory (INL) codes Griffin, BISON and RELAP-7 based on the Multiphysics Object-Oriented Simulation Environment (MOOSE).It was found that the multiphysics coupled suite is capable of simulating all the important phenomena occurring during the Depressurized Loss of Forced Cooling (DLOFC) experiments showing promising agreement with the measurements given the number of uncertainties and approximations introduced into the model.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

Sequential Decision Making (SDM) for Mesh Refinement and Model Selection in Multiscale, Multi-Physics Applications

Intelligent automation and decision support are needed to enhance computational efficiency and robustness in multiscale and multi-physics problems, including materials science, manufacturing, and climate and weather modeling. Current scientific computing approaches for enabling decisions by scientists fail to explore the role of learning, reasoning, and probabilistic planning. Often these decisions are not performed in real-time during the computation but are made prior to the start of the computation, which must be interrupted in order to make changes to the prior choices. Such interruptions at different stages of the computation increase the total computing time and the need for a human expert to frequently monitor the results. State of art scientific computing methods consist of rule-based algorithms that cannot automatically adapt to a dynamically changing computing environment. The development of a Sequential Decision Making (SDM) framework will automate scientific computing by optimizing the policies for mesh refinement, time-stepping, model and algorithm selection, resource allocation, and pre and post-processing. Our agent SDM framework for scientific computing will consist of data-driven learning (Classifier), automated reasoning (contextual knowledge), and probabilistic planning (Reinforcement Learning). In this project, we focused on three problems to demonstrate our SDM framework on a set of ordinary and partial differential equations. Classification of Lorenz system regions using Feed-Forward Neural Networks examined learning in the SDM framework. On the other hand, reasoning and planning in the SDM framework were used in two problems: adaptive time-stepping for nonlinear ODEs using on-policy RL algorithms, and adaptive mesh refinement for 2-D PDEs using off-policy RL algorithms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Scalable methods for electronic excitations and optical responses of nanostructures: mathematics to algorithms to observables

The master project under which this work is funded had as its main objective to develop computational methods for modeling electronic excited-state and optical properties of various nanostructures. The specific goals of the computer science group were primarily to develop effective numerical algorithms in Density Functional Theory (DFT) and Time Dependent Density Functional Theory (TDDFT). There were essentially four distinct stated objectives. The first objective was to study and develop effective numerical algorithms for solving large eigenvalue problems such as those that arise in Density Functional Theory (DFT) methods. The second objective was to explore so-called linear scaling methods or Methods that avoid diagonalization. The third was to develop effective approaches for Time-Dependent DFT (TDDFT). Our fourth and final objective was to examine effective solution strategies for other problems in electronic excitations, such as the GW/Bethe-Salpeter method, and quantum transport problems.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2018

Space-time discretizations using constrained first-order system least squares (CFOSLS)

This work studies finite element discretizations for three types of time-dependent PDEs, namely heat equation, scalar conservation law and wave equation, which we reformulate as first order systems in a least-squares setting, subject to a space-time conservation constraint (coming from the original PDE). Available piecewise polynomial finite element spaces in (n + 1)-dimensions for functional spaces from the (n + 1)-dimensional de Rham sequence for n = 2, 3 are used for the implementation of the method. Computational results illustrating the error behavior, iteration counts and performance of block-diagonal and monolithic geometric multigrid preconditioners are presented for the discrete CFOSLS system. The results are obtained from a parallel implementation of the methods for which we report reasonable scalability.

4D de Rham sequence↗