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DOE OSTI2026

Potential Applications of Quantum Computing at Los Alamos National Laboratory, v0.3.0

Since the scientific revolution in the 16th and 17th centuries, the process of scientific discovery has followed an iterative feedback process of observation, hypothesis development and testing with physical experiments, which is widely referred to as the scientific method. This process remained largely unchanged until the middle of the 20th century, when the emergence of digital computers empowered scientist to build and inspect detailed simulations of physical phenomena. Over the last century, computational tools have transformed modern approaches to scientific discovery by enabling fast and affordable hypothesis testing before physical experiments are conducted, shown in Figure 1-1. Some notable examples include: global climate forecasts to understand how the environment may change over decades [130]; modeling the behavior of plasma to design fusion reactors [59]; and understanding the behavior of molecules in biological processes [161, 223].

36 MATERIALS SCIENCE↗

DOE OSTI2015

VERA 3.3 Release Notes

The Virtual Environment for Reactor Applications components included in this distribution include selected computational tools and supporting infrastructure that solve neutronics, thermal-hydraulics, fuel performance, and coupled neutronics-thermal hydraulics-fuel performance problems. The infrastructure components provide a simplified common user input capability and provide for the physics integration with data transfer and coupled-physics iterative solution algorithms. Neutronics analysis can be performed for 2D lattices, 2D core and 3D core problems for pressurized water reactor geometries that can be used to calculate criticality and fission rate distributions by pin for input fuel compositions. Two neutronics capabilities are provided in this distribution including MPACT (from the University of Michigan) that supports 2D lattices and Insilico (from Oak Ridge National Laboratory) that supports 2D lattices, 2D core planes, and 3D core geometries. Both codes include integrated cross section capabilities that provide problem-specific cross sections for the problems defined. A thermal-hydraulics capability is provided with CTF (an updated version of the COBRA-TF code developed by the Pennsylvania State University) that allows thermal-hydraulics analyses for single and multiple assemblies using the simplified VERA common input. This distribution also includes an initial coupled neutronics/thermal-hydraulics capability to allow calculations of single assemblies using Insilico or MPACT coupled with CTF. The VERA fuel rod performance subcomponent BISON-CASL calculates, on a 3D basis, fuel rod temperature, fuel rod internal pressure, free gas volume, clad integrity and fuel rod waterside diameter. These capabilities allow simulation of power cycling, fuel conditioning and deconditioning, high burnup performance, power uprate scoping studies, and accident performance. Specifically targeted at VERA’s core simulator functionality (VERA-CS), the existing VERA subchannel-neutronics capability based on CTF and Insilico has been extended to use the axisymmetric 2D R-Z fuel rod modeling functionality of BISON-CASL to produce a three-way coupled neutronics, thermal-hydraulics and fuel performance capability known as Tiamat. This distribution is intended to be used for testing and evaluation of the released components of VERA. Testing within CASL has focused specifically on Westinghouse four-loop reactor geometries and conditions with example problems included in the distribution.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2016

VERA and VERA-EDU 3.5 Release Notes

The Virtual Environment for Reactor Applications components included in this distribution include selected computational tools and supporting infrastructure that solve neutronics, thermal-hydraulics, fuel performance, and coupled neutronics-thermal hydraulics problems. The infrastructure components provide a simplified common user input capability and provide for the physics integration with data transfer and coupled-physics iterative solution algorithms. Neutronics analysis can be performed for 2D lattices, 2D core and 3D core problems for pressurized water reactor geometries that can be used to calculate criticality and fission rate distributions by pin for input fuel compositions. MPACT uses the Method of Characteristics transport approach for 2D problems. For 3D problems, MPACT uses the 2D/1D method which uses 2D MOC in a radial plane and diffusion or SPn in the axial direction. MPACT includes integrated cross section capabilities that provide problem-specific cross sections generated using the subgroup methodology. The code can be executed both 2D and 3D problems in parallel to reduce overall run time. A thermal-hydraulics capability is provided with CTF (an updated version of COBRA-TF) that allows thermal-hydraulics analyses for single and multiple assemblies using the simplified VERA common input. This distribution also includes coupled neutronics/thermal-hydraulics capabilities to allow calculations using MPACT coupled with CTF. The VERA fuel rod performance component BISON calculates, on a 2D or 3D basis, fuel rod temperature, fuel rod internal pressure, free gas volume, clad integrity and fuel rod waterside diameter. These capabilities allow simulation of power cycling, fuel conditioning and deconditioning, high burnup performance, power uprate scoping studies, and accident performance. Input/Output capabilities include the VERA Common Input (VERAIn) script which converts the ASCII common input file to the intermediate XML used to drive all of the physics codes in the VERA Core Simulator (VERA-CS). VERA component codes either input the VERA XML format directly, or provide a preprocessor which can convert the XML into native input. VERAView is an interactive graphical interface for the visualization and engineering analyses of output data from VERA. The python-based software is easy to install and intuitive to use, and provides instantaneous 2D and 3D images, 1D plots, and alpha-numeric data from VERA multi-physics simulations. Testing within CASL has focused primarily on Westinghouse four-loop reactor geometries and conditions with example problems included in the distribution.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2015

Modern sensitivity analysis - 15651

Sensitivity analysis has been applied to complex models, such as performance assessment models, since at least the advent of computational tools to support such an approach to model evaluation. Initially, sensitivity analysis methods were applied to deterministic models and focused on changing one input variable at a time. Probabilistic modeling opened the door to evaluating changes in all input variables simultaneously. Standardized rank regression methods were primarily used in the last century to evaluate probabilistic models. These methods assume linearity in the rank response of the model to the inputs. At the very least this assumes monotonicity in the response, but for the most part the response needs to be near-linear. This is highly unlikely for performance assessment models that are based on differential equations, multiplication and division of variables that are usually not correlated, and conservatism that is not well understood. There are better statistical methods for evaluating highly non-linear and dynamic probabilistic models. Some of these methods were founded in the data mining industry. This century has seen a rapid development of the internet that led directly to the development of data mining techniques for massive databases. Although the goals were different, these techniques can be adapted to sensitivity analysis for complex probabilistic models, which, also, form large, or even massive, databases. These modern sensitivity analysis procedures assess the importance of every explanatory variable (input parameters) used in a probabilistic model. In practice, this means that for each endpoint of interest, every explanatory variable in the model is associated with a quantitative measure of importance. For a given explanatory variable, the importance value depends on the endpoint of interest. This global approach to sensitivity analysis allows all levels of interactions to be evaluated, so that the variation in the output can be measured at every level of possible interaction. The effects are collected together during sensitivity analysis processing, and then separated out to attribute the overall contribution of each input parameter to the model output. These global sensitivity analysis procedures have the ability to characterize non-linear and non-monotonic relationships between explanatory variables and endpoints of interest. This is critically important because of the need to characterize complex interactions among multiple explanatory variables in PA models that often have non-linear and non-monotonic effects. The options for sensitivity analysis are fully explored, including an evaluation of several methods when applying them to a well-known complex non-linear non-monotonic model. The results clearly demonstrate the relative benefit of using data mining methods over simple statistical approaches such as standardized rank regression. (authors)

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2002

Architecture-Adaptive Computing Environment: A Tool for Teaching Parallel Programming

Recently, networked and cluster computation have become very popular. This paper is an introduction to a new C based parallel language for architecture-adaptive programming, aCe C. The primary purpose of aCe (Architecture-adaptive Computing Environment) is to encourage programmers to implement applications on parallel architectures by providing them the assurance that future architectures will be able to run their applications with a minimum of modification. A secondary purpose is to encourage computer architects to develop new types of architectures by providing an easily implemented software development environment and a library of test applications. This new language should be an ideal tool to teach parallel programming. In this paper, we will focus on some fundamental features of aCe C.

Dorband, John E.↗

DOE OSTI2019

Thermal and Thermoelectric Properties of Molecular Junctions

Abstract Molecular junctions (MJs) represent an ideal platform for studying charge and energy transport at the atomic and molecular scale and are of fundamental interest for the development of molecular‐scale electronics. While tremendous efforts have been devoted to probing charge transport in MJs during the past two decades, only recently advances in experimental techniques and computational tools have made it possible to precisely characterize how heat is transported, dissipated, and converted in MJs. This progress is central to the design of thermally robust molecular circuits and high‐efficiency energy conversion devices. In addition, thermal and thermoelectric studies on MJs offer unique opportunities to test the validity of classical physical laws at the nanoscale. A brief survey of recent progress and emerging experimental approaches in probing thermal and thermoelectric transport in MJs is provided, including thermal conduction, heat dissipation, and thermoelectric effects, from both a theoretical and experimental perspective. Future directions and outstanding challenges in the field are also discussed.

Wang, Kun↗

DOE OSTI2021

The Value of Watching How Materials Grow: A Multimodal Case Study on Halide Perovskites

Material synthesis is one of the most important aspects in humankinds’ endeavor to discover and create new materials for energy applications. One strategy to tailor materials with desired functions in a rational way is by knowing how functions relate to structure, synthetic variables, arrangement of atoms and molecules, and how functions evolve during synthesis. In order to accelerate materials synthesis, discovery, and optimization by 10 times it is the right time now to integrate computational tools, synthesis, and characterization. One particular barrier to realizing this concept is the understanding of when and how phases form in real time during synthesis, which is challenging to asses by existing theoretical frameworks. In addition, transient or metastable phases with positive free energy above the lowest-free energy ground state can be revealed by such real time (in situ) measurements. Metastable materials are ubiquitous in condensed matter and can show superior properties compared to their equilibrium form. This work discusses the value of emerging multimodal in situ characterizations exemplified on hybrid halide perovskites. Finally, the ways in which the implementation of in situ measurements can advance the materials science synthesis field as well as their role to enable close-loop feedback control and autonomous synthesis are discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Polyketide synthases as a platform for chemical product design

To reduce the effects of greenhouse gas emissions on climate change, scientific efforts have sought to develop biofuels and bio‐based commodity chemicals as petrochemical replacements primarily for their environmental benefits. As the biological design space is far greater than chemical synthesis, there has been a drive to leverage this ability to create and replace fine and specialty chemicals. While polyketide synthases have traditionally been studied for their biosynthesis of pharmaceutical chemicals, the unique advantages of engineering polyketide synthases for the production of biofuels, commodity chemicals, and both pharmaceutical and nonpharmaceutical fine and specialty chemicals are discussed. With our increased understanding of polyketide biosynthetic logic, new computational tools for prospective polyketide synthesis pathways for the creation of existing and novel biochemicals are also outlined. © 2018 American Institute of Chemical Engineers AIChE J , 64: 4201–4207, 2018

Zargar, Amin↗

DOE OSTI2021

The IDAES process modeling framework and model library—Flexibility for process simulation and optimization

Abstract Energy systems and manufacturing processes of the 21st century are becoming increasingly dynamic and interconnected, which require new capabilities to effectively model and optimize their design and operations. Such next generation computational tools must leverage state‐of‐the‐art techniques in optimization and be able to rapidly incorporate new advances. To address these requirements, we have developed the Institute for the Design of Advanced Energy Systems (IDAES) Integrated Platform, which builds on the strengths of both process simulators (model libraries) and algebraic modeling languages (advanced solvers). This paper specifically presents the IDAES Core Modeling Framework (IDAES‐CMF), along with a case study demonstrating the application of the framework to solve process optimization problems. Capabilities provided by this framework include a flexible, modifiable, open‐source platform for optimization of process flowsheets utilizing state‐of‐the‐art solvers and solution techniques, fully open and extensible libraries of dynamic unit operations models and thermophysical property models, and integrated support for superstructure‐based conceptual design and optimization under uncertainty.

42 ENGINEERING↗

DOE OSTI2025

Ca X ML: Chemistry‐informed machine learning explains mutual changes between protein conformations and calcium ions in calcium‐binding proteins using structural and topological features

Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes. However, it is unclear whether the limited experimental data available can be effectively used to train models to accurately predict the charges of calcium-binding protein variants. Here, we developed a chemistry-informed, machine-learning algorithm that implements a game theoretic approach to explain the output of a machine-learning model without the prerequisite of an excessively large database for high-performance prediction of atomic charges. We used the ab initio electronic structure data representing calcium ions and the structures of the disordered segments of calcium-binding peptides with surrounding water molecules to train several explainable models. Network theory was used to extract the topological features of atomic interactions in the structurally complex data dictated by the coordination chemistry of a calcium ion, a potent indicator of its charge state in protein. Our design created a computational tool of Ca X ML, which provided a framework of explainable machine learning model to annotate ionic charges of calcium ions in calcium-binding proteins in response to the chemical changes in an environment. Our framework will provide new insights into protein design for engineering functionality based on the limited size of scientific data in a genome space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Hydroxyl radical‐driven transformations of bisphenol A and 2,4‐dinitroanisole: Experimental and computational analysis

Abstract This study used experimental and computational analysis to investigate the advanced oxidation of bisphenol A (BPA) and 2,4‐dinitroanisole (DNAN). The pseudo first‐order reaction rate constants depended on the molar peroxide ratio and were between 0.13 and 0.28 min −1 for BPA and between 0.018 and 0.032 min −1 for DNAN. The kinetic differences appear to be due in part to the energy requirements for oxidation, which depended on the reaction mechanism but were typically lower for BPA than they were for DNAN. Density functional theory (DFT) was used to develop transformation pathways that included experimentally‐detected byproducts. The most energetically favored pathway for BPA oxidation begins with the formation of hydroxylated derivatives, while for DNAN, the most energetically favorable degradation pathway begins with the substitution of the methoxy group. Overall, these findings demonstrate the power of combining experimental and computational tools to reveal transformation mechanisms during water treatment. Practitioner Points Advanced oxidation transformations for two emerging water pollutants, bisphenol A and dinitroanisole, was investigated. The observed reaction kinetics depended on molar peroxide ratio in a manner that is in keeping with previous findings. Density functional theory‐based analysis revealed reaction energy requirements and degradation pathways.

Engineering↗

DOE OSTI2024

Multi-omics Resources for Understanding Gene Regulation in Response to ER Stress in Plants

Proteotoxic stress of the endoplasmic reticulum (ER) is a potentially lethal condition that ensues when the biosynthetic capacity of the ER is overwhelmed. A sophisticated and largely conserved signaling, known as the unfolded protein response (UPR), is designed to monitor and alleviate ER stress. In plants, the emerging picture of gene regulation by the UPR now appears to be more complex than ever before, requiring multi-omics-enabled network-level approaches to be untangled. In the past decade, with an increasing access and decreasing costs of next-generation sequencing (NGS) and high-throughput protein–DNA interaction (PDI) screening technologies, multitudes of global molecular measurements, known as omics, have been generated and analyzed by the research community to investigate the complex gene regulation of plant UPR. In this chapter, we present a comprehensive catalog of omics resources at different molecular levels (transcriptomes, protein–DNA interactomes, and networks) along with the introduction of key concepts in experimental and computational tools in data generation and analyses. Finally, this chapter will serve as a starting point for both experimentalists and bioinformaticians to explore diverse omics datasets for their biological questions in the plant UPR, with likely applications also in other species for conserved mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

Identification of ultramodified proteins using top-down spectra

Post-translational modifications (PTMs) play an important role in various biological processes through changing protein structure and function. Some ultramodified proteins (like histones) have multiple PTMs forming PTM patterns that define the functionality of a protein. While bottom-up mass spectrometry (MS) has been successful in identifying individual PTMs within short peptides, it is unable to identify PTM patterns spread along entire proteins in a coordinated fashion. In contrast, top-down MS analyzes intact proteins and reveals PTM patterns along the entire proteins. However, while recent advances in instrumentation have made top-down MS accessible to many laboratories, most computational tools for top-down MS focus on proteins with few PTMs and are unable to identify complex PTM patterns. We propose a new algorithm, MS-Align-E, that identifies both expected and unexpected PTMs in ultramodified proteins. We demonstrate that MS-Align-E identifies many protein forms of histone H4 and benchmark it against the currently accepted software tools.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2020

Few-Body Bound States and Resonances in Finite Volume

Since the pioneering work of Lüscher in the 1980s it is well known that considering quantum systems in finite volume, specifically, finite periodic boxes, can be used as a powerful computational tool to extract physical observables. While this formalism has been worked out in great detail in the two-body sector, much effort is currently being invested into deriving analogous relations for systems with more constituents. This work is relevant not only for nuclear physics, where lattice methods are now able to calculate few- and many-nucleon states, but also for other fields such as simulations of cold atoms. This article discusses recent progress regarding the extraction of few-body bound-state and resonance properties from finite-volume calculations of systems with an arbitrary number of constituents.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Dissociating the phononic, magnetic and electronic contributions to thermal conductivity: a computational study in alpha-iron

Computational tools to study thermodynamic properties of magnetic materials have, until recently, been limited to phenomenological modeling or to small domain sizes limiting our mechanistic understanding of thermal transport in ferromagnets. Herein, we study the interplay of phonon and magnetic spin contributions to the thermal conductivity in a-iron utilizing non-equilibrium molecular dynamics simulations. It was observed that the magnetic spin contribution to the total thermal conductivity exceeds lattice transport for temperatures up to two-thirds of the Curie temperature after which only strongly coupled magnon-phonon modes become active heat carriers. Characterizations of the phonon and magnon spectra give a detailed insight into the coupling between these heat carriers, and the temperature sensitivity of these coupled systems. Comparisons to both experiments and ab initio data support our inferred electronic thermal conductivity, supporting the coupled molecular dynamics/spin dynamics framework as a viable method to extend the predictive capability for magnetic material properties.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Welding Defect Classification from Simulated Ultrasonic Signals

Nondestructive testing is widely used to detect and to size up discontinuities embedded in a material. Among the several ultrasonic techniques, time of flight diffraction (TOFD) combines high speed inspection, high sizing reliability and low rate of incorrect results. However, the classification of defects through ultrasound signals acquired by the TOFD technique depends heavily on the knowledge and experience of the operator and thus, this classification is still frequently questioned. Besides, this task requires long processing time due to the large amount of data to be analyzed. Nevertheless, computational tools for pattern recognition can be employed to analyze a high amount of data with large efficiency. In the present work, simulation of ultrasound propagation in two-dimensional media containing, each one, different kinds of modeled discontinuities which mimic defects in welded joints were performed. Clustering (k-means) and classification (principal component analysis and k-nearest neighbors) algorithms were employed to associate each simulated ultrasound signal with its corresponding modeled defects. The results for each method were analyzed, discussed and compared. The results are very promising.

42 ENGINEERING↗

DOE OSTI2022

Toward Discord : Code for Simulating Continuous Spin Systems

A new computational tool to simulate classical spin systems with frustrated crystal structures is presented. Complementary single- and cluster-spin flip algorithms are implemented to calculate the diffuse scattering patterns, spin-pair correlations, and thermodynamic quantities. Test cases of geometrically frustrated kagome, pyrochlore, and cubic systems are detailed. Two recent scientific cases are also shown here. This new method, together with recent developments of the rmc-discord package (https://github.com/zjmorgan/rmc-discord), represent integrated and strategic step in a complete forward and reverse Monte Carlo framework discord.

36 MATERIALS SCIENCE↗

DOE OSTI2019

A feedback regulation of CREB activation through the CUL4A and ERK signaling

CUL4A; an E3 ubiquitin ligase is involved in the degradation of negative regulators of cell cycle such as p21, p27, p53, etc., through polyubiquitination-mediated protein degradation. The functional role(s) of CUL4A proteins on their targets are well characterized; however, the transcriptional regulation of CUL4A, particularly at its promoter level is not yet studied. Therefore, in this study, using computational tools, we found cAMP responsive elements (CRE) at the locations of − 926 and − 764 with respect to transcription state site + 1 of CUL4A promoter. Hence, we investigated the role of CREB on the regulation of CUL4A transcription. Our chromatin immunoprecipitation (ChIP) data clearly showed increased levels of promoter occupancy of both CREB and pCREB on both CREs of CUL4A promoter. As expected, the expression of CUL4A increases and decreases upon the overexpression of and knocking down of CREB, respectively. Moreover, the inhibition of ERK pathway by U0126 not only reduces the CREB activation but also the CUL4A levels suggesting that CREB is the upstream activator of CUL4A transcription. The reduction of CUL4A levels upon the knocking down of CREB or by U0126 treatment increases the protein levels of CUL4A substrates such as p21 and p27. It is reported that CUL4A activates the ERK1/2 transcription and ERK1/2 pathway activates the CREB by phosphorylation. Based on our data and earlier findings, we report that CREB regulates the CUL4A levels positively which in turn activates the CREB through ERK1/2 pathway in the form of auto-regulatory looped mechanism.This suggests that CUL4A might be involved in proliferation of cancer cells by regulating the ERK1/2 and CREB signaling.

62 RADIOLOGY AND NUCLEAR MEDICINE↗