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At least 1,369 records · Page 76

Optimal Experimental Design for Inverse Problems in the Presence of Observation Correlations

Optimal experimental design (OED) is the general formalism of sensor placement and decisions on the data collection strategy for engineered or natural experiments. This problem is prevalent in many critical fields such as battery design, numerical weather prediction, geosciences, environmental and urban studies. State-of-the-art computational methods for experimental design do not accommodate correlation structure in observational errors produced by many expensive-to-operate devices such as X-ray machines, radars, and satellites. Discarding evident data correlations leads to biased results, higher expenses, and waste of valuable resources. We present a general formulation of the OED formalism for model-constrained large-scale Bayesian linear inverse problems, where measurement errors are generally correlated. The proposed approach utilizes the Hadamard product of matrices to formulate the weighted-likelihood, and is valid for both finite as well as infinite-dimensional Bayesian inverse problems. Extensive numerical experiments are carried out for empirical verification of the proposed approach using an advection-diffusion model, where the objective is to optimally place a small set of sensors, under a limited budget, to predict the concentration of a contaminant in a closed and bounded domain.

Correlated observations↗

A.I. for nuclear physics

Nuclear science is concerned with the understanding of the nature of matter, its basic constituents and their interaction to form the elements and the properties we observe. This includes the forms of matter we see around us and also exotic forms such as those that existed in the first moments after the Big Bang and that exist today inside neutron stars. The techniques, tools, and expertise needed for nuclear physics (NP) research are therefore diverse in nature. State-of-the art accelerators are being developed to illuminate the dynamical basis of the core of the atom in terms of the fundamental constituents called quarks and gluons and to increase the number of isotopes with known properties. This scientific infrastructure is reaching scales and complexities that require computational methods for tasks such as anomaly detection in operational data. New methodologies are needed to detect anomalies and to optimize operating parameters, predict failures as well as to discover new optimization algorithms.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Remembering the Work of Phillip L. Geissler: A Coda to His Scientific Trajectory

Phillip L. Geissler made important contributions to the statistical mechanics of biological polymers, heterogeneous materials, and chemical dynamics in aqueous environments. He devised analytical and computational methods that revealed the underlying organization of complex systems at the frontiers of biology, chemistry, and materials science. In this retrospective we celebrate his work at these frontiers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ab Initio Studies of Discharge Mechanism of MnO 2 in Deep-Cycled Rechargeable Zn/MnO 2 Batteries

Rechargeable alkaline Zn/MnO 2 batteries are an attractive solution for large-scale energy storage applications. Recently, Bi and Cu additives have been used to increase the cycle life and capacity of rechargeable Zn/MnO 2 batteries, with an equivalent of the full two-electron capacity realized for many cycles, in the absence of zinc. However, the mechanism of the effect of Bi and Cu on the performance of rechargeable Zn/MnO 2 batteries has not been investigated in detail. We apply first-principles density functional computational methods to study the discharge mechanisms of the unmodified and Bi/Cu-modified γ -MnO 2 electrodes in rechargeable alkaline Zn/MnO 2 batteries. Using the results of our calculations, we analyze the possible redox reaction pathways in the γ -MnO 2 electrode and identify the electrochemical processes leading to the formation of irreversible discharge reaction products, such as hausmannite and hetaerolite. Our study demonstrates the possibility of formation of intermediate Bi-Mn and Cu-Mn oxides in deep-cycled Bi/Cu-modified MnO 2 electrodes. The formation of intermediate Bi-Mn and Cu-Mn oxides could reduce the rate of accumulation of irreversible reaction products in the MnO 2 electrode and improve the rechargeability and cyclability of Zn/MnO 2 batteries.

25 ENERGY STORAGE↗

RGM: Random Geological Model Generation Package

This Fortran code is to accompany a manuscript to be submitted to Computers & Geosciences, a high-impact, peer-reviewed journal in computer methods for geosciences research. This Fortran code focuses on generation of synthetic geological models using a multi-randomization strategy. Generating high-fidelity synthetic geological models, including realistic seismic reflector migration images, faults, salt bodies, and relative geological time images, is the key for many supervised machine learning methods that aim to delineate faults and other geological properties of interest from seismic migration images. Our package contains two major functionalities: generating 2D synthetic random geological models and generating 3D synthetic random geological models. In each step of the generation process, we set random values for key properties of a geological model to improve the fidelity of the resulting geological model. The package also includes example codes on how to use the random geological model generation subroutines. We name this package RGM – Random Geological Model generation package.

Gao, Kai↗

Common Electric Power Transmission System Model JSON Schema Specification

The Common Electric Power Transmission System Model (CTM) is an intuitive, extensible, language-agnostic, and error-resistant specification of electric power network components parameter names and units, and relation between components, intended for use by the research community developing new computational methods for power systems operations and simulation. Power system datasets following the CTM specification can be read as dictionaries and manipulated in that form in most programming languages (e.g., Python, Julia, C++). This standard data structure in CTM makes it easy to work in multiple power systems domains (e.g., economic operation, reliability assessment, electricity markets, stability assessment, etc.) without requiring conversions between use-case-specific file formats with information loss in the process. This repository specifies CTM as a JSON Schema, provides documentation, derivate (code-generated) implementations of CTM, and example data and usage of the schema for important use cases.

Aravena Solis, Ignacio↗

AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

Stochastic changes in DNA methylation (i.e., spontaneous epimutations) contribute to methylome diversity in plants. Here, we describe AlphaBeta, a computational method for estimating the precise rate of such stochastic events using pedigree-based DNA methylation data as input. We demonstrate how AlphaBeta can be employed to study transgenerationally heritable epimutations in clonal or sexually derived mutation accumulation lines, as well as somatic epimutations in long-lived perennials. Application of our method to published and new data reveals that spontaneous epimutations accumulate neutrally at the genome-wide scale, originate mainly during somatic development and that they can be used as a molecular clock for age-dating trees.

59 BASIC BIOLOGICAL SCIENCES↗

Metadynamics simulations reveal mechanisms of Na + and Ca 2+ transport in two open states of the channelrhodopsin chimera, C1C2

Cation conducting channelrhodopsins (ChRs) are a popular tool used in optogenetics to control the activity of excitable cells and tissues using light. ChRs with altered ion selectivity are in high demand for use in different cell types and for other specialized applications. However, a detailed mechanism of ion permeation in ChRs is not fully resolved. Here, we use complementary experimental and computational methods to uncover the mechanisms of cation transport and valence selectivity through the channelrhodopsin chimera, C1C2, in the high- and low-conducting open states. Electrophysiology measurements identified a single-residue substitution within the central gate, N297D, that increased Ca 2+ permeability vs. Na + by nearly two-fold at peak current, but less so at stationary current. We then developed molecular models of dimeric wild-type C1C2 and N297D mutant channels in both open states and calculated the PMF profiles for Na + and Ca 2+ permeation through each protein using well-tempered/multiple-walker metadynamics. Results of these studies agree well with experimental measurements and demonstrate that the pore entrance on the extracellular side differs from original predictions and is actually located in a gap between helices I and II. Cation transport occurs via a relay mechanism where cations are passed between flexible carboxylate sidechains lining the full length of the pore by sidechain swinging, like a monkey swinging on vines. In the mutant channel, residue D297 enhances Ca 2+ permeability by mediating the handoff between the central and cytosolic binding sites via direct coordination and sidechain swinging. We also found that altered cation binding affinities at both the extracellular entrance and central binding sites underly the distinct transport properties of the low-conducting open state. This work significantly advances our understanding of ion selectivity and permeation in cation channelrhodopsins and provides the insights needed for successful development of new ion-selective optogenetic tools.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modulating ion-binding at macromolecular interfaces during (bio)mineralization: A snapshot review for calcium carbonate and calcium phosphate systems

Abstract Local environments have strict influence over (bio)mineralization in calcifying systems. This snapshot review discusses recent insights into the roles of Ca 2+ -macromolecule interactions on the nucleation of calcium carbonate and calcium phosphate minerals. Experimental findings combined with simulations/modeling are providing breakthrough information and raising important questions for future studies. The emerging picture is that both nucleation and growth are driven by local ordering of ions and water about the macromolecule interface, rather than broader properties or molecular class. Tuning macromolecular properties at the atomic scale thus provides opportunities for highly specific controls on mineralization; however, many limitations and challenges remain. We highlight studies employing in-situ atomic force microscopy (AFM) and transmission electron microscopy (TEM) to observe crystallization processes on or near macromolecular substrates. As the distribution and ability of these techniques increases, fundamental studies integrating experimental and computational methods will be crucial to inform a broad range of applications. Graphical abstract

Knight, Brenna M. (ORCID:0000000244000067)↗

Preliminary study of auto-differentiation algorithm in beam dynamics with stochastic process

Modern particle accelerator optimization requires sophisticated computational methods to address the inherently stochastic nature of beam dynamics. This research develops a framework applying AD to SDEs that specifically addresses beam dynamics challenges in particle accelerators, focusing on accurately modeling and optimizing beam behavior in regimes dominated by stochastic processes. By incorporating key physical phenomena such as synchrotron radiation, wakefield effects, and quantum excitation, the framework aims to provide auto differentiation on the figure of merit of the phase space evolution and beam dynamics. The methodology will enable effective optimization method in a dynamic system with stochastic process.

Accelerator Physics↗

Basic Research Needs for Transformative Manufacturing (Brochure)

Manufacturing is central to the nation’s prosperity and security. Manufacturing currently represents about 12% of the gross domestic product, provides nearly 13 million jobs, and accounts for about 25% of energy use. The nation’s economy relies heavily on wide-ranging manufacturing sectors - all of which share common challenges including data issues, lack of physics and chemistry-based models across scales, and resource constraints in a global environment. Furthermore, there are many hurdles that must be overcome to move basic science innovations to market. Addressing broad-ranging challenges demands a basic-science strategy that underpins applied research activities. This strategy would accelerate innovation and transform manufacturing. A Basic Research Needs workshop for Transformative Manufacturing was held in March 2020. The focus of the workshop was to identify the basic science research priorities that could accelerate innovation to transform manufacturing in the future. This was the first workshop of its kind to examine how basic energy science can drive manufacturing forward and innovate new ways to manufacture goods. Five Priority Research Directions were identified that address these science challenges: (1) innovative synthetic approaches to enable scalable assembly of matter, (2) computational methods and theoretical models to transform how manufacturing processes are controlled, (3) new characterization tools that can handle the necessary complexity, scales, and processing speeds to meet manufacturing needs, (4) new science to address opportunities relevant to sustainable and energy-efficient manufacturing, and (5) foundational approaches to co-design of materials, process, and products.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Basic Research Needs for Transformative Manufacturing

This report is based on a Basic Research Needs workshop for Transformative Manufacturing, which was held March 9 - 11, 2020. The focus of the workshop was to identify the basic science research priorities that could accelerate innovation to transform manufacturing in the future. This was the first workshop of its kind to examine how basic energy science can drive manufacturing forward and innovate new ways to manufacture goods. Five Priority Research Directions were identified that address these science challenges: (1) innovative synthetic approaches to enable scalable assembly of matter, (2) computational methods and theoretical models to transform how manufacturing processes are controlled, (3) new characterization tools that can handle the necessary complexity, scales, and processing speeds to meet manufacturing needs, (4) new science to address opportunities relevant to sustainable and energy efficient manufacturing, and (5) foundational approaches to co-design of materials, process, and products.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Roles of Carburization and Oxidation on Transition-Metal Catalyzed Surface Reactions

Many industrial chemical transformation processes are based on reactions catalyzed by transition metals. In some cases the nano-size particles used as catalysts are synthesized simultaneously or right before the initiation of the main catalytic reaction. Synthesis treatments involve complex processes such as reductions followed by calcinations in oxygenated environments coupled to the presence of gases used for the main reaction. Synthesis details are crucial because they have important consequences on the catalyst shape, size, and chemical composition, and may also affect the structure and composition of the catalyst support. All these effects may alter the main catalyzed reaction in unexpected ways. This work focuses on the synthesis of the overall catalytic system that includes catalyst and support taking place in parallel with the initial stages of the main catalyzed reaction. Two important processes are characterized: carburization and oxidation of the transition metal catalyst during synthesis or initial stages of the main reaction. The objective is to understand how the coking mechanism coupled to surface oxidation and changes in the substrate influence the dry reforming of methane taken as a model reaction. The approach uses first principles computational methods to investigate the catalyst synthesis and characterization and catalytic reaction mechanisms. These studies are complemented with experimental characterization done by the group of Dr. Renu Sharma at the National Institute of Standards and Technology (unfunded collaborator) using high resolution transmission electron microscopy. Specific goals are to identify the role of the synthesis process on the initial nanocatalyst structure and composition, and to determine how that structure and composition may evolve after being exposed to the reactants atmosphere. These studies facilitate a systematic analysis of conditions where the nanoparticle composition can be optimized regarding activity and stability. Moreover, the fundamental study of catalyst/support interactions yields valuable insights for other catalytic processes and is a first step toward controlled nanocatalyst synthesis.

36 MATERIALS SCIENCE↗

Using Raman scattering to study reacting gas flow over a catalyst

l present a series of computational methods for analyzing and correcting Raman scattering from a reacting gas flow. My work focused on the laser diagnostic measurements of formaldehyde production over a silver catalyst, specifically the Raman spectroscopy component. This technique offers a non-intrusive, in situ way to measure the coupling between the gas phase and surface activity of a catalytic reaction at relevant industrial conditions. This report outlines the steps followed for correcting the non-idealities in the data due to both the detection optics and scattering mechanics. By implementing such refinement steps, l can generate an accurate 2D spatial map of the temperature profile, number densities for major species, and relative consumption of reactants throughout the reactor cell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

BISON Capabilities for LWR Fuel Behavior Analysis During Accident and High-burnup Conditions

The U.S. Department of Energy (DOE)'s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program aims to develop predictive capabilities using computational methods for the analysis and design of advanced reactor and fuel cycle systems. This program has been supporting the development of BISON which is a high-fidelity and high-resolution fuel performance tool at the engineering scale. Increasing recent interest in applications at extended burnups motivated this study to incorporate more physically based models in BISON. This document details integration of newly implemented modeling capabilities into BISON, which includes (1) new thermal conductivity models that are valid up to 100 GWd/t, (2) models for the formation of the high-burnup structure (HBS), (3) two porosity correction methods beingapplied on the thermal conductivity due to the conducting pores during the HBS formation. BISON's results are verified and validated to test the new modeling capabilities

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Biofidelic Digital Head Model Software

Researchers at Los Alamos have extensive capabilities in biofidelic modeling, simulation and software development for predicting traumatic brain injury (TBI). Since injury-causing experiments cannot be performed on live humans, and head dummies are incapable of predicting brain deformations/strain, our approach uses magnetic resonance imaging (MRI) data for the brain combined with advanced computational methods and substructure constitutive properties to identify harmful accelerations that may develop diffused axonal injury in the brain. The goal is to develop this capability to analyze the effectiveness of personal protective equipment (PPE) such as, helmets and the advanced energy-absorbing materials used in PPE to mitigate brain injury. Los Alamos is seeking a collaborative partner (through a cooperative research and development agreement) to develop this capability toward a potential technology that will have commercial viability.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Accurate temperature determination from XRD and EXAFS measurements (Full Technical Final Report)

Measuring temperature is of fundamental importance for High Energy Density science (HED), for studying melting, phase transitions and equations of state. However, temperature determination of high pressure and high temperature (0.1-1 eV) condensed matter remains one of the biggest challenges in such experiments. This project used a combination of advanced experimental techniques and state-of-the-art computational methods to construct a framework relating the observed attenuation of X-ray diffraction (XRD) and Extended X-ray Absorption Fine Structure (EXAFS) signals due to thermal fluctuations to the actual temperature achieved in the experiments. This approach was benchmarked against low temperature resistive heating diamond anvil cell (DAC) experiments and cross-validated at higher pressure and temperature by combining the two complementary and independent techniques, diffraction and EXAFS.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The First Neptunium Dioxide Neutron Diffraction Experiment at HFIR

Here we present the first neutron diffraction experiment of a 50 mg sample of neptunium(IV) dioxide (NpO 2 ) powder at the High Flux Isotope Reactor (HFIR) using the wide-angle neutron diffractometer (WAND 2 ) HB-2C. We also provide a brief literature survey to pinpoint gaps in the crystal, electronic, and magnetic structure of NpO 2 to determine the optimum experiment to be pursued in the next HFIR user proposal cycle. Characterizing actinide materials with neutron diffraction, inelastic scattering, neutron imaging, polarized neutron studies, and small-angle neutron scattering techniques will increase our understanding of 5f electron behavior and elucidate atomic and magnetic structural properties. This strategy will help fill gaps in the literature and provide theoretical physicists with the data needed to build physical and chemical models to guide and validate computational methods. These methods may be used for predicting structural and chemical features of actinide-based materials. This proof-of-principle effort begins to uncover how to advance actinide science and technology at Oak Ridge National Laboratory (ORNL) using neutron capabilities. This effort has already sparked collaborative discussions between researchers outside the Radioisotope Science and Technology Division, including theoretical physicists from the Nuclear Nonproliferation Division and beamline scientists in the Neutron Scattering Division. We intend to continue pursuing neutron experiments and develop a scientific strategy focused on studying transuranium elements (e.g., Np, Pu, Am, and Cm) using the advanced neutron capabilities at ORNL.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗