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DOE OSTI2020

Theory of molecular emission power spectra. I. Macroscopic quantum electrodynamics formalism

In this work, we study the emission power spectrum of a molecular emitter with multiple vibrational modes in the framework of macroscopic quantum electrodynamics. The theory we present is general for a molecular spontaneous emission spectrum in the presence of arbitrary inhomogeneous, dispersive, and absorbing media. Moreover, the theory shows that the molecular emission power spectra can be decomposed into the electromagnetic environment factor and lineshape function. In order to demonstrate the validity of the theory, we investigate the lineshape function in two limits. In the incoherent limit (single molecules in a vacuum), the lineshape function exactly corresponds to the Franck–Condon principle. In the coherent limit (single molecules strongly coupled with single polaritons or photons) together with the condition of high vibrational frequency, the lineshape function exhibits a Rabi splitting, the spacing of which is exactly the same as the magnitude of exciton–photon coupling estimated by our previous theory [S. Wang et al., J. Chem. Phys. 151, 014105 (2019)]. Finally, we explore the influence of exciton–photon and electron–phonon interactions on the lineshape function of a single molecule in a cavity. The theory shows that the vibronic structure of the lineshape function does not always disappear as the exciton–photon coupling increases, and it is related to the loss of a dielectric environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Small angle scattering of diblock copolymers profiled by machine learning

We outline a machine learning strategy for quantitively determining the conformation of AB-type diblock copolymers with excluded volume effects using small angle scattering. Complemented by computer simulations, a correlation matrix connecting conformations of different copolymers according to their scattering features is established on the mathematical framework of a Gaussian process, a multivariate extension of the familiar univariate Gaussian distribution. We show that the relevant conformational characteristics of copolymers can be probabilistically inferred from their coherent scattering cross sections without any restriction imposed by model assumptions. This work not only facilitates the quantitative structural analysis of copolymer solutions but also provides the reliable benchmarking for the related theoretical development of scattering functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Best practices for first-principles simulations of epitaxial inorganic interfaces

Abstract At an interface between two materials physical properties and functionalities may be achieved, which would not exist in either material alone. Epitaxial inorganic interfaces are at the heart of semiconductor, spintronic, and quantum devices. First principles simulations based on density functional theory (DFT) can help elucidate the electronic and magnetic properties of interfaces and relate them to the structure and composition at the atomistic scale. Furthermore, DFT simulations can predict the structure and properties of candidate interfaces and guide experimental efforts in promising directions. However, DFT simulations of interfaces can be technically elaborate and computationally expensive. To help researchers embarking on such simulations, this review covers best practices for first principles simulations of epitaxial inorganic interfaces, including DFT methods, interface model construction, interface structure prediction, and analysis and visualization tools.

Physics↗

DOE OSTI2023

Effective permeability of an immiscible fluid in porous media determined from its geometric state

Based on the phenomenological extension of Darcy's law, two-fluid flow is dependent on a relative permeability function of saturation only that is process or path dependent with an underlying dependency on pore structure and wettability. For applications (fuel cells to underground CO 2 storage), it is imperative to determine the effective phase permeability relationships where the traditional approach is based on the inverse modeling of time-consuming experiments. The underlying reason is that the fundamental upscaling step from pore to Darcy scale, which links the pore structure of the porous medium to the continuum hydraulic conductivities, is not solved. Herein, we develop an artificial neural network (ANN) that relies on fundamental geometrical relationships to determine the mechanical energy dissipation during creeping immiscible two-fluid flow. Finally, the developed ANN is based on a prescribed set of state variables based on physical insights that predict the effective permeability of 4500 unseen pore-scale geometrical states with R 2 = 0.98.

42 ENGINEERING↗

DOE OSTI2021

Dynamical Components Analysis (DCA) v1.0.0

Dynamical Components Analysis is a Python implementation of the method described in "Unsupervised discovery of temporal structure in noisy data with dynamical components analysis". It implements the method as well as related data analysis functions.

Livezey, Jesse↗

DOE OSTI2021

Dynamical Components Analysis (DCA) v1.0.0

Livezey, Jesse↗

DOE OSTI2022

Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization

Background: The Fusarium solani species complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced, assembled and annotated six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins. We established a pathosystem and investigated the expression data of F. falciforme and F. keratoplasticum in Chinese softshell turtle (Pelodiscus sinensis) host. Results: Comparative analyses between the FSSC genomes revealed a spectrum of conservation patterns in chromosomes categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). LS chromosomes contribute to variations in genomes size, with up to 42.2% of variations between F. vanettenii strains. Each chromosome compartment varied in structural architectures, with FC and LS chromosomes contain higher proportions of repetitive elements with genes enriched in functions related to pathogenicity and niche expansion. We identified differences in both selection in the coding sequences and DNA methylation levels between genome features and chromosome compartments which suggest a multi-speed evolution that can be traced back to the last common ancestor of Fusarium. We further demonstrated that F. falciforme and F. keratoplasticum are opportunistic pathogens by inoculating P. sinensis eggs and identified differentially expressed genes also associated with plant pathogenicity. These included the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain. Conclusions: The high-quality genome assemblies provided new insights into the evolution of FSSC chromosomes, which also serve as a resource for studies of fungal genome evolution and pathogenesis. This study also establishes an animal model for fungal pathogens of trans-kingdom hosts.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Status Report on ASME Code Development for Nonmetallic Core Components in 2020

The purpose of this report is to provide a status update on the progress and ongoing activities of the current ASME Boiler Pressure Vessel (BPV) Code Section III, Division 5, on nonmetallic core components and assemblies which includes the design rules for graphite and ceramic composite materials. Section III is concerned with the design and construction of nuclear reactor components and Division 5 focuses on high temperature reactors (HTR). The ASME Section III Committee’s function for nuclear items other than pressure-retaining components, is to establish rules of safety related to structural integrity. The term “construction” refers to the all-inclusive effort comprising of materials, design, fabrication, examination, inspection, testing, certification, and pressure relief. The Department of Energy (DOE) supports industry codes and standards development through focused research providing the technical basis for new or modified codes and standards and the participation of subject matter experts in codes and standards committees. The activities for the nonmetallic core components and assemblies committees are the pursuit of two working groups that meet quarterly during ASME BPV Code Week meetings. The two working groups are General Requirements for Graphite and Ceramic Composite Core Components and Assemblies (GR GCCCCA) and Nonmetallic Design and Materials (NDM). The rules on general requirements for nonmetallic core components are discussed in the articles of Subsection HA subpart B. Ceramic composites were recently incorporated within the rules, and the GR GCCCCA working group is now in the process of aligning the requirements with the subsections and articles of ASME BPV Code Section III NCA, the general requirements for Division 1 and 2 of the code. The NDM working group is concerned with the design rules for graphite and composite materials for core components and assemblies discussed in Subsection HH (Class SN Nonmetallic Core Components) subpart A and subpart B which reference graphite and composite materials respectively. The bulk of the progress and work is done within this working group. A significant undertaking, with discussion that started in 2015, is to gain endorsement of ASME Section III, Division 5, by the U.S. Nuclear Regulatory Commission (NRC). In June 2018, ASME formally recommended endorsement to the NRC. The NRC has since initiated the endorsement review process, which is to be concluded early in 2021. ASME task groups on metallic structures and components, as well as non-metallic core support structures, have been formed to define potential pathways and schedules for NRC endorsement of Division 5. NRC determined to perform a review on the 2017 edition of Section III Division 5 as a baseline. As a result, the use of graphite as nonmetallic core components formed part of the review, but it excluded composite materials (which were first introduced in the 2019 edition). This report documents progress in FY 2020 directed toward ASME’s efforts to develop design codes for graphite and composites. Progress includes a major code review by NRC, the first code enquiry, and its solution, an overhaul of the treatment of Weibull Statistics, and the addition of Nonmandatory Appendices to the composites code relating to carbon-carbon composite materials.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

Gaussian Kernel Methods for Seismic Fragility and Risk Assessment of Mid-Rise Buildings

Seismic fragility functions can be evaluated using the cloud analysis method with linear regression which makes three fundamental assumptions about the relation between structural response and seismic intensity: log-linear median relationship, constant standard deviation, and Gaussian distributed errors. While cloud analysis with linear regression is a popular method, the degree to which these individual and compounded assumptions affect the fragility and the risk of mid-rise buildings needs to be systematically studied. This paper conducts such a study considering three building archetypes that make up a bulk of the building stock: RC moment frame, steel moment frame, and wood shear wall. Gaussian kernel methods are employed to capture the data-driven variations in the median structural response and standard deviation and the distributions of residuals with the intensity level. With reference to the Gaussian kernels approach, it is found that while the linear regression assumptions may not affect the fragility functions of lower damage states, this conclusion does not hold for the higher damage states (such as the Complete state). In addition, the effects of linear regression assumptions on the seismic risk are evaluated. For predicting the demand hazard, it is found that the linear regression assumptions can impact the computed risk for larger structural response values. However, for predicting the loss hazard with downtime as the decision variable, linear regression can be considered adequate for all practical purposes.

58 GEOSCIENCES↗

DOE OSTI2019

Causal hydrodynamic fluctuations in non-static and inhomogeneous backgrounds

Highlights: •The fluctuation–dissipation relation is modified by inhomogeneous backgrounds. •The constitutive equations are restricted by causality and fluctuation properties. •The structure of constitutive equation gives a natural cutoff scale of the theory. •The memory function with tensor structures in inhomogeneous backgrounds is obtained. -- Abstract: To integrate hydrodynamic fluctuations, namely thermal fluctuations of hydrodynamics, into dynamical models of high-energy nuclear collisions based on relativistic hydrodynamics, the property of the hydrodynamic fluctuations given by the fluctuation–dissipation relation should be carefully investigated. The fluctuation–dissipation relation for causal dissipative hydrodynamics with the finite relaxation time is naturally given in the integral form of the constitutive equation by the linear-response theory. While, the differential form of the constitutive equation is commonly used in analytic investigations and dynamical calculations for practical reasons. We give the fluctuation–dissipation relation for the general linear-response differential form and discuss the restrictions to the structure of the differential form, which comes from the causality and the positive semi-definiteness of the noise autocorrelation, and also the relation of those restrictions to the cutoff scale of the hydrodynamic fluctuations. We also give the fluctuation–dissipation relation for the integral form in non-static and inhomogeneous background by introducing new tensors, the pathline projectors. We find new modification terms to the fluctuation–dissipation relation for the differential form in non-static and inhomogeneous background which are particularly important in dynamical models to describe rapidly expanding systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Trifluoromethylated Phenanthroline Ligands Reduce Excited-State Distortion in Homoleptic Copper(I) Complexes

Herein, we report the synthesis and excited-state dynamics for a series of homoleptic copper(I) trifluoromethylated phenanthroline complexes with two, three, and four trifluoromethyl functional groups. Our analysis of the steady-state absorbance and emission, transient-absorption spectroscopy, and electronic-structure-theory calculations results enable in-depth analysis of the pseudo-Jahn–Teller distortion inhibition from increased steric hindrance of the trifluoromethyl functional group relative to the prototypical dimethyl phenanthroline complex. Surprisingly, our results demonstrate that the greatest degree of pseudo-Jahn–Teller distortion inhibition is achieved with trifluoromethylation of only the 2 and 9 positions by an unusual combination of steric hindrance and stabilization of a nondistorted 1 MLCT manifold observed by transient kinetic lifetimes and optimized excited-state structures. The intersystem-crossing (ISC) lifetime for the 2,9-bis(trifluoromethyl)-1,10-phenanthroline Cu(I) complex is 69 ps, while the triplet excited-state lifetime and emission quantum yield are 106 ns and 4 × 10 –3 , respectively. Further trifluoromethylation of the phenanthroline yields a greater σ bond inductive withdrawing force on the phenanthroline nitrogens, ultimately resulting in weaker coordination to the copper. Last, the surprising success of the 2,9-bis(trifluoromethyl)-1,10-phenanthroline Cu(I) complex by adjusting both ligand sterics and electronic properties outlines a new strategy for developing long-lived Cu(I) charge-transfer complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Hydration of α-UO 3 following storage under controlled conditions of temperature and relative humidity

Changes in chemical speciation of uranium oxides following storage under varied conditions of temperature and relative humidity are valuable for characterizing material provenance. In this study, subsamples of high purity α-UO 3 were stored under four sets of controlled conditions of temperature and relative humidity over several years, and then measured periodically for chemical speciation. Powder X-ray diffraction (XRD) analysis and extended X-ray absorption fine structure spectroscopy confirm hydration of α-UO 3 to a schoepite-like end product following storage under each of the varied storage conditions, but the species formed during exposure to the lower relative humidity and lower temperature condition follows different trends from those formed under the other three storage conditions (high relative humidity with high or low temperatures, and low relative humidity with a high temperature). Thermogravimetry coupled with XRD analysis was carried out to distinguish desorption pathways of water from the hydrated end products. Density functional theory calculations discern changes in the structure of α-UO 3 following incorporation of 1, 2 or 3 H 2 O molecules or 1, 2 or 3 OH groups into the orthorhombic lattice, revealing differences in lattice constants, U–O bond lengths, and U–U distances. The collective results from this analysis are in contrast to analogous studies that report that U 3 O 8 is oxidized and hydrated in air during storage under high relative humidity conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

High Thermopower in a Zn-Based 3D Semiconductive Metal–Organic Framework

Conductive metal–organic frameworks (c-MOFs) have drawn increasing attention for their outstanding performance in energy-related applications. However, the majority of reported c-MOFs are based on 2D structures. Synthetic strategies for 3D c-MOFs are under-explored, leaving unrealized functionality in both their structures and properties. Here in this paper we report a 3D c-MOF, namely Zn-HAB, designed through topological analysis. Comprising a nitrogen donor linker, hexaaminobenzene, and Zn(II) node, Zn-HAB was found to have microporosity with a band-gap of approximately 1.68 eV. The relatively large band-gap results in a modest conduc-tivity of 0.86 mS cm -1 and a high Seebeck coefficient of 200 μV K -1 at 300 K. The power factor of 3.44 nW m -1 K -2 constitutes the first report of the thermoelectric properties of an intrinsically conductive 3D MOF.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Advancing Multi-Hazard Risk and Safety Considerations for Aging Nuclear Facilities (Revision 1)

This project will demonstrate a multi-hazard time-dependent probabilistic risk assessment (PRA) approach for nuclear facilities considering aging-related deterioration of structures. A generic pressurized water reactor (PWR) reactor subjected to seismic mainshock-aftershock sequences considering the aging of the containment structure will be used as a case study to demonstrate the multi-hazard PRA approach. Using advanced modeling and simulation, seismic mainshock-aftershock fragility functions will be simulated for the containment structure considering aging effects. A multi-hazard PRA model for a generic PWR reactor will be built to quantify the multi-hazard core damage frequency (CDF) and large early release frequency (LERF) with explicit time-dependent modeling of event sequences. To date, the cascading impacts of multi-hazards are not adequately accounted for in the PRA models for nuclear facilities. In addition, for both initial and periodic evaluation of facilities to withstand natural phenomena hazards (NPH), deterioration of the SSCs due to aging and other effects is not adequately considered. By advancing multi-hazard considerations accounting for aging effects, this project will contribute to improved understanding of the safety of aging nuclear facilities. Project outcomes such as the multi-hazard CDF and LERF will also allow facility owners to optimize upgrade and retrofit protocols. This project is divided into two components: (1) advanced modeling and simulations; and (2) multi-hazard PRA. For the first component, Idaho National Laboratory’s (INL) Multi-hazard Analysis for STOchastic time-DOmaiN phenomena (MASTODON) and BlackBear codes will be used to simulate the seismic response and damage of a containment structure under cascading mainshock-aftershock sequences with aging effects. Uncertainties related to the seismic inputs, material parameters, and environmental factors such as temperature and humidity will be identified and propagated to the fragility functions. These fragility functions, which consider aging effects, will be time dependent. The second component will take the fragility information from the first component to build a multi-hazard time-dependent PRA model starting from a generic PWR model to evaluate the multi-hazard CDF and LERF and characterize the associated consequences. For this component, OpenPRA Web Application and SAPHIRE code will be used. Events such as the Fukushima Daiichi accident have highlighted the importance of considering the cascading impacts of multi-hazards for PRA. Moreover, many of the reactors in the current nuclear fleet in the United States (US) are already operating well beyond their initially planned design life, and applications for further extensions to operating licenses are being considered. Therefore, considering multi-hazard effects and aging deterioration in the NPH risk assessment process will contribute to the safety of both existing and future nuclear facilities. Outcomes of this project will thus directly benefit the standards DOE-STD-1020-16 and DOE-HDBK-1224-18.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2020

Visualizing group II intron dynamics between the first and second steps of splicing

Group II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the eukaryotic spliceosome, with potential applications as gene-editing tools. Recent biochemical and structural data have captured the intron in multiple conformations at different stages of catalysis. Here, we employ enzymatic assays, X-ray crystallography, and molecular simulations to resolve the spatiotemporal location and function of conformational changes occurring between the first and the second step of splicing. We show that the first residue of the highly-conserved catalytic triad is protonated upon 5’-splice-site scission, promoting a reversible structural rearrangement of the active site (toggling). Protonation and active site dynamics induced by the first step of splicing facilitate the progression to the second step. Our insights into the mechanism of group II intron splicing parallels functional data on the spliceosome, thus reinforcing the notion that these evolutionarily-related molecular machines share the same enzymatic strategy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Kernel Manifolds: Nonlinear‐Augmentation Dimensionality Reduction Using Reproducing Kernel Hilbert Spaces

This paper generalizes recent advances on quadratic manifold (QM) dimensionality reduction by developing kernel methods-based nonlinear-augmentation dimensionality reduction. QMs, and more generally feature map-based nonlinear corrections, augment linear dimensionality reduction with a nonlinear correction term in the reconstruction map to overcome approximation accuracy limitations of purely linear approaches. While feature map-based approaches typically learn a least squares optimal polynomial correction term, we generalize this approach by learning an optimal nonlinear correction from a user-defined reproducing kernel Hilbert space. Our approach allows one to impose arbitrary nonlinear structure on the correction term, including polynomial structure, and includes feature map and radial basis function-based corrections as special cases. Furthermore, our method has relatively low training cost and has monotonically decreasing error as the latent space dimension increases. In conclusion, we compare our approach to proper orthogonal decomposition and several recent QM approaches on data from several example problems.

kernel methods↗

DOE OSTI2023

Mott insulators with boundary zeros

The topological classification of electronic band structures is based on symmetry properties of Bloch eigenstates of single-particle Hamiltonians. In parallel, topological field theory has opened the doors to the formulation and characterization of non-trivial phases of matter driven by strong electron-electron interaction. Even though important examples of topological Mott insulators have been constructed, the relevance of the underlying non-interacting band topology to the physics of the Mott phase has remained unexplored. Here, we show that the momentum structure of the Green’s function zeros defining the “Luttinger surface" provides a topological characterization of the Mott phase related, in the simplest description, to the one of the single-particle electronic dispersion. Considerations on the zeros lead to the prediction of new phenomena: a topological Mott insulator with an inverted gap for the bulk zeros must possess gapless zeros at the boundary, which behave as a form of “topological antimatter” annihilating conventional edge states. Placing band and Mott topological insulators in contact produces distinctive observable signatures at the interface, revealing the otherwise spectroscopically elusive Green’s function zeros.

36 MATERIALS SCIENCE↗

DOE OSTI2021

A Lattice Litany for Transition Metal Oxides

In this tribute to K Alex Müeller, I describe how his early insights have influenced future decades of research on perovskite ferroelectrics and more broadly transition metal oxides (TMOs) and related quantum materials. I use his influence on my own research journey to discuss impacts in three areas: structural phase transitions, precursor structure, and quantum paraelectricity. I emphasize materials functionality in ground, metastable, and excited states arising from competitions among lattice, charge, and spin degrees of freedom, which results in highly tunable landscapes and complex networks of multiscale configurations controlling macroscopic functions. I discuss competitions between short- and long-range forces as particularly important in TMOs (and related materials classes) because of their localized and directional metal orbitals and the polarizable oxygen ions. I emphasize crucial consequences of elasticity and metal–oxygen charge transfer

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗