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DOE OSTI2022

High pressure neutron diffraction on WAND 2 with a Paris-Edinburgh press

The Paris-Edinburgh press is a widely available, highly adaptable pressure cell commonly used while collecting neutron scattering data. Here, we detail the use of the VX3 and VX5 Paris-Edinburgh presses on the Wide-Angle Neutron Diffractometer (WAND 2 ) at the High Flux Isotope Reactor at Oak Ridge National Laboratory. We first give a detailed overview of the instrument setup and alignment capabilities used at WAND 2 . We then demonstrate the high pressure capabilities through three examples. In this work, the first example focuses on diffraction data obtained from a lithium-diamond mixture to 10 GPa with the use of single toroidal cubic boron nitride anvils. Other examples include the room temperature compressions of germanium (up to 16 GPa) and the mineral malachite with double toroidal sintered diamond anvils. This work thereby represents the first studies above 10 GPa at the High Flux Isotope Reactor and opens the door for future user experiments at these elevated pressures.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

The topology of non-resonant stellarator divertors

We apply topological methods to better understand how the magnetic field in the stellarator edge can be diverted away from the confined region. Our primary method is calculating the winding numbers of closed contours, which gives information on the number and nature of fixed points within a bounded region. We first apply this to the non-resonant divertor Hamiltonian system, and present a simple explanation for the system’s diversion: trajectories are guided away from the confined region by X-points which are ‘unpaired’ i.e. do not have corresponding O-points and therefore do not resemble an island chain. We show how similar phenomena can occur in a similar, axisymmetric Hamiltonian system. Secondly, we find examples of neoclassically optimised stellarators in the quasi-symmetric stellarator repository database which divert the magnetic field via unpaired X-points. We present and discuss three examples, each containing novel phenomena which might be desirable for stellarator divertors. These examples serve as an illustration of new divertor possibilities which exist in realistic stellarators, which may ultimately have application for future experiments and reactors.

X-points, topology↗

DOE OSTI2024

Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning

Motivation: Graph representation learning is a family of related approaches that learn low-dimensional vector representations of nodes and other graph elements called embeddings. Embeddings approximate characteristics of the graph and can be used for a variety of machine-learning tasks such as novel edge prediction. For many biomedical applications, partial knowledge exists about positive edges that represent relationships between pairs of entities, but little to no knowledge is available about negative edges that represent the explicit lack of a relationship between two nodes. For this reason, classification procedures are forced to assume that the vast majority of unlabeled edges are negative. Existing approaches to sampling negative edges for training and evaluating classifiers do so by uniformly sampling pairs of nodes. Results: We show here that this sampling strategy typically leads to sets of positive and negative examples with imbalanced node degree distributions. Using representative heterogeneous biomedical knowledge graph and random walk-based graph machine learning, we show that this strategy substantially impacts classification performance. If users of graph machine-learning models apply the models to prioritize examples that are drawn from approximately the same distribution as the positive examples are, then performance of models as estimated in the validation phase may be artificially inflated. We present a degree-aware node sampling approach that mitigates this effect and is simple to implement. Availability and implementation: Our code and data are publicly available at https://github.com/monarch-initiative/negativeExampleSelection.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

AbacusHOD : a highly efficient extended multitracer HOD framework and its application to BOSS and eBOSS data

ABSTRACT We introduce the AbacusHOD model and present two applications of AbacusHOD and the AbacusSummit simulations to observations. AbacusHOD is a Halo Occupation Distribution (HOD) framework written in Python that is particle-based, multitracer, highly generalized, and highly efficient. It is designed specifically with multitracer/cosmology analyses for next-generation large-scale structure surveys in mind, and takes advantage of the volume and precision offered by the new state-of-the-art AbacusSummit cosmological simulations. The model is also highly customizable and should be broadly applicable to any upcoming surveys and a diverse range of cosmological analyses. In this paper, we demonstrate the capabilities of the AbacusHOD framework through two example applications. The first example demonstrates the high efficiency and the large HOD extension feature set through an analysis of full-shape redshift-space clustering of BOSS galaxies at intermediate to small scales ($\lt 30\, h^{-1}$ Mpc), assessing the necessity of introducing secondary galaxy biases (assembly bias). We find strong evidence for using halo environment instead of concentration to trace secondary galaxy bias, a result which also leads to a moderate reduction in the ‘lensing is low’ tension. The second example demonstrates the multitracer capabilities of the AbacusHOD package through an analysis of the extended Baryon Oscillation Spectroscopic Survey cross-correlation measurements between three different galaxy tracers: luminous red galaxies, emission-line galaxies, and quasi-stellar objects. We expect the AbacusHOD framework, in combination with the AbacusSummit simulation suite, to play an important role in a simulation-based analysis of the upcoming Dark Energy Spectroscopic Instrument data sets.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Plants use molecular mechanisms mediated by biomolecular condensates to integrate environmental cues with development

This review highlights recent literature on biomolecular condensates in plant development and discusses challenges for fully dissecting their functional roles. Plant developmental biology has been inundated with descriptive examples of biomolecular condensate formation, but it is only recently that mechanistic understanding has been forthcoming. Here, we discuss recent examples of potential roles biomolecular condensates play at different stages of the plant life cycle. We group these examples based on putative molecular functions, including sequestering interacting components, enhancing dwell time, and interacting with cytoplasmic biophysical properties in response to environmental change. We explore how these mechanisms could modulate plant development in response to environmental inputs and discuss challenges and opportunities for further research into deciphering molecular mechanisms to better understand the diverse roles that biomolecular condensates exert on life.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Quantum state reduction: Generalized bipartitions from algebras of observables

Reduced density matrices are a powerful tool in the analysis of entanglement structure, approximate or coarse-grained dynamics, decoherence, and the emergence of classicality. It is straightforward to produce a reduced density matrix with the partial-trace map by tracing out part of the quantum state, but in many natural situations this reduction may not be achievable. We investigate the general problem of identifying how the quantum state is reduced given a restriction on the observables. For example, in an experimental setting, the set of observables that can actually be measured is usually modest (compared to the set of all possible observables) and their resolution is limited. In such situations, the appropriate state-reduction map can be defined via a generalized bipartition, which is associated with the structure of irreducible representations of the algebra generated by the restricted set of observables. One of our main technical results is a general, not inherently numeric, algorithm for finding irreducible representations of matrix algebras. In our work, we demonstrate the viability of this approach with two examples of limited-resolution observables. The definition of quantum state reductions can also be extended beyond algebras of observables. To accomplish this task we introduce a more flexible notion of bipartition, the partial bipartition, which describes coarse grainings preserving information about a limited set (not necessarily algebra) of observables. We describe a variational method to choose the coarse grainings most compatible with a specified Hamiltonian, which exhibit emergent classicality in the reduced state space. We apply this construction to the concrete example of the one-dimensional Ising model. Our results have relevance for quantum information, bulk reconstruction in holography, and quantum gravity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Moment method and continued fraction expansion in Floquet operator Krylov space

Recursion methods such as Krylov techniques map complex dynamics to an effective noninteracting problem in one dimension. For example, the operator Krylov space for Floquet dynamics can be mapped to the dynamics of an edge operator of the one-dimensional Floquet inhomogeneous transverse field Ising model (ITFIM), where the latter, after a Jordan-Wigner transformation, is a Floquet model of noninteracting Majorana fermions and the couplings correspond to Krylov angles. We present an application of this showing that a moment method exists where given an autocorrelation function, one can construct the corresponding Krylov angles and from that the corresponding Floquet ITFIM. Consequently, when no solutions for the Krylov angles are obtained, it indicates that the autocorrelation is not generated by unitary dynamics. We highlight this by studying certain special cases: stable m-period dynamics derived using the method of continued fractions, exponentially decaying, and power-law decaying stroboscopic dynamics. Remarkably, our examples of stable m-period dynamics correspond to m-period edge modes for the Floquet ITFIM where, deep in the chain, the couplings correspond to a critical phase. Furthermore our results pave the way to engineer Floquet systems with desired properties of edge modes and also provide examples of persistent edge modes in gapless Floquet systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Glassy Word Problems: Ultraslow Relaxation, Hilbert Space Jamming, and Computational Complexity

We introduce a family of local models of dynamics based on “word problems” from computer science and group theory, for which we can place rigorous lower bounds on relaxation timescales. These models can be regarded either as random circuit or local Hamiltonian dynamics and include many familiar examples of constrained dynamics as special cases. The configuration space of these models splits into dynamically disconnected sectors, and for initial states to relax, they must “work out” the other states in the sector to which they belong. When this problem has a high time complexity, relaxation is slow. In some of the cases we study, this problem also has high space complexity. When the space complexity is larger than the system size, an unconventional type of jamming transition can occur, whereby a system of a fixed size is not ergodic but can be made ergodic by appending a large reservoir of sites in a trivial product state. This finding manifests itself in a new type of Hilbert space fragmentation that we call fragile fragmentation. We present explicit examples where slow relaxation and jamming strongly modify the hydrodynamics of conserved densities. In one example, density modulations of wave vector q exhibit almost no relaxation until times O ( exp ( 1 / q ) ) , at which point they abruptly collapse. We also comment on extensions of our results to higher dimensions. Published by the American Physical Society 2024

Physics↗

DOE OSTI2024

Engineering 3D Floquet Codes by Rewinding

Floquet codes are a novel class of quantum error-correcting codes with dynamically generated logical qubits arising from a periodic schedule of noncommuting measurements. We utilize the interpretation of measurements in terms of condensation of topological excitations and the rewinding of measurement sequences to engineer new examples of Floquet codes. In particular, rewinding is advantageous for obtaining a desired set of instantaneous stabilizer groups on both toric and planar layouts. Our first example is a Floquet code with instantaneous stabilizer codes that have the same topological order as the three-dimensional (3D) toric code(s). This Floquet code also exhibits a splitting of the topological order of the 3D toric code under the associated sequence of measurements, i.e., an instantaneous stabilizer group of a single copy of the 3D toric code in one round transforms into an instantaneous stabilizer group of two copies of the 3D toric code up to nonlocal stabilizers in the following round. We further construct boundaries for this 3D code and argue that stacking it with two copies of the 3D subsystem toric code allows for a transversal implementation of the logical non-Clifford controlled-controlled- Z gate. We also show that the coupled-layer construction of the X-cube Floquet code can be modified by a rewinding schedule such that each of the instantaneous stabilizer codes is finite depth equivalent to the X-cube model up to toric codes; the X-cube Floquet code exhibits a splitting of the X-cube model into a copy of the X-cube model and toric codes under the measurement sequence. Our final 3D example is a generalization of the 2D Floquet toric code on the honeycomb lattice to three dimensions, which has instantaneous stabilizer codes with the same topological order as the 3D fermionic toric code. Published by the American Physical Society2024

Physics↗

DOE OSTI2026

Composite-dimensional topological codes with boundaries and defects

We introduce new algorithms and provide example constructions of stabilizer models for the gapped boundaries, domain walls, and 0D defects of Abelian composite-dimensional twisted quantum doubles. Using the physically intuitive concept of condensation, our algorithm explicitly describes how to construct the boundary and domain-wall stabilizers starting from the bulk model. This extends the utility of Pauli stabilizer models in describing nontranslationally invariant topological orders with gapped boundaries. To highlight this utility, we provide a series of examples, including a new family of quantum error-correcting codes where the double of ℤ4 is coupled to instances of the double semion (DS) phase. We discuss the codes' utility in the burgeoning area of quantum error correction with an emphasis on the interplay between deconfined anyons, logical operators, error rates, and decoding. We also augment our construction, built using algorithmic tools to describe the properties of explicit stabilizer layouts at the microscopic lattice level, with dimensional counting arguments and macroscopic-level constructions building on pants decompositions. The latter outlines how such codes' representation and design can be automated. Our results are validated by a series of error-correcting threshold calculations comparing our codes' performance with that of standard surface codes. To do so, we introduce a composite-dimensional belief-propagation decoder with ordered statistics that utilizes combination sweeps. Going beyond our worked-out examples, we expect our explicit step-by-step algorithms to pave the path for higher-dimensional codes to be discovered and implemented in near-future architectures that take advantage of various hardware platforms.

Mousa, Mohamad [Purdue University]↗

DOE OSTI2021

Missing-Data Nonparametric Coherency Estimation

Chave recently proposed an estimator for multitaper spectral density where the time series contains missing values. In this article we generalize this technique to a multitaper estimator of coherence and phase and show that one can also obtain bootstrapped confidence intervals. Additionally, we give two examples. The first is a toy example in which the true coherence is known. In the second example we show that the multitaper missing-data coherence estimator computed on real data with a single gap comprising 11% of the data outperforms the Daniell-smoothed coherence estimator where there are no gaps. The case where the two time series have different missing indices is also discussed.

42 ENGINEERING↗

DOE OSTI2020

Vector Field Decompositions Using Multiscale Poisson Kernel

Extraction of multiscale features using scale-space is one of the fundamental approaches to analyze scalar fields. However, similar techniques for vector fields are much less common, even though it is well known that, for example, turbulent flows contain cascades of nested vortices at different scales. The challenge is that the ideas related to scale-space are based upon iteratively smoothing the data to extract features at progressively larger scale, making it difficult to extract overlapping features. Instead, we consider spatial regions of influence in vector fields as scale, and introduce a new approach for the multiscale analysis of vector fields. Rather than smoothing the flow, we use the natural Helmholtz-Hodge decomposition to split it into small-scale and large-scale components using progressively larger neighborhoods. Our approach creates a natural separation of features by extracting local flow behavior, for example, a small vortex, from large-scale effects, for example, a background flow. We demonstrate our technique on large-scale, turbulent flows, and show multiscale features that cannot be extracted using state-of-the-art techniques.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Sampling in Long-Screened Wells: Issues, Misconceptions, and Solutions

The issues associated with long-screened wells (LSWs) (and open boreholes) at contaminated sites are well documented in the groundwater literature but are still not fully appreciated in practice. As established in seminal and review papers going back over three decades, the interpretation of sampling results from LSWs is challenging in the presence of vertical hydraulic gradients and borehole flow; furthermore, LSWs allow for vertical redistribution of contamination between aquifer layers. Acknowledgment of these issues has led to the development of new technologies and well designs to enable discrete-zone monitoring (DZM), yet LSWs remain common for many reasons, for example, as multipurpose wells, for geophysical logging, and (or) as legacy installations. Despite the literature on LSWs and despite the adoption of DZM at many sites, the use of LSWs persists and the challenges of interpreting sampling results from LSWs remain. In this issue paper, we provide a conceptual overview of the problems posed by LSWs and review existing literature and past work to improve the interpretation of sampling in LSWs. We draw on experience from previous studies at the Hanford Site in eastern WA, USA, and use synthetic examples to illustrate key concepts and challenges for interpretation. A recently published analytical modeling framework is used to develop illustrative synthetic examples and demonstrate a workflow for building scientific intuition to understand issues around interpreting samples from LSWs, which is critical to effective characterization and groundwater remediation at sites with LSWs.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

A seed-like proteome in oil-rich tubers

There are numerous examples of plant organs or developmental stages that are desiccation-tolerant and can withstand extended periods of severe water loss. One prime example are seeds and pollen of many spermatophytes. However, in some plants, also vegetative organs can be desiccation-tolerant. One example are the tubers of yellow nutsedge ( Cyperus esculentus ), which also store large amounts of lipids similar to seeds. Interestingly, the closest known relative, purple nutsedge ( Cyperus rotundus ), generates tubers that do not accumulate oil and are not desiccation-tolerant. We generated nanoLC-MS/MS-based proteomes of yellow nutsedge in five replicates of four stages of tuber development and compared them to the proteomes of roots and leaves, yielding 2257 distinct protein groups. Our data reveal a striking upregulation of hallmark proteins of seeds in the tubers. A deeper comparison to the tuber proteome of the close relative purple nutsedge ( C. rotundus ) and a previously published proteome of Arabidopsis seeds and seedlings indicates that indeed a seed-like proteome was found in yellow but not purple nutsedge. This was further supported by an analysis of the proteome of a lipid droplet-enriched fraction of yellow nutsedge, which also displayed seed-like characteristics. One reason for the differences between the two nutsedge species might be the expression of certain transcription factors homologous to ABSCISIC ACID INSENSITIVE3, WRINKLED1, and LEAFY COTYLEDON1 that drive gene expression in Arabidopsis seed embryos.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Atomic-Level, Energy-Conversion Heat Transfer

Abstract Heat is stored in quanta of kinetic and potential energies in matter. The temperature represents the equilibrium and excited occupation (boson) of these energy conditions. Temporal and spatial temperature variations and heat transfer are associated with the kinetics of these equilibrium excitations. During energy-conversion (between electron and phonon systems), the occupancies deviate from equilibria, while holding atomic-scale, inelastic spectral energy transfer kinetics. Heat transfer physics reaches nonequilibrium energy excitations and kinetics among the principal carriers, phonon, electron (and holes and ions), fluid particle, and photon. This allows atomic-level tailoring of energetic materials and energy-conversion processes and their efficiencies. For example, modern thermal-electric harvesters have transformed broad-spectrum, high-entropy heat into a narrow spectrum of low-entropy emissions to efficiently generate thermal electricity. Phonoelectricity, in contrast, intervenes before a low-entropy population of nonequilibrium optical phonons becomes a high-entropy heat. In particular, the suggested phonovoltaic cell generates phonoelectricity by employing the nonequilibrium, low-entropy, and elevated temperature optical-phonon produced population—for example, by relaxing electrons, excited by an electric field. A phonovoltaic material has an ultranarrow electronic bandgap, such that the hot optical-phonon population can relax by producing electron-hole pairs (and power) instead of multiple acoustic phonons (and entropy). Examples of these quanta and spectral heat transfer are reviewed, contemplating a prospect for education and research in this field.

Engineering↗

DOE OSTI2022

Surrogate Modeling of Nonlinear Dynamic Systems: A Comparative Study

Surrogate models play a vital role in overcoming the computational challenge in designing and analyzing nonlinear dynamic systems, especially in the presence of uncertainty. This paper presents a comparative study of different surrogate modeling techniques for nonlinear dynamic systems. Four surrogate modeling methods, namely, Gaussian process (GP) regression, a long short-term memory (LSTM) network, a convolutional neural network (CNN) with LSTM (CNN-LSTM), and a CNN with bidirectional LSTM (CNN-BLSTM), are studied and compared. All these model types can predict the future behavior of dynamic systems over long periods based on training data from relatively short periods. The multi-dimensional inputs of surrogate models are organized in a nonlinear autoregressive exogenous model (NARX) scheme to enable recursive prediction over long periods, where current predictions replace inputs from the previous time window. Three numerical examples, including one mathematical example and two nonlinear engineering analysis models, are used to compare the performance of the four surrogate modeling techniques. The results show that the GP-NARX surrogate model tends to have more stable performance than the other three deep learning (DL)-based methods for the three particular examples studied. The tuning effort of GP-NARX is also much lower than its deep learning-based counterparts.

42 ENGINEERING↗

DOE OSTI2022

Critical Shear Stress for Erosion Under Laminar Jet Flow

Particle erosion is an important process in both natural and manmade environments. For example, in natural environments particle or sediment erosion rates determine the course of rivers, depth of streams, and fate of deltas. The interplay between erosion rates and flow patterns can have dramatic impact on shorelines. Where hydrodynamic jet flows or rip currents change direction, sediments may accumulate or disperse altering the shape of coastlines and the ecosystems and economies that rely on them. In man-made systems, jet flows may be used to mobilize particles from surfaces or within industrial scale mixing tanks. For example, in the nuclear industry, impinging jet mixers may be used to mobilize and suspend sludges at the bottom of waste tanks. In each of these examples, the Shields diagram is useful to determine the conditions under which erosion occurs. This diagram plots the scaled critical shear stress for erosion as a function of the particle size as embedded in particle Reynolds numbers, Archimedes numbers, or their equivalents. Although the data, that carries a large spread, is largely in agreement with mathematical models, for the smallest particles, model predictions diverge from each other and from experimental data. Indeed, there is substantial uncertainty about the Shields diagrams at relatively small particle sizes and flow rates. Here we evaluate critical shear stresses for erosion under laminar jet flow. To date critical shear stresses for erosion, as embodied in Shields diagrams, have largely been developed for turbulent flow both experimental and mathematically. However, curves on the Shields diagrams diverge among various models at lower particle Reynolds numbers. Indeed, how critical shear stresses for erosion develop under fully laminar jet flow conditions (not simply laminar boundary layers under turbulent flow) remains unclear. Here we address this gap, which is particularly important for mobilization of the smallest particles. We find the Shields parameter to be inversely proportional to the particle Reynolds numbers under laminar jet flow conditions similar to turbulent conditions.

critical shear stresses, erosion rates, effective ↗

DOE OSTI2020

Role of consistent terminology in XPS reproducibility

The use of inconsistent and incorrect terminology in scientific publications contributes to misunderstanding, confusion, and erroneous results in the scientific literature. This issue is of particular importance in x-ray photoelectron spectroscopy (XPS) that is in widespread use for many different purposes by scientists with diverse backgrounds. A set of surface analysis terminology, approved through consensus by international experts, has been developed by International Organization for Standardization Technical Committee TC201 on Surface Chemical Analysis. To encourage wide use, the terminology is accessible at several web sites free of charge. This short overview provides examples to highlight the importance of agreed terminology in eliminating confusion between similar terms. Examples are provided of terms that are commonly misused or confused in the literature. Other examples highlight terminology that provides a common basis for comparing instrument parameters and performance. As science advances, it is important to clarify terminology for describing evolving concepts and developments important to XPS.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗