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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Cellular fluidics

The natural world provides many examples of multiphase transport and reaction processes that have been optimized by evolution. These phenomena take place at multiple length and time scales and typically include gas–liquid–solid interfaces and capillary phenomena in porous media. Many biological and living systems have evolved to optimize fluidic transport. However, living things are exceptionally complex and very difficult to replicate, and human-made microfluidic devices (which are typically planar and enclosed) are highly limited for multiphase process engineering. In this paper, we introduce the concept of cellular fluidics: a platform of unit-cell-based, three-dimensional structures—enabled by emerging 3D printing methods—for the deterministic control of multiphase flow, transport and reaction processes. We show that flow in these structures can be ‘programmed’ through architected design of cell type, size and relative density. We demonstrate gas–liquid transport processes such as transpiration and absorption, using evaporative cooling and CO 2 capture as examples. We design and demonstrate preferential liquid and gas transport pathways in three-dimensional cellular fluidic devices with capillary-driven and actively pumped liquid flow, and present examples of selective metallization of pre-programmed patterns. Our results show that the design and fabrication of architected cellular materials, coupled with analytical and numerical predictions of steady-state and dynamic behaviour of multiphase interfaces, provide deterministic control of fluidic transport in three dimensions. Cellular fluidics may transform the design space for spatial and temporal control of multiphase transport and reaction processes.

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

A novel random forest approach to revealing interactions and controls on chlorophyll concentration and bacterial communities during coastal phytoplankton blooms

Abstract Increasing occurrence of harmful algal blooms across the land–water interface poses significant risks to coastal ecosystem structure and human health. Defining significant drivers and their interactive impacts on blooms allows for more effective analysis and identification of specific conditions supporting phytoplankton growth. A novel iterative Random Forests (iRF) machine-learning model was developed and applied to two example cases along the California coast to identify key stable interactions: (1) phytoplankton abundance in response to various drivers due to coastal conditions and land-sea nutrient fluxes, (2) microbial community structure during algal blooms. In Example 1, watershed derived nutrients were identified as the least significant interacting variable associated with Monterey Bay phytoplankton abundance. In Example 2, through iRF analysis of field-based 16S OTU bacterial community and algae datasets, we independently found stable interactions of prokaryote abundance patterns associated with phytoplankton abundance that have been previously identified in laboratory-based studies. Our study represents the first iRF application to marine algal blooms that helps to identify ocean, microbial, and terrestrial conditions that are considered dominant causal factors on bloom dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Assessing the potential of deep learning for protein–ligand docking

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein–ligand docking have recently been introduced, so far no previous works have systematically studied the behaviour of the latest docking and structure prediction methods within the broadly applicable context of: (1) using predicted (apo) protein structures for docking (for example, for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (for example, for enzyme design); and (3) having no previous knowledge of binding pockets (for example, for generalization to unknown pockets). To enable a deeper understanding of the real-world utility of docking methods, we introduce PoseBench, a comprehensive benchmark for broadly applicable protein–ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein–ligand docking and protein–ligand structure prediction using both primary ligand and multiligand benchmark datasets, the latter of which we introduce to the DL community. Empirically, using PoseBench, we find that: (1) DL cofolding methods generally outperform comparable conventional and DL docking baseline algorithms, but popular methods such as AlphaFold 3 are still challenged by prediction targets with new protein–ligand binding poses; (2) certain DL cofolding methods are highly sensitive to their input multiple sequence alignments, whereas others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting new or multiligand protein targets.

Morehead, Alex [Lawrence Berkeley National Laborat↗
DOE OSTI2026

Perspective: Magnon-magnon coupling in hybrid magnonics

The internal coupling of magnetic excitations (magnons) with themselves has created a new research sub-field in hybrid magnonics, i.e., magnon-magnon coupling, which focuses on materials discovery and engineering for probing and controlling magnons in a coherent manner. This is enabled by, one, the abundant mechanisms of introducing magnetic interactions, with examples of exchange coupling, dipolar coupling, Ruderman–Kittel–Kasuya–Yosida (RKKY) coupling, and Dzyaloshinskii–Moriya interaction (DMI) coupling, and two, the vast knowledge of how to control magnon band structure, including field and wavelength dependences of frequencies, for determining the degeneracy of magnon modes with different symmetries. In particular, we discuss how magnon-magnon coupling is implemented in various materials systems, with examples of magnetic bilayers, synthetic antiferromagnets, nanomagnetic arrays, layered van der Waals magnets, and (DMI spin-orbit torque materials) in magnetic multilayers. Here, we then introduce new concept of applications for these hybrid magnonic materials systems, with examples of frequency up/down conversion and magnon-exciton coupling, and discuss what properties are desired for achieving those applications.

Materials science↗
DOE OSTI2021

Methods for neutron diffraction studies on hydride superconductors and other metal hydrides

High-pressure neutron diffraction is an extremely useful technique in the quest for making and understanding novel hydride superconductors. Neutron diffraction can be used to directly determine elemental stoichiometries and atomic positions of many light elements such as hydrogen or deuterium, even in the presence of heavy elements such as rare-earth metals. In this work, we report on the current status and ongoing developments on high-pressure neutron diffraction for hydride superconductors and other metal hydrides with a special focus on current advancements at the Spallation Neutrons and Pressure (SNAP) beamline of the Spallation Neutron Source at Oak Ridge National Laboratory. For broader context, an overview of high-pressure neutron diffractometers and pressure cells is included together with insight into critical sample considerations. There, attention is given to the requirements for powdered hydride samples and the need for deuterium rather than hydrogen. Additionally, the advantages of angular access and data representation as possible at SNAP are described. We demonstrate the current capability for high-pressure neutron diffraction on two different samples created via hydrogen gas loading, specifically pure deuterium and nickel-deuteride. The deuterium example highlights the usefulness of adding sample materials that facilitate the formation of a good powder while the nickel-deuteride example demonstrates that atomic deuterium positions and stoichiometry can be directly determined. Both examples highlight the importance of large scattering apertures. These enable investigation of the data resolved by scattering angle that is needed to identify parasitic peaks and background features. Finally, future directions beyond current high-pressure neutron powder diffraction are also discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Direct stellarator coil optimization for nested magnetic surfaces with precise quasi-symmetry

We present a robust optimization algorithm for the design of electromagnetic coils that generate vacuum magnetic fields with nested flux surfaces and precise quasi-symmetry. The method is based on a bilevel optimization problem, where the outer coil optimization is constrained by a set of inner least squares optimization problems whose solutions describe magnetic surfaces. The outer optimization objective targets coils that generate a field with nested magnetic surfaces and good quasi-symmetry. The inner optimization problems identify magnetic surfaces when they exist, and approximate surfaces in the presence of magnetic islands or chaos. We show that this formulation can be used to heal islands and chaos, thus producing coils that result in magnetic fields with precise quasi-symmetry. We show that the method can be initialized with coils from the traditional two-stage coil design process, as well as coils from a near-axis expansion optimization. We present a numerical example where island chains are healed and quasi-symmetry is optimized up to surfaces with aspect ratio 6. Another numerical example illustrates that the aspect ratio of nested flux surfaces with optimized quasi-symmetry can be decreased from 6 to approximately 4. In conclusion, the last example shows that our approach is robust and a cold-start using coils from a near-axis expansion optimization.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Creating large Fock states and massively squeezed states in optics using systems with nonlinear bound states in the continuum

The quantization of the electromagnetic field leads directly to the existence of quantum mechanical states, called Fock states, with an exact integer number of photons. Despite these fundamental states being long-understood, and despite their many potential applications, generating them is largely an open problem. For example, at optical frequencies, it is challenging to deterministically generate Fock states of order two and beyond. Here, we predict the existence of an effect in nonlinear optics, which enables the deterministic generation of large Fock states at arbitrary frequencies. The effect, which we call an n-photon bound state in the continuum, is one in which a photonic resonance (such as a cavity mode) becomes lossless when a precise number of photons n is inside the resonance. Based on analytical theory and numerical simulations, we show that these bound states enable a remarkable phenomenon in which a coherent state of light, when injected into a system supporting this bound state, can spontaneously evolve into a Fock state of a controllable photon number. This effect is also directly applicable for creating (highly) squeezed states of light, whose photon number fluctuations are (far) below the value expected from classical physics (i.e., shot noise). In conclusion, we suggest several examples of systems to experimentally realize the effects predicted here in nonlinear nanophotonic systems, showing examples of generating both optical Fock states with large n (n > 10), as well as more macroscopic photonic states with very large squeezing, with over 90% less noise (10 dB) than the classical value associated with shot noise.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
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↗