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DOE OSTI2021

Heterogeneity and Hysteresis in the Polymer Collapse of Single Core–Shell Stimuli-Responsive Plasmonic Nanohybrids

Broad application of polymeric stimuli-responsive smart nanohybrids requires understanding the mechanisms governing active control. Ensemble techniques have identified inhomogeneous polymer collapse in microgels that potentially arise from heterogeneous interchain interactions and differences in core size. A single-particle examination would establish the influence of core size and internal polymer network heterogeneity on local interactions that contribute to the observed inhomogeneous polymer collapse dynamics of nanohybrids. Using single-particle dark-field spectroscopy, we investigated the complex polymer collapse profiles of core–shell plasmonic nanohybrids comprising thermoresponsive poly(N-isopropylacrylamide) (pNIPAM)-encapsulated gold nanorods (AuNRs). We report that the polymer collapse behavior was independent of the core size. For thinner polymer shells, we observed hysteresis in the collapse of AuNR@pNIPAMs, likely related to local pNIPAM aggregation due to interchain hydrogen bonding. For thicker polymer shells, we observed a broad polymer collapse distribution that we attributed to a two-step phase transition that arises from a polymer network density gradient. Furthermore, our single-particle approach relates the internal heterogeneity of the polymer network of nanohybrids to the mechanisms underlying heterogeneous phase transitions that traditional, ensemble-averaged approaches are unable to discern.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Machine learning visualization tool for exploring parameterized hydrodynamics

We are interested in the computational study of shock hydrodynamics, i.e. problems involving compressible solids, liquids, and gases that undergo large deformation. These problems are dynamic and nonlinear and can exhibit complex instabilities. Due to advances in high performance computing it is possible to parameterize a hydrodynamic problem and perform a computational study yielding $\mathscr{O} (TB)$ of simulation state data. We present an interactive machine learning tool that can be used to compress, browse, and interpolate these large simulation datasets. This tool allows computational scientists and researchers to quickly visualize 'what-if' situations, perform sensitivity analyses, and optimize complex hydrodynamic experiments.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Numerical investigation of multiphase flow through self-affine rough fractures

Multiphase flow through fractures has great significance in subsurface energy recovery and gas storage applications. Different fracture and flow properties affect flow through a fracture which is difficult to control in laboratory experiments. Here, we perform lattice Boltzmann simulations in an ensemble of synthetically generated fractures. Drainage simulations are performed at different capillary numbers, wettability, and viscosity ratios. We track the invading front and quantify breakthrough saturations and show that roughness and wettability have a strong effect on fluid invasion through a complex fracture. Invading a more viscous fluid results in more stable displacement regardless of the capillary number while at very low capillary numbers, fluid migration is dependent on the inherent structure of the fracture. We develop a fluid displacement phase diagram in a single rough fracture and compare our results from that in the literature. Finally, we extend the phase diagrams across multiple fractures and demonstrate the importance of natural fracture features of roughness and wettability in identifying stable versus unstable displacement regimes during multiphase flow through rough fractures. Our work presents an end-to-end numerical pathway for testing on experimental data and expanding numerical data sets for testing combinations of different physical phenomenon and make valuable predictions on fluid flow through rough fractures.

02 PETROLEUM↗

DOE OSTI2020

Screening of Therapeutic Agents for COVID-19 Using Machine Learning and Ensemble Docking Studies

The current pandemic demands a search for therapeutic agents against the novel coronavirus SARS-CoV-2. In this work, we present an efficient computational strategy that combines machine learning (ML)-based models and high-fidelity ensemble docking studies to enable rapid screening of possible therapeutic ligands. Targeting the binding affinity of molecules for either the isolated SARS-CoV-2 S-protein at its host receptor region or the S-protein:human ACE2 interface complex, we screen ligands from drug and biomolecule data sets that can potentially limit and/or disrupt the host-virus interactions. Top scoring one hundred eighty-seven ligands (with 75 approved by the Food and Drug Administration) are further validated by all atom docking studies. Important molecular descriptors ( 2 χ n , topological surface area, and ring count) and promising chemical fragments (oxolane, hydroxy, and imidazole) are identified to guide future experiments. Overall, this work expands our knowledge of small-molecule treatment against COVID-19 and provides a general screening pathway (combining quick ML models with expensive high-fidelity simulations) for targeting several chemical/biochemical problems.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Revealing the evolution of order in materials microstructures using multi-modal computer vision

The development of high-performance materials for microelectronics, energy storage, and extreme environments depends on our ability to describe and direct property-defining microstructural order. Our present understanding is typically derived from laborious manual analysis of imaging and spectroscopy data, which is difficult to scale, challenging to reproduce, and lacks the ability to reveal latent associations needed for mechanistic models. Here, we demonstrate a multi-modal machine learning (ML) approach to describe order from electron microscopy analysis of the complex oxide La 1−x Sr x FeO 3 . We construct a hybrid pipeline based on fully and semi-supervised classification, allowing us to evaluate both the characteristics of each data modality and the value each modality adds to the ensemble. We observe distinct differences in the performance of uni- and multi-modal models, from which we draw general lessons in describing crystal order using computer vision.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Impact of the Earth’s Density Profile on Atmospheric Neutrino Oscillations

As atmospheric neutrinos traverse the Earth, the matter potential influences their oscillation probabilities in intricate ways, enhancing and suppressing the conversion of one neutrino’s flavor to another along the propagation. Comprehending their behavior within Earth’s complex density profile, primarily described by the Preliminary Reference Earth Model (PREM) [1], is essential for accurately describing oscillations and determining expected atmospheric neutrino event rates in the DUNE Far Detector. In this study, we address this challenge by considering an ensemble of Earth models constrained by astronomical measurements of the planet’s mass and moment of inertia. We evaluate how variations in densities and layer boundaries can affect oscillation probabilities and event rates, and what implications this could have on various physics analyses.

Ismerio Oliveira, Marcelo [Rio de Janeiro, Pont. U↗

DOE OSTI2020

Toward Resilient Heterogeneous Computing Workflow through Kokkos-DataSpaces Integration

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Design and Performance of Kokkos Staging Space toward Scalable Resilient Application Couplings

With the growing number of applications designed for heterogeneous HPC devices, application programmers and users are finding it challenging to compose scalable workflows as ensembles of these applications, that are portable, performant and resilient. The Kokkos C++ library has been designed to simplify this cumbersome procedure by providing an intra-application uniform programming model and portable performance. However, assembling multiple Kokkos-enabled applications into a complex workflow is still a challenge. Although Kokkos enables a uniform programming model, the inter-application data exchange still remains a challenge from both performance and software development cost perspectives. In order to address this issue, we propose Kokkos data staging memory space, an extension of Kokkos' data abstraction (memory space) for heterogeneous computing systems. This new abstraction allows to express data on a virtual shared-space for multiple Kokkos applications, thus extending Kokkos to support inter-application data exchange to build an efficient application workflow. Additionally, we study the effectiveness of asynchronous data layout conversions for applications requiring different memory access patterns for the shared data. Our preliminary evaluation with a synthetic benchmark indicate the effectiveness of this conversion adapted to three different scenarios representing access frequency and use patterns of the shared data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Calibration and Uncertainty Estimation Using the Ensemble Kalman Filter with a Large Subsurface Flow and Transport Model - 20321

At routinely monitored groundwater contamination sites, periodically measured environmental conditions such as groundwater levels and contaminant concentrations are used to inform and confirm a conceptual site model (CSM) and guide the development and calibration of a numerical groundwater flow and transport model. The calibration of groundwater flow and transport models after each measurement (sampling) event can illuminate deficiencies in a CSM, identify areas where additional monitoring is warranted, and predict the behavior of the system to guide decision making. However, manual and automated (e.g. PEST) model calibration tools can be time-consuming and computationally expensive to implement after each sampling event. Perhaps as a result, such calibration tools generally utilize all available monitoring data simultaneously rather than sequentially assimilating monitoring data one sampling event at a time as the results from sampling become available. A more real-time data assimilation approach may reduce parameter uncertainty, quantify the value of additional monitoring data, and produce a usable model more quickly and with less effort. To mitigate the potential time-consuming aspects of manual and widely applied automated calibration techniques, a data assimilation algorithm called the ensemble Kalman filter (EnKF) was evaluated as a relatively efficient method of model calibration and uncertainty assessment via the sequential integration of monitoring data into a model. The EnKF was able to successfully and efficiently assimilate monitoring and modeling data to calibrate a complex flow and transport model at a real-world site with significant subsurface heterogeneity, uncertainty, and 12 years of monitoring data (over 4,000 individual measurements of groundwater levels and over 2,500 measurements of contaminant concentrations). Starting with an uncalibrated model data from annual sampling events were sequentially assimilated, and the resultant predication errors and estimated parameter uncertainties were tracked. After all monitoring data were assimilated, both flow and transport residuals at the end of the EnKF process were comparable to those produced via a concurrent PEST calibration effort but required fewer model simulations. Both uncertainty and prediction errors decreased over time. In a real-time application, the adequacy of the model could be assessed after each sampling event. The benefits of such a real-time approach to utilizing monitoring data include reduced costs (in the form of model updates or site characterization efforts), early flagging of possible errors in the CSM, and a reduced risk of overfitting and corresponding increased confidence in model predictions. This tool may be particularly useful compared to other calibration techniques (e.g. manual, PEST) when model runtimes are long, calibration parameters are many, or parameter uncertainty is large. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Determining Infrared Optical Constants for Dolomite using Single Angle Reflectance and Spectroscopic Ellipsometry

The optical constants, namely the real (n) and imaginary (k) parts of the complex refractive index, are of particular interest to generate the infrared (IR) spectra of liquid and solid materials in different morphologies. To obtain n/k, however, most materials are typically not found in the monolithic forms necessary to easily measure n/k, and thus require the use of other methods such as pressing powders to form planar, specularly-reflective pellets. In this work dolomite crystals are measured using fixed-angle IR reflectance spectroscopy in both 1) a monolithic form with the crystal fixed in epoxy and polished, but data are also recorded from 2) pressed-pellet forms of powders of the same mineral using the same spectroscopic protocols. First results for the two methods are compared. It was found that the measured reflectance can vary by as much as a factor of two between the dolomite crystals and the pressed powder forms. For the two-sample preparation approaches the preliminary spectra are compared and the implications and limitations of each method for determining the optical constants of given materials are discussed. Comparison to literature data suggest that polarization effects likely account for the differing amplitude results for reflectance (and hence the k -vectors): Dolomite is known to be biaxial with significantly differing ordinary and extraordinary rays; the pressed pellet method measures an ensemble of microcrystals in randomly oriented positions, whereas the single crystal maintains just one orientation relative to the optical axis.

ellipsometry, dolomite, complex refractive index, ↗

DOE OSTI2022

Experimental realization of an extended Fermi-Hubbard model using a 2D lattice of dopant-based quantum dots

The Hubbard model is an essential tool for understanding many-body physics in condensed matter systems. Artificial lattices of dopants in silicon are a promising method for the analog quantum simulation of extended Fermi-Hubbard Hamiltonians in the strong interaction regime. However, complex atom-based device fabrication requirements have meant emulating a tunable two-dimensional Fermi-Hubbard Hamiltonian in silicon has not been achieved. Here, we fabricate 3 × 3 arrays of single/few-dopant quantum dots with finite disorder and demonstrate tuning of the electron ensemble using gates and probe the many-body states using quantum transport measurements. By controlling the lattice constants, we tune the hopping amplitude and long-range interactions and observe the finite-size analogue of a transition from metallic to Mott insulating behavior. We simulate thermally activated hopping and Hubbard band formation using increased temperatures. As atomically precise fabrication continues to improve, these results enable a new class of engineered artificial lattices to simulate interactive fermionic models.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Programmable interactions and emergent geometry in an array of atom clouds

Interactions govern the flow of information and the formation of correlations between constituents of many-body quantum systems, dictating phases of matter found in nature and forms of entanglement generated in the laboratory. Typical interactions decay with distance and thus produce a network of connectivity governed by geometry—such as the crystalline structure of a material or the trapping sites of atoms in a quantum simulator. However, many envisioned applications in quantum simulation and computation require more complex coupling graphs including non-local interactions, which feature in models of information scrambling in black hole, and mappings of hard optimization problems onto frustrated classical magnets. Here we describe the realization of programmable non-local interactions in an array of atomic ensembles within an optical cavity, in which photons carry information between atomic spins. By programming the distance dependence of the interactions, we access effective geometries for which the dimensionality, topology and metric are entirely distinct from the physical geometry of the array. As examples, we engineer an antiferromagnetic triangular ladder, a Möbius strip with sign-changing interactions and a treelike geometry inspired by concepts of quantum gravity. The tree graph constitutes a toy model of holographic duality, in which the quantum system lies on the boundary of a higher-dimensional geometry that emerges from measured correlations. Overall, our work provides broader prospects for simulating frustrated magnets and topological phases, investigating quantum optimization paradigms and engineering entangled resource states for sensing and computation.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

Interpreting the Operando XANES of Surface-Supported Subnanometer Clusters: When Fluxionality, Oxidation State, and Size Effect Fight.

X-ray absorption near edge structure (XANES) spectroscopy is widely used for operando catalyst characterization. We show that, for highly fluxional supported nanoclusters, the customary extraction of the oxidation state of the metal from the XANES data by fitting to the bulk standards is highly questionable. The XANES signatures as well as the apparent oxidation state for such clusters arise from a complex combination of many factors, and not only from the chemical composition in reaction conditions (e.g., oxygen content in oxidizing atmosphere). The thermally accessible isomerization and population of several structurally distinct cluster forms, cluster-support interaction, and intrinsic size effects all impact the metal oxidation state and XANES signal. We demonstrate this on copper oxide clusters with different compositions, Cu4Ox(x = 2-5) and Cu5Oy (y = 3, 5), deposited on amorphous alumina and ultrananocrystalline diamond, for which we computed the XANES spectra and compare the results to the experiment. We show in addition that fitting the experimental spectrum to calculated spectra of supported clusters can, in contrast, provide good agreement and insight into the spectrum-composition-structure relation. Experimental XANES interpreted using the proposed fitting scheme shows the partial reduction of Cu oxide clusters at rising temperatures, and pinpoints the specific stoichiometries that dominate in the ensemble of cluster states as the temperature changes.

Zandkarimi, Borna↗

DOE OSTI2020

Characterizing intracellular proteomes for microbes: An experimental approach using label-free protein quantitation

Genomic and transcriptomic studies generate a rich source of molecular information; however, neither a static genome nor the presence of a messenger RNA provides the most direct insight into the functional state of a microbial cell at any given time. Rather, it is the ensemble of proteins (i.e., proteome) that is the primary workhorse for most biological processes that are concurrent and coordinately active in a living cell. Currently, mass-spectrometry-based (MS) technologies provide unprecedented information into the composition of the proteome, shedding light on the numerous complex biological processes actively shaping observed phenotypes. Herein, we detail a protocol for the exploration of intracellular proteomes through the large-scale, unbiased identification of proteins and their relative abundances using liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS). In general, this protocol is applicable to both microbial and eukaryotic systems.

Abraham, Paul↗

DOE OSTI2020

Enabling Large-Scale Condensed-Phase Hybrid Density Functional Theory Based Ab Initio Molecular Dynamics. 1. Theory, Algorithm, and Performance

By including a fraction of exact exchange (EXX), hybrid functionals reduce the self-interaction error in semilocal density functional theory (DFT) and thereby furnish a more accurate and reliable description of the underlying electronic structure in systems throughout biology, chemistry, physics, and materials science. However, the high computational cost associated with the evaluation of all required EXX quantities has limited the applicability of hybrid DFT in the treatment of large molecules and complex condensed-phase materials. To overcome this limitation, we describe a linear-scaling approach that utilizes a local representation of the occupied orbitals (e.g., maximally localized Wannier functions (MLWFs)) to exploit the sparsity in the real-space evaluation of the quantum mechanical exchange interaction in finite-gap systems. In this work, we present a detailed description of the theoretical and algorithmic advances required to perform MLWF-based ab initio molecular dynamics (AIMD) simulations of large-scale condensed-phase systems of interest at the hybrid DFT level. We focus our theoretical discussion on the integration of this approach into the framework of Car–Parrinello AIMD, and highlight the central role played by the MLWF-product potential (i.e., the solution of Poisson’s equation for each corresponding MLWF-product density) in the evaluation of the EXX energy and wave function forces. We then provide a comprehensive description of the exx algorithm implemented in the open-source Quantum ESPRESSO program, which employs a hybrid MPI/OpenMP parallelization scheme to efficiently utilize the high-performance computing (HPC) resources available on current- and next-generation supercomputer architectures. Furthermore, this is followed by a critical assessment of the accuracy and parallel performance (e.g., strong and weak scaling) of this approach when AIMD simulations of liquid water are performed in the canonical (NVT) ensemble. With access to HPC resources, we demonstrate that exx enables hybrid DFT-based AIMD simulations of condensed-phase systems containing 500–1000 atoms (e.g., (H₂O)₂₅₆) with a wall time cost that is comparable to that of semilocal DFT. In doing so, exx takes us one step closer to routinely performing AIMD simulations of complex and large-scale condensed-phase systems for sufficiently long time scales at the hybrid DFT level of theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Evaluating Probability of Containment Effectiveness at a GCS Sites using integrated assessment modeling approach with Bayesian decision Networks

Improved scientific and engineering understanding of the behavior of geologic CO2 storage together with established regulatory framework and incentive structures raise the prospects for accelerated, large-scale deployment of this greenhouse gas emissions reduction approach. Incentive structures call for the establishment of appropriate verification and accounting approaches to support claims of the integrity of a geologic storage complex and to justify taking credit for long-term storage. In this study, we present a framework for assessing the probability of containment effectiveness over the lifetime of a geologic carbon storage site (e.g., after 70 years of injection and post-injection site performance) using forward stochastic model realizations based on site characterization data and using a monitoring-informed Bayesian network based on hypothetical detectability from surface seismic surveys over the site injection and post-injection phases. The National Risk Assessment Partnership’s open-source Integrated Assessment Model (NRAP-Open-IAM) was utilized to develop an ensemble of 10,000 a priori stochastic forecasts of CO2 containment. Those simulations were used to train the Bayesian network model to estimate the prior probabilities of the CO2 leakage mass into overlying, monitorable aquifers considering the uncertainties in the reservoir properties, permeability of potentially leaky wells and the overlying aquifers. The conditional probabilities in the Bayesian network were either learned from the NRAP-Open-IAM simulations or derived from the predefined detection thresholds for the monitoring method. Observations obtained from monitoring, over time during the site operation phases were then used to generate updated posterior probabilities of containment (and any loss from containment) in the Bayesian network by propagating the prior probabilities through the conditional probabilities. We demonstrate how to construct and use the Bayesian network for verifying the long-term storage complex effectiveness informed by monitoring based on the NRAP-Open-IAM simulations previously developed for the FutureGen 2.0 site. This approach may have relevance for stake holders to demonstrate secure geologic storage, provide a defensible, probabilistic approach to claim credit for geologic storage, and to estimate the likelihood that any fraction of the claimed credit may need to be refunded to the creditor based on available monitoring information.

Bayesian network, Risk assessment, Monitoring, car↗

DOE OSTI2023

Operando studies reveal active Cu nanograins for CO 2 electroreduction

Carbon dioxide electroreduction facilitates the sustainable synthesis of fuels and chemicals. Although Cu enables CO 2 -to-multicarbon product (C 2+ ) conversion, the nature of the active sites under operating conditions remains elusive. Importantly, identifying active sites of high-performance Cu nanocatalysts necessitates nanoscale, time-resolved operando techniques. Here, we present a comprehensive investigation of the structural dynamics during the life cycle of Cu nanocatalysts. A 7 nm Cu nanoparticle ensemble evolves into metallic Cu nanograins during electrolysis before complete oxidation to single-crystal Cu 2 O nanocubes following post-electrolysis air exposure. Operando analytical and four-dimensional electrochemical liquid-cell scanning transmission electron microscopy shows the presence of metallic Cu nanograins under CO 2 reduction conditions. Correlated high-energy-resolution time-resolved X-ray spectroscopy suggests that metallic Cu, rich in nanograin boundaries, supports undercoordinated active sites for C–C coupling. Quantitative structure–activity correlation shows that a higher fraction of metallic Cu nanograins leads to higher C 2+ selectivity. A 7 nm Cu nanoparticle ensemble, with a unity fraction of active Cu nanograins, exhibits sixfold higher C 2+ selectivity than the 18 nm counterpart with one-third of active Cu nanograins. Importantly, the correlation of multimodal operando techniques serves as a powerful platform to advance our fundamental understanding of the complex structural evolution of nanocatalysts under electrochemical conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Mind the gap: the discrepancy between simulation and reality drives interpretations of the Galactic Center Excess

The Galactic Center Excess (GCE) in GeV gamma rays has been debated for over a decade, with the possibility that it might be due to dark matter annihilation or undetected point sources such as millisecond pulsars (MSPs). This study investigates how the gamma-ray emission model (γEM) used in Galactic center analyses affects the interpretation of the GCE's nature. To address this issue, we construct an ultra-fast and powerful inference pipeline based on convolutional Deep Ensemble Networks. We explore the two main competing hypotheses for the GCE using a set of γEMs with increasing parametric freedom. We calculate the fractional contribution (f src ) of a dim population of MSPs to the total luminosity of the GCE and analyze its dependence on the complexity of the γEM. For the simplest γEM, we obtain fsrc = 0.10 ± 0.07, while the most complex model yields f src = 0.79 ± 0.24. In conclusion, we find that the statement about the nature of the GCE (dark matter or not) strongly depends on the assumed γEM. The quoted results for f src do not account for the additional uncertainty arising from the fact that the observed gamma-ray sky is out-of-distribution concerning the investigated γEM iterations. We quantify the reality gap between our γEMs using deep-learning-based One-Class Deep Support Vector Data Description networks, revealing that all employed γEMs have gaps to reality. Finally, our study casts doubt on the validity of previous conclusions regarding the GCE and dark matter, and underscores the urgent need to account for the reality gap and consider previously overlooked "out of domain" uncertainties in future interpretations.

79 ASTRONOMY AND ASTROPHYSICS↗