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DOE OSTI2022

U.S. Department of Energy: National Virtual Biotechnology Laboratory (Technical Report)

With funding from the CARES Act, the U.S Department of Energy (DOE) established the National Virtual Biotechnology Laboratory (NVBL) in March 2020 to address key challenges associated with the COVID-19 crisis. The NVBL brought together the broad scientific and technical expertise and resources of DOE’s 17 national laboratories to help tackle medical supply shortages, discover potential drugs to fight the virus, develop and validate COVID-19 testing methods, model disease spread and impact across the nation, and understand virus transport in buildings and the environment. National laboratory resources leveraged for this effort include a suite of world-leading user facilities broadly available to the research community, such as light and neutron sources, nanoscale science research centers, sequencing and biocharacterization facilities, and high-performance computing facilities. As part of the NVBL framework, DOE rapidly assembled five project teams to (1) identify new targets for medical therapeutics; (2) develop innovations in testing capabilities; (3) provide epidemiological and logistical support; (4) understand viral fate and transport in the environment; and (5) address supply chain bottlenecks by harnessing extensive additive manufacturing capabilities. Each research team was charged with defining high-impact projects that could be completed in a 6-month sprint while coordinating their developments with academia, other government agencies, and the private sector. Within months, NVBL teams used DOE’s high-performance computers and light and neutron sources to identify promising candidates for antibodies and antivirals that universities and drug companies are now evaluating. NVBL researchers also developed new diagnostic targets and sample collection approaches, and supported efforts by the U.S. Food and Drug Administration, Centers for Disease Control and Prevention, and U.S. Department of Defense to establish national guidelines used in administering millions of tests. Researchers used artificial intelligence and high-performance computing to produce near-real-time data analysis to forecast disease transmission, stress on public health infrastructure, and economic impact, which supported decision-makers at the local, state, and national levels. To minimize virus uptake and protect human health, NVBL teams studied how to control indoor virus movement. Researchers also produced innovations in materials and advanced manufacturing that mitigated shortages in test kits and personal protective equipment, creating nearly 1,000 new jobs. Through its NVBL framework, DOE has contributed significantly to the nation’s COVID response, demonstrating in only a few months the critical impact of its national laboratories. NVBL’s accomplishments demonstrate not only the powerful resource represented by DOE’s national laboratories working together to meet national needs, but also the effectiveness of the integrated NVBL framework for rapidly responding to emergencies with research and development solutions. Going forward, the NVBL is poised to apply the unique capabilities and expertise of the national laboratory complex to future national and international emergencies, both natural and engineered. Through this framework, DOE will continue to be an integral component of agency-wide efforts to prepare for and respond to biorisks and other crises. This technical report describes the goals, progress, and results of NVBL’s five project teams—Molecular Design for COVID-19 Therapeutics, COVID-19 Testing, Epidemiological Modeling, Viral Fate and Transport, and Materials and Manufacturing of Critical Supplies—and lists each team’s publications and research output.

42 ENGINEERING↗

DOE OSTI2021

C3PU:Real-Time Predictive Charge Control Software for Battery Management Systems (Code for Charge Control and Predictive Unit) [SWR-21-48]

C3PU sets up a model predictive control formulation for the optimal charging control of battery packs and can be deployed for real-time operation on an embedded microprocessor. C3PU uses electrochemical and thermal models of battery packs to predict the charging trajectories of the battery pack over a time horizon under different operating conditions. It then selects the optimal charging trajectory such that a pre-defined objective is minimized, which in the present state of the code is to minimize the charging duration of the battery pack. The optimal charging trajectory is obtained by solving an underlying mathematical problem. However, C3PU is flexible to incorporate other charging objectives. The underlying battery models can be swapped as well, as long as they follow certain mathematical properties. Mathematically, optimal control problems (in this case, optimally controlling the charging current of the battery pack) are computationally expensive. C3PU implements advanced numerical techniques, namely pseudo-spectral optimization, to reduce the computational burden of the underlying problem to solve. This allows for the problem to be solved in real-time in an embedded system. Once the optimal charging trajectory is computed over a time horizon, C3PU can package such data and send it out via appropriate communication protocols.

Mishra, Partha↗

DOE OSTI2025

Nature of molybdenum carbide surfaces for catalytic hydrogen dissociation using machine-learned potentials: an ensemble-averaged perspective

Molybdenum carbides with an electronic structure similar to noble metals have gained attention as a promising low-cost catalyst for biomass valorization and the hydrogen evolution reaction. However, our fundamental understanding of the catalyst surface and how different phases of these catalysts behave at varying reaction conditions is limited to ground state density functional theory calculations as ab initio molecular dynamics (AIMD) is computationally prohibitive at relevant length and time scales. Here, in this work, we train a multi-atomic cluster expansion (MACE) machine-learned interatomic potentials (MLIP) to study hydrogen dissociation and dynamics over Mo, δ-MoC, α-Mo 2 C, and β-Mo 2 C surfaces at varying temperatures and hydrogen partial pressures. Our simulations identify unique and different molecular and atomic hydrogen adsorption sites on different surfaces that do not depend on the temperature. At low hydrogen pressures, the surface coverage is monolayer, which transitions to two-layer adsorption at higher pressures. We find that atomic hydrogen diffusion and recombinations are preferred over molybdenum atom hollow sites, while the diffusion over carbon-terminated facets was negligible, signifying particularly strong C–H interactions. In contrast, molecular hydrogen adsorption occurs mostly atop Mo or the bridging sites. At a comparable hydrogen loading, β-Mo 2 C (001) is the most active surface for hydrogen dissociation reaction. This work provides insights into the dynamic nature of the hydrogen dissociation chemistry and the diversity of hydrogen adsorption sites on molybdenum carbides.

08 HYDROGEN↗

DOE OSTI2022

Scaling Superconducting Quantum Computers with Chiplet Architectures

Fixed-frequency transmon quantum computers (QCs) have advanced in coherence times, addressability, and gate fidelities. Unfortunately, these devices are restricted by the number of on-chip qubits, capping processing power and slowing progress toward fault-tolerance. Although emerging transmon devices feature over 100 qubits, building QCs large enough for meaningful demonstrations of quantum advantage requires overcoming many design challenges. For example, today’s transmon qubits suffer from significant variation due to limited precision in fabrication. As a result, barring significant improvements in current fabrication techniques, scaling QCs by building ever larger individual chips with more qubits is hampered by device variation. Severe device variation that degrades QC performance is referred to as a defect. Here, we focus on a specific defect known as a frequency collision. When transmon frequencies collide, their difference falls within a range that limits two-qubit gate fidelity. Frequency collisions occur with greater probability on larger QCs, causing collision-free yields to decline as the number of on-chip qubits increases. As a solution, we propose exploiting the higher yields associated with smaller QCs by integrating quantum chiplets within quantum multi-chip modules (MCMs). Yield, gate performance, and application-based analysis show the feasibility of QC scaling through modularity. Our results demonstrate that chiplet architectures, relative to monolithic designs, benefit from average yield improvements ranging from 9.6 – 92.6 × for ≲5 qubit machines. In addition, our simulations explore the design space of chiplet systems and discover configurations that demonstrate average two-qubit gate infidelity reductions that are at best 0.815 × their monolithic counterpart. Lastly, we observe that carefully-selected modular systems achieve fidelity improvements on a range of benchmark circuits.

quantum architecture↗

DOE OSTI2024

Enabling Parallel Performance and Portability of Solid Mechanics Simulations Across CPU and GPU Architectures

Efficiently simulating solid mechanics is vital across various engineering applications. As constitutive models grow more complex and simulations scale up in size, harnessing the capabilities of modern computer architectures has become essential for achieving timely results. This paper presents advancements in running parallel simulations of solid mechanics on multi-core CPUs and GPUs using a single-code implementation. This portability is made possible by the C++ matrix and array (MATAR) library, which interfaces with the C++ Kokkos library, enabling the selection of fine-grained parallelism backends (e.g., CUDA, HIP, OpenMP, pthreads, etc.) at compile time. MATAR simplifies the transition from Fortran to C++ and Kokkos, making it easier to modernize legacy solid mechanics codes. We applied this approach to modernize a suite of constitutive models and to demonstrate substantial performance improvements across different computer architectures. This paper includes comparative performance studies using multi-core CPUs along with AMD and NVIDIA GPUs. Results are presented using a hypoelastic–plastic model, a crystal plasticity model, and the viscoplastic self-consistent generalized material model (VPSC-GMM). The results underscore the potential of using the MATAR library and modern computer architectures to accelerate solid mechanics simulations.

Morgan, Nathaniel (ORCID:0000000276118449)↗

DOE OSTI2021

Large scale multi-node simulations of $\mathbb{Z}_2$ gauge theory quantum circuits using Google Cloud Platform

Simulating quantum field theories on a quantum computer is one of the most exciting fundamental physics applications of quantum information science. Dynamical time evolution of quantum fields is a challenge that is beyond the capabilities of classical computing, but it can teach us important lessons about the fundamental fabric of space and time. Whether we may answer scientific questions of interest using near-term quantum computing hardware is an open question that requires a detailed simulation study of quantum noise. Here we present a large scale simulation study powered by a multi-node implementation of qsim using the Google Cloud Platform. We additionally employ newly-developed GPU capabilities in qsim and show how Tensor Processing Units -- Application-specific Integrated Circuits (ASICs) specialized for Machine Learning -- may be used to dramatically speed up the simulation of large quantum circuits. We demonstrate the use of high performance cloud computing for simulating $\mathbb{Z}_2$ quantum field theories on system sizes up to 36 qubits. We find this lattice size is not able to simulate our problem and observable combination with sufficient accuracy, implying more challenging observables of interest for this theory are likely beyond the reach of classical computation using exact circuit simulation.

Gustafson, Erik↗

DOE OSTI2021

Fast All-sky Radiation Model for Solar applications (FARMS) [SWR-16-18]

The Fast All-sky Radiation Model for Solar applications (FARMS) is used to compute cloudy irradiance. Radiative transfer (RT) models simulating broadband solar radiation have been widely used by atmospheric scientists to model solar resources for various energy applications such as operational forecasting. Due to the complexity of solving the RT equation, the computation under cloudy conditions can be extremely time consuming though many approximations (e.g. two-stream approach and delta-M truncation scheme) have been utilized. Thus, a more efficient RT model is crucial for model developers as a new option for approximating solar radiation at the land surface with minimal loss of accuracy. We have developed a fast all-sky radiation model for solar applications (FARMS) using the simplified clear-sky RT model, REST2, and simulated cloud transmittances and reflectances from the Rapid Radiation Transfer Model (RRTM) with a sixteen-stream Discrete Ordinates Radiative Transfer (DISORT). Simulated lookup tables (LUTs) of cloud transmittances and reflectances were created by varying cloud optical thicknesses, cloud particle sizes, and solar zenith angles. Equations with optimized parameters were fitted to the cloud transmittances and reflectances to develop the model. Using this model the all-sky solar irradiance at the land surface can be computed rapidly by combining REST2 with the cloud transmittances and reflectances. This new RT model is more than 1000 times faster than those currently utilized in solar resource assessment and forecasting since it does not explicitly solve the RT equation for each individual cloud condition. Our results indicate the accuracy of the fast radiative transfer model is comparable to or better than two-stream approximation in term of computing cloud transmittance and solar radiation.

Xie, Yu↗

DOE OSTI2023

Fast All-sky Radiation Model for Solar applications (FARMS) 2023 [SWR-16-18]

Xie, Yu↗

DOE OSTI2024

WFOT: A Wave Function Overlap Tool between Single- and Multi-Reference Electronic Structure Methods for Spectroscopy Simulation

We report the development of a novel diagnostic tool, named wave function overlap tool (WFOT), designed to evaluate the overlap between wave functions computed at single-reference [i.e., time-dependent density functional theory or configuration interaction singles (CIS)] and multireference (i.e., CASSCF/CASPT2) electronic structure levels of theory. It relies on truncating the single- and multireference WFs to CIS-like expansions spanning the same configurational space and maximizing the molecular orbital overlap by means of a unitary transformation. To demonstrate the functionality of the tool, we calculate the transient spectrum of acetylacetone by evaluating excited state absorption signals with multireference quality on top of single-reference on-the-fly dynamics simulations. Semiautomatic spectra generation is facilitated by interfacing the tool with the COBRAMM package, which also allows one to use WFOT with several quantum chemistry codes such as Gaussian, NWChem, and OpenMolcas. Finally, other exciting possibilities for the utilization of the code beyond the simulation of transient absorption spectroscopy are eventually discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Enabling dynamic 3D coherent diffraction imaging via adaptive latent space tuning of generative autoencoders

Abstract Coherent diffraction imaging (CDI) is an advanced non-destructive 3D X-ray imaging technique for measuring a sample’s electron density. The main challenge of CDI is loss of phase information in diffraction intensity measurements, resulting in lengthy iterative reconstruction processes that can return non-unique solutions, which pose challenges for experiments attempting to track dynamic sample evolution through multiple states. As the increased brightness of fourth-generation light sources enables faster sample measurements and drives operando experiments with Bragg CDI, there is a growing need for faster reconstruction techniques that can keep pace. We have developed an adaptive generative autoencoder approach for uniquely tracking a sample’s electron density as it dynamically evolves. Our approach adaptively tunes the low-dimensional latent embedding of a generative autoencoder, enabling a computationally efficient manner to account for time-varying shifting distributions in real-time. Analytic proof of convergence is provided as well as numerical demonstration of sample tracking with noisy measurements.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Evolution of texture and internal stresses within polycrystalline rock salt using in situ 3D synchrotron computed tomography and 3D X-ray diffraction

Over time rock salt caverns have been extensively used as reliable repositories for hazardous waste such as nuclear waste, oil or compressed gases. Undisturbed rock salt deposits in nature are usually impermeable and have very low porosity. However, rock salt formations under excavation stresses can develop crack networks, which increase their porosities; and in the case of a connected crack network within the media, rock salt may become permeable. Although the relationship between the permeability of rock salt and the applied stresses has been reported in the literature, a microscopic study that investigates the properties influencing this relationship, such as the evolution of texture and internal stresses, has yet to be conducted. This study employs in situ 3D synchrotron micro-computed tomography and 3D X-ray diffraction (3DXRD) on two small-scale polycrystalline rock salt specimens to investigate the evolution of the texture and internal stresses within the specimens. The 3DXRD technique measures the 3D crystal structure and lattice strains within rock salt grains. The specimens were prepared under 1D compression conditions and have shown an initial {111} preferred texture, a dominant {110}$\langle1\bar{1}0\rangle$ slip system and no fully connected crack network. The {111} preferred texture under the unconfined compression experiment became stronger, while the {111}$\langle1\bar{1}0\rangle$ slip system became more prominent. The specimens did not have a fully connected crack network until applied axial stresses reached about 30 MPa, at a point where the impermeability of the material becomes compromised due to the development of multiple major cracks.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Modeling laser-wakefield accelerators using the time-averaged ponderomotive approximation in a Lorentz boosted frame

Future, high-fidelity simulations of multi-GeV-class laser Wakefield accelerators (LWFAs) will need to model the propagation of high-intensity laser drivers over meter-scale plasmas with high spatial and temporal resolutions, thus requiring high amounts of computational resources. Various techniques have been devised over the years to reduce the computational cost of such simulations, including the time-averaged ponderomotive approximation, and the use of the Lorentz boosted frame technique. In this paper we discuss the combination of these two computational techniques, highlighting the resulting significant reduction in the computational cost of LWFA simulations and the limitations of this approach. The combination of the two techniques can potentially become essential for the modeling of a multi-TeV, LWFA-based collider.

Laser Wakefield Acceleration↗

DOE OSTI2022

Form factors and spectral densities from Lightcone Conformal Truncation

We use the method of Lightcone Conformal Truncation (LCT) to obtain form factors and spectral densities of local operators $\mathcal{O}$ in $\phi^4$ theory in two dimensions. We show how to use the Hamiltonian eigenstates from LCT to obtain form factors that are matrix elements of a local operator $\mathcal{O}$ between single-particle bra and ket states, and we develop methods that significantly reduce errors resulting from the finite truncation of the Hilbert space. We extrapolate these form factors as a function of momentum to the regime where, by crossing symmetry, they are form factors of $\mathcal{O}$ between the vacuum and a two-particle asymptotic scattering state. We also compute the momentum-space time-ordered two-point functions of local operators in LCT. These converge quickly at momenta away from branch cuts, allowing us to indirectly obtain the time-ordered correlator and the spectral density at the branch cuts. We focus on the case where the local operator $\mathcal{O}$ is the trace Θ of the stress tensor.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Simple holographic models of black hole evaporation

Several recent papers have shown a close relationship between entanglement wedge reconstruction and the unitarity of black hole evaporation in AdS/CFT. The analysis of these papers however has a rather puzzling feature: all calculations are done using bulk dynamics which are essentially those Hawking used to predict information loss, but applying ideas from entanglement wedge reconstruction seems to suggest a Page curve which is consistent with information conservation. Why should two different calculations in the same model give different answers for the Page curve? In this note we present a new pair of models which clarify this situation. Our first model gives a holographic illustration of unitary black hole evaporation, in which the analogue of the Hawking radiation purifies itself as expected, and this purification is reproduced by the entanglement wedge analysis. Moreover a smooth black hole interior persists until the last stages the evaporation process. Our second model gives an alternative holographic interpretation of the situation where the bulk evolution leads to information loss: unlike in the models proposed so far, this bulk information loss is correctly reproduced by the entanglement wedge analysis. This serves as an illustration that quantum extremal surfaces are in some sense kinematic: the time-dependence of the entropy they compute depends on the choice of bulk dynamics. In both models no bulk quantum corrections need to be considered: classical extremal surfaces are enough to do the job. We argue that our first model is the one which gives the right analogy for what actually happens to evaporating black holes, but we also emphasize that any complete resolution of the information problem will require an understanding of non-perturbative bulk dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Assessing free tropospheric quasi-equilibrium for different GCM resolutions using a cloud-resolving model simulation of tropical convection

Abstract This study examines the free-tropospheric quasi-equilibrium at different global climate model (GCM) resolutions using the simulation of tropical convection by a cloud-resolving model during the Tropical Western Pacific International Cloud Experiment. The simulated dynamic and thermodynamic fields within the model domain are averaged over subdomains of different sizes equivalent to different GCM resolutions. These coarse-grained fields are then used to compute CAPE and its change with time, and their relationships with simulated convection. Results show that CAPE change with time is controlled predominantly by variations of thermodynamic properties in the planetary boundary layer for all subdomain sizes ranging from 64 to 4 km. Lag correlation analysis shows that CAPE generation by the free-tropospheric dynamical advection (dCAPE ls ) leads convective precipitation but is in phase with convective mass flux at 600 mb and 500 mb vertical velocity for all subdomain sizes. However, the correlation coefficients and regression slopes decrease as the subdomain size decreases for subdomain sizes smaller than 16 km. This is probably due to increased randomness of convection and more scale-dependence of the relationships when the subdomain size reaches the grey zone. By examining the sensitivity of the relationships of convection with dCAPE ls to temporal scales in different subdomain size, it shows that the quasi-equilibrium between dCAPE ls and convection holds well for timescales of 30 min or longer at all subdomain sizes. These results suggest that the free tropospheric quasi-equilibrium assumption may still be useable even for GCM resolutions in the grey zone.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Developing a system for in vivo imaging of maize roots containing iodinated contrast media in soil using synchrotron XCT and XRF

We sought to develop a novel experimental system which enabled application of iodinated contrast media to in vivo plant roots intact in soil and was compatible with time-resolved synchrotron X-ray computed tomography imaging. The system was developed to overcome issues of low contrast to noise within X-ray computed tomography images of plant roots and soil environments, the latter of which can complicate image processing and result in the loss of anatomical information. To demonstrate the efficacy of the system we employ the novel use of both synchrotron X-ray computed tomography and synchrotron X-ray fluorescence mapping to capture the translocation of the contrast media through root vasculature into the leaves. With the application of contrast media we identify fluid flow in root vasculature and visualise anatomical features, which are otherwise often only observable in ex vivo microscopy, including: the xylem, metaxylem, pith, fibres in aerenchyma and leaf venation. We are also able to observe interactions between aerenchyma cross sectional area and solute transport in the root vasculature with depth. Our novel system was capable of successfully delivering sufficient contrast media into root and leaf tissues such that anatomical features could be visualised and internal fluid transport observed. We propose that our system could be used in future to study internal plant transport mechanisms and parameterise models for fluid flow in plants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Temperature-dependent mechanical properties and crystal plasticity parameters for additively manufactured Haynes-214 alloy: Experiments and numerical modeling

Our experimental mechanical testing data demonstrated that the additively manufactured (AM) laser powder bed fusion (L-PBF) Haynes-214 alloy exhibits non-linear mechanical properties as the temperature rises from ambient to 870 °C. Crystal plasticity (CP) simulations provide an effective approach to gaining deeper insights into microstructure-property linkages under thermomechanical loading. This method can reduce the need for costly high-temperature mechanical testing while accounting for the effects of crystallographic texture and grain morphology on the mechanical behavior of AM materials. However, calibrating a CP model is time-consuming because individual simulations are computationally expensive and hundreds (or more) of iterations over parameter sets may be required. To address this issue, we have designed a machine learning-differential evolution (ML-DE) CP framework that can accurately interpolate the tensile properties of AM L-PBF Haynes-214 alloy across a wide temperature range from ambient to 870 °C, with minimal reliance on experimental data. The framework uses electron backscatter diffraction (EBSD) measurements to generate statistically equivalent microstructural volume elements to serve as inputs to the CP modeling framework. Stress–strain curves were generated from 1000 CP simulations, which serve as the training data set for the three ML regression algorithms explored: linear, extra-trees, and multi-layer perceptron. These three regression models were independently evaluated to compare their efficiency and identify the most suitable algorithm for the given problem. Results revealed that the extra-trees ML regressor outperforms the other models in both qualitative and quantitative aspects with an R 2 of 0.98. Subsequently, the differential evolution optimization approach is employed to calibrate the ML-based CP material parameters with experimental results obtained at various temperatures. Finally, temperature-dependent CP material parameters are formulated. The effectiveness and efficiency of the designed framework are validated through comparison with experimental results, demonstrating a high degree of agreement. These calibrated parametric constitutive equations enable further use of the CP model to study the deformation behavior of this alloy under a wide range of thermo-mechanical loading conditions.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Prediction of local concentration fields in porous media with chemical reaction using a multi scale convolutional neural network

The study of solute transport in porous media is of interest in many chemical engineering systems. Some example applications include packed bed catalytic reactors, filtration devices, and batteries. The pore scale modeling of these systems is time consuming and may require large computing resources, for this reason computational fluid dynamics (CFD) simulations are not practical if a large number of simulations is required, like in multiscale modeling, where a model at a large scale calls for pore scale simulations. It has been shown that neural networks can be trained with a dataset of flow simulations and then predict fields orders of magnitude faster, and with less computational resources, in new domains. However, it is crucial to provide the neural network with an effective description of the domain and the undergoing operating conditions to be able to train models that generalize accurately in unseen samples. Therefore, research is needed to employ neural networks in new complex systems. The appropriate training of a network for predicting coupled flow and solute transport processes is an outstanding problem due to the complex interplay between geometry and operating conditions. In this work, we train a multi scale convolutional neural network (MSNet) with a diverse dataset of simulations of transport and chemical reaction in porous media to predict the local concentration fields in images of porous media. Our dataset contains a wide diversity of sphere pack arrangements under different operating conditions (Péclet and Reynolds numbers). Further, we train a robust model by employing different input descriptors that represent the medium and the different operating conditions of each system. Our trained model is able to provide nearly instantaneous predictions, compared to around twenty hours of the CFD workflow, with less than 3.5% error on new geometries and transport conditions. Thus the model could be easily integrated in a multiscale workflow where fast response is needed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗