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DOE OSTI2025

Computational tools and data integration to accelerate vaccine development: challenges, opportunities, and future directions

The development of effective vaccines is crucial for combating current and emerging pathogens. Despite significant advances in the field of vaccine development there remain numerous challenges including the lack of standardized data reporting and curation practices, making it difficult to determine correlates of protection from experimental and clinical studies. Significant gaps in data and knowledge integration can hinder vaccine development which relies on a comprehensive understanding of the interplay between pathogens and the host immune system. In this review, we explore the current landscape of vaccine development, highlighting the computational challenges, limitations, and opportunities associated with integrating diverse data types for leveraging artificial intelligence (AI) and machine learning (ML) techniques in vaccine design. We discuss the role of natural language processing, semantic integration, and causal inference in extracting valuable insights from published literature and unstructured data sources, as well as the computational modeling of immune responses. Furthermore, we highlight specific challenges associated with uncertainty quantification in vaccine development and emphasize the importance of establishing standardized data formats and ontologies to facilitate the integration and analysis of heterogeneous data. Through data harmonization and integration, the development of safe and effective vaccines can be accelerated to improve public health outcomes. Looking to the future, we highlight the need for collaborative efforts among researchers, data scientists, and public health experts to realize the full potential of AI-assisted vaccine design and streamline the vaccine development process.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Hardware accelerated dynamic work creation on a graphics processing unit

A processor core is configured to execute a parent task that is described by a data structure stored in a memory. A coprocessor is configured to dispatch a child task to the at least one processor core in response to the coprocessor receiving a request from the parent task concurrently with the parent task executing on the at least one processor core. In some cases, the parent task registers the child task in a task pool and the child task is a future task that is configured to monitor a completion object and enqueue another task associated with the future task in response to detecting the completion object. The future task is configured to self-enqueue by adding a continuation future task to a continuation queue for subsequent execution in response to the future task failing to detect the completion object.

Gutierrez, Anthony↗

DOE OSTI2023

Hardware accelerated dynamic work creation on a graphics processing unit

Gutierrez, Anthony T.↗

DOE OSTI2026

Qualifying LaBr3:Ce+Sr detector performance for the Mu2e experiment at Fermilab Using the ELBE Accelerator

A LaBr3:Ce+Sr detector will be used to measure the stopped muon captures at the Mu2e experiment at Fermilab. It has been benchmarked in a test beam experiment performed at the ELBE electron accelerator located at the Helmholtz-Zentrum Dresden-Rossendorf, Germany. ELBE’s pulsed bremsstrahlung beam line was set to deliver an average γ -ray energy of between 4–5 MeV. The detector response was mapped to match Mu2e beam conditions, including rates up to 1 Mcps, energy flux, and time structure. A radioactive calibration source was used to mimic the characteristic 1808.7 keV γ -ray, emitted during the atomic muon nuclear capture in the Mu2e aluminum stopping target. The detector energy resolution was measured as a function of the average energy flux: up to 1 TeV/s for 0.34 s, the steady-operation beam-on time and up to 4 TeV/s for 5 ms to get a conservative estimate of the effect of high intensity Mu2e beam fluctuations. The PMT gain variation as a function of the beam spill length and average intensity has been parametrized and corrected for. When a PMT gain correction corresponding to the average beam-spill intensity is applied, the residual effect of beam intensity fluctuations around the average degrades the energy resolution, σ E γ /E γ , at 1808.7 keV from 0.66% to 0.83%.

Huang, Shihua [Purdue U., West Lafayette]↗

DOE OSTI2025

Anomalous lattice relaxation dynamics in optimally doped La 2−𝑥⁢ Sr 𝑥 ⁢CuO 4

The atomic lattice plays a critical role in the emergence of high-𝑇 𝑐 superconductivity in cuprates. While the dynamics associated with electron-lattice coupling typically unfold on picosecond-to-femtosecond timescales, we present an x-ray photon correlation spectroscopy investigation on an optimally doped La-based cuprate that reveals a strong response of kilosecond-scale lattice relaxation dynamics to the superconducting state. Notably, an anomaly emerges around 𝑇 𝑐 : upon cooling into the superconducting state, the average atomic relaxation lifetime decreases, i.e., dynamics accelerate. This indicates a significant change in the local disorder-induced strain field dynamics at the superconducting transition, highlighting a remarkable coupling between superconductivity and the lattice on quasistatic timescales.

Petsch, A. N. [SLAC National Accelerator Laborator↗

DOE OSTI2023

Precision engineering of biological function with large-scale measurements and machine learning

As synthetic biology expands and accelerates into real-world applications, methods for quantitatively and precisely engineering biological function become increasingly relevant. This is particularly true for applications that require programmed sensing to dynamically regulate gene expression in response to stimuli. However, few methods have been described that can engineer biological sensing with any level of quantitative precision. Here, we present two complementary methods for precision engineering of genetic sensors: in silico selection and machine-learning-enabled forward engineering. Both methods use a large-scale genotype-phenotype dataset to identify DNA sequences that encode sensors with quantitatively specified dose response. First, we show that in silico selection can be used to engineer sensors with a wide range of dose-response curves. To demonstrate in silico selection for precise, multi-objective engineering, we simultaneously tune a genetic sensor’s sensitivity (EC 50 ) and saturating output to meet quantitative specifications. In addition, we engineer sensors with inverted dose-response and specified EC 50 . Second, we demonstrate a machine-learning-enabled approach to predictively engineer genetic sensors with mutation combinations that are not present in the large-scale dataset. We show that the interpretable machine learning results can be combined with a biophysical model to engineer sensors with improved inverted dose-response curves.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Niowave Ancillary Systems – FY21: In Partial Fulfillment of the Deliverable Requirement for Niowave Ancillary Systems Support by LANL

Niowave Inc. produces medical radioisotopes within the US. Lead-bismuth eutectic (LBE) is irradiated using an electron beam to produce neutrons that are used in the production of Molybdenum-99 (Mo-99). The medical community relies on a steady supply of Mo-99 which is primarily used in medical diagnostic imaging. The irradiation of LBE results in high temperatures within the molten metal, this work focusses on the design of ancillary systems associated with the liquid metal system. The LBE is initially at a temperature of 200°C and flows over a steel plate to create a waterfall. The electron beam is then aimed at the waterfall to generate neutrons. The peak temperatures of the LBE post irradiation depend on the beam energy of the LINAC. For a 15 MeV and 20 kW beam, the temperatures can range between 300°C and 350°C. The LBE is cycled through the system to create a closed loop that requires the post-irradiation LBE to be cooled back to 200°C. This work focuses on the heat exchanger and condenser system responsible for the cooling of the post-irradiation LBE.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Structural dynamics modeling of spent nuclear fuel during hypothetical package drop events

The response of spent nuclear fuel (SNF) to hypothetical package drop events is of particular interest in the scope of spent fuel storage and transportation because of the mechanical shock encountered in such scenarios. Previous testing and modeling by the U.S. Department of Energy has demonstrated that the shock and vibration environment of normal shipping and handling conditions (excluding package drop events) is relatively benign and does not challenge the integrity of spent nuclear fuel. Cask drop events are worth considering because SNF packages are required to withstand free drops onto unyielding surfaces as part of their licensing basis. The acceleration experienced during drop events can be orders of magnitude higher, and thus more advanced models are needed to encompass potential nonlinear behavior of the fuel, such as spacer grid buckling and rod-to-rod impact. This work describes a number of finite element models developed to calculate the response of spent nuclear fuel to various hypothetical drop events that have been validated by package and fuel assembly drop tests conducted in the last decade. Sensitivity of the model response to factors such as package drop orientation, secondary impacts, and irradiated material properties as well as their potential impacts to fuel cladding integrity, was also investigated. Cask drops are not expected as a regular occurrence during SNF transportation, but this work helps raise the understanding of SNF mechanical loads to the point of consistency with the package design requirements.

Kadooka, Kevin↗

DOE OSTI2024

Compensation of Third-order Resonances in the High Intensity Regime

As the Fermilab Accelerator Complex enters the high-intensity era, the Recycler Ring (RR) needs to mitigate the detrimental effect of third-order resonance crossing. Third-order resonance lines can be compensated to first order by cancelling out the global Resonance Driving Terms (RDTs) using the response matrix method. This compensation scheme has been proven to work at low intensities, i.e., in the single-particle regime. In order to evaluate the effectiveness of this compensation scheme at higher intensities, this study looks at dynamic and static tune scans, with and without resonance compensation, and different space charge tune shifts. Special care was taken in order to disentangle effects from space charge tune shift, structure resonances and space charge driven resonances.

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

Repetitive proteins that undergo large conformational changes evade structural prediction algorithms

Protein structure prediction algorithms, such as AlphaFold, have accelerated protein design and advanced the understanding of the relationship between amino acid sequence and protein structure. However, these algorithms are limited in their ability to predict the structures of conformationally dynamic, intrinsically disordered, and stimuli-responsive proteins. To evaluate sequence-to-structure predictions of such challenging proteins, we explored a class of conformationally dynamic, repeats-in-toxin (RTX) proteins. RTX proteins adopt intrinsically disordered conformations in the absence of calcium and undergo reversible folding into β-roll structures upon binding to calcium. RTX proteins are characterized by tandem repeats of the sequence GGXGXDXUX, in which X can be any amino acid and U is an aliphatic amino acid. We designed RTX sequence variants with global substitutions of nonconserved amino acids, tandem repeats of consensus sequences GGAGXDTLY, and tandem repeats of scrambled sequences GGAGXDTYL. AlphaFold2 and AlphaFold3 predicted that all of these RTX variants adopt β-roll structures, characteristic of wild-type RTX bound to calcium. However, modeling the predicted structures with molecular dynamics simulations and characterizing the protein variants with circular dichroism spectroscopy, small-angle x-ray scattering, and x-ray crystallography revealed that variants adopt diverse, sequence-dependent structures in the absence and presence of calcium. To better design proteins for applications in biotechnology and sustainability, it is critical to build predictive tools that consider intrinsically disordered protein states and validate these tools with multi-mode, multi-scale experimental data.

Chang, Marina P. [Stanford Univ., CA (United State↗

DOE OSTI2021

Ionizing radiation effects in SONOS-based neuromorphic inference accelerators

Here, we evaluate the sensitivity of neuromorphic inference accelerators based on Silicon-Oxide-Nitride-Oxide-Silicon (SONOS) charge trap memory arrays to total ionizing dose (TID) effects. Data retention statistics were collected for 16 Mbit of 40 nm SONOS digital memory exposed to ionizing radiation from a Co-60 source, showing good retention of the bits up to the maximum dose of 500 krad(Si). Using this data, we formulate a rate-equation-based model for the TID response of trapped charge carriers in the ONO stack, and predict the effect of TID on intermediate device states between ‘program’ and ‘erase’. This model is then used to simulate arrays of low-power, analog SONOS devices that store 8-bit neural network weights and support in situ matrix-vector multiplication. We evaluate the accuracy of the irradiated SONOS-based inference accelerator on two image recognition tasks – CIFAR-10 and the challenging ImageNet dataset – using state-of-the-art convolutional neural networks, such as ResNet-50. We find that across the datasets and neural networks evaluated, the accelerator tolerates a maximum TID between 10 krad(Si) and 100 krad(Si), with deeper networks being more susceptible to accuracy losses due to TID.

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

A GPU ‐Accelerated 3D Unstructured Mesh Based Particle Tracking Code for Multi‐Species Impurity Transport Simulation in Fusion Tokamaks

ABSTRACT This paper presents the multi‐species global impurity transport capability developed in a GPU‐accelerated fully 3D unstructured mesh‐based code, GITRm, to simultaneously track multiple impurity species and handle interactions of these impurities with mixed‐material surfaces. Different computational approaches to model particle‐surface interaction or surface response have been developed and compared. Sheath electric field is taken into account by employing a fast distance‐to‐boundary calculation, which is carried out in parallel on distributed or partitioned meshes on multiple GPUs without the need for any inter‐process communication during the simulation. Several example cases, including two for the DIII‐D tokamak, that is, one with the SAS‐V divertor and the other with the collector probes, are used to demonstrate the utility of the current multi‐species capability. For the DIII‐D probe case, the capability of GITRm to resolve the spatial distribution of particles in localized regions, such as diagnostic probes, within non‐axisymmetric tokamak geometries is demonstrated. These simulations involve up to 320 million particles and utilize up to 48 GPUs.

Nath, Dhyanjyoti D. [Scientific Computation Resear↗

DOE OSTI2023

Observation and Modeling of the Thermal Runaway of High-Capacity Pouch Cells Due to an Internal Short Induced by an Indenter

Owing to the complexity of coupling mechanical and electrical solvers for finite element analysis (FEA) of mechanical abuse of a battery, the simulation should be performed by incorporating a local short circuit model activated based on the status of battery elements. However, the approach should also consider various other conditions of the battery simulated, such as the initial state of charge (SOC), for precise simulations of the internal short. This study proposes an approach developed with a mechanical model and single-particle battery model, along with a reaction kinetics model for thermal abuse using LS-DYNA. Several key parameters were selected, such as the activation criteria, kinetic abuse and element integration points during the internal short circuit induced by the indenter. The impact of these key parameters in the FEA on thermal runaway response for various initial SOCs from 25 to 100 % were analyzed. The FEA results obtained were compared against experimental results with various parameters such as activation criterion of internal short, kinetic abuse based on accelerating rate calorimetry (ARC) data. Finally, the root causes of the discrepancy between the FEA and experimental results are discussed regarding integration point what solver can make difference during calculation.

ENERGY STORAGE↗

DOE OSTI2024

Uniaxial strain tuning of charge modulation and singularity in a kagome superconductor

Tunable quantum materials hold great potential for applications. Of special interest are materials in which small lattice strain induces giant electronic responses. The kagome compounds AV 3 Sb 5 (A = K, Rb, Cs) provide a testbed for electronic tunable states. In this study, through angle-resolved photo- emission spectroscopy, we provide comprehensive spectroscopic measure- ments of the electronic responses induced by compressive and tensile strains on the charge-density-wave (CDW) and van Hove singularity (VHS) in CsV 3 Sb 5 . We observe a tripling of the CDW gap magnitudes with ~ 1% strain. Simulta- neously, changes of both energy and mass of the VHS are observed. Combined, this reveals an anticorrelation between the unconventional CDW order para- meter and the mass of the VHS, and highlight the role of the latter in the superconducting pairing. The substantial electronic responses uncover a rich strain tunability of the versatile kagome system in studying quantum inter- plays under lattice variations.

electronic properties and materials↗

DOE OSTI2023

Multiple emission components in the Cygnus cocoon detected from Fermi -LAT observations

Star-forming regions may play an important role in the life cycle of Galactic cosmic rays (CRs), notably as home to specific acceleration mechanisms and transport conditions. Gamma-ray observations of Cygnus X have revealed the presence of an excess of hard-spectrum gamma-ray emission, possibly related to a cocoon of freshly accelerated particles. We seek an improved description of the gamma-ray emission from the cocoon using ~13 yr of observations with the Fermi-Large Area Telescope (LAT) and use it to further constrain the processes and objects responsible for the young CR population. We developed an emission model for a large region of interest, including a description of interstellar emission from the background population of CRs and recent models for other gamma-ray sources in the field. Thus, we performed an improved spectro-morphological characterisation of the residual emission including the cocoon. The best-fit model for the cocoon includes two main emission components: an extended component FCES G78.74+1.56, described by a 2D Gaussian of extension r 68 = 4.4° ± 0.1° -0.1° +0.1° and a smooth broken power law spectrum with spectral indices 1.67 ± 0.05 -0.01 +0.02 and 2.12 ± 0.02 -0.01 +0.00 below and above 3.0 ± 0.6 -0.2 +0.0 GeV, respectively; and a central component FCES G80.00+0.50, traced by the distribution of ionised gas within the borders of the photo-dissociation regions and with a power law spectrum of index 2.19 ± 0.03 -0.01 +0.00 that is significantly different from the spectrum of FCES G78.74+1.56. An additional extended emission component FCES G78.83+3.57, located on the edge of the central cavities in Cygnus X and with a spectrum compatible with that of FCES G80.00+0.50, is likely related to the cocoon. For the two brightest components FCES G80.00+0.50 and FCES G78.74+1.56, spectra and radial-azimuthal profiles of the emission can be accounted for in a diffusion-loss framework involving one single population of non-thermal particles with a flat injection spectrum. Particles span the full extent of FCES G78.74+1.56 as a result of diffusion from a central source, and give rise to source FCES G80.00+0.50 by interacting with ionised gas in the innermost region. For this simple diffusion-loss model, viable setups can be very different in terms of energetics, transport conditions, and timescales involved, and both hadronic and leptonic scenarios are possible. The solutions range from long-lasting particle acceleration, possibly in prominent star clusters such as Cyg OB2 and NGC 6910, to a more recent and short-lived release of particles within the last 10–100 kyr, likely from a supernova remnant. The observables extracted from our analysis can be used to perform detailed comparisons with advanced models of particle acceleration and transport in star-forming regions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Statistical Multiobjective Optimization of Thiospinel CoNi 2 S 4 Nanocrystal Synthesis via Design of Experiments

Thiospinels, such as CoNi 2 S 4 , are showing promise for numerous applications, including as catalysts for the hydrogen evolution reaction, hydrodesulfurization, and oxygen evolution and reduction reactions; however, CoNi 2 S 4 has not been synthesized as small, colloidal nanocrystals with high surface-area-to-volume ratios. Traditional optimization methods to control nanocrystal attributes such as size typically rely upon one variable at a time (OVAT) methods that are not only time and labor intensive but also lack the ability to identify higher-order interactions between experimental variables that affect target outcomes. Herein, we demonstrate that a statistical design of experiments (DoE) approach can optimize the synthesis of CoNi 2 S 4 nanocrystals, allowing for control over the responses of nanocrystal size, size distribution, and isolated yield. After implementing a 2 5–2 fractional factorial design, the statistical screening of five different experimental variables identified temperature, Co:Ni precursor ratio, Co:thiol ratio, and their higher-order interactions as the most critical factors in influencing the aforementioned responses. Second-order design with a Doehlert matrix yielded polynomial functions used to predict the reaction parameters needed to individually optimize all three responses. A multiobjective optimization, allowing for the simultaneous optimization of size, size distribution, and isolated yield, predicted the synthetic conditions needed to achieve a minimum nanocrystal size of 6.1 nm, a minimum polydispersity (σ/$\bar{d}$) of 10%, and a maximum isolated yield of 99%, with a desirability of 96%. The resulting model was experimentally verified by performing reactions under the specified conditions. Furthermore, our work illustrates the advantage of multivariate experimental design as a powerful tool for accelerating control and optimization in nanocrystal syntheses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

BETO 2021 Peer Review - ChemCatBio Data Hub 2.6.2.500

The goal of the ChemCatBio DataHub project is to accelerate the catalyst and process development cycle by developing transformational tools for prediction and collaboration in catalyst R&D. The project is currently focused on the development of the Catalyst Property Database (CPD), a free and public resource released in September 2020. The CPD was designed in response to the observation that when data, such as computed reaction energetics, is used in catalyst design, it is almost always generated by the researchers seeking to use it, even if similar data has been published previously. One barrier to data reuse that results in this duplication of effort is the difficult process of finding and applying published data, which can be slow, error-prone, and manual. The CPD seeks to overcome these challenges by creating a centralized, searchable database of quality catalyst property data. At present, the CPD contains computed adsorption energies for intermediates along catalytic pathways. During FY21 and FY22, development of the CPD continues with a focus on external users and meeting their requirements. A batch upload capability, training and curation procedures, user interviews, and a demonstration of the CPD's utility in accelerating catalyst research are planned. Overall, the Data Hub project and CPD aim to reduce the time and cost of catalyst research by harnessing the power of data in catalyst discovery.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2022

Machine Intelligence-Centered System for Automated Characterization of Functional Materials and Interfaces

Classic design of experiment relies on a time-intensive workflow that requires planning, data interpretation, and hypothesis building by experienced researchers. Here, in this paper, we describe an integrated, machine-intelligent experimental system which enables simultaneous dynamic tests of electrical, optical, gravimetric, and viscoelastic properties of materials under a programmable dynamic environment. Specially designed software controls the experiment and performs on-the-fly extensive data analysis and dynamic modeling, real-time iterative feedback for dynamic control of experimental conditions, and rapid visualization of experimental results. The system operates with minimal human intervention and enables time-efficient characterization of complex dynamic multifunctional environmental responses of materials with simultaneous data processing and analytics. The system provides a viable platform for artificial intelligence (AI)-centered material characterization, which, when coupled with an AI-controlled synthesis system, could lead to accelerated discovery of multifunctional materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗