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DOE OSTI2022

Fed-DeepONet: Stochastic Gradient-Based Federated Training of Deep Operator Networks

The Deep Operator Network (DeepONet) framework is a different class of neural network architecture that one trains to learn nonlinear operators, i.e., mappings between infinite-dimensional spaces. Traditionally, DeepONets are trained using a centralized strategy that requires transferring the training data to a centralized location. Such a strategy, however, limits our ability to secure data privacy or use high-performance distributed/parallel computing platforms. To alleviate such limitations, in this paper, we study the federated training of DeepONets for the first time. That is, we develop a framework, which we refer to as Fed-DeepONet, that allows multiple clients to train DeepONets collaboratively under the coordination of a centralized server. To achieve Fed-DeepONets, we propose an efficient stochastic gradient-based algorithm that enables the distributed optimization of the DeepONet parameters by averaging first-order estimates of the DeepONet loss gradient. Then, to accelerate the training convergence of Fed-DeepONets, we propose a moment-enhanced (i.e., adaptive) stochastic gradient-based strategy. Finally, we verify the performance of Fed-DeepONet by learning, for different configurations of the number of clients and fractions of available clients, (i) the solution operator of a gravity pendulum and (ii) the dynamic response of a parametric library of pendulums.

Moya, Christian↗

DOE OSTI2024

Role of Nuclear Science User Facilities (NSUF) in Nuclear Energy Materials Research

The Nuclear Science User Facilities (NSUF) is one of a diverse number of U.S. Department of Energy (DOE) user facilities established to provide researchers with the most advanced tools of modern science. The NSUF is unique and represents a consortium of capabilities distributed across the U.S. at twenty-one institutions. The NSUF is centered at and managed from the Idaho National Laboratory (INL), where it was originally founded, but it coordinates activities at twenty “partner” institutions that include universities, the Center for Advanced Energy Studies (CAES), national laboratories, and a nuclear industry vendor. These institutions have capabilities that include neutron, ion, and gamma irradiation, hot cells, advanced materials characterization equipment, and high-performance computing resources. Many of these capabilities were beyond reach for most researchers before NSUF. The NSUF provides researchers to access these capabilities at no cost to nuclear energy researchers to produce the highest quality research results to increase understanding of advanced nuclear energy technologies important to DOE-NE and support national priorities by adapting to the needs of DOE-NE programs, industry, and new innovative concepts for sustainable nuclear future.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

WLCG Transition from X.509 to Tokens. Status, Plans, and Timeline

Since 2017, the Worldwide LHC Computing Grid (WLCG) has been working towards enabling token-based authentication and authorization throughout its entire middleware stack. Following the initial publication of the WLCG Token Schema v1.0 in 2019, OAuth2.0 token workflows have been integrated across grid middleware. There are many complex challenges to be addressed before the WLCG can be end-to-end token-based, including not just technical hurdles but also interoperability with the wider authentication and authorization landscape. This paper presents the status of the WLCG coordination and deployment work, and how it relates to software providers and partner communities. The authors also detail how the WLCG token transition timeline has progressed, and how it has changed since its publication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three-dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe, PDBe.org) as an open-source, web-based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. Across RCSB.org, the RCSB PDB research-focused web portal, Mol* has been implemented to support single-mouse-click atomic-level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small-molecule ligands, ions, water molecules, or other macromolecules. RCSB.org Mol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within various RCSB.org tools—allowing users to view polymer sequence and structure-based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available at RCSB.org, Standalone Mol* is freely available for visualizing any atomic-level or multi-scale biostructure at rcsb.org/3d-view.

3D biostructure↗

DOE OSTI2024

Gas-Phase Coordination of Phosphine-Chalcogenides to the Uranyl Cation

It is generally believed that actinides exhibit an increased covalency in bonding to soft-donor atoms such as nitrogen and sulfur compared to the lanthanides. The explanation is that the greater spatial extent of the 5f orbitals in the actinides compared to the 4f orbitals in the lanthanides accounts for this behavior. However, recent computational studies on lanthanide and actinide complexes with sulfur-donor atom ligands suggest that while calculated metrics of bond covalency could increase for actinide complexes with sulfur ligands, the overall stability of the complexes decreased. While many studies of actinide covalency were conducted in the condensed phases, this work investigates the intrinsic interaction between actinides and soft-donor ligands compared with oxygen in the gas phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Gas-Phase Coordination of Phosphine-Chalcogenides to the Uranyl Cation

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Efficient and generalizable nested Fourier-DeepONet for three-dimensional geological carbon sequestration

Geological carbon sequestration (GCS) involves injecting CO2 into subsurface geological formationsfor permanent storage. Numerical simulations could guide decisions in GCS projects by predictingCO 2 migration pathways and the pressure distribution in storage formation. However, these simula-tions are often computationally expensive due to highly coupled physics and large spatial-temporalsimulation domains. Surrogate modelling with data-driven machine learning has become a promis-ing alternative to accelerate physics-based simulations. Among these, the Fourier neural operator(FNO) has been applied to three-dimensional synthetic subsurface models. Despite its good accuracyin simulating CO 2 plume migration, it requires large computational resources in training and alsolacks generalizability. Here, to further improve performance, we have developed a nested Fourier-DeepONet by combining the expressiveness of the FNO with the modularity of a deep operatornetwork (DeepONet). This new framework is twice as efficient as a nested FNO for training and has atleast 80% lower GPU memory requirement due to its flexibility to treat temporal coordinates sepa-rately. These performance improvements are achieved without compromising prediction accuracy.In addition, the generalization and extrapolation ability of nested Fourier-DeepONet beyond thetraining range has been thoroughly evaluated. Nested Fourier-DeepONet outperformed the nestedFNO for extrapolation in time with more than 50% reduced error. It also exhibited good extrapolationaccuracy beyond the training range in terms of reservoir properties, number of wells, and injectionrate.

Lee, Jonathan E. [Department of Chemical and Envir↗

DOE OSTI2025

Structural biology at the National Synchrotron Light Source II

The structural biology program at the National Synchrotron Light Source II presents a coordinated set of instruments, software and research opportunities for the interested user. We describe in some detail the research capabilities enabled by the Center for BioMolecular Structure. The evolution of the resources is described in detail, considering three major themes: automation, micro-focusing and computation prediction.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Alkali Metal Ions Dictate the Structure and Reactivity of an Iron(II) Imido Complex

The presence of redox innocent metal ions has been proposed to modulate the reactivity of metal ligand multiple bonds; however, insight from structure/function relationships is limited. Here, alkali metal reduction of the Fe(III) imido complex [Ph 2 B( t BuIm) 2 Fe=NDipp] (1) provides the series of structurally characterized Fe(II) imido complexes [Ph 2 B( t BuIm) 2 Fe=NDippLi(THF) 2 ] (2), [Ph 2 B( t BuIm) 2 Fe=NDippNa(THF) 3 ] (3), and [Ph 2 B( t BuIm) 2 Fe=NDippK] 2 (4), in which the alkali metal cations coordinate the imido ligand. Structural investigations demonstrate that the alkali metal ions modestly lengthen the Fe=N bond distance from that in the charge separated complex [Ph 2 B( t BuIm) 2 Fe=NDipp][K(18-C-6)THF 2 ] (5), with the longest bond observed for the smallest alkali metal ion. In contrast to 5, the imido ligands in 2–4 can be protonated and alkylated to afford Fe(II) amido complexes. Combined experimental and computational studies reveal that the alkali metal polarizes the Fe=N bond, and the basicity of imido ligand increases according to 5 < 4 ≈ 3 < 2. The basicity of the imido ligands influences the relative rates of reaction with 1,4-cyclohexadiene, specifically by gating access to complex 5, which is the species that is active for HAT. All complexes 2–4 react with benzophenone form metastable Fe(II) intermediates that subsequently eliminate the metathesis product Ph 2 C=NDipp, with relative rates dependent on the alkali metal ion. By contrast, the same reaction with 5 does not lead to the formation of Ph 2 C=NDipp. Furthermore, these results demonstrate that the coordination of alkali metal ions dictate both the structure and reactivity of the imido ligand and moreover can direct the reactivity of reaction intermediates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Ultra-large-scale ab initio quantum chemical computation of bio-molecular systems: The case of spike protein of SARS-CoV-2 virus

The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intramolecular bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic bonding, partial charge distribution and the role played by hydrogen bond network are discussed. In the interaction among structural domains, we present new insights for crucial hinge-like movement and fusion process. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Framework for Large-scale Implementation of Wholesale-Retail Transactive Control Mechanism

Transactive energy is a control technique that uses market mechanisms to achieve desired control objectives. Several simulation studies and field demonstrations were carried out in recent years, but all focused on small scale systems and purpose-built simplified models which are not always capable of pointing out all the advantages and shortcomings of transac- tive energy methods. This work describes a co-simulation framework built on a hierarchical control architecture that allows for conducting studies of the impacts of a very large-scale deployment of transactive energy. The hierarchical transactive control architecture adopted in this work helps with alleviating computation and communication burden to facilitate a more effective large scale real-time market operation among device level resources and the system level operators. The co-simulation framework is evaluated an integrated power sys- tem model of unprecedented scale composed of the Western Electricity Coordination Council (WECC) transmission system with tens of thousands of distribution systems deployed with flexible device-level distributed energy resources (DERs) using off-the-shelf simulators.

Transactive energy, market-based controls, DER int↗

DOE OSTI2023

Compression of tokamak boundary plasma simulation data using a maximum volume algorithm for matrix skeleton decomposition

This report demonstrates satisfactory data compression of SOLPS-ITER simulation output ranging from 2D fields, 1D profiles, and 0D scalar variables with a novel matrix decomposition approach. The singular value decomposition (SVD) scales poorly for large matrix sizes and is unsuited to the application on high dimensional data common to fusion plasma physics simulation. In this work, we employ the columns-submatrix-rows (CUR) matrix factorization technique in order to compute a low-rank approximation up to two orders of magnitude faster than the SVD, but within a nominal L2-norm relative error of ε = 10 –2 . In addition, the CUR approach maintains the original format of the data, in its extracted columns and rows, allowing for interpretable data storage at the original resolution of the simulation. We utilize an iterative algorithm to compute the CUR decomposition of simulation output by maximizing the volume, or linearly independent information content, of a low-rank submatrix contained within the data. Experiments over $\textit{n} × \textit{n}$ randomized test matrices with embedded rank-deficient features show that this maximum volume implementation of CUR matrix approximation has reduced asymptotic computational complexity on the order of n compared to the SVD, which scales approximately as $n^3$. These results show that the CUR technique can be used to effectively select time step snapshots (columns) of over 140 SOLPS-ITER output variables and the associated discretized coordinate timeseries (rows) allowing for reconstruction of the complete simulation dynamics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Laser-Induced Thermal Decomposition of Uranium Coordination Compounds with Non-oxidic Ligands to Produce Nitride and Carbide Materials

The production of ceramics from uranium coordination compounds can be achieved through thermal processing if an excess amount of the desired atoms (i.e., C or N), or reactive gaseous products (e.g., methane or nitrogen oxide) is made available to the reactive uranium metal core via decomposition/fragmentation of the surrounding ligand groups. Here, computational thermodynamic approaches were utilized to identify the temperatures necessary to produce uranium metal from some starting compounds—UI 4 (TMEDA) 2 , UCl 4 (TMEDA) 2 , UCl 3 (pyridine) x , and UI 3 (pyridine) 4 . Experimentally, precursors were irradiated by a laser under various gaseous environments (argon, nitrogen, and methane) creating extreme reaction conditions (i.e., fast heating, high temperature profile >2000 °C, and rapid cooling). Despite the fast dynamics associated with laser irradiation, the central uranium atom reacted with the thermal decomposition products of the ligands yielding uranium ceramics. Residual gas analysis identified vaporized products from the laser irradiation, and the final ceramic products were characterized by powder X-ray diffraction. The composition of the uranium precursor as well as the gaseous environment had a direct impact on the production of the final phases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Co(salen)-Catalyzed Oxidation of Lignin Models to Form Benzoquinones and Benzaldehydes: A Computational and Experimental Study

Lignin is a highly abundant polyphenolic polymer that imparts mechanical strength to plant biomass. Transition-metal complexes can catalyze lignin oxidation to produce value-added products, but low catalytic efficiency has hampered their use in industry. Identifying the chemical and structural factors that govern catalytic activity is a prerequisite to rational design of catalysts with improved activity. In this study, we combine computational and experimental approaches to investigate the mechanism of Co(salen)-catalyzed oxidation of the monomeric lignin models syringyl (S), vanillyl (G), and 4-hydroxybenzyl alcohol (H) to produce benzoquinone and benzaldehyde products. Experimentally, S oxidation to form dimethoxybenzoquinone proceeded efficiently with a Co(salen) catalyst coordinated by a pyridine ligand, but G and H did not undergo oxidation. Density functional theory calculations reveal that catalyst regeneration is energetically unfavorable in the presence of H, which prevents oxidation. In contrast, S readily facilitates catalyst regeneration. Formation of methoxybenzoquinone from G was achieved experimentally by adding bulky, noncoordinating bases. These findings provide a fundamental baseline for enhancing the activity of Co-Schiff base catalysts toward lignin-like molecules by adding sterically hindered nitrogenous bases or potentially by including a cocatalyst that promotes catalyst regeneration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Olefin Coupling Catalyzed by (Pybox)Os Complexes via Osmacyclopentane Intermediates: Comparison with Isoelectronic (Phebox)Ir

(Pybox)Os is found to catalyze alkene hydrovinylation, effecting the dimerization of ethylene, tail-to-tail coupling of propene and 1-butene, and cross-coupling of ethylene with higher α-olefins. This reactivity contrasts with the previously reported dehydrogenative coupling of ethylene to give butadiene catalyzed by the isoelectronic fragment (Phebox)Ir. The reaction mechanism was investigated through computational and experimental means. Both the Os- and Ir-catalyzed reactions proceed through a [2 + 2 + 1] cyclization of the corresponding bis-olefin complex to yield an experimentally observed metallacyclopentane intermediate. In both cases, the metallacyclopentane undergoes β- H elimination, via a dechelated κ 2 -pincer-ligated intermediate, to yield a σ−π-but-3-enyl hydride complex or derivative. Both the greater reactivity and the distinct chemoselectivity of the Os system relative to the Ir system are attributable to C−H reductive elimination by the σ−π-but-3-enyl hydride having a barrier for Os much lower than that for Ir. This lower barrier to C−H elimination for Os is unexpected given that the thermodynamic driving force for elimination is much less for Os than for Ir. Computational studies of model complexes were conducted, comparing (Pybox)Os(L)(CH 3 )(H) with the isoelectronic (Phebox)Ir(L)(CH 3 )(H). The results indicate that the more facile kinetics with Os relative to Ir may be general for C−H elimination from six-coordinate d 6 complexes of the two metals, as well as for the microscopic reverse, i.e., C−H addition to the corresponding four-coordinate d 8 species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

The reaction mechanism of the Ideonella sakaiensis PETase enzyme

Abstract Polyethylene terephthalate (PET), the most abundantly produced polyester plastic, can be depolymerized by the Ideonella sakaiensis PETase enzyme. Based on multiple PETase crystal structures, the reaction has been proposed to proceed via a two-step serine hydrolase mechanism mediated by a serine-histidine-aspartate catalytic triad. To elucidate the multi-step PETase catalytic mechanism, we use transition path sampling and likelihood maximization to identify optimal reaction coordinates for the PETase enzyme. We predict that deacylation is likely rate-limiting, and the reaction coordinates for both steps include elements describing nucleophilic attack, ester bond cleavage, and the “moving-histidine” mechanism. We find that the flexibility of Trp185 promotes the reaction, providing an explanation for decreased activity observed in mutations that restrict Trp185 motion. Overall, this study uses unbiased computational approaches to reveal the detailed reaction mechanism necessary for further engineering of an important class of enzymes for plastics bioconversion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Edge ICRF simulations in 3D geometry: From MHD equilibrium to coupling determination

We present in this work a consistent numerical scheme that allows the computation of 3D magnetic fields a nd 3D density profiles and their usage in ion cyclotron range of frequencies (ICRF) coupling simulations. We first utilize the PARVMEC code to compute the 3D free-boundary plasma equilibrium in the ideal magnetohydrodynamic (MHD) approximation. Since the PARVMEC solution is only defined within the last closed flux surface (LCFS), the magnetic field domain is extended to the scrape-off layer (SOL) via the BMW code, which computes a divergence-free magnetic field solution arising from the external conductors’ vacuum field a nd t he PARVMEC flux surface currents. This magnetic reconstruction is then used in the EMC3-EIRENE transport code in order to compute 3D density profiles. In the last step, the RAPLICASOL code is utilized to compute the ICRF antenna S-matrices resulting from the 3D density profiles. We exemplify this scheme for the ASDEX Upgrade tokamak. A new implementation of a curved model for the ASDEX Upgrade ICRF 2-strap antenna in RAPLICASOL allows simulations in realistic geometry, without any coordinate transformations.

Lopez, Graham↗

DOE OSTI2021

Advance Reactor Operational Technology Architecture Categorization

Seven generation III+ and generation IV nuclear reactor types, based on twelve reactor concepts surveyed, are examined using functional decomposition to extract relevant operational technology (OT) architecture information. This information is compared to existing nuclear power plants (NPPs) OT architectures to highlight novel and emergent cyber risks associated with next generation NPPs. These insights can help inform operational technology architecture requirements that will be unique to a given reactor type. Next generation NPPs have streamlined OT architectures relative to the current generation II commercial NPP fleet. Overall, without compensatory measures that provide sufficient and efficient cybersecurity controls, next generation NPPs will have increased cyber risk. Verification and validation of cyber-physical testbeds and cyber risk assessment methodologies may be an important next step to reduce cyber risk in the OT architecture design and testing phase. Coordination with safety requirements can result in OT architecture design being an iterative process.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗