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DOE OSTI2022

A Julia Framework for Graph-Structured Nonlinear Optimization

Graph theory provides a convenient framework for modeling and solving structured optimization problems. Under this framework, the modeler can arrange/assemble the components of an optimization model (variables, constraints, objective functions, and data) within nodes and edges of a graph, and this representation can be used to visualize, manipulate, and solve the problem. In this work, we present a Julia framework for modeling and solving graph-structured nonlinear optimization problems. Our framework integrates the modeling package Plasmo.jl (which facilitates the construction and manipulation of graph models) and the nonlinear optimization solver MadNLP.jl (which provides capabilities for exploiting graph structures to accelerate solution). We illustrate with a simple example how model construction and manipulation can be performed in an intuitive manner using Plasmo.jl and how the model structure can be exploited by MadNLP.jl. We also demonstrate the scalability of the framework by targeting a large-scale, stochastic gas network problem that contains over 1.7 million variables.

Cole, David↗

DOE OSTI2025

Higher Dimensionality in the Mg–Co–B System: Synthesis and Structure of Incommensurate Composite Mg 1+ε Co 4 B 4

Guided by high-temperature in situ X-ray diffraction, the discovery and synthesis of Mg 1+ε Co 4 B 4 (ε ≈ 0.272) using a MgH 2 hydride precursor is reported, along with a detailed crystal structure description and measurement of magnetic properties. The mismatch in lattice periodicities between Mg and Co–B substructures places Mg 1+ε Co 4 B 4 in the family of incommensurate composite crystals and prompted structural refinement in a (3 + 1)-dimensional model. The structure of Mg 1+ε Co 4 B 4 (P4 2 /ncm(00γ)s00s, a = 6.75847(7) Å, c = 3.94007(8) Å, q = (0, 0, 1.2721(3))) was refined from neutron powder diffraction and high-resolution powder X-ray diffraction data and confirmed by scanning transmission electron microscopy and electron diffraction. Mg 1+ε Co 4 B 4 is isostructural to Nd 1+ε Fe 4 B 4 and several related ternary borides with 0.07 ≤ ε ≤ 0.17, with Mg occupying the rare-earth site. Satellite reflections in the electron diffraction patterns hinted at positional modulation of the transition metal–boron substructure by Mg atoms, but this could not be refined from the neutron or X-ray diffraction data. Low-temperature magnetic measurements show no indications of long-range magnetic ordering or superconductivity down to 5 K. DFT calculations confirmed the absence of a magnetically ordered ground state and the stability of a 5:4 supercell (ε = 0.25) relative to the fully commensurate structure. Neutron diffraction and synthesis from elemental Mg demonstrated that Mg 1+ε Co 4 B 4 is not a hydrogen-stabilized phase. Mg 1+ε Co 4 B 4 represents the second compound reported in the Mg–Co–B system and the first superspace symmetry model of a Nd 1+ε Fe 4 B 4 -type incommensurate composite compound refined from powder diffraction data.

chemical structure↗

DOE OSTI2021

Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis

Counterfactual inference is a useful tool for comparing outcomes of interventions on complex systems. It requires us to represent the system in form of a structural causal model, complete with a causal diagram, probabilistic assumptions on exogenous variables, and functional assignments. Specifying such models can be extremely difficult in practice. The process requires substantial domain expertise, and does not scale easily to large systems, multiple systems, or novel system modifications. At the same time, many application domains, such as molecular biology, are rich in structured causal knowledge that is qualitative in nature. This manuscript proposes a general approach for querying a causal knowledge graph with a causal question and converting the qualitative result into a quantitative structural causal model that can learn from data to answer the question. Here, we demonstrate the feasibility, accuracy and versatility of this approach using two case studies in systems biology. The first demonstrates the appropriateness of the underlying assumptions and the accuracy of the results. The second demonstrates the versatility of the approach by querying a knowledge base for the molecular determinants of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced cytokine storm and performing counterfactual inference to predict the causal effect of medical countermeasures for severely ill COVID-19 patients.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Analysis of Two Models for the Angular Structure of the Outflows Producing the Swift/XRT “Larger-angle Emission” of Gamma-Ray Bursts

The quasi-instantaneous emission from a relativistic surface endowed with a Lorentz factor that decreases away from the outflow symmetry axis can naturally explain the three phases observed by Swift X-Ray Telescope (XRT) in gamma-ray bursts (GRBs) and their afterglows (GRB tail, afterglow plateau, and postplateau) based only on the angular change of the relativistic Doppler boost across the outflow surface. We develop further the analytical formalism of the “larger-angle emission” model for the case of “n-exponential” outflows (where the Lorentz factor Γ dependence of the angular location θ is Γ ~ exp{-(θ/θ c ) n }), and compare its ability to account for the X-ray emission of XRT afterglows relative to that of “power-law” outflows (Γ ∼ θ −g ). Power-law outflows yield longer afterglow plateaus, followed by slower postplateau flux decays than n-exponential outflows, features which may be used in identifying which type of angular structure is at work in a given afterglow. Identifying the Γ(θ) angular structure that accommodates XRT light curves is slightly complicated by the fact that the afterglow X-ray light curve is also determined by how two characteristics of the comoving-frame emission spectrum (peak energy $E'_p$ and peak intensity $i'_p$) change with the angular location or, equivalently, with the Lorentz factor. Here, we assume power-law Γ dependences of those spectral characteristics and find that, unlike power-law outflows, n-exponential outflows cannot account for plateaus with a temporal dynamical range larger than 100 (2 dex in logarithmic space). To capture all the information contained in XRT afterglow measurements (0.3–10 keV unabsorbed flux and effective spectral slope), we calculate 0.3 and 10 keV light curves using a broken-power-law emission spectrum of peak energy and low- and high-energy slopes that are derived from the effective slope measured by XRT. This economical peak energy determination is found to be consistent with the results of more expensive spectral fits. The angular distributions of the Lorentz factor, comoving frame peak energy, and peak intensity (Γ(θ), $E'_p$(θ), $i'_p$(θ)) constrain the (yet-to-be determined) convolution of various features of the production of relativistic jets by solar-mass black holes and of their propagation through the progenitor/circumburst medium, while the $E'_p$(Γ) and $i'_p$(Γ) dependences may constrain the GRB dissipation mechanism and the GRB emission process.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Ultrafast x-ray and electron scattering of free molecules: A comparative evaluation

Resolving gas phase molecular motions with simultaneous spatial and temporal resolution is rapidly coming within the reach of x-ray Free Electron Lasers (XFELs) and Mega-electron-Volt (MeV) electron beams. These two methods enable scattering experiments that have yielded fascinating new results, and while both are important methods for determining transient molecular structures in photochemical reactions, it is important to understand their relative merits. In the present study, we evaluate the respective scattering cross sections of the two methods and simulate their ability to determine excited state molecular structures in light of currently existing XFEL and MeV source parameters. Using the example of optically excited N-methyl morpholine and simulating the scattering patterns with shot noise, we find that the currently achievable signals are superior with x-ray scattering for equal samples and on a per-shot basis and that x-ray scattering requires fewer detected signal counts for an equal fidelity structure determination. Importantly, within the independent atom model, excellent structure determinations can be achieved for scattering vectors only to about 5 Å−1, leaving larger scattering vector ranges for investigating vibrational motions and wavepackets. Electron scattering has a comparatively higher sensitivity toward hydrogen atoms, which may point to applications where electron scattering is inherently the preferred choice, provided that excellent signals can be achieved at large scattering angles that are currently difficult to access.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

New heat flux model for non-axisymmetric divertor infrared structures

A convective heat flux model for perturbed plasmas, based on guiding center ion drift in vacuum elds (A. Wingen, et al., Phys. Plasmas 21 (2014) 012509), has been updated. The old model only considered ion heat flux, while here also electron heat flux is included. The updated model predicts divertor heat flux distributions in non-axisymmetric (3D) plasmas with applied Resonant Magnetic Perturbation (RMP) fields, and includes electric scalar potentials. It is found that a radial electric field in the near Scrape-o Layer (SOL) can considerably shift the footprints toroidally, leading to a smearing out eff ect of the incident heat flux, while a simple model for sheath potential has little impact on footprints. Various approaches to model electron heat flux are studied. A convective electron model, based on collisionless free streaming, is found to yield the best agreement with measurements, while a conductive model requires a at temperature gradient inside lobes to yield acceptable peak heat ux values. A heuristic heat flux layer approach, based on a fixed layer width also requires a limited heat flux inside the last closed flux surface (LCFS); by selecting various locations of the LCFS, the results of the conductive or convective model can be recovered respectively. The sum of ion and electron heat fluxes, both obtained by the convective model, is compared to experimental data for multiple time slices in DIII-D. Strike point splitting is observed with peak heat fluxes and layer widths that compare well to infrared camera (IR) measurements.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

CryoPDK Development for 22nm FDSOI CryoCMOS

Cryogenic Process Design Kits (PDKs) are an indispensable tool in the design of complex integrated circuits across a wide spectrum of applications, from noble element detectors to Quantum Information Science, Superconducting Nanowire Single Photon Detectors (SNSPDs), and precision atomic clocks. The development of PDK-compatible SPICE models is a complex endeavor requiring test structures, measurements, model extraction and fitting. We will present the cryogenic modeling and development of a cryo-PDK for a 22nm FDSOI CMOS process for operation at 3.8 Kelvin.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Continued Verification of MOOSE Structural Mechanics Tools for Modeling Core Bowing Phenomena in Fast Reactors

Under the U.S. Department of Energy Office of Nuclear Energy’s Advanced Modeling and Simulation (NEAMS) Program, an integrated multiphysics approach is being developed to model the core bowing phenomena important to liquid metal-cooled fast reactors. Core bowing is an important passive safety mechanism whereby increased power (which leads to temperature and flux gradients) influences the core to bow into less reactive configurations when the restraint system is properly designed. The phenomenon includes a complex interplay of radiation transport, duct temperature calculations involving fluid flow and heat transfer, and thermo-mechanical responses to the induced temperature and flux gradients. Structural material properties are also important to determining inelastic response to longer term flux gradients which cause irradiation creep and swelling. While core bowing provides a strong negative reactivity feedback when the restraint system is designed properly, it also results in additional forces between assemblies which increase the loads required to extricate them during refueling or control rod movement. Therefore, the restraint system must be designed with these tradeoffs in mind. The first stage of the work, which commenced in FY21 and continues through FY22, assesses thermo-mechanical modeling tools for producing core bowing predictions consistent with conventional tools. The Multiphysics Object Oriented Simulation Environment (MOOSE) Tensor Mechanics and Contact Modules are employed. This status report describes work on additional thermo-mechanical benchmark verification problems with increased complexity from the examples demonstrated in FY21. Several benchmark verification examples were selected from the IAEA verification and validation report. These examples involve clusters of ducts representative of a sector of a hexagonal reactor core which bow into each other and cause contact and load pad elevations, as well as single ducts subjected to irradiation fields undergoing swelling and subsequent bowing. The MOOSE-based results were compared to both IAEA benchmark participants’ results, analytic equations as available, and NUBOW-3D, a beam model code developed by Argonne National Laboratory. In every case, the MOOSE results agreed with other simulations results, providing additional verification basis of the tools for this particular physics application.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

LigninGraphs: lignin structure determination with multiscale graph modeling

Lignin is an aromatic biopolymer found in ubiquitous sources of woody biomass. Designing and optimizing lignin valorization processes requires a fundamental understanding of lignin structures. Experimental characterization techniques, such as 2D-heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra, could elucidate the global properties of the polymer molecules. Computer models could extend the resolution of experiments by representing structures at the molecular and atomistic scales. We introduce a graph-based multiscale modeling framework for lignin structure generation and visualization. The framework employs accelerated rejection-free polymerization and hierarchical Metropolis Monte Carlo optimization algorithms. We obtain structure libraries for various lignin feedstocks based on literature and new experimental NMR data for poplar wood, pinewood, and herbaceous lignin. The framework could guide researchers towards feasible lignin structures, efficient space exploration, and future kinetics modeling. Its software implementation in Python, LigninGraphs, is open-source and available on GitHub.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Data for Spatial Analysis of Cell Patterning to Aid Genetic and Phenotypic Understanding of Grass Stomatal Density: A Case Study in Maize

Biological processes involve complex hierarchies where composite traits result from multiple component traits. However, holistically understanding of how sets of component traits interact to underpin genotype-to-phenotype relationships is generally lacking. Stomatal density (SD) is a tractable model system for exploring how high-throughput phenotyping (HTP) data could be exploited by a new spatial analysis approach to better understand a developmentally and functionally important trait. SD is a composite trait, resulting from various components related to cell identity and size, which are themselves governed by a series of spatio-developmental processes. Data from 192 recombinant inbred lines of maize [Zea mays (L.)] were analyzed by a new stomatal patterning phenotype (SPP) to (1) describe the average spatial probability distribution of the nearest neighboring stomata; (2) derive a core set of component traits related to cell size, cell packing, and positional probabilities; (3) build a structural equation model of component traits underlying SD; and (4) identify stomatal patterning quantitative trait loci (QTL). The core set of SPP-derived traits explained 74% of the variation in SD. Analyzing SPP component traits allowed some loci previously identified as generic SD QTL to be recognized as specific to lateral versus longitudinal elements of stomatal patterning. Therefore, this study highlights how novel insights can be gained by decomposing a composite trait (e.g., SD) into a set of component traits that were present in HTP data but not previously exploited.

AI/ML↗

DOE OSTI2025

Atomistic Modeling of the Interphase Structure between Alumina and Al12Fe2Cr Quasicrystal Approximant

Molecular dynamics simulations are performed to study the stability of an fcc metallic interlayer phase between an iron aluminide quasicrystal approximant (QCA) phase (84.2 Al, 5.7 Fe, 5.4 Ni, and 4.7 at.% Cr) and aluminum oxides (α-Al 2 O 3 and γ-Al 2 O 3 ). The presence of the interlayer phase was experimentally observed in some regions of the inner diameter surface of a TPBAR cladding tube. The simulations employed existing many-body (MEAM and EAM) interatomic potentials to describe atomic interactions in the interlayer and QCA phases, and Buckingham+Coulomb pair interactions for the alumina and between the alumina and the QCA (or fcc). Interface systems of QCA/alumina, fec/alumina, and QCA/fcc are modeled and the fracture energy of the interfaces is calculated. Based on the fracture energies, for the γ-Al 2 O 3 , both MEAM and EAM suggest that the fcc interlayer phase would not form. For the α-Al 2 O 3 , the MEAM predicts that the fcc phase would form, however, the EAM predicts that it forms only if the α-Al 2 O 3 is Al-terminated at the interface. For the O-terminated α-Al 2 O 3 , the EAM predicts the fcc phase would not form, consistent with the results for γ-Al 2 O 3 .

36 MATERIALS SCIENCE↗

DOE OSTI2022

New insights on carbon black suspension rheology—Anisotropic thixotropy and antithixotropy

We report a detailed experimental study of peculiar thixotropic dynamics of carbon black (CB, Vulcan XC-72) suspensions in mineral oil, specifically the observation of sequential stress increase then decrease at a fixed shear rate in a step-down test. We verify that such dynamics, though peculiar, come from a true material response rather than experimental artifacts. We also reveal how this long-time stress decay is associated with antithixotropic structural change rather than viscoelastic stress relaxation by using orthogonal superposition (OSP) rheometry to probe viscoelastic moduli during the step-down tests. The orthogonal storage and loss moduli are present, showing this two-timescale recovery then decay response, which demonstrates that this response is antithixotropic, and it involves shear-induced structuring. We further show a mechanical anisotropy in the CB suspension under shear using OSP. Based on the rheological results, a microstructural schematic is proposed, considering qualitatively thixotropic structure build-up, antithixotropic densification, and anisotropic structure evolution. Our observation for these CB suspensions is outside the standard paradigm of thixotropic structure-parameter models, and the elastic response provides us with new insight into the transient dynamics of CB suspensions.

Mechanics↗

DOE OSTI2022

Multi-objective optimization of root phenotypes for nutrient capture using evolutionary algorithms

Root phenotypes are avenues to the development of crop cultivars with improved nutrient capture, which is an important goal for global agriculture. The fitness landscape of root phenotypes is highly complex and multidimensional. It is difficult to predict which combinations of traits (phene states) will create the best performing integrated phenotypes in various environments. Brute force methods to map the fitness landscape by simulating millions of phenotypes in multiple environments are computationally challenging. Evolutionary optimization algorithms may provide more efficient avenues to explore high dimensional domains such as the root phenotypic space. We coupled the three-dimensional functional–structural plant model, SimRoot, to the Borg Multi-Objective Evolutionary Algorithm (MOEA) and the evolutionary search over several generations facilitated the identification of optimal root phenotypes balancing trade-offs across nutrient uptake, biomass accumulation, and root carbon costs in environments varying in nutrient availability. Our results show that several combinations of root phenes generate optimal integrated phenotypes where performance in one objective comes at the cost of reduced performance in one or more of the remaining objectives, and such combinations differed for mobile and non-mobile nutrients and for maize (a monocot) and bean (a dicot). Functional–structural plant models can be used with multi-objective optimization to identify optimal root phenotypes under various environments, including future climate scenarios, which will be useful in developing the more resilient, efficient crops urgently needed in global agriculture.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Multipole-based Cable Braid Magnetic Penetration Model for Conducting Wires

In this report, we investigate the effects of conductor losses in a multipole-based cable braid magnetic penetration model. Our multipole model uses a mesh of the actual cable geometry, which enables us to model more complicated structures. After summarizing the first principles model formulation, we consider a one-dimensional array of wires, for which an analytical solution is known in the lossless case. We extend this solution to the lossy case by using a complex-valued radius. We also model this structure analytically using a conformal-mapping solution. We then compare both the self-impedance and the transfer impedance results from our first principles cable braid electromagnetic penetration model to those obtained using the analytical solutions. An analysis for various frequencies (and skin depths) usually encountered in cable modeling is reported. These results are found in good agreement up to a radius to half spacing ratio of about 0.7, demonstrating a robustness needed for many commercial and non-commercial cables.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Voltage Calculations in Secondary Distribution Networks via Physics-Inspired Neural Network Using Smart Meter Data

The increasing penetration of distributed energy resources (DERs) leads to voltage issues across distribution networks, necessitating voltage calculations by utilities. Electric model-free voltage calculation offers an enticing solution. However, most researches mainly focus on primary distribution networks ignoring secondary distribution networks and commonly overlook extreme voltage case calculations, which require the model’s extrapolation abilities. Here, in addressing the gaps, this paper presents a customized physics-inspired neural network (PINN) model, the structure of which is inspired by the derived coupled power flow model of primary-secondary distribution networks. To ensure precision and rapid convergence, a crafted training framework for the PINN model is proposed. The PINN’s “structure-mimetic” design enables superior extrapolation for unseen scenarios and enhances physical information awareness. We demonstrate this through two applications: hosting capacity analysis and customer-transformer connectivity. The effectiveness and advantages of the proposed PINN model are validated on two public testing systems and one utility distribution feeder model.

Distribution network↗

DOE OSTI2024

Lattice Design and Advanced Modeling to Guide the Design of High-Performance Lightweight Structural Materials

Lightweight structural materials are required to increase the mobility of fission batteries. The materials must feature a robust combination of mechanical properties to demonstrate structural resilience. The primary objective of this project is to produce lightweight structural materials whose strength-to-weight ratios exceed those of the current widely used structural materials such as 316L stainless steels (316L SS). To achieve this, advanced modeling and simulation tools were employed to design lattice structures with different lattice parameters and different lattice types. A process was successfully developed for transforming lattice-structures models into Multiphysics Object Oriented Simulation Environment (MOOSE) inputs. Finite element modeling (FEM) was used to simulate the uniaxial tensile testing of the lattice-structured parts to investigate the stress distribution at a given displacement. The preliminary results showed that the lattice-structured sample displayed a lower Young’s modulus in comparison with the solid material and that the unit cell size of the lattice had a minimal effect. The novelty here is to apply up-front modeling to determine the best structure for the application before actually producing the sample. The approach of using modeling as a guiding tool for preliminary material design can significantly save time and cost for material development.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Beyond real: alternative unitary cluster Jastrow models for molecular electronic structure calculations on near-term quantum computers

Near-term quantum devices require wavefunction ansätze that are expressive while also of shallow circuit depth in order to both accurately and efficiently simulate molecular electronic structure. While the unitary coupled cluster ansatz (e.g., UCCSD) has become a standard, the high gate count associated with the implementation of this limits its feasibility on noisy intermediate-scale quantum (NISQ) hardware. k -Fold unitary cluster Jastrow (uCJ) ansätze mitigate this challenge by providing O( kN 2 ) circuit scaling and favorable linear depth circuit implementation. Previous work has focused on the real orbitalrotation (Re-uCJ) variant of uCJ, which allows an exact (Trotter-free) implementation. Here we extend and generalize the k -fold uCJ framework by introducing two new variants, Im-uCJ and g-uCJ, which incorporate imaginary and fully complex orbital rotation operators, respectively. Similar to Re-uCJ, both of the new variants achieve quadratic gate-count scaling. Our results focus on the simplest k = 1 model, and show that the uCJ models frequently maintain energy errors within chemical accuracy (∼1 kcal mol −1 ). Both g-uCJ and Im-uCJ are more expressive in terms of capturing electron correlation and are also more accurate than the earlier Re-uCJ ansatz. We further show that Im-uCJ and g-uCJ circuits can also be implemented exactly, without any Trotter decomposition. Numerical tests using k = 1 on H 2 , H 3 + , Be 2 , C 2 H 4 , C 2 H 6 and C 6 H 6 in various basis sets confirm the practical feasibility of these shallow Jastrow-based ansätze for applications on near-term quantum hardware.

Tkachenko, Nikolay V. [University of California, B↗