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DOE OSTI2025

Model Calibration with Markov Chain Monte Carlo Tutorial

The purpose of this tutorial is to demonstrate how to use Markov chain Monte Carlo (MCMC) to calibrate a model. By calibration, we mean the selection of model parameters (and, when relevant, structures). A common goal in model development and diagnostics is calibration, or the identification of model structures and parameters which are consistent with data. While models can be calibrated through hand-tuning parameters or minimizing simple error metrics such as root-mean-square-error (RMSE), these approaches can underrepresent the probabilistic nature of the data-generating process, as well as the potential for multiple model configurations to be consistent with the data. Probabilistic uncertainty quantification, which is the topic of this notebook, can address these concerns. This tutorial is presented as an appendix to the e-book: Addressing Uncertainty in MultiSector Dynamics Research.

Markov chain Monte Carlo↗

DOE OSTI2020

Model-Independent Study of Structure in B + → D + D - K + Decays

The only anticipated resonant contributions to B + → D + D - K + decays are charmonium states in the D + D - channel. A model-independent analysis, using LHCb proton-proton collision data taken at center of-mass energies of $\sqrt{s}$ = 7, 8, and 13 TeV, corresponding to a total integrated luminosity of 9 fb -1 , is carried out to test this hypothesis. The description of the data assuming that resonances only manifest in decays to the D + D - pair is shown to be incomplete. This constitutes evidence for a new contribution to the decay, potentially one or more new charm-strange resonances in the D + K - channel with masses around 2.9 GeV/c 2

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

An FEM-Based Peridynamic Model for Failure Analysis of Unidirectional Fiber-Reinforced Laminates

To predict the mixed damage modes of unidirectional fiber-reinforced polymer (FRP) laminates under dynamic loading, an FEM-based peridynamic model is introduced in this paper. Based on its geometric structure and material composition, a long fiber lamina is considered a transversely isotropic medium as a result of homogenization at the meso-scale. The laminated structure is modeled by stacking surface mesh layers with arbitrary fiber angles along the thickness direction. The peridynamic bonds between Gauss points connect the separated elements. These bonds are classified as inner-layer bonds and inter-layer bonds. To represent the anisotropy of a laminate, the micro-elastic modulus of the inner-layer and inter-layer bonds is calculated from the anisotropic engineering material constants separately. To capture complex failure behaviors of laminate structures, an empirical damage model is proposed for the tension/ compression breakage of peridynamic bonds. This damage model can control the in-plane and delamination failure process. Finally, benchmark tests are conducted to validate the elastic response of laminates under dynamic loading. In terms of damage analysis, the proposed model can capture the complex damage modes and resistive force of laminate structures.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Small-Signal Angle Stability-Oriented False Data Injection Cyber-Attacks on Power Systems

The small-signal angle stability (SSAS) of a power system is determined by the property of operation points. The widely applied false data injection (FDI) cyber-attack, however, is able to stealthily mislead the optimal power flow (OPF) and thus compromise operation points, leading to damages to the SSAS margin. Here, to provide insights for cyber defenders, this paper proposes and investigates a stealthy SSAS-oriented FDI cyber-attack focusing on two attacking purposes, i.e., the SSAS margin and operation cost, with higher priority on the former one. First, this paper establishes a novel bi-level model with an implicit SSAS constraint based on a structure preserving model to compromise operation points. Then, for the SSAS interarea mode in a typical two-area system, this paper formulates closed-form expressions of how the SSAS margin and operation cost behave with respect to stealthy injections. By comparison, for the SSAS local mode in general power systems, this paper proposes a moving target cyber-attack-based hierarchical solution algorithm. Simulation results on a two-area system, a Kundur 11 bus system, and a modified IEEE 14 bus system demonstrate the significant damaging effects of the proposed SSAS-oriented FDI cyber-attack and the conflict between the two attacking purposes.

Benders decomposition↗

DOE OSTI2025

Structure–property relations of binary ferrite melts

Molten ferrite systems are used in the smelting and refining processes in steelmaking, to reduce the loss of metals in slags and to accelerate reaction rates. Here, high-energy x-ray diffraction experiments have been performed on aerodynamically levitated molten spheres of 43BaO–57FeO X and 43SrO–57FeO X at 1873 K using laser beam heating. The composition was varied within the range of x = 1–1.5 by changing the oxygen partial pressure of the levitation gas. The corresponding x-ray pair distribution functions have been interpreted using empirical potential structure refinement (EPSR) modeling. In oxygen-rich melts (x = 1.5), our EPSR models indicate very similar structures for the different alkaline-earth liquids, with both the Ba–O and Sr–O coordination numbers to be ∼8.4 and the total Fe–O coordination numbers ∼5.7. However, our models show that in reducing environments, the Fe 3+ and Fe 2+ ions exhibit very different behaviors in the Ba- and Sr-ferrite liquids. In the Ba-ferrite melt, the Fe 3+ –O coordination number decreases from 5.7 (at x = 1.5) to 5.2 (at x = 1.07), whereas Fe 2+ –O remains constant at ∼5.0 across the same compositional range. In the Sr melts, both the Fe 2+ –O and Fe 3+ –O coordination numbers rise from ∼5.7 (at x = 1.5) to 6.3 (at x = 1.07). All models show the structures to be heterogeneous with intertwined nanometer sized clusters or channels of Ba/Sr–O and Fe–O polyhedra that grow as oxygen content is reduced. Changes in the viscosity and electrical properties are interpreted in terms of the number of bridging and non-bridging oxygens associated with FeO 4 tetrahedra and concentration of charge carriers, respectively.

Benmore, Chris J. [Argonne National Laboratory (AN↗

DOE OSTI2023

Modeling the interfacial failure and resulting mechanical properties of z-pinned additively manufactured composites

The mechanical properties of Fused Filament Fabrication (FFF) parts are limited in the build direction, albeit advantages such as design flexibility and in-house customization. Here, in this paper, a novel z-pinning approach that enhances mechanical properties in the build direction by depositing material across multiple layers within the part was investigated through numerical simulations and validated experimentally. A finite element model for z-pinned composite structures was developed by assigning fiber-orientation dependent material properties obtained using a micromechanics approach to beads and pins. The bead-to-bead and pin-to-pin adhesions within the z-pinned structures were modeled using a cohesive traction separation law. The properties of cohesive elements for carbon fiber-reinforced polylactic acid (CF-PLA) z-pinned composites were calibrated using tensile experiments. The elastic modulus and tensile strength of CF-PLA z-pinned composites in the build direction were predicted with the developed numerical model. The numerical investigation on various geometrical parameters revealed that the largest pin volume increases the stiffness and tensile strength by 40% and thus, has the greatest influence on the mechanical properties of the z-pinned composites. The effect of z-pin geometrical parameters on the mechanical properties was summarized to aid in the design of z-pinned additively manufactured composite structures.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure

Coarse-grained modeling can be used to explore general theories that are independent of specific chemical detail. In this paper, we present cg_openmm, a Python-based simulation framework for modeling coarse-grained hetero-oligomers and screening them for structural and thermodynamic characteristics of cooperative secondary structures. cg_openmm facilitates the building of coarse-grained topology and random starting configurations, setup of GPU-accelerated replica exchange molecular dynamics simulations with the OpenMM software package, and features a suite of postprocessing thermodynamic and structural analysis tools. In particular, native contact analysis, heat capacity calculations, and free energy of folding calculations are used to identify and characterize cooperative folding transitions and stable secondary structures. In this work, we demonstrate the capabilities of cg_openmm on a simple 1–1 Lennard-Jones coarse-grained model, in which each residue contains 1 backbone and 1 side-chain bead. By scanning both nonbonded and bonded force-field parameter spaces at the coarse-grained level, we identify and characterize sets of parameters which result in the formation of stable helices through cooperative folding transitions. Furthermore, we show that the geometries and stabilities of these helices can be tuned by manipulating the force-field parameters.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution. (Model and code can be found at imageomics.github.io/phylo-diffusion)

Khurana, Mridul↗

DOE OSTI2023

Lifetime and Degradation Study of Poly(Methyl Methacrylate) via a Data-Driven Study Protocol Approach

We report to optimize and extend the service life of polymeric materials in outdoor environments, a domain knowledge-based and data-driven approach was utilized to quantitatively investigate the temporal evolution of degradation modes, mechanisms, and rates under various stepwise accelerated exposure conditions. Six formulations of poly(methyl methacrylate) (PMMA) with different combinations of stabilizing additives, including one unstabilized formulation, were exposed in three accelerated weathering conditions. Degradation was dependent on wavelength as samples in UV light at 340 nm (UVA) exposure showed the most yellowing. The unstabilized PMMA formulation showed much higher yellowness index values (59.5) than stabilized PMMA formulations (2–12). Urbach edge analysis shows a shift toward longer wavelength from 285 to 500 nm with increasing exposure time and an increased absorbance around 400 nm of visible region as the unstabilized samples increase in yellowing. The degradation mechanisms of PMMA were tracked using induced absorbance to dose at specific wavelengths that correspond to known degradation mechanisms. The degradation pathway of PMMA was modeled in a framework using network structural equation modeling (netSEM). netSEM showed changes in degradation pathway as PMMA transition stages of degradation.

36 MATERIALS SCIENCE↗

DOE OSTI2021

The local structure of 0.5Ba(Zr 0.2 Ti 0.8 )O 3 -0.5(Ba 0.7 Ca 0.3 )TiO 3 from neutron total scattering measurements and multi-edge X-ray absorption analysis

Neutron total scattering measurements and multi-edge X-ray absorption analysis were performed on a 0.5Ba(Zr 0.2 Ti 0.8 )O 3 -0.5(Ba 0.7 Ca 0.3 )TiO 3 powder sample. The TiIII-II edges showed that titanium is distorted in the rhombohedral [111] direction (in a BaTiO 3 -like chemical and bonding environment). Extended X-ray fine structure analysis (EXAFS) was performed on the zirconium K-edge and it was found that zirconium resides in the center of the ZrO 6 octahedra in cubic symmetry. Furthermore, the local structure was initially modelled with the orthorhombic Amm2 space group with unsatisfactory results. To better model the local structure, the results from the EXAFS analysis were incorporated into the small-box pair distribution function (PDF) refinements and the best fit of the observed data was a combination of barium calcium titanate (BCT) and barium calcium zirconate (BCZ) phases.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Dense Ru single-atoms integrated with sulfoacids for cellulose valorization to isosorbide

Metal-acid bifunctional catalysts are the unity of two opposites (metal-acid repelling) for cellulosic biomass valorization to isosorbide. It is challenging to improve the selectivity of metal hydrogenation catalysts and their synergism with acids for catalytic hydrolysis and dehydration to achieve substantial isosorbide. Herein, dense Ru single-atoms (10.1 wt% of Ru SAs) are anchored on sulfoacid-functionalized hollow mesoporous carbon shells, designed by assembling silica and 8-hydroxyquinoline-modified chitosan (HQ-CTS) through in situ Stöber templating strategy before pyrolysis and acid treatment. Based on X-ray absorption fine structure and computational modeling results, the structure of Ru SAs is determined as RuN 4 , which is more selective for a transitional glucose hydrogenation to sorbitol than Ru001 of Ru clusters. A lower-energy barrier of 1.21 (0.72) eV is delivered over RuN 4 (Ru001) for glucose hydrogenation (isomerization). These Ru SAs are integrated with sulfoacids (SO 3 H) but resistent against acids, rendering enhanced isosorbide yield in water as compared to Ru clusters, via a one-pot cascade reaction under harsh conditions (220 °C, 6 MPa H 2 ). The elaborately fabricated dense Ru SAs and sulfoacids, achieved by varying the addition time of HQ-CTS during the in situ Stöber templating process, improve the synergism of glucose hydrogenation with cellulose hydrolysis and sorbitol dehydration. In conclusion, this study provides a new idea for rational design of high-performance metal-acid bifunctional catalysts toward one-pot conversion of cellulose to isosorbide.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Wave energy resources assessment for the multi-modal sea state of Hawaii

This paper describes development and validation of a 32-year wave hindcast for Hawaii as part of the wave energy resources assessment for the Exclusive Economic Zones of the US and affiliated territories. The nested model system comprises structured WAVEWATCH III models for the entire globe and the Central North Pacific as well as an unstructured SWAN model around the Hawaiian Islands with wind forcing from the Global Forecast System Reanalysis and its regional downscaling. The development effort follows the standards introduced by the International Electrotechnical Commission (IEC). The hindcast dataset was firstly validated with buoy measurements in terms of the six IEC wave energy resources parameters including the omnidirectional wave power ????, significant wave height ????????0, energy period ????????, spectral width ????0, direction of maximum directionally resolved wave power ?????????? ????????, and directionality coefficient ????. The comparison shows good overall agreement but with greater uncertainties for the spectral parameters ????0, ???????????????????? , and ???? formulated for narrow band spectra. The multimodal sea state in Hawaii always includes a mix of short-period wind seas, long-period swells from the North and South Pacific as well as waves with moderate periods from multiple sources. We partition the hindcast spectra based on the respective period ranges and directions and validate the partitioned spectral energy and parameters with measured values for implementation in wave energy resources assessment. The partitioned wave parameters from the hindcast allow separate seasonal descriptions of wind seas, north and south swells, and moderate-period waves for in-depth understanding of the wave climate and resources in Hawaii.

Li, Ning↗

DOE OSTI2026

An agentic artificially intelligent X-ray scientist

Executing experimental tasks in both normal research laboratories and large-scale scientific facilities often requires extensive human supervision and remains a key challenge on the path to fully autonomous, artificial intelligence (AI)-driven science. Here we demonstrate a large language model-driven agent that autonomously performs X-ray sample alignment on a synchrotron beamline by planning actions, executing instrumental commands, interpreting observations and iterating towards experimental goals. Based on existing large language models with structured tool-use via the model context protocol, our AI X-ray scientist was guided and tested using an in-house-built virtual experimental setup that mirrors a six-circle diffractometer at an operational synchrotron beamline. The agentic workflow developed in the virtual environment was directly deployed on a real beamline, where it correctly identified reference reflections and determined the orientation matrix, an essential first step in any type of single-crystal scattering experiment. Our AI X-ray scientist responded effectively to unexpected experimental conditions, demonstrating adaptive problem-solving and readiness for addressing practical experimental situations. Our study provides a step towards autonomous operation across diverse experimental environments at large-scale scattering facilities.

Chen, Zhantao (ORCID:0000000319543868)↗

DOE OSTI2022

First Sagittarius A* Event Horizon Telescope Results. IV. Variability, Morphology, and Black Hole Mass

In this paper we quantify the temporal variability and image morphology of the horizon-scale emission from Sgr A*, as observed by the EHT in 2017 April at a wavelength of 1.3 mm. We find that the Sgr A* data exhibit variability that exceeds what can be explained by the uncertainties in the data or by the effects of interstellar scattering. The magnitude of this variability can be a substantial fraction of the correlated flux density, reaching ~100% on some baselines. Through an exploration of simple geometric source models, we demonstrate that ring-like morphologies provide better fits to the Sgr A* data than do other morphologies with comparable complexity. We develop two strategies for fitting static geometric ring models to the time-variable Sgr A* data; one strategy fits models to short segments of data over which the source is static and averages these independent fits, while the other fits models to the full data set using a parametric model for the structural variability power spectrum around the average source structure. Both geometric modeling and image-domain feature extraction techniques determine the ring diameter to be 51.8 ± 2.3 μas (68% credible intervals), with the ring thickness constrained to have an FWHM between ~30% and 50% of the ring diameter. To bring the diameter measurements to a common physical scale, we calibrate them using synthetic data generated from GRMHD simulations. This calibration constrains the angular size of the gravitational radius to be ${4.8}_{-0.7}^{+1.4}$ μas, which we combine with an independent distance measurement from maser parallaxes to determine the mass of Sgr A* to be ${4.0}_{-0.6}^{+1.1}\times {10}^{6}$ M⊙.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Modeling the impact of structure and coverage on the reactivity of realistic heterogeneous catalysts

Adsorbates often cover the surfaces of catalysts densely as they carry out reactions, dynamically altering their structure and reactivity. Understanding adsorbate-induced phenomena and harnessing them in our broader quest for improved catalysts is a substantial challenge that is only beginning to be addressed. Here, in this work, we chart a path toward a deeper understanding of such phenomena by focusing on emerging in silico modeling methodologies, which will increasingly incorporate machine learning techniques. We first examine how adsorption on catalyst surfaces can lead to local and even global structural changes spanning entire nanoparticles, and how this affects their reactivity. We then evaluate current efforts and the remaining challenges in developing robust and predictive simulations for modeling such behavior. Last, we provide our perspectives in four critical areas—integration of artificial intelligence, building robust catalysis informatics infrastructure, synergism with experimental characterization, and adaptive modeling frameworks—that we believe can help surmount the remaining challenges in rationally designing catalysts in light of these complex phenomena.

catalytic mechanisms↗

DOE OSTI2023

Theory and Simulation of Ultrafast Multidimensional Nonlinear X-ray Spectroscopy of Molecules (Final Report)

Emerging X-ray free electron laser (XFEL) beam sources offer new types of probes of matter with unprecedented spatial and temporal resolutions. These experimental advances must be met by robust theoretical and computational tools that provide predictive modeling capacity of the underlining electronic and structural dynamics. The latter will be essential for the design of sophisticated multi-pulse experiments and for their interpretation. The proposed research effort will focus on developing cutting- edge simulation tools for nonlinear multidimensional X-ray/optical spectroscopies and aims to address key questions in Priority Research Opportunities 1 (Probing and controlling electron motion within a molecule) and 3 (Capturing rare events and intermediate states in the transformation of matter) as mentioned in the BES Roundtable Report “Opportunities for Basic Research at the Frontiers of XFEL Ultrafast Science”. XFEL multidimensional nonlinear techniques, which combine sequences of X-ray and possibly optical pulses, provide a unique experimental toolbox for probing the dynamics of core and valence electronic excitations, as well as material structure. Predictive modeling of these dynamical processes requires the combination of analytical theory for nonlinear interactions of light and matter, robust quantum-chemical methodologies for the accurate description of electronic structure of various materials, and multiscale ab initio electron and nuclear dynamics techniques operating beyond Born-Oppenheimer approximation. These challenges will be addressed with three research thrusts (i) Develop and implement theoretical apparatus for modeling a broad range of multidimensional spectroscopic techniques enabled by present and upcoming XFEL facilities. This thrust also includes the incorporation of a computational module in the DOE supported open-source NWChem computational chemistry package as well as the development of other open-source codes ready for dissemination across a broad user base; (ii) Propose and design new multi-pulse experiments that make use of the capabilities of the incoming LCLS-II facility; (iii) Perform selected applications to specific molecular systems that can be carried out at LCLS-II and demonstrate how these X-ray sources may be used to study nonadiabatic dynamics through conical interactions, electronic correlations in multi-core excitons, and charge transfer/energy transfer processes. The proposed research will be carried out by a multi-disciplinary four-institution research team which combines academia and national laboratories and spans the broad and necessary expertise in theoretical spectroscopy, nonlinear optics, quantum chemistry, molecular non-adiabatic dynamics and code development. The work will be performed in a highly interactive team environment with junior researchers shared between institutions thus cementing cross- disciplinary interactions. The developed simulation tools will be immediately deployed for XFEL facility users, both experimentalists and theorists, via freely distributed codes and databases. Altogether, this project will facilitate establishing XFEL-based multidimensional spectroscopies as a novel diagnostic tool for monitoring electronic and structural dynamics in molecular materials.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2025

Fully Bayesian Analysis With Model Inadequacy Correction For Nuclear Graphite Property Models With Hierarchical Variance Structure

Nuclear-grade graphites are extensively utilized in the core designs of various advanced nuclear reactors. Within the reactor environment, graphite is subjected to prolonged exposure to extreme conditions, including high temperatures, radiation, and potentially molten salt and oxygen. Such exposure can induce several degradation mechanisms in graphite, such as nonuniform volumetric strains caused by irradiation and thermal expansion, leading to stresses that may compromise the performance of graphite components. Assessing component integrity, forecasting component performance over the reactor's lifespan, and developing design standards necessitate robust tools for predicting fracture initiation and propagation in graphite structural components within nuclear reactors. This code enables the Bayesian calibration of properties for nuclear-grade graphites. Using a hierarchical Bayesian approach, multiple experimental data sources are combined to develop Gaussian process models for the properties. Using the Kennedy O'Hagan framework, the uncertainties due inadequacies in the model and the inherent spread in the experimental data are quantified.

Dhulipala, Som Lakshmi NarasimhaLakshmi Narasimha ↗

DOE OSTI2021

Highly Accurate Experimental Heave Decay Tests with a Floating Sphere: A Public Benchmark Dataset for Model Validation of Fluid–Structure Interaction

Highly accurate and precise heave decay tests on a sphere with a diameter of 300 mm were completed in a meticulously designed test setup in the wave basin in the Ocean and Coastal Engineering Laboratory at Aalborg University, Denmark. The tests were dedicated to providing a rigorous benchmark dataset for numerical model validation. The sphere was ballasted to half submergence, thereby floating with the waterline at the equator when at rest in calm water. Heave decay tests were conducted, wherein the sphere was held stationary and dropped from three drop heights: a small drop height, which can be considered a linear case, a moderately nonlinear case, and a highly nonlinear case with a drop height from a position where the whole sphere was initially above the water. The precision of the heave decay time series was calculated from random and systematic standard uncertainties. At a 95% confidence level, uncertainties were found to be very low—on average only about 0.3% of the respective drop heights. Physical parameters of the test setup and associated uncertainties were quantified. A test case was formulated that closely represents the physical tests, enabling the reader to do his/her own numerical tests. The paper includes a comparison of the physical test results to the results from several independent numerical models based on linear potential flow, fully nonlinear potential flow, and the Reynolds-averaged Navier–Stokes (RANS) equations. A high correlation between physical and numerical test results is shown. The physical test results are very suitable for numerical model validation and are public as a benchmark dataset.

42 ENGINEERING↗