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DOE OSTI2024

Predicting RNA structure and dynamics with deep learning and solution scattering

Advanced deep learning and statistical methods can predict structural models for RNA molecules. However, RNAs are flexible, and it remains difficult to describe their macromolecular conformations in solutions where varying conditions can induce conformational changes. Small-angle x-ray scattering (SAXS) in solution is an efficient technique to validate structural predictions by comparing the experimental SAXS profile with those calculated from predicted structures. There are two main challenges in comparing SAXS profiles to RNA structures: the absence of cations essential for stability and charge neutralization in predicted structures and the inadequacy of a single structure to represent RNA’s conformational plasticity. We introduce a solution conformation predictor for RNA (SCOPER) to address these challenges. This pipeline integrates kinematics-based conformational sampling with the innovative deep learning model, IonNet, designed for predicting Mg 2+ ion binding sites. Validated through benchmarking against 14 experimental data sets, SCOPER significantly improved the quality of SAXS profile fits by including Mg 2+ ions and sampling of conformational plasticity. We observe that an increased content of monovalent and bivalent ions leads to decreased RNA plasticity. Therefore, carefully adjusting the plasticity and ion density is crucial to avoid overfitting experimental SAXS data. SCOPER is an efficient tool for accurately validating the solution state of RNAs given an initial, sufficiently accurate structure and provides the corrected atomistic model, including ions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Fracturing process of micro-concrete under uniaxial and triaxial compression: Insights from in-situ X-ray mechanical tests

This paper presents an experimental study of concrete at meso-scale (aggregates, macro-pores and mortar matrix) in order to get a better understanding of the local failure mechanisms known to drive the macroscopic mechanical behaviour of the material. The main originality comes from conducting in-situ X-ray mechanical tests on micro-concrete samples of realistic composition (including cement, sand, aggregates and water), under uniaxial compression and, for the first time, under triaxial compression at 5 MPa, 10 MPa and 15 MPa confining pressures. A timeseries analysis of the set of 3D images coming from each test allows for the measurement of the 3D kinematic fields (displacement and strain fields) throughout the experiments. The different failure patterns observed for each loading path are discussed, along with a quantification of the 3D fracturing processes at the scale of the largest heterogeneities (aggregates and macro-pores). With an increasing level of confinement, the transition from brittle to ductile response is observed, as well as an increase of the strength of the material. The pronounced impact of the meso-scale heterogeneities of concrete on their local failure mechanisms is highlighted. It is shown that strain localisation mainly originates between aggregates and mortar matrix, with the shape and location of the largest aggregates and macro-pores essentially driving the propagation of the cracking network.

36 MATERIALS SCIENCE↗

DOE OSTI2023

An extended three-field principle to scale-bridge the granular micromechanics of polymer-bonded particulate materials

Observed phenomena of damage, viscoelasticity, and viscoplasticity in polymer-bonded particulate materials (PBPM), like polymer-bonded explosive (PBX), are accommodated in a scale-bridging constitutive model based on granular micromechanics. An extended three-field variational principle with min - max optimization problem is introduced to homogenize the bonded aggregates’ grain-scale contact mechanics. Similarly to prior applications of a three-field principle, volume constraints are invoked to embed microscale-to-macroscale correspondences for kinematic and static volumetric measures, like mean strain and its energy-conjugate stress invariant. Unlike prior applications, our three-field principle realizes a strain-driven model for effective constitutive behavior due to bonded intergranular contact. In conclusion, the resultant micro-sphere integration-based homogenization is demonstrated in comparison to existing publicly-available measurements to capture the extreme tension/compression constitutive asymmetry exhibited by PBPMs (specifically PBX-9501) during material softening.

42 ENGINEERING↗

DOE OSTI2024

Crack opening calculation in phase-field modeling of fluid-filled fracture: A robust and efficient strain-based method

The phase-field method has become popular for the numerical modeling of fluid-filled fractures, thanks to its ability to represent complex fracture geometry without algorithms. However, the algorithm-free representation of fracture geometry poses a significant challenge in calculating the crack opening (aperture) of phase-field fracture, which governs the fracture permeability and hence the overall hydromechanical behavior. Although several approaches have been devised to compute the crack opening of phase-field fracture, they require a sophisticated algorithm for post-processing the phase-field values or an additional parameter sensitive to the element size and alignment. Here, we develop a novel method for calculating the crack opening of fluid-filled phase-field fracture, which enables one to obtain the crack opening without additional algorithms or parameters. Here we transform the displacement-jump-based kinematics of a fracture into a continuous strain-based version, insert it into a force balance equation on the fracture, and apply the phase-field approximation. Through this procedure, we obtain a simple equation for the crack opening which can be calculated with quantities at individual material points. We verify the proposed method with analytical and numerical solutions obtained based on discrete representations of fractures, demonstrating its capability to calculate the crack opening regardless of the element size or alignment.

58 GEOSCIENCES↗

DOE OSTI2023

Ground vehicle lane-keeping assistance system via differential flatness output feedback control and algebraic derivative estimation

Vehicle run-off-road is one of the most frequent and fatal traffic accidents in the United States. Various lane-keeping assistance (LKA) systems have been developed in the last decade to help drivers stay on the road. Most of them are built upon linear driver–vehicle–road (DVR) models and treat road curvature as a disturbance. Albeit effective, their control performance would degrade if road curvature varies rapidly. Here, this paper proposes a novel nonlinear DVR model by integrating a driver steering model into vehicle–road kinematics, which explicitly considers road curvature. Particularly, this nonlinear DVR system has been proven to be differentially flat, and a flatness-based LKA system is designed. Additionally, Model-Free Control is introduced to compensate for system modeling errors. Hardware-in-the-loop simulations and diver-in-the-loop experiments validate the proposed control framework and demonstrate the performance enhancement with respect to a representative linear robust LKA system.

42 ENGINEERING↗

DOE OSTI2021

LeptonInjector and LeptonWeighter: A neutrino event generator and weighter for neutrino observatories

In this work, we present a high-energy neutrino event generator, called LeptonInjector, alongside an event weighter, called LeptonWeighter. Both are designed for large-volume Cherenkov neutrino telescopes such as IceCube. The neutrino event generator allows for quick and flexible simulation of neutrino events within and around the detector volume, and implements the leading Standard Model neutrino interaction processes relevant for neutrino observatories: neutrino-nucleon deep-inelastic scattering and neutrino-electron annihilation. In this paper, we discuss the event generation algorithm, the weighting algorithm, and the main functions of the publicly available code, with examples. Program summary: Program Titles: LeptonInjector and LeptonWeighter CPC Library link to program files: https://doi.org/10.17632/662gkpjfd9.1 Developer's repository links: https://github.com/icecube/LeptonInjector and https://github.com/icecube/LeptonWeighter Licensing provisions: GNU Lesser General Public License, version 3. Programming Language: C++11 External Routines: • Boost • HDF5 • nuflux (https://github.com/icecube/nuflux) • nuSQuIDS (https://github.com/arguelles/nuSQuIDS) • Photospline (https://github.com/icecube/photospline) • SuiteSparse (https://github.com/DrTimothyAldenDavis/SuiteSparse) Nature of problem: LeptonInjector: Generate neutrino interaction events of all possible topologies and energies throughout and around a detector volume. LeptonWeighter: Reweight Monte Carlo events, generated by a set of LeptonInjector Generators, to any desired physical neutrino flux or cross section. Solution method: LeptonInjector: Projected ranges of generated leptons and the extent of the detector, in terms of column depth, are used to inject events in and around the detector volume. Event kinematics follow distributions provided in cross section files. LeptonWeighter: Event generation probabilities are calculated for each Generator, which are then combined into a generation weight and used to calculate an overall event weight.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Simulating low-energy neutrino interactions with MARLEY

Monte Carlo event generators are a critical tool for the interpretation of data obtained by neutrino experiments. Several modern event generators are available which are well-suited to the GeV energy scale used in studies of accelerator neutrinos. However, theoretical modeling differences make their immediate application to lower energies difficult. In this paper, I present a new event generator, MARLEY, which is designed to better address the simulation needs of the low-energy (tens of MeV and below) neutrino community. The code is written in C++14 with an optional interface to the popular ROOT data analysis framework. The current release of MARLEY (version 1.2.0) emphasizes simulations of the reaction 40 Ar ( ν e , e − ) 40 K ⁎ but is extensible to other channels with suitable user input. This paper provides detailed documentation of MARLEY's implementation and usage, including guidance on how generated events may be analyzed and how MARLEY may be interfaced with external codes such as Geant4. Further information about MARLEY is available on the official website at http://www.marleygen.org. Program title:MARLEY 1.2.0 CPC Library link to program files:https://doi.org/10.17632/4v7zxnc8j3.1 Developer's respository link:http://github.com/MARLEY-MC/marley Code Ocean capsule:https://codeocean.com/capsule/9868179 Licensing provisions: GNU General Public License 3.0 Programming language: C++14 External routines/libraries used: GNU Scientific Library [1,2] (required), ROOT [3,4] (optional) Nature of problem: Simulation of neutrino-nucleus scattering events at energies of tens-of-MeV and below Solution method: Initial two-to-two scattering kinematics are sampled using the allowed approximation differential cross section and tables of precomputed nuclear matrix elements. Subsequent de-excitations of the remnant nucleus are simulated using a Monte Carlo implementation of the Hauser-Feshbach statistical model and tabulated γ-ray decay schemes for discrete nuclear levels. Additional comments including restrictions and unusual features: Input data are provided with the code that are suitable for producing simulations of the charged-current reaction 40 Ar ( ν e , e − ) 40 K ⁎ , coherent elastic neutrino-nucleus scattering on spin-zero target nuclei, and neutrino-electron elastic scattering on any atomic target. Preparation of new reaction input files (whose format is documented in Appendix B) would enable other reaction channels and nuclear targets to be handled by the existing code framework. Although there is no maximum neutrino energy enforced by the code itself, realistic neutrino-nucleus scattering events may be generated up to roughly 50 MeV. Above this energy, the effects of forbidden nuclear transitions, which are neglected in the current treatment of the cross sections (see section 2.1), become increasingly important.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

Simulation of dark bremsstrahlung in Geant4

A technique for the simulation of dark bremsstrahlung for electrons and muons in GEANT4 is presented. The total cross section is calculated using the Weizsäcker-Williams approximation and the outgoing kinematics are produced by scaling events produced in MadGraph/MadEvent to lower incident lepton energies, allowing the simulation to account for thick targets and lepton sources without fixed energies. In conclusion, compared with dedicated samples produced at an arbitrary particle energy, typical precision of better than 5% is achieved.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Principal Landau determinants

We reformulate the Landau analysis of Feynman integrals with the aim of advancing the state of the art in modern particle-physics computations. We contribute new algorithms for computing Landau singularities, using tools from polyhedral geometry and symbolic/numerical elimination. Inspired by the work of Gelfand, Kapranov, and Zelevinsky (GKZ) on generalized Euler integrals, we define the principal Landau determinant of a Feynman diagram. We illustrate with a number of examples that this algebraic formalism allows to compute many components of the Landau singular locus. We adapt the GKZ framework by carefully specializing Euler integrals to Feynman integrals. For instance, ultraviolet and infrared singularities are detected as irreducible components of an incidence variety, which project dominantly to the kinematic space. We compute principal Landau determinants for the infinite families of one-loop and banana diagrams with different mass configurations, and for a range of cutting-edge Standard Model processes. Furthermore, our algorithms build on the Julia package this http URL and are implemented in the new open-source package this http URL available at this https URL.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

A universal implementation of radiative effects in neutrino event generators

Due to the similarities between electron-nucleus (eA) and neutrino-nucleus scattering (νA), eA data can contribute key information to improve cross-section modeling in eA and hence in νA event generators. However, to compare data and generated events, either the data must be radiatively corrected or radiative effects need to be included in the event generators. We implemented a universal radiative corrections program that can be used with all reaction mechanisms and any eA event generator. Our program includes real photon radiation by the incident and scattered electrons, and virtual photon exchange and photon vacuum polarization diagrams. It uses the “extended peaking” approximation for electron radiation and neglects charged hadron radiation. This method, validated with GENIE, can also be extended to simulate νA radiative effects. This work facilitates data-event-generator comparisons used to improve νA event generators for the next-generation of neutrino experiments. Program Title: emMCRadCorr CPC Library link to program files:https://doi.org/10.17632/hmsxg82vnf.1 Developer's repository link:https://github.com/e4nu/emMCRadCorr Licensing provisions: AGPLv3 Programming language:C++ Nature of problem: Radiative effects can significantly modify the event kinematics and the resulting cross-sections. Such effects must be accounted for when comparing event generators to eA data. Existing radiative correction codes are tailored to specific processes and topologies, and are limited to a restricted phase space defined by the spectrometer acceptance. Therefore, a more general approach is required to apply radiative corrections to semi-inclusive and exclusive eA measurements. Solution method: Our program incorporates real photon radiation from both the incident and scattered electrons, as well as virtual photon exchange and photon vacuum polarization effects. It employs the “extended peaking” approximation for electron radiation while neglecting contributions from charged hadron radiation. The code is fully decoupled from event generator codes and can be used for all event generators in the market.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

A branch-and-price algorithm for a team orienteering problem with fixed-wing drones

This paper formulates a team orienteering problem with multiple fixed-wing drones and develops a branch-and-price algorithm to solve the problem to optimality. Fixed-wing drones, unlike rotary drones, have kinematic constraints associated with them, thereby preventing them to make on-the-spot turns and restricting them to a minimum turn radius. This paper presents the implications of these constraints on the drone routing problem formulation and proposes a systematic technique to address them in the context of the team orienteering problem. Furthermore, a novel branch-and-price algorithm with branching techniques specific to the constraints imposed due to fixed-wing drones are proposed. Extensive computational experiments on benchmark instances corroborating the effectiveness of the algorithms are also presented.

42 ENGINEERING↗

DOE OSTI2024

Bayesian calibration and uncertainty quantification of a rate-dependent cohesive zone model for polymer interfaces

In this work we present a rate-dependent cohesive zone model for the fracture of polymeric interfaces and performs a Bayesian calibration, an uncertainty quantification, and a sensitivity analysis for the model. The proposed cohesive zone model accounts for both reversible elastic and irreversible rate-dependent separation sliding deformation at the interface. The viscous dissipation due to the irreversible opening at the interface is modeled using elastic-viscoplastic kinematics that incorporates the effects of strain rate. Inverse calibration of parameters for such complex models through trial and error is challenging due to the large number of parameters of the model. Moreover, the calibrated parameter values are often non-unique and uncertain when the available experimental data is limited. To tackle this challenge, we employ a Bayesian calibration approach to identify parameters from experimental data, the resulting parameters significantly enhance the accuracy of the model. To quantify the uncertainty associated with the inverse parameter estimation, a modular Bayesian approach is employed to calibrate the unknown model parameters, accounting for the parameter uncertainty of the cohesive zone model. The advantages of the Bayesian calibration over a deterministic parameter fit are demonstrated. Further, to quantify the model uncertainties, such as incorrect assumptions or missing physics, a discrepancy function is introduced, which significantly improves the model’s prediction. Finally, the total uncertainty of the model is quantified in a predictive setting. A sensitivity analysis is performed to assess how changes in the input variables of the model affect the peak load, facilitating the identification of a concise set of highly influential parameters. The present approach can be used for calibration and uncertainty quantification for other complex computational mechanics models. It should also facilitate the designing of interface materials under uncertainty.

42 ENGINEERING↗

DOE OSTI2025

A structured framework for predicting sustainable aviation fuel properties using liquid-phase FTIR and machine learning

Sustainable aviation fuels have the potential to improve efficiency, reduce emissions, and enhance energy security. To help identify viable sustainable aviation fuels and accelerate research, machine learning models have been developed to predict relevant physicochemical properties. However, many models have limited applicability, leverage data from complex analytical techniques with confined spectral ranges, or use feature decomposition methods that offer limited interpretability. Using liquid-phase Fourier Transform Infrared (FTIR) spectra, this study presents a structured method for creating accurate and interpretable property prediction models for neat molecules, aviation fuels, and blends. Liquid FTIR spectra can be collected quickly and consistently, offering high reliability, sensitivity, and component specificity using less than 2 ml of sample. The method first decomposes FTIR spectra into fundamental building blocks using non-negative matrix factorization (NMF) to enable scientific analysis of FTIR spectra attributes and fuel properties. The NMF features are then used to create five ensemble models for predicting final boiling point, flash point, freezing point, density at 15°C, and kinematic viscosity at -20°C. All models were trained using experimental property data from neat molecules, aviation fuels, and blends. The models accurately predict key properties across a broad range of neat molecules and representative fuels and blends, while enabling interpretation of relationships between compositional elements, such as functional groups or chemical classes, and their resulting properties. This demonstrates strong potential to support sustainable aviation fuel research and development. The models and data are available on an interactive web tool.

Fourier transform infrared spectroscopy↗

DOE OSTI2025

Development, validation, and verification of multi-pass thermo-mechanical welding simulations using the open-source MOOSE framework: NeT TG4 benchmark weldment

This study develops and validates a sequentially coupled thermo-mechanical welding simulation for the three-pass 316L stainless steel NeT TG4 benchmark weldment using the open-source Multiphysics Object-Oriented Simulation Environment (MOOSE) and the Nuclear Engineering Material model Library (NEML). A diffused ellipsoidal heat source was calibrated against thermocouple data and weld macrographs to accurately model the fusion zone geometry and transient thermal fields. Material hardening is represented using the Lemaitre-Chaboche mixed isotropic-kinematic hardening model, while four annealing models - no annealing, single-stage at 1050 °C and 1300 °C, and two-stage at 800 °C/1300 °C - were implemented to assess the impact of annealing models on the accuracy of the predicted welding-induced plasticity, distortions, and residual stresses. The predictions were validated against experimental measurements and benchmarked against results from commercial software, demonstrating that thermo-mechanical MOOSE welding simulations achieve comparable accuracy with enhanced computational efficiency. This work highlights the potential of using open-source finite element frameworks like MOOSE for advanced manufacturing simulations.

Ji, Wendy [Australian Nuclear Science and Technolo↗

DOE OSTI2026

In situ quantification of fracture slip induced by hydraulic injections in a deep borehole: A comparison of two different borehole techniques

In situ measurements of fracture deformation during fluid injection are rare, yet essential for understanding the mechanical response of fractured rock. In this study, we evaluate the reliability of two methods by comparing their slip vector estimates: high-resolution borehole acoustic televiewer images captured before and after injection tests, and displacement data from a three-component borehole deformation probe recorded during the injections. Acoustic televiewer images capture only final in-plane displacement, whereas three-component borehole deformation measurements provide full 3D, transient fracture movement. Four injection tests in a fractured granitic rock mass along an inclined borehole at the Bedretto Underground Laboratory (Switzerland), beneath more than 1100 m of overburden, were analyzed. The two methods yielded consistent kinematics and comparable slip magnitudes, typically in the range of 0.2 – 0.6 mm. Angular differences between estimated slip directions ranged from 0.2° to 28°. For two test intervals with pre-existing fractures optimally oriented for slip, the measured slip vectors agreed with forward-modeled slip vectors based on the regional in situ stress field, supporting the Wallace–Bott hypothesis. Measurable shear displacement was identified in two test intervals containing fractures oriented nearly perpendicular to the least principal stress, including a newly formed hydraulic fracture. This demonstrates that even fractures unfavorably oriented for slip can undergo shear due to local stress perturbations around an inclined borehole.

Acoustic televiewer↗

DOE OSTI2022

A unified finite strain gradient-enhanced micropolar continuum approach for modeling quasi-brittle failure of cohesive-frictional materials

Here, in this work, a novel framework for modeling quasi-brittle crack propagation and shear band dominated failure of cohesive-frictional materials like concrete, mortar, rock, tough ceramics, energetic materials, but also granular materials like sands or powders in terms of a unified continuum approach is proposed. It is based on a combination of the gradient-enhanced continuum with gradients of internal variables for representing quasi-brittle cracking, and the micropolar continuum, accounting for the deformation of the microstructure. For developing the gradient-enhanced micropolar framework, the set of balance equations and the kinematic relations are derived, and the constitutive relations are established in a general manner. The framework is formulated in a geometrically exact setting, based on the thermodynamically sound theory of hyperelasto-plasticity, and the numerical implementation by means of the finite element method is discussed. For assessing the approach, realizations of this new approach in terms of constitutive models for particular materials are developed. They are applied to numerical benchmark examples, investigating various loading conditions, and the obtained results are validated by means of a comparison with experiments from the literature.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Periodic boundary conditions for arbitrary deformations in molecular dynamics simulations

A generalization of the Lees-Edwards periodic boundary conditions (gLE-PBC) for molecular dynamics (MD) simulations is developed to allow for arbitrary deformations to be applied to the domain. The gLE-PBC domain remains a rectangular cuboid regardless of the applied deformation in contrast with the Lagrangian-rhomboid periodic boundary conditions (LR-PBC) where the domain deforms according to the applied deformation. Furthermore, the kinematics of gLE-PBC are validated against pure shear. The gLE-PBC method for interacting systems is then validated against the LR-PBC method and analytical solutions for a solid under isotropic compression, one-dimensional shearing, three-dimensional extension and shearing and for a liquid under Couette flow. Bulk physical properties extracted from the gLE-PBC simulations agree well with values calculated from equilibrium MD simulations. Three dimensional shearing and a deformation with a full velocity gradient matrix are also simulated, showing the range of problems gLE-PBC can explore.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

A sharp interface Lagrangian-Eulerian method for flexible-body fluid-structure interaction

This paper introduces a sharp-interface approach to simulating fluid-structure interaction (FSI) involving flexible bodies described by general nonlinear material models and across a broad range of mass density ratios. This new flexible-body immersed Lagrangian-Eulerian (ILE) scheme extends our prior work on integrating partitioned and immersed approaches to rigid-body FSI. Our numerical approach incorporates the geometrical and domain solution flexibility of the immersed boundary (IB) method with an accuracy comparable to body-fitted approaches that sharply resolve flows and stresses up to the fluid-structure interface. Unlike many IB methods, our ILE formulation uses distinct momentum equations for the fluid and solid subregions with a Dirichlet-Neumann coupling strategy that connects fluid and solid subproblems through simple interface conditions. As in earlier work, we use approximate Lagrange multiplier forces to treat the kinematic interface conditions along the fluid-structure interface. This penalty approach simplifies the linear solvers needed by our formulation by introducing two representations of the fluid-structure interface, one that moves with the fluid and another that moves with the structure, that are connected by stiff springs. This approach also enables the use of multi-rate time stepping, which allows us to use different time step sizes for the fluid and structure subproblems. Our fluid solver relies on an immersed interface method (IIM) for discrete surfaces to impose stress jump conditions along complex interfaces while enabling the use of fast structured-grid solvers for the incompressible Navier-Stokes equations. The dynamics of the volumetric structural mesh are determined using a standard finite element approach to large-deformation nonlinear elasticity via a nearly incompressible solid mechanics formulation. This formulation also readily accommodates compressible structures with a constant total volume, and it can handle fully compressible solid structures for cases in which at least part of the solid boundary does not contact the incompressible fluid. Selected grid convergence studies demonstrate second-order convergence in volume conservation and in the pointwise discrepancies between corresponding positions of the two interface representations as well as between first and second-order convergence in the structural displacements. The time stepping scheme is also demonstrated to yield second-order convergence. To assess and validate the robustness and accuracy of the new algorithm, comparisons are made with computational and experimental FSI benchmarks. Test cases include both smooth and sharp geometries in various flow conditions. Furthermore, we also demonstrate the capabilities of this methodology by applying it to model the transport and capture of a geometrically realistic, deformable blood clot in an inferior vena cava filter.

97 MATHEMATICS AND COMPUTING↗