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DOE OSTI2025

Structural switching dynamically controls the doubly pseudoknotted Rous sarcoma virus–programmed ribosomal frameshifting element

A hallmark of retrovirus replication is the translation of two different polyproteins from one RNA through programmed –1 frameshifting. This is a mechanism in which the actively translating ribosome is induced to slip in the 5′ direction at a defined codon and then continues translating in the new reading frame. Programmed frameshifting controls the stoichiometry of viral proteins and is therefore under stringent evolutionary selection. Forty years ago, the first frameshifting stimulatory element was discovered in the Rous sarcoma virus. The ~120 nt RNA segment was predicted to contain a pseudoknot, but its 3D structure has remained elusive. Now, we have determined cryoEM and X-ray crystallographic structures of this classic retroviral element, finding that it adopts a butterfly-like double-pseudoknot fold. One “wing” contains a dynamic pyrimidine-rich helix, observed crystallographically in two conformations and in a third conformation via cryoEM. The other wing encompasses the predicted pseudoknot, which interacts with a second unexpected pseudoknot through a toggle residue, A2546. This key purine switches conformations between structural states and tunes the stability of interacting residues in the two wings. We find that its mutation can modulate frameshifting by as much as 50-fold, likely by altering the relative abundance of different structural states in the conformational ensemble of the RNA. Taken together, our structure–function analyses reveal how a dynamic double pseudoknot junction stimulates frameshifting by taking advantage of conformational heterogeneity, supporting a multistate model in which high Shannon entropy enhances frameshifting efficiency.

Science & Technology - Other Topics↗

DOE OSTI2020

Single Crystal Plasticity Model with Deformation Twinning for the High Rate Deformation of β-HMX

Deformation twinning is an active deformation mechanism during loading along certain crystallographic directions of β-cyclotetramethylene tetranitramine (β-HMX). In this work, a finite strain thermomechanical model is extended to include twinning as a deformation mechanism in addition to plastic slip. The stress is derived from the free energy expression including a term representing the equation of state. The crystal plasticity framework is used to divide the total strain into inelastic and elastic component, where the elastic part is used in the expression for the free energy. The twin systems are treated as pseudo slip systems and the shear rate on the twin systems is evaluated in terms of the twin resistance and the projection of the stress tensor. The model parameters were calibrated against a set of plate impact experiments performed on β-HMX by Dick et al. The remaining plate impact experiments are used to evaluate the predictive capability of the model. The quality of the model fits and predictions is discussed from a physical and modeling perspective. Particularly, the role of twin modeling on results is highlighted. Finally, the model is used to explore the relationship between the propensity for twinning and crystal orientation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Limited modified gravity

In this work, we systematically assess several limiting cases of modified gravity, where particular theoretical or observational conditions hold. This framework includes the well known scalar-tensor gravity and No Slip Gravity and No Run Gravity, and we extend it to three new limits: only Run, Only Light, and Only Growth Gravities. These limits give simplifications that allow deeper understanding of modified gravity, including demonstration that gravitational effects on light and matter can have opposite signs in their deviation from general relativity. We also show observational predictions for the different cosmic structure growth rates fσ8 and the ratio of gravitational wave standard siren luminosity to photon standard candle luminosity distance relations, defining a new statistic DG that emphasizes their complementarity and ability to distinguish models.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Modeling of the thermo-mechanical response and texture evolution of WE43 Mg alloy in the dynamic recrystallization regime using a viscoplastic self-consistent formulation

This paper presents a microstructure sensitive model for predicting mechanical response and texture evolution of metals in the dynamic recrystallization regime. A recently proposed viscoplastic self-consistent (VPSC) formulation for the prediction of recrystallization driven by strain energy and intragranular misorientation is extended to hexagonal close-packed (hcp) metals. The model is applied to the dynamic recrystallization of magnesium alloy WE43 at different temperatures and strain rates. Model predictions in terms of stress-strain response and texture evolution are compared to the experimental measurements and acceptable agreement is achieved. According to the model predictions, superplastic behavior of nuclei was found to be the dominant softening mechanism at high temperatures and low strain rates. High concentration of precipitates at the grain boundaries and presence of alloying elements are the likely causes of low boundary mobility, resulting in nucleation dominated dynamic recrystallization. Relatively strong basal compression textures indicate dominant activity of basal slip, which can be achieved only through large difference in slip resistance between soft basal and hard prismatic and pyramidal modes.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Time domain probabilistic seismic risk analysis using ground motion prediction equations of Fourier amplitude spectra

Modeling of Fourier amplitude spectra (FAS) of seismic motions has gained much attention in engineering seismology. In the past few years, several ground motion prediction equations (GMPEs) and inter-frequency correlation structure of FAS have been established. Due to many preferable characteristics of FAS, probabilistic seismic hazard/risk analysis is rapidly changing from ergodic, spectrum acceleration Sa(T 0 )-based approach to non-ergodic, site-specific, FAS-based approach. This paper presents time domain intrusive framework for probabilistic seismic risk analysis using GMPE of FAS. Herein, methodology for time domain stochastic ground motion modeling based on GMPEs of FAS is presented in some detail. The simulated uncertain motions are modeled as a random process and represented by polynomial chaos Karhunen-Loève expansion. The random process excitations are further propagated into the uncertain structural system using Galerkin stochastic finite element method (SFEM). Probabilistic evolution of structural response is solved, and such solution is used to develop seismic risk for any damage state. The presented framework is illustrated through seismic risk analysis of a four-story building subjected to possible earthquakes from two strike slip faults. The influences of the epistemic uncertainties in source stress drop Δσ and site attenuation κ0 on seismic risk are investigated. The need for non-ergodic seismic risk analysis with source-specific and site specific characterizations is emphasized.

58 GEOSCIENCES↗

DOE OSTI2025

Coupled geomechanical investigation of depletion-induced fault reactivation

Fault reactivation during subsurface fluid production pose significant challenges to safe and sustainable resource extraction. Here, this study presents a three-dimensional coupled geomechanical framework to investigate the processes driving fault reactivation, capturing the interactions between reservoir dynamics and geomechanical responses. Verification against theoretical estimations based on linear poroelasticity confirms the model's capacity in representing reservoir background stress responses. However, the study reveals that relying solely on background stress states can underestimate or overestimate fault reactivation potential, emphasizing the importance of including localized stress perturbations such as differential compaction and stress redistribution. Applied to a fault (M1) inspired by the geological characteristics of the Groningen field, the model shows slip initiation at 2965 m depth with 16.0 MPa depletion, aligning with field observations where seismicity occurred at approximately 3 km depth after 15.8 MPa depletion. Parametric studies reveal: (1) inelastic reservoir compaction delays fault reactivation and mitigates fault slip by reducing stress concentration, (2) higher intermediate in-situ stress magnitudes decrease the Coulomb Failure Stress (CFS) increase rate and reduce fault slip, (3) larger fault offsets amplify shear stress near the offset zone, promoting earlier reactivation and longer rupture propagation, and (4) fault permeability significantly influences pressure diffusion, with low-permeability faults leading to sharper stress changes and earlier fault destabilization. These insights highlight the critical role of geological and mechanical parameters in fault reactivation and provide a predictive framework for mitigating induced seismicity risks.

Coupled geomechanical modeling↗

DOE OSTI2020

New Opportunities to Study Earthquake Precursors

The topic of earthquake prediction has a long history, littered with failed attempts. Part of the challenge is that possible precursory signals are usually reported after the event, and the systematic relationships between potential precursors and main events, should they exist, are unclear. Furthermore, several recent studies have shown the potential of new approaches to simultaneously detect earthquake foreshocks and slow-slip phenomena through ground deformation, seismic, and gravitational transients—weeks to months before large subduction zone earthquakes. The entire international community of earthquake researchers should be engaged in deploying instrumentation, sharing data in real time, and improving physical models to resolve the extent to which slow slip events and earthquake swarms enhance the likelihood (or not) for later, larger earthquakes.

58 GEOSCIENCES↗

DOE OSTI2022

INGENIOUS - Great Basin Regional Dataset Compilation

This is the regional dataset compilation for the INnovative Geothermal Exploration through Novel Investigations Of Undiscovered Systems (INGENIOUS) project. The primary goal of this project is to accelerate discoveries of new, commercially viable hidden geothermal systems while reducing the exploration and development risks for all geothermal resources. These datasets will be used in INGENIOUS as input features for predicting geothermal favorability throughout the Great Basin study area. Datasets consist of shapefiles, geotiffs, tabular spreadsheets, and metadata that describe: 2-meter temperature probe surveys, quaternary faults and volcanic features, geodetic shear and dilation models, heat flow, magnetotellurics (conductance), magnetics, gravity, paleogeothermal features (such as sinter and tufa deposits), seismicity, spring and well temperatures, spring and well aqueous geochemistry analyses, thermal conductivity, and fault slip and dilation tendency. For additional project information, see the INGENIOUS project site linked in the submission. Terms of use: These datasets are provided "as is", and the contributors assume no responsibility for any errors or omissions. The user assumes the entire risk associated with their use of these data and bears all responsibility in determining whether these data are fit for their intended use. These datasets may be redistributed with attribution (see citation information below). Please refer to the license information on this page for full licensing terms and conditions.

15 GEOTHERMAL ENERGY↗

DOE OSTI2020

Hydrogen Transport in a Model 9979 Shipping Package with Inner Convenience Cans

Radiolytic hydrogen production and accumulation inside containment packages is a concern at any facility responsible for their packaging, storage, transportation, and/or disposal. When hydrogen gas accumulates to concentrations above the Lower Flammability Limit (LFL) which is 4% or 40,000 ppm in air, the possibility of a deflagration or explosion increases. This concern persists over the course of the package lifetime which is unlimited when disposed of by burial or in permanent repositories. Here, we report on a numerical model used to predict the concentration of hydrogen within each layer of a Model 9979 package containing a convenience can assembly. Simulations show the hydrogen concentration to always be highest in the inner convenience can containing the radioactive source. When the radioactive source is within the Los Alamos National Laboratory (LANL) Packaging Limits, the hydrogen concentration is shown to remain well below the LFL at all times including packaging, storage, transportation, and disposal. A hydrogen transport model is presented for a Model 9979 package system containing a nested arrangement of convenience cans, which are tin oxide coated steel cans of various sizes with a slip-lid assembly. The inner convenience can contains the radioactive source material along with an unknown quantity of incidental water acquired from humid air or processing. While visible organic materials such as paper and plastics were purposely excluded from the inner can, it is not possible to claim the wastes are entirely organic free. The inner convenience can is tape sealed and placed into a plastic bag which is horsetail closed (i.e., twisted and taped). The bagged can is placed into an outer convenience can that is also tape sealed. The can assembly is then placed into the 30 gallon drum and subsequently placed inside the 55 gallon drum in the 9979 package. Here we assume hydrogen gas is produced in the inner convenience can from alpha radiolysis of water at a rate dependent on the quantity of uranium isotopes and water present. The hydrogen transport model was used to calculate hydrogen accumulations within the package’s five layers at different times and conditions. These simulations serve two purposes; (i) to build confidence in the model by comparing predicted values to measured values, and (ii) to check the steady state hydrogen concentrations that are approached at long times in the package’s lifetime. Model simulations were compared to gas samples taken from the 30 gallon drum after storage at LANL’s Chemistry and Metallurgy Research (CMR) building for around 500 days. Hydrogen concentration calculations over much longer periods (i.e., more than 270 years) included extreme storage durations, transportation at extreme cold temperatures, and disposal of packages assuming different average temperatures.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2026

Roadrunner

SAND2026-17073O Roadrunner software provides a comprehensive platform for simulating the mechanical behavior of crystalline materials under various loading conditions, allowing users to investigate the effects of dislocation slip hardening and damage evolution. Developed as a fork of the Multiphysics Object Oriented Simulation Environment (MOOSE) software from Idaho National Laboratory, Roadrunner is optimized for high-performance computing and can simulate large-scale problems, enabling researchers to explore complex scenarios. Its applications include material design and optimization in aerospace and automotive industries, investigation of failure mechanisms in structural materials, and development of predictive models for crystalline materials under various loading conditions. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Lim, Hojun [Sandia National Lab. (SNL-CA), Livermo↗

DOE OSTI2024

DECOVALEX-2023: Task G, SAFENET Final Report

DECOVALEX Task G deals with fracture mechanics at several scales using a combined approach of experimental work, related model development, benchmarking and experimental analysis. Fig. 0.1 provides a graphical abstract for Task G. The experimental basis for the related mechanical (M), hydro-mechanical (HM), and thermo-mechanical (TM) processes comes from the rock mechanics laboratories of Universities of Freiberg (TUBAF) and Edinburgh, as well as the Korea Institute of Civil Engineering and Building Technology (KICT). The experimental work in the rock laboratories is closely linked to the underground research laboratories (URLs) Reiche Zeche (Germany), KURT (Korea), and Mont Terri (Switzerland). The scientific key questions are related to fracture permeability evolution under THM conditions, anisotropy effects on fracturing processes, and thermal fracture slip, which are being addressed in specific steps of the task. A large variety of numerical methods have been developed and applied for experimental analysis, ranging from continuum to discontinuum approaches. A detailed comparison of mechanical and hydro-mechanical processes is given in the section 3 via the benchmarking exercises. As a result of DECOVALEX-2023 Task G we further improved our understanding and predictability of fracturing processes under THM conditions. This was based on robust numerical simulation methods and in-depth experimental analysis.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

EQSIM—A multidisciplinary framework for fault-to-structure earthquake simulations on exascale computers, part II: Regional simulations of building response

The existing observational database of the regional-scale distribution of strong ground motions and measured building response for major earthquakes continues to be quite sparse. As a result, details of the regional variability and spatial distribution of ground motions, and the corresponding distribution of risk to buildings and other infrastructure, are not comprehensively understood. Utilizing high-performance computing platforms, emerging high-resolution, physics-based ground motion simulations can now resolve frequencies of engineering interest and provide detailed synthetic ground motions at high spatial density. This provides an opportunity for new insight into the distribution of infrastructure seismic demands and risk. In the work presented herein, the EQSIM fault-to-structure computational framework described in a companion paper, McCallen et al., is employed to investigate the regional-scale response of buildings to large earthquakes. A representative M = 7.0 strike-slip event is used to explore the distribution and amplitude of building demand, and comparisons are made between building response computed with fault-to-structure simulations and building response computed with existing measured near-fault earthquake records. New information on the distribution and variability of building response from high-performance parallel simulations is described and analyzed, and favorable first comparisons between building response predicted with both fault-to-structure simulations and real ground motions records are presented.

58 GEOSCIENCES↗

DOE OSTI2023

Coupled Investigation of Fracture Permeability Impact on Reservoir Stress and Seismic Slip Behavior

Our goal is to develop, apply and validate a holistic thermal, hydrologic, mechanical, and chemical (THMC) workflow that includes evaluation of induced seismic slip in EGS reservoirs. We will integrate experimental and modeling approaches to reduce parameter uncertainty and better predict/mitigate seismic hazard at EGS sites. Our novel approach couples 3D physics-based earthquake simulations with THMC models (THMc+E). This capability will enable improve engineering decisions at Utah-FORGE and move EGS operations toward repeatable, robust, economically viable, and socially accepted development. For example, our THMC+E models will predict circulation scenarios and related seismic hazard for a suite of flow rates and under uncertainty, thus enabling evaluation of optimal circulation strategy. Laboratory experiments will be performed to constrain key model parameters and Bayesian techniques will provide a probabilistic evaluation of parameters used in models. THMC+E simulations will enable exploration various circumstances that may hinder EGS success and develop mitigation strategies.

58 GEOSCIENCES↗

DOE OSTI2024

5-2428: Fracture Permeability Impact on Seismic Slip Behavior

58 GEOSCIENCES↗

DOE OSTI2020

Multiscale formulation of frictional contact mechanics at the pore scale

Direct numerical simulation (DNS) yields the highest fidelity predictions of mechanical deformation at the pore scale, but is prohibitively expensive for analyzing large or many samples. Discrete element methods (DEM) are an efficient alternative, but are limited to granular media and incapable of estimating or controlling prediction errors. We present a pore-level multiscale method (PLMM) that approximates DNS efficiently and with controllable accuracy. We focus on the linear elastic response of a consolidated geologic porous medium with arbitrary microstructure, heterogeneous mineralogy, containing cracks or defects. PLMM decomposes the solid phase into non-overlapping subdomains, on which local basis functions are constructed. The bases are then coupled with a global interface problem that accounts for slip or stick contact conditions between the subdomains. PLMM produces an initial, but accurate, approximation to DNS that can be iteratively improved. It is amenable to parallelism and allows for different mesh, models, and physics in each subdomain. An algebraic interpretation of PLMM as a preconditioner is also presented to allow non-intrusive implementation into existing solvers. Lastly, this work extends previous developments of PLMM in fluid dynamics to solid mechanics and enables future extensions towards modeling coupled flow and mechanics problems.

42 ENGINEERING↗

DOE OSTI2024

Quantification of grain boundary effects on the geometrically necessary dislocation density evolution and strain hardening of polycrystalline Mg 4Al using in situ tensile testing in scanning electron microscope and HR-EBSD

In situ tensile testing in a scanning electron microscope (SEM) in conjunction with high-resolution electron backscatter diffraction (HR-EBSD) under load was used to characterize the evolution of geometrically necessary dislocation (GND) densities at individual grain boundaries as a function of applied strain in a polycrystalline Mg—4Al alloy. The increase in GND density was investigated at plastic strains of 0 %, 0.6 %, 2.2 %, 3.3 % from the area including 76 grains and correlated with (i) geometric compatibility between slip systems across grain boundaries, and (ii) plastic incompatibility. We develop expressions for the grain boundary GND density evolution as a function of plastic strain and plastic incompatibility, from which uniaxial tensile stress-strain response of polycrystalline Mg—4Al are computed and compared with experimental measurement. The findings in this study contribute to understanding the mechanisms governing the strain hardening response of single-phase polycrystalline alloys and more reliable prediction of mechanical behaviors in diverse microstructures.

Geometrically necessary dislocations↗

DOE OSTI2021

Identification of crystal plasticity model parameters by multi-objective optimization integrating microstructural evolution and mechanical data

Crystal plasticity models evolve a polycrystalline yield surface using meso-scale descriptions of deformation mechanisms. The activation of deformation mechanisms is governed by crystallography and a set of model parameters, which are typically calibrated through the fitting of mechanical data such as stress–strain curves and elastic lattice strains. Microstructural data such as phase fractions and texture evolution are used for verifying crystal plasticity parameters. In this study, we use a multi-objective genetic algorithm to identify hardening parameters from flow stress curves with an option to incorporate texture into the optimization approach. Robust, generalized objective functions are developed and used to identify sets of parameters pertaining to dislocation density-based hardening laws in visco-plastic and elasto-plastic self-consistent (VPSC and EPSC) homogenization models. First, the parameters are identified for pure Nb directly from texture using an objective function based on generalized spherical harmonics. Since texture evolution is driven by the relative contribution of active slip systems, the parameters governing the evolution of slip resistance ratios can be recovered from fitting discrete textures at a series of strains. Next, a comprehensive set of load reversal data for dual phase (DP) 780 steel is used to fit a hardening law and a back-stress law in EPSC. Finally, parameters pertaining to a complex hardening law for the evolution of slip and twinning in pure α-Ti are identified. Remarkably, using texture as an objective in combination with stress–strain objectives constrains the model of Ti to fully reproduce not only stress–strain and texture evolution but also hierarchical twinning measurements as a function of initial grain size and texture. Furthermore, given an appropriate model fit to representative experimental texture evolution, underlying twin volume fractions contributing to texture evolution can be predicted.

42 ENGINEERING↗

DOE OSTI2021

Combined Structural Analysis of Core and Image Log of TGH 76-31 South East of Mt Baker, Washington State

Despite active volcanism, few geothermal energy resources have been developed in the Cascades Range. Temperature Gradient Hole 76-31 was drilled to ~440 m measured depth to probe for zones where fractures provide fluid conduits that transport deep volcanic heat to shallow depths that could support baseload, carbon neutral electrical generation. These zones were predicted by a Play Fairway assessment (PFA) of resource potential along a zone 11 km west-southwest of the summit of Mount Baker Volcano. Rock core, temperature logs, and an acoustic image log were obtained. By comparison to outcrops, the core has been initially interpreted as the Chilliwack group comprised of partially metamorphosed basaltic to andesitic volcanics. Core mapping reveals complex, steeply dipping networks of fractures and brecciation along slickensided strike slip faults; clay alteration is common in many of these structures. The majority of fractures are thoroughly healed by layers of chlorite and calcite; preservation of pyrite indicates anoxic conditions. The majority of fracture porosity resides in very dense fractures a few centimeters or less in length. The image log provides good insights into attitude of fractures that fully transect the core, but generally underestimates fracture density. The combination of complex, non-planar fracture zones containing many short fractures and healing promote misinterpretation of natural fracture attitude and density in the image log. The healing and anoxic minerals are consistent with the conductive temperature gradient measured in the well below a shallow isothermal zone, although, several fractures are open or only partially healed and resulted in fluid entries into the well. Here, the equilibrated measured temperature gradient of 64ºC/km and calculated heat flow of 145 mW/m2 is more than twice the regional average, indicating local influence of the Mt Baker magmatic system at the Little Park Creek TGH site.

Cascades↗