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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 OSTI2026

How earthquakes organize stress

Stress is not uniform in the Earth. Therefore, we must use natural experiments to measure the distribution of stresses and related quantities, rather than single values. For instance, dynamic triggering shows that faults are uniformly distributed over their loading cycles in Southern California. The probability that a fault ruptures across a barrier measures the in situ energy distribution. Fault roughness reflects the distribution of strength. These natural experiments produce observable distributions that are surprisingly consistent and suggest some degree of self-organization in the Earth’s crust. Once established, the functional form of the distributions can be used to track changes in response to earthquakes as well as to distinguish fundamentally different fault systems. Transient fault locking before stress release in laboratory experiments can be interpreted as a consequence of self-organization of fault stress. The robust self-organization of multiple variables in earthquake systems suggests that the most consequential mechanical outcome of earthquakes may be the redistribution of stress and the strain energy associated with it. The low friction on a fault during seismic slip as inferred by temperature measurements of the Tohoku earthquake is consistent with dissipation playing a secondary role to this redistribution process. Through stress redistribution and interaction, subduction zone faults tend to synchronize, perhaps due to their geometric simplicity, while the continental system of Southern California cannot synchronize, perhaps due to the complexity of the fault network. Earthquakes organize stress in the crust and produce a suite of well-defined, consistent distributions.

earthquakes↗

DOE OSTI2019

Void growth by dislocation adsorption

Here, we propose a dislocation adsorption-based mechanism for void growth in metals, wherein a void grows as dislocations from the bulk annihilate at its surface. The basic process is governed by glide and cross-slip of dislocations at the surface of a void. Using molecular dynamics simulations we show that when dislocations are present around a void, growth occurs more quickly and at much lower stresses than when the crystal is initially dislocation-free. Finally, we show that adsorption-mediated growth predicts an exponential dependence on the hydrostatic stress, consistent with the well-known Rice-Tracey equation.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Ultrahigh strength and plasticity in laser rapid solidified Al–Si nanoscale eutectics

As-cast Al–20wt.% Si alloys were processed via laser rapid solidification (LRS) techniques to create eutectic microstructures with nanoscale interconnected, nanotwinned Si fibers. LRS morphologies exhibit higher flow stress, exceeding 800 MPa and uniform plastic deformation above 20% compared to as-cast alloy that fractures at strains below 8% at flow strength of approximately 200 MPa. The strengthening mechanisms of LRS morphologies are interpreted in terms of the interfacial constraints: increase in yield strength as well as strain hardening rate due to nanoscale confined slip in fibrous Al–Si eutectic, and load transfer and eventual plasticity in the nanoscale Si fibers.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Formation and dissociation of shear-induced high-energy dislocations: insight from molecular dynamics simulations

Solid-phase processing (SPP) allows one to create complex microstructures, not achievable via thermal processing alone. The resulting structures exhibit a rich palette of defects, both thermal and non-thermal, including defect substructures, such as dislocation networks. It is essential to understand the mechanisms of deformation and defect structure formation to guide SPP towards achieving desired microstructures and material properties. In this study, large-scale molecular dynamics simulations are used to investigate the effects of inhomogeneous strain distribution, that mimics deformation conditions of tribological tests, on the evolution of defects under severe shear deformation in polycrystalline Al. Analysis of defect nucleation and reaction pathways reveals that strong geometric constraints suppress the nucleation and slide of low energy dislocation 1/2$\langle110\rangle${111} but promote the nucleation and slide of high energy dislocations, such as [$1\bar1$0] (001) and 1/2 [$1\bar1$$\bar2$]($1\bar1$1). Further, a rough contact surface, characteristic to tribological tests, imposes an inhomogeneous stress field leading to inhomogeneous defect substructures due to location-dependent activation of slip systems. The results suggest that high-energy dislocations can dominate the evolution of grain structures in highly constrained environments, which should be considered in modeling plastic deformation and grain refinement during SPP.

42 ENGINEERING↗

DOE OSTI2024

Resolving crystallographic geometrically necessary dislocations in three dimensions in a hexagonal close packed titanium alloy

Abstract Geometrically necessary dislocation (GND) content is measured from mm 3 -scaled Ti7Al three-dimensional (3D) microstructural data using a theory extended for hexagonal close packed crystals, which accounts for basal, prismatic and pyramidal ⟨ c + a ⟩ type dislocation content. The Ti7Al samples have been mechanically pre-strained to two different strain levels, and will then be strained along the same axis in uniaxial tension during simulation. Both inter- and intragranular GNDs across the microstructures have been characterized, with a large contribution of pyramidal ⟨ c + a ⟩ GNDs, consistent with the relative slip activity involved in pre-straining. The spatially resolved crystallographic GND distributions within the 3D microstructures are used to instantiate a microstructure model for forward modeling deformation simulations by a dislocation density hardening elasto-viscoplastic fast Fourier transform framework. Coarsening the voxel resolution during the initial microstructure construction procedure is shown to strongly impact both the magnitude and spatial distribution of the GNDs and in turn the forward deformation response of the pre-strained material. This study indicates that the voxel resolution desired when transferring from measured to model microstructures need not only be proportionally scaled with the microstructure but also sufficiently fine to capture the subgranular orientation gradients that may already be present in the material.

Materials Science↗

DOE OSTI2022

Shape-driven, emergent behavior in active particle mixtures

Abstract Active particle systems can vary greatly from one-component systems of spheres to mixtures of particle shapes at different composition ratios. We investigate computationally the combined effect of anisotropy and stoichiometry on the collective behavior of two-dimensional active colloidal mixtures of polygons. We uncover three emergent phenomena not yet reported in active Brownian particle systems. First, we find that mixtures containing hexagons exhibit micro-phase separation with large grains of hexagonal symmetry. We quantify a measurable, implicit ‘steric attraction’ between the active particles as a result of shape anisotropy and activity. This calculation provides further evidence that implicit interactions in active systems, even without explicit attraction, can lead to an effective preferential attraction between particles. Next, we report stable fluid clusters in mixtures containing one triangle or square component. We attribute the fluidization of the dense cluster to the interplay of cluster destabilizing particles, which introduce grain boundaries and slip planes into the system, causing solid-like clusters to break up into fluid clusters. Third, we show that fluid clusters can coexist with solid clusters within a sparse gas of particles in a steady state of three coexisting phases. Our results highlight the potential for a wide variety of behavior to be accessible to active matter systems and establish a route to control active colloidal systems through simple parameter designs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

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 OSTI2021

Cosmology at high redshift — a probe of fundamental physics

An observational program focused on the high redshift (2<z<6) Universe has the opportunity to dramatically improve over upcoming LSS and CMB surveys on measurements of both the standard cosmological model and its extensions. Using a Fisher matrix formalism that builds upon recent advances in Lagrangian perturbation theory, we forecast constraints for future spectroscopic and 21-cm surveys on the standard cosmological model, curvature, neutrino mass, relativistic species, primordial features, primordial non-Gaussianity, dynamical dark energy, and gravitational slip. We compare these constraints with those achievable by current or near-future surveys such as DESI and Euclid, all under the same forecasting formalism, and compare our formalism with traditional linear methods. Here, our Python code FishLSS — used to calculate the Fisher information of the full shape power spectrum, CMB lensing, the cross-correlation of CMB lensing with galaxies, and combinations thereof — is publicly available.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

A joint analysis of 3D clustering and galaxy × CMB-lensing cross-correlations with DESI DR1 galaxies

The spectroscopic data from DESI Data Release 1 (DR1) galaxies enables the analysis of 3D clustering by fitting galaxy power spectra and reconstructed correlation functions in redshift space. Given low measurements of the amplitude of structure from cosmic shear at z ∼ 1, redshift space distortions (RSD) + Baryon Acoustic Oscillation (BAO) signals from DESI galaxies combined with weak lensing can break degeneracies and provide a tight alternative constraint on the z ∼ 1 amplitude of structure. In this paper we perform joint analyses that combine full-shape + post-reconstruction information from the DESI DR1 BGS and LRG samples along with angular cross-correlations with Planck PR4 and ACT DR6 CMB lensing maps. We show that adding galaxy-lensing cross-correlations tightens clustering amplitude constraints, improving σ 8 uncertainties by 30% over RSD+BAO alone. We also include angular galaxy-galaxy and galaxy-lensing spectra using photometric samples from the DESI Legacy Survey to further improve constraints. Our headline results are σ 8 = 0.803 ± 0.017, Ω m = 0.3037 ± 0.0069, and S 8 = 0.808 ± 0.017. Given DESI's preference for higher σ 8 compared to lower values from BOSS, we perform a catalog-level comparison of LRG samples from both surveys. We test sensitivity to dark energy assumptions by relaxing our ΛCDM prior and allowing for evolving dark energy via the w 0 - w a parameterization. We find our S 8 constraints to be relatively unchanged despite a 3.5σ tension with the cosmological constant model when combining with the Union3 supernova likelihood. Finally we test general relativity (GR) by allowing the gravitational slip parameter (γ) to vary, and find γ = 1.17 ± 0.11 in mild (∼ 1.5σ) tension with the GR value of 1.0.

cosmological parameters from LSS↗

DOE OSTI2022

Frictional properties of Opalinus Clay: influence of humidity, normal stress and grain size on frictional stability

SUMMARY The Opalinus Clay (OPA) is a clay-rich formation considered as a potential host rock for radioactive waste repositories and as a caprock for carbon storage in Switzerland. Its very low permeability (10−19 to 10−21 m2) makes it a potential sealing horizon, however the presence of faults that may be activated during the lifetime of a repository project can compromise the long-term hydrological confinement, and lead to mechanical instability. Here, we have performed laboratory experiments to test the effect of relative humidity (RH), grain size (g.s.) and normal stress on rate-and-state frictional properties and stability of fault laboratory analogues corresponding to powders of OPA shaly facies. The sifted host rock powders at different grain size fractions (<63 μm and 63 < g.s. < 125 μm), at room (∼25 per cent) and 100 per cent humidity, were slid in double-direct shear configuration, under different normal stresses (5–70 MPa). We observe that peak friction, μpeak and steady-state friction, μss, depend on water vapour content and applied normal stress. Increasing relative humidity from ∼25 per cent RH (room humidity) to 100 per cent RH causes a decrease of frictional coefficient from 0.41 to 0.35. The analysis of velocity-steps in the light of rate-and-state friction framework shows that the stability parameter (a–b) is always positive (velocity-strengthening), and it increases with increasing sliding velocity and humidity. The dependence of (a–b) on slip rate is lost as normal stress increases, for each humidity condition. By monitoring the variations of the layer thickness during the velocity steps, we observe that dilation (Δh) is directly proportional to the sliding velocity, decreases with normal stress and is unaffected by humidity. Microstructural analysis shows that most of the deformation is accommodated within B-shear zones, and the increase of normal stress (σn) promotes the transition from strain localization and grain size reduction to distributed deformation on a well-developed phyllosilicate network. These results suggest that: (1) the progressive loss of velocity dependence of frictional stability parameter (a–b) at σn > 35 MPa is dictated by a transition from localized to distributed deformation and (2) water vapour content does not affect the deformation mechanisms and dilation, whereas it decreases steady-state friction (μss), and enhances fault stability.

58 GEOSCIENCES↗

DOE OSTI2019

Simulation of site and topographic effects on ground motion in Los Alamos, NM mesas

Mesas, which consist of an elevated area of land with a flat top and steep cliffs at the sides, are one of the common geological formations present in the Los Alamos region. Previous research has shown that geological formations such as sedimentary canyons can amplify soil response during earthquakes. There have also been parametric studies to understand the response of an idealized and isolated mountain/canyon under inclined plane waves. In this study, a 2-D linear anelastic soil domain, with topography modelled after the Los Alamos region with many mesas and canyons, is considered to understand site-specific topographic effects in the presence of non-isolated topographical features. Various earthquake sources configurations ranging from point sources to finite faults with varying rupture length, dip angles and spatial slip distributions are considered. To isolate the effect of topography, three other soil domains—a homogeneous half-space, homogeneous half-space with mesas and canyons, and a computational domain with just the soil properties from the Los Alamos region on a flat soil domain is also considered. 2-D site-response analyses of these soil domains under earthquake excitation show that the free-field response of the soil can be amplified or de-amplified depending on the topography of the region and the location of the station relative to the fault. These studies also show that even relatively small mesas with height less than 100 m can significantly amplify the response (by a factor of 2 or more), which differ from the much smaller amplification factors (≤1.2) specified by standard building codes such as Eurocode-8 (2000) for topographical features with a similar slope. De-amplifications are also fairly common, especially close to the canyons. The results from this study agree qualitatively with those from the ambient vibration study conducted by Stolte et al. on a mesa from the Los Alamos region. Furthermore, such site-specific studies provide important insights into the variability of the topographic amplification factors within a region of interest. Such knowledge is important in the design of safety-related critical infrastructure located within that region.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Theoretical description of atomtronic Josephson junctions in an optical lattice

Experimental realizations of “atomtronic” Josephson junctions have recently been created in annular traps in relative rotation with respect to potential barriers that generate the weak links. If these devices are additionally subjected to an optical lattice potential, then they can incorporate strong-coupling Mott physics within the design, which can modify the behavior and can allow for interesting new configurations of barriers and of superfluid flow patterns. We examine theoretically the behavior of a Bose superfluid in an optical lattice in the presence of an annular trap and a barrier across the annular region which acts as a Josephson junction. As the superfluid is rotated, circulating super-currents appear. Beyond a threshold superfluid velocity, phase slips develop, which generate vortices. We use a finite temperature strong-coupling expansion about the mean-field solution of the Bose Hubbard model to calculate various properties of such devices. Additionally, we discuss some of the rich behavior that can result when there are Mott regions within the system.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2026

Controlling Deformation in Al/Ti: How Interface Roughness and Orientation Drive Bimetal Mechanics

The microstructural characteristics and morphology of interfaces in metals can be crucial in governing the initiation of plasticity and early deformation mechanisms under extreme conditions. During high-strain-rate deformation, these interfaces significantly affect dislocation nucleation, twinning, and other mechanisms that directly impact material strength and failure. Despite their importance, a substantial knowledge gap remains between the observed macroscopic material behavior and the underlying role of bimetal interfaces in plasticity initiation. Here, to address this gap, large-scale molecular dynamics simulations are performed on Al/Ti bimetal structures to examine the effect of interface characteristics on the onset of plasticity under uniaxial compression. Specifically, this study investigates how interface roughness (flat vs waveform interfaces) modifies the initiation of plastic events in the microstructure. Atomistic simulations indicate that interface roughness (a microscopic behavior) reduces the stress required for dislocation nucleation, thereby reducing the peak stress relative to a flat interface. For the square interface, the step height strongly influences plasticity initiation by setting the separation of locally flat regions. Varying the interface rotation relative to the loading direction (macroscopic behavior) reveals that the peak stress for both flat and waveform interfaces initially decreases and then increases with rotation, accompanied by a shift in dominant mechanisms—from Al twinning (flat) to interface sliding and Ti-dominated phase transformation and twinning at lower angles. The change in the stress-strain slope during initial compression reflects how rotation alters the resolved shear stress and activates different slip systems. Overall, the study provides valuable insights into the role of bimetal interfaces in controlling plasticity initiation and early deformation pathways for Al/Ti under extreme loading conditions.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Pervasive symmetry-lowering nanoscale structural fluctuations in the cuprate La 2−𝑥 ⁢Sr 𝑥 ⁢Cu⁢O 4

The cuprate superconductors are among the most widely studied quantum materials, yet there remain fundamental open questions regarding their electronic properties and the role of structural degrees of freedom. Recent neutron and x-ray scattering measurements uncovered exponential scaling with temperature of the strength of orthorhombic fluctuations in the tetragonal phase of La 2−𝑥⁢ Sr 𝑥 ⁢Cu⁢O 4 and Tl 2 ⁢Ba 2 ⁢Cu⁢O 6+𝛿 , unusual behavior that closely resembles prior results for the emergence of superconducting fluctuations, and that points to a common origin rooted in inherent correlated structural inhomogeneity. Here, in this study, we use neutron and x-ray diffuse scattering to provide further insight into structural fluctuations in La 2−𝑥 ⁢Sr 𝑥 ⁢Cu⁢O 4 . We perform measurements up to temperatures that approach the melting point of the undoped parent compound, and we investigate the effects of in situ in-plane uniaxial elastic stress and plastic deformation. Our neutron scattering results for the parent compound La 2 ⁢Cu⁢O 4 reveal that short-range orthorhombic fluctuations persist to the maximum experimental temperature of nearly 1000 K, i.e., to a significant fraction of the crystallization temperature. At this temperature, the spatial characteristic length extracted from the momentum-space data is still about three lattice constants. The neutron scattering experiment enables quasistatic discrimination and reveals that the response is increasingly dynamic at higher temperatures. We also find that neither compressive elastic stress along the tetragonal [110] direction nor irreversible plastic deformation activating the ⟨100⟩⁢[001] slip system significantly alter the robust orthorhombic fluctuations. Overall, these results support the notion that these fluctuations couple to subtle, underlying inhomogeneity that underpins the cuprate phase diagram. Finally, in La 1.8⁢ Sr 0.2⁢ Cu⁢O 4 , we uncover low-energy structural fluctuations at a nominally forbidden reflection that are distinct from the orthorhombic distortions. While the origin of these fluctuations is not clear, they might be related to the presence of extended defects such as dislocations or stacking faults.

Spieker, R. J. [Univ. of Minnesota, Minneapolis, M↗

DOE OSTI2020

Instantons in chiral magnets

In this work, we exhaustively construct instanton solutions and elucidate their properties in one-dimensional antiferromagnetic chiral magnets based on the $\textit{O}(3)$ nonlinear sigma model description of spin chains with the Dzyaloshinskii-Moriya (DM) interaction. By introducing an easy-axis potential and a staggered magnetic field, we obtain a phase diagram consisting of ground-state phases with two points (or one point) in the easy-axis dominant cases, a helical modulation at a fixed latitude of the sphere, and a tricritical point allowing helical modulations at an arbitrary latitude. We find that instantons (or skyrmions in two-dimensional Euclidean space) appear as composite solitons in different fashions in these phases: temporal domain walls or wall-antiwall pairs (bions) in the easy-axis dominant cases, dislocations (or phase slips called merons) with fractional instanton numbers in the helical state, and isolated instantons and calorons living on the top of the helical modulation at the tricritical point. We also show that the models with DM interaction and an easy-plane potential can be mapped into those without them, providing a useful tool to investigate the model with the DM interaction.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Controllable vortex shedding from dissipative exchange flows in ferromagnetic channels

Ferromagnetic channels subject to spin injection at one extremum sustain long-range coherent textures that carry spin currents known as dissipative exchange flows (DEFs). In the weak injection regime, spin currents carried by DEFs decay algebraically and extend through the length of the channel, a regime known as spin superfluidity. Similar to fluids, these structures are prone to phase slips that manifest as vortex-antivortex pairs. In this work, we numerically study vortex shedding from DEFs excited in a magnetic nanowire with a physical obstacle. Using micromagnetic simulations, we find regimes of laminar flow and vortex shedding as a function of obstacle position tunable by the spin injection sign and magnitude. Vortex-antivortex pairs translate forward (VF regime) or backward (VB regime) with respect to the detector's extremum, resulting in well-defined spectral features. Qualitatively similar results are obtained when temperature, anisotropy, and weak nonlocal dipole fields are included in the simulations. These results provide clear features associated with DEFs that may be detected experimentally in devices with nominally identical boundary conditions. Furthermore, our results suggest that obstacles can be considered as DEF control gates, opening an avenue to manipulate DEFs via physical defects.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Two types of superconducting pairs in stripe-ordered La 2 - x Ba x CuO 4 ( x = 1 / 8 ) : Evidence from resistivity measurements

Recent angle-resolved c-axis resistivity measurements of the stripe-ordered La 2-x Ba x CuO 4 (LBCO) with x = 1/8 revealed an unexpected dependence on the direction of the in-plane magnetic field. We argue that these and other available data for the c-axis transport point to the existence of superconducting pairs of two different types in the x = 1/8 LBCO below the stripe ordering temperature. The pairs of one type carry finite momentum and are confined to the Cu-O planes; the pairs of other type (probably the conventional d wave with zero momentum) propagate along narrow conducting channels traversing the sample in the c-axis direction. The evidence for this comes from the observed exponential temperature dependence of the c-axis resistivity ρ c (T ) which we attribute to the thermally excited slips of the superconducting phase and flux flows. We present a simple theory to fit the observed π/2-periodic dependence of ρ c on the direction of the in-plane magnetic field and the other data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗