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DOE OSTI2025

Data for "Viral Delivery of Recombinases Activates Heritable Genetic Switches in Plants"

Viral vectors provide an increasingly versatile platform for transformation-free reagent delivery to plants. RNA viral vectors can be used to induce gene silencing, overexpress proteins, or introduce gene editing reagents; however, they are often constrained by carrying capacity or restricted tropism in germline cells. Site-specific recombinases that catalyze precise genetic rearrangements are powerful tools for genome engineering that vary in size and, potentially, efficacy in plants. In this work, we show that viral vectors based on tobacco rattle virus (TRV) deliver and stably express four recombinases ranging in size from ∼0.6 to ∼1.5 kb and achieve simultaneous marker removal and reporter activation through targeted excision in transgenic Nicotiana benthamiana lines. TRV vectors with Cre, FLP, CinH, and Integrase13 efficiently mediated recombination in infected somatic tissue and led to heritable modifications at high frequency. An excision-activated Ruby reporter enabled simple and high-resolution tracing of infected cell lineages without the need for molecular genotyping. Together, our experiments broaden the scope of viral recombinase delivery and offer insights into infection dynamics that may be useful in developing future viral vectors.

gene editing↗

DOE OSTI2025

A New Vehicle-to-Vehicle Communication System: Visual-Enhanced Cooperative Traffic Operations

The advent of Connected and Autonomous Vehicles (CAVs) has highlighted the necessity for robust communication systems between vehicles and their environment. This study introduces a novel vehicle-to-vehicle (V2V) communication system, termed the Visual-Enhanced Cooperative Traffic Operations (VECTOR) system. The VECTOR system addresses the need for robust communication by converting dynamic data (including velocity and yaw angle data) into binary code, which is displayed on an LED panel mounted on the top of the vehicle. Following vehicles detect this panel and decode the information using a camera, implementing a visual-based communication method. VECTOR system employs a comprehensive five-module process. Initially, polynomial fitting techniques are applied to velocity data over fixed time intervals using third-degree polynomials, with validation via R² and MSE metrics. The second module converts velocity and yaw angle data into binary form, thereby enhancing detection and processing efficiency. The third module focuses on improving detection stability across various environmental conditions to enhance traffic safety. The fourth module decodes the binary data back into trajectory information, ensuring the fidelity of velocity and yaw angles. The final module integrates eco-control through the VECTOR system, employing advanced control algorithms to minimize energy consumption in CAVs. Experimental evaluations conducted using a modified CAV test platform based on the Lincoln MKZ demonstrate the feasibility and efficiency of the VECTOR system, achieving a 75% R-squared accuracy rate in replicating original velocity data. This methodology not only highlights potential applications but also underscores significant implications for advancing CAV technology.

Ma, Ke↗

DOE OSTI2026

J/ψ photoproduction at the threshold with GlueX

High-statistics total cross sections for the vector meson photoproduction at the threshold: γp → ωp (from A2 at MAMI, ELPH, and CBELSA), γp → ϕp (from CLAS6 at JLab and LEPS at SPring-8), and γp → J/ψp (from GlueX at JLab) allow one to extract the absolute value of vector meson nucleon scattering length using Vector Meson Dominance (VMD) model. The “young” vector meson hypothesis may explain the fact that the obtained scattering length values for the nucleon. ϕ-meson compared to the typical hadron size of approximately ∼ 1 fm indicates that the proton is more transparent for the ϕ-meson compared to the ω-meson and is much less transparent than the J/ψ-meson. The extended analysis of Υ-meson photoproduction using quasi-data from the QCD approach is in perfect agreement with the light-meson findings using experimental data. Finally, the ability of J-PARC to measure $π^{–}p → ϕn$ and $π^{–}p → J/ψn$ at the threshold, which are free from the VMD model, is presented. It enables one to understand the dynamics of $s\bar{s}$ and $c\bar{c}$ production at threshold and to search for the effects of LHCb’s heavy quark exotic states.

Vector meson nucleon scattering length↗

DOE OSTI2024

Transient anisotropic kernel for probabilistic learning on manifolds

PLoM (Probabilistic Learning on Manifolds) is a method introduced in 2016 for handling small training datasets by projecting an Itô equation from a stochastic dissipative Hamiltonian dynamical system, acting as the MCMC generator, for which the KDE-estimated probability measure with the training dataset is the invariant measure. PLoM performs a projection on a reduced-order vector basis related to the training dataset, using the diffusion maps (DMAPS) basis constructed with a time-independent isotropic kernel. In this paper, we propose a new ISDE projection vector basis built from a transient anisotropic kernel, providing an alternative to the DMAPS basis to improve statistical surrogates for stochastic manifolds with heterogeneous data. The construction ensures that for times near the initial time, the DMAPS basis coincides with the transient basis. For larger times, the differences between the two bases are characterized by the angle of their spanned vector subspaces. The optimal instant yielding the optimal transient basis is determined using an estimation of mutual information from Information Theory, which is normalized by the entropy estimation to account for the effects of the number of realizations used in the estimations. Consequently, this new vector basis better represents statistical dependencies in the learned probability measure for any dimension. Three applications with varying levels of statistical complexity and data heterogeneity validate the proposed theory, showing that the transient anisotropic kernel improves the learned probability measure.

Diffusion maps↗

DOE OSTI2024

Nanometric modulations of the magnetic structure of the element Nd

The rare earth neodymium arguably exhibits the most complex magnetic ordering and series of magnetic phase transitions of the elements. Here we report the results of small-angle neutron scattering (SANS) measurements as a function of temperature and applied magnetic field to study magnetic correlations on nanometer length scales in Nd. We support these results with additional neutron diffraction, thermodynamic and synchrotron x-ray measurements. The SANS measurements reveal the presence of modulation vectors characterizing the ordered spin configuration which exhibit changes in magnitude and direction that are phase dependent. Between 5.9 and 7.6 K an additional modulation vector is observed with magnitude Q = 0.12 Å -1 . This scattering appears to originate from order of the Nd layers which contain a center of inversion. Tracking this modulation vector as a function of magnetic field indicates a phase boundary at ≈1 T. The modulation vectors observed in this study establish the presence of nanometer length scale spin textures which are likely stabilized by frustrated Ruderman–Kittel–Kasuya–Yosida (RKKY) interactions.

36 MATERIALS SCIENCE↗

DOE OSTI2026

The X17 with Chiral Couplings

In recent years, the ATOMKI collaboration has performed a series of measurements of excited nuclei, observing a resonant excess of electron-positron pairs at large opening angles compared to the Standard Model prediction. The excess has been hypothesized to be due to the production of a new spin-1 or spin-0 particle, X17, with a mass of about 17 MeV. Recently, the PADME experiment has reported an excess in the $e^+e^-$ cross section at center-of-mass energies near 17 MeV, perhaps further hinting at the existence of a new state. Studies of the spin-1 case have hitherto focused on either vector {\em or} axial-vector couplings to quarks and leptons, whereas UV theories more naturally produce {\em both} vector and axial-vector (\textit{i.e.} chiral) couplings, analogous to the Standard Model weak interactions. We consider the ATOMKI anomalies in the context of an $X$ with chiral couplings to quarks and explore the parameter space that can explain the ATOMKI anomalies, contrasting them with experimental constraints. We find that it is possible to accommodate the reported ATOMKI signals. However, the $99\%$ CL region is in tension with null results from searches for atomic parity violation and direct searches for new low mass physics coupled to electrons. This tension is found to be driven by the magnitude of the reported excess in the transition of $^{12}{\rm C}(17.23)$, which drives the best-fit region towards excluded couplings.

Fieg, Max H. [UC, Irvine; UC, Irvine (main); Fermi↗

DOE OSTI2024

Constraining neutrinophilic mediators at FASER ν , FLArE, and FASER ν 2

High energy collider neutrinos have been observed for the first time by the FASER ν experiment. The detected spectrum of collider neutrinos scattering off nucleons can be used to probe neutrinophilic mediators with GeV-scale masses. We find that constraints on the pseudoscalar (axial vector) neutrinophilic mediator are close to the scalar (vector) case since they have similar cross section in the neutrino massless limit. We perform an analysis on the measured muon spectra at FASER ν , and find that the bounds on the vector mediator from the current FASER ν data are comparable to the existing bounds at m Z ′ ≈ 0.2 GeV . We also study the sensitivities to a neutrinophilic mediator at future Forward Physics Facilities including FLArE and FASER ν 2 by using both the missing transverse momentum and the charge identification information. We find that FLArE and FASER ν 2 can impose stronger bounds on both the scalar and vector neutrinophilic mediators than the existing bounds. The constraints on the scalar mediator can reach 0.08 (0.1) for m ϕ ≲ 1 GeV with (without) muon charge identification at FASER ν 2 . Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Vesicular Stomatitis Virus Transmission Dynamics Within Its Endemic Range in Chiapas, Mexico

Vesicular stomatitis virus (VSV), comprising vesicular stomatitis New Jersey virus (VSNJV) and vesicular stomatitis Indiana virus (VSIV), emerges from its focus of endemic transmission in Southern Mexico to cause sporadic livestock epizootics in the Western United States. A dearth of information on the role of potential arthropod vectors in the endemic region hampers efforts to identify factors that enable endemicity and predict outbreaks. In a two-year, longitudinal study at five cattle ranches in Chiapas, Mexico, insect taxa implicated as VSV vectors (blackflies, sandflies, biting midges, and mosquitoes) were collected and screened for VSV RNA, livestock vesicular stomatitis (VS) cases were monitored, and serum samples were screened for neutralizing antibodies. VS cases were reported during the rainy (n = 20) and post-rainy (n = 2) seasons. Seroprevalence against VSNJV in adult cattle was very high (75–100% per ranch) compared with VSIV (0.6%, all ranches). All four potential vector taxa were sampled, and VSNJV RNA was detected in each of them (11% VSNJV-positive of 874 total pools), while VSIV RNA was only detected in four pools of mosquitoes. Our findings indicate that VSNJV is the dominant serotype across our sampling sites with a variety of potential insect vectors involved in its transmission throughout the year. Although no livestock cases were reported in Chiapas during the dry season, VSNJV was detected in insects during this period, suggesting that mechanisms other than transmission from livestock support VSV endemicity.

Virology↗

DOE OSTI2026

An mRNA vaccine encoding the Ebola virus glycoprotein induces high neutralizing antibody titers and provides strong protection against lethal infections in mouse models

Ebola virus (EBOV) is the causative agent of Ebola disease (EBOD), a viral hemorrhagic fever with a notably high case fatality rate. Current treatments for EBOD are limited to monoclonal antibodies or two licensed viral vector vaccines, a recombinant vesicular stomatitis virus (rVSV)-vectored vaccine or an adenovirus and modified vaccinia Ankara regimen. However, comparisons of protection, efficacy, and durability with alternative nucleotide platforms remain understudied. Here, we evaluated the immunogenicity of an mRNA vaccine expressing the EBOV glycoprotein (GP) in parallel with rVSV- and DNA-based vaccine platforms. The mRNA EBOV-GP vaccine, formulated in lipid nanoparticles, elicited significantly higher levels of total IgG and neutralizing antibody titers compared to the rVSV-EBOV-GP vaccine. Linear antibody epitope analysis indicated a preference for targeting the mucin-like domain in EBOV-GP1 following rVSV-based vaccination, while the mRNA platform distinctly targeted the internal fusion loop of EBOV-GP2. After characterizing the immunogenicity of the mRNA vaccine, two models of EBOD were used to demonstrate its protective efficacy: a surrogate rVSV-based challenge model of EBOD using type-I interferon deficient C57BL/6 mice and infection of BALB/c mice with authentic mouse-adapted EBOV. In both studies, the EBOV mRNA vaccine fully protected the mouse cohorts against morbidity and mortality. Additionally, the EBOV mRNA vaccine produced greater neutralizing antibody titers compared to the DNA EBOV-GP vaccine. These results suggest that an mRNA vaccine expressing EBOV-GP can induce robust, functional humoral responses that are protective against EBOD, warranting further development as an alternative to, or as part of a vaccine strategy including, viral vectored vaccines.

DNA vaccines↗

DOE OSTI2025

Energy-enhanced dimension eight SMEFT effects in VBF Higgs production

We study Higgs boson production via vector boson fusion at the LHC, focusing on the process pp → H + jj and capturing the leading energy-enhanced contributions within the Standard Model Effective Field Theory (SMEFT) up to order 1/Λ$^{4}$. Employing energy-scaling arguments, we predict the magnitude of each higher-dimensional operator’s contribution. Utilizing the geometric formulation of SMEFT, our analysis incorporates dimension-eight operators not previously considered. We find that the kinematics of vector boson fusion — characterized by two highly forward jets — tend to suppress contributions from higher-dimensional operators, requiring a lower scale Λ for SMEFT effects to become observable. This suggests that the SMEFT remains valid for lower Λ than expected. Combined with the fact that LEP constrains the dimension-six operators with the most considerable impact on vector boson fusion, a regime exists where dimension-eight operators can have significant effects. In many cases, these dimension-eight operators also influence associated production processes like pp → HV(jj), though differences in analysis cuts and kinematics mean this is not always the case. Our findings provide insights that could refine the search for SMEFT signals in collider experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Search for new particles in final states with a boosted top quark and missing transverse momentum in proton-proton collisions at $\sqrt{s}$ = 13 TeV with the ATLAS detector

A search for events with one top quark and missing transverse momentum in the final state is presented. The fully hadronic decay of the top quark is explored by selecting events with a reconstructed boosted top-quark topology produced in association with large missing transverse momentum. The analysis uses 139 fb -1 of proton-proton collision data at a centre-of-mass energy of $\sqrt{s}$ = 13 TeV recorded during 2015-2018 by the ATLAS detector at the Large Hadron Collider. The results are interpreted in the context of simplified models for Dark Matter particle production and the single production of a vector-like T quark. Without significant excess relative to the Standard Model expectations, 95% confidence-level upper limits on the corresponding cross-sections are obtained. The production of Dark Matter particles in association with a single top quark is excluded for masses of a scalar (vector) mediator up to 4.3 (2.3) TeV, assuming m χ = 1 GeV and the model couplings λ q = 0.6 and λ χ = 0.4 (a = 0.5 and g χ = 1). The production of a single vector-like T quark is excluded for masses below 1.8 TeV assuming a coupling to the top quark κ T = 0.5 and a branching ratio for T → Zt of 25%.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Constraining non-standard neutrino interactions with neutral current events at long-baseline oscillation experiments

We explore, for the first time, neutral-curren t events at long-baseline experiments to constrain vector and axial-vector neutrino non-standard interactions (NSI) with quarks. We leverage the flavor dependence of NSIs to perform an oscillation analysis in the neutral- current channel. We first introduce a framework to parametrize the effect of NSI on the cross section. Then, as an example, we analyze NOvA neutral-current data which provides significantly improved constraints on the axial-vector NSI parameters ${\varepsilon}_{\mu \mu}^A$, ${\varepsilon}_{\tau \tau}^A$ and ${\varepsilon}_{e\mu}^A$. This is highly complementary to constraints from SNO data, which, differently from long-baseline neutral current data, is not sensitive to isospin conserving NSIs ${\varepsilon}_u^A$ = ${\varepsilon}_d^A$. Additionally, we disfavor large values of the diagonal vectorial NSI ${\varepsilon}_{\mu \mu}^{VV}$ and ${\varepsilon}_{\tau \tau}^V$ which originate from the LMA-Dark solution. We also highlight the complementarity between NSI searches at oscillation experiments using charged current and neutral current channels.

neutrino interactions↗

DOE OSTI2024

Non-standard neutrino interactions mediated by a light scalar at DUNE

Abstract We investigate the effect on neutrino oscillations generated by beyond-the-standard-model interactions between neutrinos and matter. Specifically, we focus on scalar-mediated non-standard interactions (NSI) whose impact fundamentally differs from that of vector-mediated NSI. Scalar NSI contribute as corrections to the neutrino mass matrix rather than the matter potential and thereby predict distinct phenomenology from the vector-mediated ones. Similar to vector-type NSI, the presence of scalar-mediated neutrino NSI can influence measurements of oscillation parameters in long-baseline neutrino oscillation experiments, with a notable impact on CP measurement in the case of DUNE. Our study focuses on the effect of scalar NSI on neutrino oscillations, using DUNE as an example. We introduce a model-independent parameterization procedure that enables the examination of the impact of all non-zero scalar NSI parameters simultaneously. Subsequently, we convert DUNE’s sensitivity to the NSI parameters into projected sensitivity concerning the parameters of a light scalar model. We compare these results with existing non-oscillation probes. Our findings reveal that the region of the light scalar parameter space sensitive to DUNE is predominantly excluded by non-oscillation probes, especially when considering all nonzero parameters simultaneously for DUNE.

Physics↗

DOE OSTI2024

Beyond the Holographic Entropy Cone via Cycle Flows

Motivated by bit threads, we introduce a new prescription for computing entropy vectors outside the holographic entropy cone. By utilizing cycle flows on directed graphs, we show that the maximum cycle flow associated to any subset of vertices, which corresponds to a subsystem, manifestly obeys purification symmetry. Furthermore, by restricting ourselves to a subclass of directed graphs, we prove that the maximum cycle flow obeys both subadditivity and strong subadditivity, thereby establishing it as a viable candidate for the entropy associated to the subsystem. Lastly, we demonstrate how our model generalizes the entropy vectors obtainable via conventional flows in undirected graphs, as well as conjecture that our model similarly generalizes the entropy vectors arising from hypergraphs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

A Particle-in-Cell Method for Plasmas with a Generalized Momentum Formulation, Part II: Enforcing the Lorenz Gauge Condition

In a previous paper Christlieb et al. (A particle-in-cell method for plasmas with a generalized momentum formulation, part I: Model formulation, 2024), we developed a new particle-in-cell (PIC) method for the relativistic Vlasov–Maxwell system in which the electromagnetic fields and the equations of motion for the particles were cast in terms of scalar and vector potentials through a Hamiltonian formulation. This new method evolved the potentials under the Lorenz gauge using integral equation methods. New methods to construct spatial derivatives of the potentials that converge at the same rates as the fields were also presented. The new particle method was compared against standard explicit discretizations, including the well-known FDTD-PIC method, for a range of applications involving sheaths and particle beams. Here, this paper extends this new class of methods by focusing on the enforcement the Lorenz gauge condition in both exact and approximate forms using co-located meshes. A time-consistency property of the proposed field solver for the vector potential form of Maxwell’s equations is established, which is shown to preserve the equivalence between the semi-discrete Lorenz gauge condition and the analogous semi-discrete continuity equation. Using this property, we present three methods to enforce a semi-discrete gauge condition. The first method introduces an update for the continuity equation that is consistent with the discretization of the Lorenz gauge condition. Both the finite difference and spectral implementations satisfy this discrete gauge condition to machine precision. The second approach we propose enforces a semi-discrete continuity equation using the boundary integral solution to the field equations. The potential benefit of this approach is that it eliminates spatial derivatives that appear on the particle data, namely the current density, which is often calculated by linear combinations of low-order spline basis functions. This method is ideally suited to boundary integral equation methods that invert multi-dimensional operators without dimensional splitting techniques and will be the subject of future work. The third approach introduces a gauge correcting method that makes direct use of the gauge condition to modify the scalar potential and uses local maps for both the charge and current densities. This results in a gauge error, as the maps do not enforce the continuity equation. The vector potential coming from the current density is taken to be exact, and using the Lorenz gauge, we compute a correction to the scalar potential that makes the two potentials satisfy the gauge condition. This method also enforces the gauge condition to machine precision. We demonstrate two of the proposed methods in the context of periodic domains. Problems defined on bounded domains, including those with complex geometric features remain an ongoing effort. However, this work shows that it is possible to design computationally efficient methods that can effectively enforce the Lorenz gauge condition in a non-staggered PIC formulation.

97 MATHEMATICS AND COMPUTING↗

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 OSTI2024

Spatial imaging of polarized deuterons at the Electron-Ion Collider

We study diffractive vector meson production at small-x in the collision of electrons and polarized deuterons e + d $\uparrow$ . We consider the polarization dependence of the nuclear wave function of the deuteron, which results in an azimuthal angular dependence of the produced vector meson when the deuteron is transversely polarized. The Fourier coefficients extracted from the azimuthal angular dependence of the vector meson differential cross-section exhibit notable differences between longitudinally and transversely polarized deuterons. The angular dependence of the extracted effective deuteron radius provides direct insight into the structure of the polarized deuteron wave function. Furthermore, we observe slightly increased gluon saturation effects when the deuteron is longitudinally polarized compared to the transversely polarized case. The small-x observables studied in this work will be accessible at the future Electron-Ion Collider.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Comparing quantum annealing and spiking neuromorphic computing for sampling binary sparse coding QUBO problems

We consider the problem of computing a sparse binary representation of an image. Given an image and an overcomplete, non-orthonormal basis, we aim to find a sparse binary vector indicating the minimal set of basis vectors that when added together best reconstruct the given input. We formulate this problem with an L 2 loss on the reconstruction error, and an L 0 loss on the binary vector enforcing sparsity. First, we solve the sparse representation QUBOs by solving them both on a D-Wave quantum annealer with Pegasus chip connectivity, as well as on the Intel Loihi 2 spiking neuromorphic processor using a stochastic Non-equilibrium Boltzmann Machine (NEBM). Second, using Quantum Evolution Monte Carlo with Reverse Annealing and iterated warm starting on Loihi 2 to evolve the solution quality from the respective machines. We demonstrate that both quantum annealing and neuromorphic computing are suitable for solving binary sparse coding QUBOs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗