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At least 37 records · Page 2

A conserved viral RNA fold enables nuclease resistance across kingdoms of life

Abstract Viral exoribonuclease-resistant RNA (xrRNA) structures block cellular nucleases to produce subgenomic viral RNAs during infection. High sequence variability among xrRNAs from distantly related viruses raises questions about the shared molecular features that enable these RNAs to withstand the strong unwinding forces of exoribonucleases. Here, we present the first structure of a plant-virus xrRNA in its active conformation and uncover universal principles of xrRNA folding. Comparison with the structure of a human-pathogenic flavivirus xrRNA reveals that both share a core structural motif—a protective ring encircling the RNA’s 5′ end—despite lacking sequence similarity. Disrupting this core motif through targeted mutagenesis eliminates exoribonuclease-resistance and attenuates viral infection. We identify hundreds of related structures across multiple virus families, supporting the conservation of this mechanism. Our study demonstrates how distantly related RNA viruses have converged on a common structural strategy to inhibit cellular nucleases, with a universal ring topology as the defining feature of viral xrRNAs.

Biochemistry & Molecular Biology

EIC Physics from Lattice QCD: investigations beyond leading twist

This project proposes theoretical studies of Quantum Chromodynamics (QCD), the theory describing the strong nuclear force among the building blocks (quarks and gluons) of the visible matter. These appear only confined within hadrons, that make up more than 99% of the mass of the matter. Understanding QCD will significantly advance many aspects of science, from the sub-nuclear interactions to astrophysics, and a quantitative theoretical description is imperative. However, this is a challenging task because QCD is a highly nonlinear theory. We propose hadron structure calculations within lattice QCD (LQCD), an ideal ab initio approach based on space-time discretization, which allows the study of the properties of fundamental particles numerically. This is done by defining the continuous equations on a discrete four-dimensional lattice, which results in equations with hundreds of billions of degrees of freedom, and must be simulated in powerful computers.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Why Do Nuclei Stick Together?

Although quantum chromodynamics (QCD) has long been accepted as the underlying theory of the strong nuclear force, connecting the structure and interactions of nuclei to the fundamental parameters of QCD remains challenging. In this talk, I will present new results from lattice QCD and effective field theory that explore how nuclear interactions look in a world where the quarks are much heavier than they are in nature, and discuss lessons that can be learned for nuclear physics as well as searches for physics beyond the Standard Model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Primordial Black Hole Triggered Type Ia Supernovae. I. Impact on Explosion Dynamics and Light Curves

Primordial black holes (PBHs) in the asteroid-mass window are compelling dark matter candidates, made plausible by the existence of black holes and by the variety of mechanisms of their production in the early Universe. If a PBH falls into a white dwarf (WD), the strong tidal forces can generate enough heat to trigger a thermonuclear runaway explosion, depending on the WD’s mass and the PBH’s orbital parameters. In this work, we investigate the WD explosion triggered by the passage of a PBH. We perform 2D simulations of the WD undergoing thermonuclear explosion in this scenario, with the predicted ignition site as a parameter assuming the deflagration–detonation transition model. We study the explosion dynamics, and predict the associated light curves and nucleosynthesis. We find that the model sequence predicts light curves which align with the Phillips relation (B max versus ΔM 15 ). Our models hint at a unifying approach in triggering Type Ia supernovae without involving two distinctive evolutionary tracks.

Dark matter

Short-range correlations in nuclei

Atomic nuclei are held together by the strong nuclear force acting between protons and neutrons (nucleons). While the long range, averaged part of this force is well described by the nuclear shell model, the short-range and tensor components create a fascinating substructure: pairs of nucleons that momentarily approach each other very closely, acquiring large relative momenta. These short-range correlated (SRC) pairs account for roughly 20% of all nucleons in any nucleus and almost all of the high momentum nucleons. This chapter provides an introduction to SRC pairs: their origin in the nucleon-nucleon tensor force, the experimental methods used to study them, principally deep inelastic and quasielastic electron and proton scattering, and the comprehensive picture that has emerged over the past three decades.

FOS: Physical sciences

Zooming in: SCREAM at 100 m using regional refinement over the San Francisco Bay Area

Pushing global climate models to large-eddy simulation (LES) scales over complex terrain has remained a major challenge. This study presents the first known implementation of a global model – SCREAM (Simple Cloud-Resolving E3SM Atmosphere Model) – at 100 m horizontal resolution using a regionally refined mesh (RRM) over the San Francisco Bay Area. Two hindcast simulations were conducted to test performance under both strong synoptic forcing and weak, boundary-layer-driven conditions. We demonstrate that SCREAM can stably run at LES scales while realistically capturing topography, surface heterogeneity, and coastal processes. The 100 m SCREAM-RRM substantially improves near-surface wind speed, temperature, humidity, and pressure biases compared to the baseline 3.25 km simulation, and better reproduces fine-scale wind oscillations and boundary-layer structures. These advances leverage SCREAM's scale-aware SHOC turbulence parameterization, which transitions smoothly across scales without tuning. Performance tests show that while CPU-only simulations remain costly, GPU acceleration with SCREAMv1 on NERSC's Perlmutter system enables two-day hindcasts to complete in under two wall-clock days. Our results open the door to LES-scale studies of orographic flows, boundary-layer turbulence, and coastal clouds within a fully comprehensive global modeling framework.

Geosciences

First Measurement of the Isospin-Dependence of Nuclear Structure Functions at 12 GeV Jefferson Lab

The structure functions of protons and neutrons provide crucial insight into how the strong nuclear force, as described by Quantum Chromodynamics (QCD), manifests at everyday energies, allowing us to better understand precisely how quarks and gluons interact to form the basic building blocks of almost all visible mass in our universe. Despite more than 40 years of experimental and theoretical effort, the EMC effect – the observation that nuclear structure functions appear to be modified from those of free nucleons – is still not fully understood. One open question that remains is whether or not the modification of quark distributions is the same for all quark flavors. Determining the flavor (isospin) dependence of the EMC effect, which is predicted by several models, is essential for coming to a complete understanding of how QCD manifests in nuclei. To this end, inclusive electron Deep Inelastic Scattering (DIS) from nuclei with approximately constant atomic mass number A and variable proton-to-neutron ratio N/Z was measured in Jefferson Lab experiment E12-10-008 to look for isospin-dependent modification of nuclear structure functions. The preliminary EMC ratios presented here cover a kinematic range of 2.8 < Q2 < 8.1 GeV2 and 0.18 < xBj < 1.0. The size of the EMC effect in these nuclei is extracted by calculating the slope of the EMC ratio as a function of Bjorken x (xBj ) over the ranges 0.3 < xBj < 0.6 and 0.3 < xBj < 0.7; these slopes then are compared with existing world data. Our preliminary results do not appear to indicate significant isospin-dependence of the EMC effect, though a more careful study is needed once all results are confirmed.

Cotton, Cameron William [Univ. of Virginia, Charlo

Exotic Hadrons: A Subatomic Bestiary

Particle physicists study unfamiliar forms of matter – matter that hasn’t commonly existed in the cosmos since fractions of a second after the universe began. It has allowed scientists to dive down into an ever-decreasing set of size scales, from molecules, to atoms, to protons and neutrons, and even to quarks. The world of quarks can be a confusing one, but over the past couple decades, it has gotten even more complicated. Using powerful particle accelerators researchers have begun to create and study a truly new form of matter, one in which quarks are combined in unusual ways and one which will teach us some interesting new things about the strong nuclear force.

Lincoln, Don [Fermilab] (ORCID:0000000205997407)

Exploring Resonance Structures in the Partial-Wave Analysis of ¿p0 Photoproduction at GlueX

This thesis studies what happens when a photon (¿) collides with a proton (p) and produces a neutral omega (¿) and pion (p0) pair, with a recoiling proton (p'), expressed as ¿p ¿ ¿p0p'. We study this and other reactions to better understand the strong nuclear force; one of the four fundamental forces that govern all the physics of the universe. This force is specifically responsible for the binding and decay of subatomic particles, such as the ones here. While we understand the ¿ and p0, what we are actually interested in is a short-lived unknown particle X that decays via X ¿ ¿p0. There are a multitude of possible particles X can be, and so our focus in this work is to find out what X is by determining its properties from the particles we measure. We do this via an intricate analysis procedure known as “partial-wave analysis”. By analogy, one can think of our particle detector as a buoy, and the particles we want to analyze (X) as pebbles hitting a pond. The waves created by the pebble will move our buoy, giving us information about the pebble that produced the wave. However, when multiple pebbles hit our pond, the waves overlap and interfere with each other. Our buoy only can measure the complicated interfering result of all the waves. To disentangle this, our partial-wave analysis works by modeling this interference pattern so that we may infer the properties of the pebbles (particles) we produced. In this thesis, we review the relevant experimental history in photoproduction and related production mechanisms, as well as the theoretical foundations that motivate our measurement. We describe the methods used to collect our data at the GlueX experiment stationed at the Jefferson Lab accelerator facility in Newport News, Virginia. We then detail the selections we apply to ensure our events are almost exclusively ¿p ¿ ¿p0p'. We cover the intensity model, how we verify its capabilities, and finally present our results together with systematic studies. Our primary result is the detection of a b1(1235) meson interfering with a wide JPC = 1-- vector state, measured via a mass-independent partial-wave analysis. It provides precise experimental results that can be used as input for theoretical models of the reaction, yielding conclusions about the procedures responsible for how our universe behaves at its most basic level.

Scheuer, Kevin [College of William and Mary, Willi

Direct measurement of thermal Knudsen forces in rarefied gas environments

At micro- and nanoscales, momentum transfer between surfaces is influenced by various physical mechanisms, including quantum fluctuations, electromagnetic interactions, electric charges, and the dynamics of (rarefied) gases. Under non-isothermal conditions, rarefied gases give rise to thermal Knudsen forces whose magnitudes strongly depend on the gas species and surface characteristics. Knudsen forces are particularly relevant in nanotechnology, optical manipulation, and aerospace systems, where gas rarefaction occurs due to highly confined geometries, sub-micrometer length scales, and reduced particle densities. Despite their significance, predictive modeling of Knudsen forces is limited by a lack of comprehensive experimental data across diverse materials and surface morphologies. Here, in this work, we present a highly sensitive and adaptable measurement platform capable of directly quantifying Knudsen forces using a suspended, interchangeable micro-cantilever within controlled rarefied helium and nitrogen environments. The system integrates optical fiber interferometry to precisely capture out-of-plane displacements at sub-micrometer resolution, driven by Knudsen forces. From the empirical data, we derive a robust correlation linking the magnitudes of Knudsen forces to energy accommodation coefficients, offering deeper insights into the underlying gas–surface interaction mechanisms.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC

Including the vacuum energy in stellarator coil design

Being three-dimensional, stellarators have the advantage that plasma currents are not essential for creating rotational-transform; however, the external current-carrying coils in stellarators can have strong geometrical shaping, which can complicate the construction. Reducing the inter-coil electromagnetic forces acting on strongly shaped 3D coils and the stress on the support structure while preserving the favorable properties of the magnetic field is a design challenge. In this work, we recognize that the inter-coil forces are the gradient of the vacuum magnetic energy. We introduce an objective functional built on the usual quadratic flux on a prescribed target surface together with a weighed penalty on the vacuum energy. The Euler–Lagrange equation for stationary states is derived, and numerical illustrations are computed using a modern stellarator optimization framework. A study of the effect of the energy functional on the inter-coil forces is conducted and the energy is shown to be a promising quantity in producing coils with low forces.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

How Thermodynamic, Electronic, and Steric Factors Influence Mesitylcopper Oligomers

Mesitylcopper (CuMes) is a highly versatile organocopper reagent used in both organic and inorganic syntheses. It has previously been shown that CuMes exists as a tetrameric or pentameric cyclic oligomer [CuMes] n (n = 4, 5), both in solution and in the solid state. The bonding arrangement between the [CuMes] units has qualitatively been described as localized three-center twoelectron (3c-2e) bonds. However, the electronic, structural, and thermodynamic forces driving this aggregation are still not well understood. For this reason, we employed density functional theory (DFT) calculations to study mesitylcopper as a monomeric [CuMes] unit and [CuMes]n oligomers with n = 2 to n = 7. We found that there is a strong electronic driving force for aggregation caused by strong mixing between the Cu’s d orbitals and Mes’s π orbitals in oligomers larger than the dimer. This mixing is only optimized in oligomers with n ≥ 3, where the mesityl group is no longer bonded to a single copper center but instead becomes a bridging ligand. Beyond the trimer, steric and entropic factors become relevant for determining the relative stabilities of the different aggregates, with midsized oligomers (n = 4−5) having the optimal balance between the electronic Cu−C bonding character, Cu···Cu attractive forces, entropy, reduced internal ring strain, and reduced steric interactions between the mesityl groups.

Copper

Observed Temperature and Moisture Advection Characteristics in the Southern Great Plains

Until recently, advection profiles in the planetary boundary layer have been difficult to quantify from observations. As a result, not much is known about its basic characteristics, like magnitude and diurnal cycles, or how these differ as a function of large-scale environments. Here, to provide insight into advective characteristics, a Green’s Theorem–based method for calculating profiles of advection in the lowest 3 km from an array of ground-based thermodynamic and kinematic profiling instruments has been applied to 2 years of observations from the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) observing site. Since advection largely depends on synoptic-scale forcing, a self-organizing map (SOM) was used to classify days based on mean sea level pressure analyses; from that, the diurnal evolution of vertical profiles of advection for different synoptic environments was quantified. The overall mean magnitude of the potential temperature advection is approximately ±3 K h −1 , while the moisture advection is approximately ±1.5 g kg −1 h −1 , with substantial variability in the sign and magnitude of the advective tendencies at different heights and throughout the diurnal cycle. Advection magnitude is strongly connected to the strength of synoptic-scale forcing, which varies depending on the time of year. Variability in advection is larger for potential temperature than it is for moisture, and strongly forced environments, like midlatitude cyclones, feature greater variability in the advection magnitude than weakly forced or quiescent environments.

advection

Mediation of Colloidal Encounter Dynamics by Surface Roughness

Rigorous understanding on the self-assembly of colloidal nanocrystals is crucial to develop tailored nanostructured materials for energy storage, sensing, and optical fields. Despite extensive studies on the self-assembly, a mechanistic understanding of self-assembly under an external field still remains an ongoing challenge. Here, in this work, we used optical tweezers that impose an external attractive force field, resulting in the self-assembly of alpha-phase sodium yttrium fluoride nanocrystals. The dynamic force that is strongly dependent on the surface roughness of the nanocrystals is shown to be a decisive factor for a direct contact between the nanocrystals, manifested by the roughness-dependent hydrodynamic resistivity and Langevin dynamic simulations. Our study provides direct evidence that the role of dynamics is equally important in understanding the self-assembly, which has been rarely observed in the self-assembly in contrast with many studies on the equilibrium forces. These results may have further impact in other fields, such as having explanatory power for the probability of nonclassical crystal growth or the structure of viral spike proteins that affect the probability of viruses binding with cells.

Felsted, Robert G. [Univ. of Washington, Seattle,

Thermochemistry of Layered and Two-Dimensional Niobium Carbo-Chalcogenides

Two-dimensional transition metal carbo-chalcogenides (TMCCs) represent a novel class of layered materials with tunable electronic structures and high chemical versatility, making them promising candidates for energy and environmental applications. In this work, the structural and thermochemical properties of a series of TMCCs are investigated. High-temperature oxidative solution calorimetry, conducted at 800 °C in molten sodium molybdate (3Na2O·4MoO3), was used to determine the enthalpies of oxidation and formation from the elements at 25 °C, enabling a comprehensive thermodynamic assessment. Comparison of these enthalpies reveals distinct stability trends across the series. Cu0.67Nb2S2C exhibits the most exothermic oxidation enthalpy, indicating a strong thermodynamic driving force for oxidation and reduced resistance to oxidative degradation. Its positive enthalpy of formation from the elements suggests lower thermodynamic stabilization relative to the other compositions, consistent with the energetic influence of Cu and residual Fe within the Nb–S–C framework. In contrast, delaminated Nb2S2C exhibits poor oxidative stability but a highly exothermic enthalpy of formation, consistent with a defect-rich, metastable structural state rather than enhanced lattice stability. These findings establish correlations between crystal structure and energetic stability, providing insights into the design of robust TMCC-based materials for advanced energy and environmental technologies.

Cassell, Nakeshma [Clemson University]

Observation of quantum effects on radiation reaction in strong fields

Radiation reaction, the force experienced by an accelerated charge due to radiation emission, has long been the subject of extensive theoretical and experimental research. Experimental verification of a quantum, strong-field description of radiation reaction is fundamentally important, and has wide-ranging implications for astrophysics, laser-driven particle acceleration, next-generation particle colliders and inverse-Compton photon sources for medical and industrial applications. However, the difficulty of accessing regimes where strong field and quantum effects dominate inhibited previous efforts to observe quantum radiation reaction in charged particle dynamics with high significance. We report the first high significance (> 5σ) observation of strong-field radiation reaction on electron spectra where quantum effects are substantial. We obtain the first, quantitative, strong evidence favouring the quantum-continuous and quantum-stochastic models over the classical model; the quantum models perform comparably. The lower electron energy losses predicted by the quantum models accounts for their improved performance. Model comparison was performed using a novel Bayesian framework which has widespread utility for laser-particle collision experiments, including those utilising conventional accelerators, where some collision parameters cannot be measured directly.

Los, Eva E. [Imperial College London (United Kingd

IOTA experiment for proton pulse compression at extreme space-charge

The longitudinal compression of intense proton bunches with strong space-charge force is an essential component of a proton driver for a muon collider. We propose a proton bunch compression experiment at the Integrable Optics Test Accelerator (IOTA) storage ring at Fermilab to explore optimal radio frequency (RF) cavity and lattice configurations. IOTA is a compact fixed-energy storage ring dedicated to beam physics R&D that can circulate a 2.5-MeV proton beam with extreme space-charge. Using ImpactX and its 3D space-charge solver, simulations indicate that bunch length can be rapidly reduced by a factor of at least two, without appreciable degradation in transverse beam quality, even under strong space-charge conditions. However, longitudinal defocusing presents a large effect in short-pulsed proton beams, and the optimization of bunch compression under such conditions is discussed.

Simons, Benjamin [Northern Illinois U.; Fermilab]