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At least 955 records · Page 53

Cut site preference allows influenza A virus PA-X to discriminate between host and viral mRNAs

Many viruses block host gene expression to take over the infected cell. This process, termed host shutoff, is thought to promote viral replication by preventing antiviral responses and redirecting cellular resources to viral processes. Several viruses from divergent families accomplish host shutoff through RNA degradation by endoribonucleases. However, viruses also need to ensure expression of their own genes. The influenza A virus endoribonuclease PA-X solves this problem by sparing viral mRNAs and some host RNAs necessary for viral replication. Here, to understand how PA-X distinguishes between RNAs, we characterized PA-X cut sites transcriptome-wide using 5' rapid amplification of complementary DNA ends coupled to high-throughput sequencing. This analysis, along with RNA structure predictions and validation experiments using reporters, shows that PA-Xs from multiple influenza strains preferentially cleave RNAs at GCUG tetramers in hairpin loops. Importantly, GCUG tetramers are enriched in the human but not the influenza transcriptome. Moreover, optimal PA-X cut sites inserted in the influenza A virus genome are quickly selected against during viral replication in cells. This finding suggests that PA-X evolved these cleavage characteristics to preferentially target host over viral mRNAs in a manner reminiscent of cellular self versus non-self discrimination.

59 BASIC BIOLOGICAL SCIENCES↗

Observing the onset of pressure-driven K-shell delocalization

The gravitational pressure in many astrophysical objects exceeds one gigabar (one billion atmospheres), creating extreme conditions where the distance between nuclei approaches the size of the K shell. This close proximity modifies these tightly bound states and, above a certain pressure, drives them into a delocalized state. Both processes substantially affect the equation of state and radiation transport and, therefore, the structure and evolution of these objects. Still, our understanding of this transition is far from satisfactory and experimental data are sparse. Here, in this work, we report on experiments that create and diagnose matter at pressures exceeding three gigabars at the National Ignition Facility where 184 laser beams imploded a beryllium shell. Bright X-ray flashes enable precision radiography and X-ray Thomson scattering that reveal both the macroscopic conditions and the microscopic states. The data show clear signs of quantum-degenerate electrons in states reaching 30 times compression, and a temperature of around two million kelvins. At the most extreme conditions, we observe strongly reduced elastic scattering, which mainly originates from K-shell electrons. We attribute this reduction to the onset of delocalization of the remaining K-shell electron. With this interpretation, the ion charge inferred from the scattering data agrees well with ab initio simulations, but it is significantly higher than widely used analytical models predict.

79 ASTRONOMY AND ASTROPHYSICS↗

Dissociated prismatic loop punching by bubble growth in FCC metals

Abstract Materials performance can be significantly degraded due to bubble generation. In this work, the bubble growth process is elaborated in Cu by atomistic modeling to bridge the gap of experimental observations. Upon continuous He implantation, bubble growth is accommodated first by nucleation of dislocation network from bubble surface, then formation of dissociated prismatic dislocation loop (DPDL), and final DPDL emission in $$\langle 110\rangle$$ ⟨ 110 ⟩ directions. As the DPDL is found capable of collecting He atoms, this process is likely to assist the formation of self-organized bubble superlattice, which has been reported from experiments. Moreover, the pressurized bubble in solid state manifests the shape of an imperfect octahedron, built by Cu $$\{111\}$$ { 111 } surfaces, consistent with experiments. These atomistic details integrating experimental work fill the gap of mechanistic understanding of athermal bubble growth in Cu. Importantly, by associating with nanoindentation testings, DPDL punching by bubble growth arguably applies to various FCC (face-centered cubic) metals such as Au, Ag, Ni, and Al.

36 MATERIALS SCIENCE↗

Kubernetes for the Deep Underground Neutrino Experiment Data Acquisition

The Deep Underground Neutrino Experiment (DUNE) is a next-generation long-baseline neutrino experiment based in the USA which is expected to start taking data in 2029. DUNE aims to precisely measure neutrino oscillation parameters by detecting neutrinos from the LBNF beamline (Fermilab) at the Far Detector, 1,300 kilometres away, in South Dakota at the Sanford Underground Research Facility. The Far Detector will consist of four cryogenic Liquid Argon Time Projection Chamber detectors of 17 kT, each producing more than 1 TB/sec of data. The main requirements for the data acquisition system are the ability to run continuously for extended periods of time, with a 99% up-time requirement, and the functionality to record both beam neutrinos and low energy neutrinos from the explosion of a neighbouring supernova, should one occur during the lifetime of the experiment. The key challenges are the high data rates that the detectors generate and the deep underground environment, which places constraints on power and space. To overcome these challenges, DUNE plans to use a highly optimised C++ software suite and a server farm of about 110 nodes continuously running about two hundred multicore processes located close to the detector, 1.5 kilometres underground. Thirty nodes will be at the surface and will run around two hundred processes simultaneously. DUNE is studying the use of the Kubernetes framework to manage containerised workloads and take advantage of its resource definitions and high up-time services to run the DAQ system. Progress in deploying these systems at the CERN neutrino platform on the prototype DUNE experiments is reported.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Shock Hugoniot measurements of single-crystal 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) compressed to 83 GPa

We present laser-driven shock Hugoniot measurements of single-crystal (SC) 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) between 15 and 83 GPa, spanning pressures below and well above the Chapman–Jouguet pressure of ~28 GPa for TATB formulations (TATB grains mixed with plastic binders at 5–10 wt. %). The new SC data are generally ~3% more compressible than previously published data on neat and formulated TATB measured in gas-gun and explosive-driven experiments. An exception is at compressions in the density of ~1.5 (~30–40 GPa), where our new SC data exhibit significantly lower pressures than previous results on overdriven TATB formulations, suggesting that our SC samples remain largely unreacted below 35 GPa over the short nanosecond-time scales inherent to our laser-driven experiments. We report these novel equation-of-state measurements are a critical step toward understanding TATB in its most fundamental form and improving predictive modeling of TATB-based explosives.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The effect of laser entrance hole foil thickness on MagLIF-relevant laser preheat

The magnetized liner inertial fusion (MagLIF) scheme relies on coupling laser energy into an underdense fuel raising the fuel adiabat at the start of the implosion. To deposit energy into the fuel, the laser must first penetrate a laser entrance hole (LEH) foil which can be a significant energy sink and introduce mix. In this paper, we report on experiments investigating laser energy coupling into MagLIF-relevant gas cell targets with LEH foil thicknesses varying from 0.5 μm to 3 μm. Two-dimensional (2D) axisymmetric simulations match the experimental results well for 0.5 μm and 1 μm thick LEH foils but exhibit whole-beam self-focusing and excessive penetration of the laser into the gas for 2 μm and 3 μm thick LEH foils. Additionally, better agreement for the 2 μm-thick foil is found when using a different thermal conductivity model in 2D simulations, while only 3D Cartesian simulations come close to matching the 3 μm-thick foil experiments. The study suggests that simulations may over-predict the tendency for the laser to self-focus during MagLIF preheat when thicker LEH foils are used. This effect is pronounced with 2D simulations where the azimuthally symmetric density channel effectively self-focuses the rays that are forced to traverse the center of the plasma. The extra degree of freedom in 3D simulations significantly reduces this effect. The experiments and simulations also suggest that, in this study, the amount of energy coupled into the gas is highly correlated with the laser propagation length regardless of the LEH foil thickness.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Cavity molecular dynamics simulations of vibrational polariton-enhanced molecular nonlinear absorption

We report recent experiments have observed that the chemical and photophysical properties of molecules can be modified inside an optical Fabry– Pérot microcavity under collective vibrational strong coupling (VSC) conditions, and such modification is currently not well understood by theory. In an effort to understand the origin of such cavity-induced phenomena, some recent studies have focused on the effect of the cavity environment on the nonlinear optical response of the molecular subsystem. Here, we use a recently proposed protocol for classical cavity molecular dynamics simulations to numerically investigate the linear and the nonlinear response of liquid carbon dioxide under such VSC conditions following an optical pulse excitation. We find that applying a strong pulse of excitation to the lower hybrid light–matter state, i.e., the lower polariton (LP), can lead to an overall molecular nonlinear absorption that is enhanced by up to two orders of magnitude relative to the excitation outside the cavity. This polariton-enhanced multiphoton absorption also causes an ultrashort LP lifetime (0.2 ps) under strong illumination. Unlike usual polariton relaxation processes—whereby polaritonic energy transfers directly to the manifold of singly excited vibrational dark states—under the present mechanism, the LP transfers energy directly to the manifold of higher vibrationally excited dark states; these highly excited dark states subsequently relax to the manifold of singly excited states with a lifetime of tens of ps. Because the present mechanism is generic in nature, we expect these numerical predictions to be experimentally observed in different molecular systems and in cavities with different volumes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Design and simulation of multilayer coatings for a multi-channel Wolter-like x-ray imager with large field of view and high resolution

X-ray diagnostics are key instruments for understanding the physics behind inertial confinement fusion experiments. We report on the multilayer design optimization for the Toroidal X-ray Imager (TXI), a hard x-rays microscope instrument designed by Commissariat à l’énergie atomique (CEA) and Laboratoire Charles Fabry (LCF) to be installed on the National Ignition Facility. TXI includes six channels designed for three different energy bands centered on 8.7, 13, and 17.5 keV. Each channel is made up of two toroidal mirrors arranged in a Wolter-like configuration. The required field of view is 800 × 400 µm2, and the resolution should be better than 5 µm. In addition, we seek to estimate the spatial distribution of the temperature, which requires no spectral overlap of the different energy bands and a good spectral homogeneity of the image produced. The development of the multilayer coatings was performed in a two-step method. First, the coatings were optimized to obtain proper energy bands. Then, an x-ray tracing code was used to calculate the integrated optical response of each channel and adjust the response of the mirror to fulfill the requirements. To fulfill all the specifications, we propose an original design using a combination of two aperiodic coatings, one with a narrow bandwidth and the other one with a larger bandwidth.

hard x-rays↗

Evaluating nonlocal heat transport in directly driven chromium spheres using x-ray spectroscopy

We report on experiments investigating heat transport in laser-generated plasmas using directly driven chromium spheres. The spheres are fielded at the OMEGA laser facility and are driven with laser intensities of 5×10 14 Wcm −2 . Plasma conditions in the corona and scattered light are measured experimentally and compared against predictions from two-dimensional (2D) radiation-hydrodynamic simulations using different heat transport models. Spectroscopic analysis of x-ray self-emission is used as an additional diagnostic. X-ray emission is integrated over a large region of the plasma, probing regions that are not observed by localized optical Thomson scattering. In particular, x-ray emission peaks near the plasma critical density, so emission from optically thin lines provides information on plasma conditions where nonlocal transport is most likely to be significant. Three common heat transport models are considered: local transport with flux limiters f = 0.15 and f = 0.03, and the nonlocal Schurtz–Nicolai–Busquet (SNB) model. Consistent with previous work, both the high-flux (f = 0.15) and SNB models show good agreement with experimentally measured plasma conditions in the corona despite overpredicting laser absorption, whereas the low-flux (f = 0.03) model fails to match any experimental data. Conditions inferred from x-ray self-emission line ratios support this conclusion during the period of laser peak power, although synthetic spectra for all models fail to match the experiment during the transient portions of the pulse. For these reasons, the low-flux model is again rejected.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Measuring the robustness of predictive probability for early stopping in two-group comparisons

We report physical experiments are often expensive and time-consuming. Test engineers must certify the compatibility of aircraft and their weapon systems before they can be deployed in the field, but the testing required is time consuming, expensive, and resource limited. Adopting Bayesian adaptive designs is a promising way to borrow from the successes seen in the clinical trials domain. The use of predictive probability (PP) to stop testing early and make faster decisions is particularly appealing given the aforementioned constraints. Given the high-consequence nature of the tests performed in the national security space, a strong understanding of new methods is required before being deployed. Although PP has been thoroughly studied for binary data, there is less work with continuous data, where many reliability studies are interested in certifying the specification limits of components. A simulation study evaluating the robustness of this approach indicates early stopping based on PP is reasonably robust to minor assumption violations, especially when only a few interim analyses are conducted. The simulation study also compares PP to conditional power, showing its relative strengths and weaknesses. A post-hoc analysis exploring whether release requirements of a weapon system from an aircraft are within specification with desired reliability resulted in stopping the experiment early and saving 33% of the experimental runs.

97 MATHEMATICS AND COMPUTING↗

First-principles calculation of Hubbard U for Terbium metal under high pressure

Abstract Using density functional theory (DFT) and linear response approaches, we compute the on-site Hubbard interaction U of elemental Terbium (Tb) metal in the pressure range ∼ 0–65 GPa. The resulting first-principles U values with experimental crystal structures enable us to examine the magnetic properties of Tb using a DFT+U method. The lowest-energy magnetic states in our calculations for different high-pressure Tb phases—including hcp, α -Sm, and dhcp—are found to be compatible with the corresponding magnetic ordering vectors reported in experiments. The result shows that the inclusion of Hubbard U substantially improves the accuracy and efficiency in modeling correlated rare-earth materials. Our study also provides the necessary U information for other quantum many-body techniques to study Tb under extreme pressure conditions.

36 MATERIALS SCIENCE↗

Impact of divertor material on neutral recycling and discharge fueling in DIII-D

We report that experiments with the lower divertor of DIII-D during the Metal Rings Campaign (MRC) show that the fraction F of atomic D in the total recycling flux is material-dependent and varies through the ELM cycle, which may affect divertor fueling. Between ELMs, F C ~ 10% and FW ~ 40%, consistent with expectations if all atomic recycling is due to reflections. During ELMs, F C increases to 50% and F W to 60%. In contrast, the total D recycling coefficient including atoms and molecules R stays close to unity near the strike point where the surface is saturated with D. During ELMs, R can deviate from unity, increasing during high energy ELM-ion deposition (net D release) and decreasing at the end of the ELM which leads to ability of the target to trap the ELM-deposited D. The increase of R > 1 in response to an increase in ion impact energy Ei has been studied with small divertor target samples using Divertor Materials Evaluation System (DiMES). An electrostatic bias was applied to DiMES to change E i by 90 eV. On all studied materials including C, Mo, uncoated and W-coated TZM (>99% Mo, Ti, and Zr alloy), W, and W fuzz, an increase of E i transiently increased the D yield (and R) by ~10%. On C there was also an increase in the molecular D 2 yield, probably due to ion-induced D 2 desorption. Despite the measured increase in F on W compared to C, attached H-mode shots with OSP on W during MRC did not demonstrate a higher pedestal density. About 8% increase in the edge density could be seen only in attached L-mode scenarios. The difference can be explained by higher D trapping in the divertor and lower divertor fueling efficiency in H- versus L-mode.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Analysis of MHD stability and active mode control on KSTAR for high confinement, disruption-free plasma

Long-pulse plasma operation at high normalized beta, $β_N$, above the $\textit{n}$= 1 ideal MHD no-wall stability limit in KSTAR is presently limited by tearing instabilities rather than resistive wall modes. H-mode plasma operation during the recent KSTAR device campaign produced discharges having strong $\textit{m/n}$= 2/1 tearing instabilities at $β_N$ lower than the ideal MHD no-wall beta limit. The unstable tearing mode consequently reduced plasma confinement and toroidal plasma rotation significantly. We report the experiment confirmed that an extended duration of electron cyclotron heating (ECH) at the initial phase of the discharge plays a critical role in mode destabilization. To study destabilizing mechanisms that affect the mode growth, the stability of the observed tearing modes from plasmas with significantly different $β_N$ is computed by using the resistive DCON code and the M3D-C 1 code. Equilibrium reconstructions that include constraints from internal profile diagnostics, and computed fast particle pressure are used as input for reliable computation of stability. The classical tearing stability index, Δ', from resistive DCON is computed to be unstable when the island is fully saturated with large amplitude, while the unstable mode is not computed by M3D-C 1 . The modified Rutherford equation (MRE) describing the evolution of the island width has been constructed for KSTAR plasmas by using plasma parameters computed by the TRANSP code. The MRE model estimates a saturated island width corresponding to ~10% of the plasma minor radius for equilibrium at high $β_N$ 3 having a stable Δ' from the resistive DCON. In preparation for long-pulse plasma operation at higher beta utilizing increased plasma heating power, a resistive wall mode (RWM) active feedback control algorithm has been completed and enabled on KSTAR. To accurately determine the $\textit{n}$= 1component produced by RWMs, an algorithm has been developed that includes magnetic sensor compensation of the prompt applied field and the field from the induced current on the passive conductors. Use of multiple toroidal sensor arrays is enabled by modifying the sensor toroidal angles assumed in mode decomposition to include the effect of varied mode helicities in the outboard region where the mode measurement is made. This analysis on stability, transport, and control provides the required foundation for disruption prediction and avoidance research on KSTAR.

resistive wall mode (RWM)↗

The role of RF-induced E×B flows in the mitigation of scrape-off-layer convective transport during ion cyclotron resonance heating

Abstract While multiple experiments have reported a decrease in intermittent fluctuations in the far Scrape-Off-Layer (SOL) during ion cyclotron resonance heating (Antar et al 2010 Phys. Rev. Lett. 105 165001, Li et al 2022 Nucl. Eng. Technol. 54 207–19, Antar et al 2012 Nucl. Fusion 52 103005), the physical mechanism behind this observation has not been fully established yet. In this work, we demonstrate, for the first time, a direct correlation between the amplitude of RF-induced E×B flows and turbulence suppression in the far SOL. Using the Gas Puff Imaging (GPI) diagnostic on Alcator C-Mod, we show again that Ion Cyclotron Range of Frequencies can significantly alter the flow in the SOL and introduce a shear layer in regions magnetically connected close to the antenna (Cziegler et al 2012 Plasma Phys. Control. Fusion 54 105019). With the 4-strap field-aligned antenna operated in dipole phasing, the ratio of the power coupled by the central two straps to the power coupled by the outer two straps was varied. The resulting RF-induced radial electric field magnitude thus varied, and we show that the impact on the far SOL turbulence correlates with the modified E×B velocity. We then apply a newly-developed blob tracking algorithm (Han et al 2022 Sci. Rep. 12 18142) to higher-resolution GPI videos in order to directly observe the process of blob shearing by RF-induced E×B flows. We show that the radially sheared poloidal flows act as a transport barrier by stretching, stopping, and destroying filaments, which is consistent with the observed difference in turbulence statistics.

Diab, R. (ORCID:0000000342065868)↗

Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering

Abstract Time-resolved small-angle X-ray experiments are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in the folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 24.3 to 12.6 Å. The collapse is monophasic and is complete in <600 ms. Additional hand-mixing pH-jump kinetic studies show that slower kinetic steps follow the collapse. The folded and unfolded states at equilibrium were further characterized by SAXS studies and other biophysical tools, showing that G4 unfolding was complete at alkaline pH, but not in LiCl solution as is often claimed. The SAXS Ensemble Optimization Method analysis reveals models of the unfolded state as a dynamic ensemble of flexible oligonucleotide chains with a variety of transient hairpin structures. These results suggest a G4 folding pathway in which a rapid collapse, analogous to molten globule formation seen in proteins, is followed by a confined conformational search within the collapsed particle to form the native contacts ultimately found in the stable folded form.

Biochemistry & Molecular Biology↗

Measurement of the longitudinal flow-plane decorrelation using multiplane cumulants in $\sqrt{s_{NN}}$ = 200 GeV Au+Au, Ru+Ru, and Zr+Zr collisions

Measurements of the variation of anisotropic flow-plane angles (𝛹 𝑛 ) with rapidity, commonly known as the flow-plane decorrelation, provide important insights into the initial conditions of the matter produced in heavy-ion collisions. Here, in this paper, using data collected by the STAR experiment, we report the first measurement of the four-plane correlator observable 𝑇 𝑛 ⁡{𝑏⁢𝑎;𝑑⁢𝑐}=⟨⟨sin⁡[𝑛⁢(𝛹$^𝑏_𝑛$ − 𝛹$^𝑎_𝑛$)]⁢sin⁡[𝑛⁢(𝛹$^𝑑_𝑛$ − 𝛹$^𝑐_𝑛$)]⟩⟩, where superscripts 𝑎, 𝑏, 𝑐, and 𝑑 denote sequential pseudorapidity (𝜂) regions with 𝑎 corresponding to the most backward region, 𝑏 and 𝑐 close to mid-rapidity with 𝜂 𝑏 < 0 and 𝜂 𝑐 > 0, and 𝑑 being the most forward. The measurement is performed for the elliptic and triangular flow (i.e.~𝑛 = 2 and 3) in Au+Au and isobar (Ru+Ru, Zr+Zr) collisions at $\sqrt{s_{NN}}$=200~GeV. The goal of calculating the correlation of the flow-plane angle variations from backward to mid-central, and from mid-central to forward regions, is to probe the systematic variation of flow angle over a wide 𝜂 range. In mid-central collisions (10−30% centrality), we find 𝑇 2 ⁡{𝑏⁢𝑎;𝑑⁢𝑐} =−0.004 ±0.001⁢(s⁢t⁢a⁢t) ±0.002⁢(s⁢y⁢s⁢t) independent of the collision system. Such a small value of 𝑇 2 favors a random-walk'' variation of the flow-plane angles, where the rapidity correlation length is smaller than the entire region under study. These measurements provide new information on the decorrelation patterns in the system and offer a quantitative estimate of possible systematic variations in anisotropic flow angles such astwist’’ between forward and backward regions. This opens new opportunities for understanding the three-dimensional structure and the time evolution of the quark-gluon plasma created in heavy-ion collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Measurement of turbulent velocity and bounds for thermal diffusivity in laser shock compressed foams by x-ray photon correlation spectroscopy

Experimental benchmarking of transport coefficients under extreme conditions is required for validation of differing theoretical models. To date, measurement of transport properties of dynamically compressed samples remains a challenge with only a limited number of studies able to quantify transport in high pressure and temperature matter. x-ray photon correlation spectroscopy utilizes coherent x-ray sources to measure time correlations of density fluctuations, thus providing measurements of length and timescale-dependent transport properties. Here, we present a first-of-a-kind experiment to conduct x-ray photon correlation spectroscopy in laser shock compression experiments. We report measurement of the turbulent velocity in the wake of a laser driven supersonic shock and place an upper bound on thermal diffusivity in a solid density plasma on nanosecond timescales.

High-energy-density plasmas↗

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↗