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At least 559 records · Page 31

Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora

Abstract Background Over their evolutionary history, corals have adapted to sea level rise and increasing ocean temperatures, however, it is unclear how quickly they may respond to rapid change. Genome structure and genetic diversity contained within may highlight their adaptive potential. Results We present chromosome-scale genome assemblies and linkage maps of the critically endangered Atlantic acroporids,Acropora palmataandA. cervicornis. Both assemblies and linkage maps were resolved into 14 chromosomes with their gene content and colinearity. Repeats and chromosome arrangements were largely preserved between the species. The family Acroporidae and the genusAcroporaexhibited many phylogenetically significant gene family expansions. Macrosynteny decreased with phylogenetic distance. Nevertheless, scleractinians shared six of the 21 cnidarian ancestral linkage groups as well as numerous fission and fusion events compared to other distantly related cnidarians. Genetic linkage maps were constructed from oneA. palmatafamily and 16A. cervicornisfamilies using a genotyping array. The consensus maps span 1,013.42 cM and 927.36 cM forA. palmataandA. cervicornis, respectively. Both species exhibited high genome-wide recombination rates (3.04 to 3.53 cM/Mb) and pronounced sex-based differences, known as heterochiasmy, with 2 to 2.5X higher recombination rates estimated in the female maps. Conclusions Together, the chromosome-scale assemblies and genetic maps we present here are the first detailed look at the genomic landscapes of the critically endangered Atlantic acroporids. These data sets revealed that adaptive capacity of Atlantic acroporids is not limited by their recombination rates. The sister species maintain macrosynteny with few genes with high sequence divergence that may act as reproductive barriers between them. In the AtlanticAcropora, hybridization between the two sister species yields an F1 hybrid with limited fertility despite the high levels of macrosynteny and gene colinearity of their genomes. Together, these resources now enable genome-wide association studies and discovery of quantitative trait loci, two tools that can aid in the conservation of these species.

Biotechnology & Applied Microbiology↗

Turbulence and E × B flow correlations across the L-H transition in DIII-D deuterium and hydrogen plasmas

The isotope dependence of the low- to high confinement-mode (L- to H-mode) transition power threshold P LH presents significant challenges for the initial (non-nuclear) hydrogen operations phase of the international thermonuclear experimental reactor (ITER). Here, we examine the isotope dependence of turbulence and E × B flow correlation properties in the L-mode edge plasma, leading up to the L-H transition. At marginal auxiliary power (near P LH ), turbulence is initially suppressed periodically during limit cycle oscillations (LCO) that precede the transition to sustained H-mode confinement. Here, we present evidence that the long-range (toroidal) correlation of the E × B edge plasma flow across the LCO phase is much weaker in hydrogen than in deuterium in the DIII-D tokamak, congruent with the higher threshold power P LH required to access LCO and H-mode in hydrogen. Concomitantly, the time required to initially quench edge turbulence via localized edge E × B flow shear is significantly longer in hydrogen (1–1.5 ms) than in deuterium (approx. 100 µs). No toroidal long-range correlation of the turbulence amplitude is observed, in agreement with expectations based on the relatively short poloidal turbulence correlation length. Radial edge turbulence and flow correlation lengths are longer in deuterium than in hydrogen plasmas as one would expect from ‘naïve’ gyro-Bohm isotope transport scaling, despite the substantially higher thermal flux across the last closed flux surface in hydrogen before the L-H transition. This article is part of a discussion meeting issue 'H-mode transition and pedestal studies in fusion plasmas'.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Fusing 4D coded thermoacoustic, electromagnetic, and acoustic/seismic wavefields for subsurface characterization and imaging of fluid flow in porous media

This research program aims to address critical challenges in subsurface exploration and monitoring of anthropogenic CO 2 storage by advancing quantitative dynamic sensing and imaging technologies. Two primary applications—petrophysical assessment of hydrocarbon reservoirs (C1) and CO 2 storage monitoring (C2)—require significant innovation to overcome three barriers (B1-B3). These barriers include the need for enhanced understanding of interactions between physical wave fields (thermoacoustic, electromagnetic, acoustic/seismic, and X-ray) with fluid-filled porous media, the development of multi-sensor data fusion for real-time imaging, and upscaling microscopic quantum effects for macroscopic observations. The project’s objective was to establish a unified 4D coded sensing and imaging approach, integrating EM, AC/S, and TA fields for multi-scale and multi-physics material characterization and subsurface imaging.

58 GEOSCIENCES↗

Impact of Magnetic Field Configuration on Heat Transport in Stellarators and Heliotrons

We assess the magnetic field configuration in modern fusion devices by comparing experiments with the same heating power, between a stellarator and a heliotron. The key role of turbulence is evident in the optimized stellarator, while neoclassical processes largely determine the transport in the heliotron device. Gyrokinetic simulations elucidate the underlying mechanisms promoting stronger ion scale turbulence in the stellarator. Similar plasma performances in these experiments suggests that neoclassical and turbulent transport should both be optimized in next step reactor designs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Three dimensional low-mode areal-density non-uniformities in indirect-drive implosions at the National Ignition Facility

To achieve hotspot ignition, an inertial confinement fusion implosion must achieve high hotspot pressure that is inertially confined by a dense shell of DT fuel. This requires a symmetric implosion having high in-flight shell velocity and high areal density at stagnation. The size of the driver and scale of the capsule required can be minimized by maintaining a high efficiency of energy coupling from the imploding shell to the hotspot. Significant 3D low mode asymmetries, however, are commonly observed in indirect-drive implosions and reduce the coupling of shell kinetic energy to the hotspot. To better quantify the magnitudes and impacts of shell density asymmetries, we have developed new analysis techniques and analytic models [Hurricane et al., Phys. Plasmas 27(6), 062704 (2020)]. To build confidence in the underlying data, we have also developed an analytic neutron transport model to cross-compare two independent measurements of asymmetry, which shows excellent agreement across shots for mode-1 (ℓ = 1). This work also demonstrates that asymmetry can introduce potential sampling bias into down-scattered ratio measurements causing the solid-angle-average and uncertainty-weighted-average down-scattered ratios to differ significantly. Diagnosing asymmetries beyond mode-1 (ℓ > 1) presents significant challenges. Using new diagnostic instruments and analysis techniques, however, evidence of significant Legendre mode P2 (ℓ = 2, m = 0) and additional 3D asymmetries (ℓ > 1, m ≠ 0) are beginning to emerge from the high precision activation diagnostic data (real-time nuclear activation detectors) and down-scattered neutron imaging data.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Stellarators as a fast path to fusion

Herein this paper is focused on three points: (1) overcoming obstacles to tokamak power plants may require a configuration modification as large as that of a stellarator. (2) The demonstrated reliability of the computational design of stellarators should change fusion strategy. (3) Deployment of carbon-free energy sources is mandated by the thirty-year doubling of carbon dioxide emissions. Carbon-free energy options must be developed and fully deployed within a few doubling times. Unit size and cost of electricity are only relevant in comparison to alternative worldwide energy solutions. Intermittency, site specificity, waste management, and nuclear proliferation make fusion attractive as the basis for a carbon-free energy system compared to the alternatives. Nonetheless, fusion is not an option for deployment until a power plant has successfully operated. A critical element in a minimal time and risk program is the use of computational design as opposed to just extrapolation. Only the stellarator has an empirical demonstration of the reliable computational design through large changes in configuration properties and scale. The computational design of stellarators should proceed while the inventions necessary for a more tokamak-like power plant are sought. The cost of computational design is extremely small, but adequate time is required for the development of ideas that maximize attractiveness and minimize risk. Rapid power-plant construction without many intermediate steps may seem risky, but the price is small compared to the cost of trillions of dollars for each year's delay in addressing carbon-dioxide emissions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Wisconsin In Situ Penning (WISP) gauge: A versatile neutral pressure gauge to measure partial pressures in strong magnetic fields

A new type of in-vessel Penning gauge, the Wisconsin In Situ Penning (WISP) gauge, has been developed and successfully operated in the Wendelstein 7-X (W7-X) island divertor baffle and vacuum vessel. The capacity of the quantitative measurements of the neutral reservoir for light impurities, in particular, helium, is important for tokamaks as well as stellarator divertors in order to avoid fuel dilution and radiative energy loss. Penning gauges assisted by spectroscopy are a powerful tool to obtain the total neutral pressure as well as fractional neutral pressures of specific impurities. The WISP gauge is a miniaturized Penning gauge arrangement, which exploits the ambient magnetic field of magnetic confinement fusion experiments to establish the Penning discharge. Then, in situ spectroscopy is conducted to separate the fractional neutral pressures of hydrogen, helium, and possibly also other impurities. The WISP probe head was qualified using the magnetic field of the Magnetized Dusty Plasma Experiment at Auburn University between 0.25 T and 3.5 T [E. Thomas et al ., J. Plasma Phys. 81, 345810206 (2015)]. The in-depth quantitative evaluation for hydrogen and helium will be shown as well as an exploration of nitrogen, argon, and neon. A power law scaling between current I and pressure p, I = f (Gas,V) p n⁽Gas, B⁾ , was shown. The factor f is gas and anode potential dependent, while n is gas and magnetic field strength dependent. Pressure measurements from 0.1 mbar and down to 1 × 10 -5 mbar were achieved, demonstrating a reliable operating range for relevant pressure levels in the divertor and main vessel regions in current and future fusion devices, with a time resolution of up to 1 kHz. The lowest achievable pressure measurement increases with an increase in B and can be shifted with the anode potential V . At W7-X, the WISP probe head was mounted on an immersion tube setup that passes through the cryostat and places the probe head close to the plasma. Two probe heads were positioned in different divertor pump gaps, top and bottom, and one close to the plasma on the midplane in one module. The gauges were in situ calibrated together with the ASDEX pressure gauges [G. Haas and H.-S. Bosch, Vacuum 51, 39 (1998)]. Data were taken during the entire operation phase 1.2b, and measurements were coherent with other neutral gas pressure gauges. For the spectroscopic partial pressure measurements, channels of a spectroscopic detection system based on photo-multipliers, a so-called filterscope [R. J. Colchin et al ., Rev. Sci. Instrum. 74, 2068 (2003)], provided by the Oak Ridge National Lab were used.

47 OTHER INSTRUMENTATION↗

Formation of turing patterns in strongly magnetized electric discharges

Abstract Pattern formation and self-organization in many biological and non-biological systems can be explained through Turing’s activator-inhibitor model. Here we show how this model can be employed to describe the formation of filamentary structures in a low-pressure electric discharge exposed to a strong magnetic field. Theoretical investigation reveals that the fluid equations describing a magnetized plasma can be rearranged to take the mathematical form of Turing’s activator-inhibitor model. Numerical simulations based on the equations derived from this approach could reproduce the various patterns observed in the experiments. Also, it is shown that a density imbalance between electrons and ions exists in the bulk of the magnetized plasma that generates an electric field structure transverse to the applied magnetic field. This electric field is responsible for the stability of the filamentary patterns in the magnetized plasma over time scales much longer than the characteristic time scales of the electric discharge.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Top Yukawa coupling measurement at the muon collider

We have presented a detailed study about the prospects for the measurement of the top Yukawa coupling in the vector boson fusion production of a top quark pair at high energy muon colliders. By employing the effective W approximation and the high energy limit for the helicity amplitudes of the subprocess W + W − → t t ¯ , we have derived the energy scaling of the statistical signal significance in the presence of the anomalous couplings by focusing on the interference term only. The sensitivity on the top Yukawa coupling decreases as the bin energy increases. For the anomalous triple gauge boson couplings and the gauge-boson-fermion couplings with E 2 energy growing behavior, the signal significance has mild increase at the beginning and starts to decrease for s ^ t t ¯ ∼ 0.2 s μ + μ − . The 95% CL on the anomalous top Yukawa coupling is projected to be 5.6% (1.7%) at a 10 (30) TeV muon collider, which is comparable to the sensitivity of 2% at the 100 TeV collider. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

Perturbed Ion Temperature and Toroidal Flow Profile Measurements in Rotating Neoclassical Tearing Mode Magnetic Islands

The perturbed ion temperature and toroidal flow were measured in rotating Neoclassical Tearing Modes (NTM) in a tokamak for the first time. These toroidally and radially resolved profiles were obtained by impurity ion spectroscopy in a 2,1 NTM in DIII-D. In agreement with drift-kinetic simulations, the electron temperature profile is flat, while the ion temperature gradient is restored across the magnetic island O-point in the presence of fast ions; the perturbed flow has minima in the O-points and maxima at the X-points. Furthermore, these measurements provide the first confirmation of the theoretically expected ion temperature and flow response to a magnetic island needed to predict the NTM on set threshold scaling for ITER and other future tokamaks.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Enhanced production of taxadiene in Saccharomyces cerevisiae

Cost-effective production of the highly effective anti-cancer drug, paclitaxel (Taxol ® ), remains limited despite growing global demands. Low yields of the critical taxadiene precursor remains a key bottleneck in microbial production. In this study, the key challenge of poor taxadiene synthase (TASY) solubility in S. cerevisiae was revealed, and the strains were strategically engineered to relieve this bottleneck. Multi-copy chromosomal integration of TASY harbouring a selection of fusion solubility tags improved taxadiene titres 22-fold, up to 57 ± 3 mg/L at 30 °C at microscale, compared to expressing a single episomal copy of TASY. The scalability of the process was highlighted through achieving similar titres during scale up to 25 mL and 250 mL in shake flask and bioreactor cultivations, respectively at 20 and 30 °C. Maximum taxadiene titres of 129 ± 15 mg/L and 127 mg/L were achieved through shake flask and bioreactor cultivations, respectively, of the optimal strain at a reduced temperature of 20 °C. The results of this study highlight the benefit of employing a combination of molecular biology and bioprocess tools during synthetic pathway development, with which TASY activity was successfully improved by 6.5-fold compared to the highest literature titre in S. cerevisiae cell factories.

59 BASIC BIOLOGICAL SCIENCES↗

Phase Contrast Imaging Diagnostic on DIII-D (1994-2007); Phase Contrast Imaging Diagnostic on DIII-D and Alcator C-Mod (2007-2010); Experimental Study of Waves, Turbulence and Transport, and Model Validation with Phase Contrast Imaging on DIII-D and Alcator C-Mod (2010-2012); Phase Contrast Imaging Diagnostic Upgrade on DIII-D for Measuring High-k Turbulence and Alfven modes (2021-2016); Phase Contrast Imaging Diagnostic Upgrade on DIII-D for Full Multi-Scale Measurements (2016-2020) (Final Report)

This report describes the first twenty-five years of development and use of the Phase Contrast Imaging (PCI) diagnostic for measuring plasma fluctuations on the DIII–D tokamak. One of the key challenges in moving tokamak technology forward to the stage of a nuclear reactor remains understanding how energy and particles are transported across the magnetic field by the action of turbulence and waves, and PCI provides a highly flexible and capable measurement of these fluctuations. The PCI diagnostic uses a laser beam to probe the plasma and optical filtering to produce an amplitude variation on a linear detector array which provides an image of the density waves in the plasma. The PCI covers an exceptional range in frequency and wavelength of the measured fluctuations, allowing observation of plasma-sized magnetohydrodynamic (MHD) modes and ion- and electron-scale turbulence. Modulation of the beam amplitude allows measurement of radio frequency (RF) waves.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Resolution requirements for energy conservation in kinetic plasma simulations

The kinetic codes used to model the coupled dynamics of electromagnetic fields and charged particle transport have requirements for spatial, temporal, and charge resolution. These requirements may vary by the solution technique and scope of the problem. In this report, we investigate the resolution limits in the energy-conserving implicit particle-in-cell code CHICAGO. This report has the narrow aim of determining the maximum acceptable grid spacing for the dense plasmas generated in models of z-pinch target gases and power-flow electrode plasmas. In the 2D sample problem, the plasma drifts without external forces with velocity of 10 cm/µs. Simulations are scaled by plasma density to maintain uniform strides across the plasma and from the plasma to the boundaries. Additionally, the cloud-in-cell technique is used with 400 particles per cell and Δ t = 0.85× the Courant limit. For the linear cloud distribution, the criterion for conserving energy is Δ E/E tot < 0.01 for 50,000 time steps. The grid resolution is determined to crudely be Δx ≲ 3 l s , where l s is the electron collisionless skin depth. For the second-order cloud distribution the criterion is Δ E/E tot < 0.005 yielding Δx ≤ 15 l s . These scalings are functions of the chosen v d , Δ t , particles-per-cell, and number of steps.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

High-Temperature Oxidation Behavior of Wrought and Additive Manufactured H282 in Direct-Fired Supercritical CO2 Power Cycle Environments

Materials selection is a key concern for corrosion resistance in high temperature and pressure direct-fired supercritical CO2 power cycles. The effect of elevated pressure on corrosion resistance can be critical, as impurities within the supercritical fluid such as H2O and O2 can result in additional corrosion behaviors. Utilizing additive manufacturing (AM) methods for construction of power cycle components requiring both compact and complex designs could be advantageous. AM H282 produced by laser powder bed fusion was exposed to direct-fired conditions (95CO2 – 4H2O – 1 O2) at 750 °C at both atmospheric pressure and supercritical conditions (20 MPa) for up to 4,000 hours. Oxidation behavior, sub-surface carbide formation, and chromia scale volatilization was dependent upon AM preparation techniques and surface modifications. These results are discussed in terms of the potential compatibility issues that may arise when using AM alloys in high temperature regions of direct-fired sCO2 power cycles, particularly for thin-walled components.

Carney, Casey↗

SciDAC ISEP: Integrated Simulation of Energetic Particles in Burning Plasmas

The objective of the SciDAC Center for Integrated Simulation of Energetic Particles in Burning Plasmas (ISEP) is to improve physics understanding of energetic particle (EP) confinement and EP interactions with burning thermal plasmas through large-scale simulations. The ISEP center will develop a multiscale and multiphysics ISEP framework for a predictive capability of EP physics and deliver an EP module incorporating both first-principles simulations and high fidelity reduced transport models to the fusion whole device modeling (WDM) project. The ISEP framework will enable us to perform long time, global kinetic simulations of EP physics in burning plasmas, by utilizing the full power of the next generation supercomputers. Our research and development activities will build on fruitful collaborations with computer scientists and applied mathematicians to offer enabling technologies for performance scalability, portability, solvers, coupling for integration with the fusion WDM project, and long-term preservation of data.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Oxidation Behavior of Heat-Resistant Type $\mathrm{HK}$ Steel ($\mathrm{HK30Nb}$) at 800 °C

We report the cyclic oxidation behavior of HK30Nb heat-resistant steel processed by laser powder bed fusion (LPBF) was compared to its cast counterpart during exposures in air and air + 10% H 2 O at 800 °C. The specific finer microstructure and lower Mn of the LPBF alloy resulted in lower oxidation rates in dry air and faster establishment of a continuous Cr 2 O 3 scale in air + 10% H 2 O compared to coarse-grained cast HK30Nb with higher Mn. Differences in alloy mechanical strength and therefore their ability to accommodate high temperature and oxidation-induced stresses as well as differences in thermal expansion coefficients between the alloy and the formed oxides (Cr 2 O 3 only for the LPBF and Cr 2 O 3 and MnCr 2 O 4 for the cast specimens) during temperature cycling were found to result in a greater extent of spallation for the LPBF than for the cast alloy in dry air at 800 °C.

36 MATERIALS SCIENCE↗

Bound on hot-spot mix in high-velocity, high-adiabat direct-drive cryogenic implosions based on comparison of absolute x-ray and neutron yields

In laser-driven implosions for laboratory fusion, the comparison of hot-spot x-ray yield to neutron production can serve to infer hot-spot mix. For high-performance direct-drive implosions, this ratio depends sensitively on the degree of equilibration between the ion and electron fluids. A scaling for x-ray yield as a function of neutron yield and characteristic ion and electron hot-spot temperatures is developed on the basis of simulations with varying degrees of equilibration. We apply this model to hot-spot x-ray measurements of direct-drive cryogenic implosions typical of the direct-drive designs with best ignition metrics. Furthermore, the comparison of the measured x-ray and neutron yields indicates that hot-spot mix, if present, is below a sensitivity estimated as ~ 2% by-atom mix of ablator plastic into the hot spot.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Self-consistent theory of the Darrieus–Landau and Rayleigh–Taylor instabilities with self-generated magnetic fields

The Rayleigh–Taylor (RT) and Darrieus–Landau (DL) instabilities are studied in an inertial confinement fusion context within the framework of small critical-to-shell density ratio D R and weak acceleration regime, i.e., large Froude number Fr. The quasi-isobaric analysis in Sanz et al. is completed with the inclusion of non-isobaric and self-generated magnetic-field effects. The analysis is restricted to perturbation wavelengths k~1 larger than the conduction length scale at the ablation front, yet its validity ranges from wavelengths shorter and larger than the conduction layer width (distance between the ablation front and the critical surface). The use of a sharp boundary model leads to a single analytical expression of the dispersion relation encompassing both instabilities. The two new effects come into play by modifying the perturbed mass and momentum fluxes at the ablation front. The momentum flux (perturbed pressure at the spike) is the predominant stabilizing mechanism in the RT instability (overpressure) and the driving mechanism in the DL instability (underpressure). The non-isobaric effects notably modify the scaling laws in the DL limit, leading to an underpressure scaling as ~k –11/15 rather than ~k –2/5 obtained in the quasi-isobaric model. The magnetic fields are generated due to misalignment between pressure and density gradients (Biermann battery effect). They affect the hydrodynamics by bending the heat flux lines. Within the framework of this paper, they enhance ablation, resulting in a stabilizing effect that peaks for perturbation wavelengths comparable to the conduction layer width. Here, the combination of parameters D R Fr 2/3 defines the region of predominance of each instability in the dispersion relation. It is proven that the DL region falls outside of the parameter range in inertial confinement fusion.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗