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DOE OSTI2014

Stellar age spreads in clusters as imprints of cluster-parent clump densities

It has recently been suggested that high-density star clusters have stellar age distributions much narrower than that of the Orion Nebula Cluster, indicating a possible trend of narrower age distributions for denser clusters. We show this effect to likely arise from star formation being faster in gas with a higher density. We model the star formation history of molecular clumps in equilibrium by associating a star formation efficiency per free-fall time, ε{sub ff}, to their volume density profile. We focus on the case of isothermal spheres and we obtain the evolution with time of their star formation rate. Our model predicts a steady decline of the star formation rate, which we quantify with its half-life time, namely, the time needed for the star formation rate to drop to half its initial value. Given the uncertainties affecting the star formation efficiency per free-fall time, we consider two distinct values: ε{sub ff} = 0.1 and ε{sub ff} = 0.01. When ε{sub ff} = 0.1, the half-life time is of the order of the clump free-fall time, τ{sub ff}. As a result, the age distributions of stars formed in high-density clumps have smaller full-widths at half-maximum than those of stars formed in low-density clumps. When the star formation efficiency per free-fall time is 0.01, the half-life time is 10 times longer, i.e., 10 clump free-fall times. We explore what happens if the duration of star formation is shorter than 10τ{sub ff}, that is, if the half-life time of the star formation rate cannot be defined. There, we build on the invariance of the shape of the young cluster mass function to show that an anti-correlation between the clump density and the duration of star formation is expected. We therefore conclude that, regardless of whether the duration of star formation is longer than the star formation rate half-life time, denser molecular clumps yield narrower star age distributions in clusters. Published densities and stellar age spreads of young clusters and star-forming regions actually suggest that the timescale for star formation is of order 1-4τ{sub ff}. We also discuss how the age bin size and uncertainties in stellar ages affect our results. We conclude that there is no need to invoke the existence of multiple cluster formation mechanisms to explain the observed range of stellar age spreads in clusters.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2015

KINK AND SAUSAGE MODES IN NONUNIFORM MAGNETIC SLABS WITH CONTINUOUS TRANSVERSE DENSITY DISTRIBUTIONS

We examine the influence of a continuous density structuring transverse to coronal slabs on the dispersive properties of fundamental standing kink and sausage modes supported therein. We derive generic dispersion relations (DRs) governing linear fast waves in pressureless straight slabs with general transverse density distributions, and focus on cases where the density inhomogeneity takes place in a layer of arbitrary width and in arbitrary form. The physical relevance of the solutions to the DRs is demonstrated by the corresponding time-dependent computations. For all profiles examined, the lowest order kink modes are trapped regardless of longitudinal wavenumber k. A continuous density distribution introduces a difference to their periods of ≲13% when k is the observed range relative to the case where the density profile takes a step function form. Sausage modes and other branches of kink modes are leaky at small k, and their periods and damping times are heavily influenced by how the transverse density profile is prescribed, in particular the length scale. These modes have sufficiently high quality to be observable only for physical parameters representative of flare loops. We conclude that while the simpler DR pertinent to a step function profile can be used for the lowest order kink modes, the detailed information on the transverse density structuring needs to be incorporated into studies of sausage modes and higher order kink modes.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

Maximization of ICRF power by SOL density tailoring with local gas injection

We report that experiments have been performed under the coordination of the International Tokamak Physics Activity (ITPA) on several tokamaks, including ASDEX Upgrade (AUG), JET and DIII-D, to characterize the increased Ion cyclotron range of frequency (ICRF) antenna loading achieved by optimizing the position of gas injection relative to the RF antennas. On DIII-D, AUG and JET (with the ITER-Like Wall) a 50% increase in the antenna loading was observed when injecting deuterium in ELMy H-mode plasmas using mid-plane inlets close to the powered antennas instead of divertor injection and, with smaller improvement when using gas inlets located at the top of the machine. The gas injection rate required for such improvements (similar to 0.7 x 10(22) el s(-1) in AUG, similar to 1.0 x 10(22) el s(-1) in JET) is compatible with the use of this technique to optimize ICRF heating during the development of plasma scenarios and no degradation of confinement was observed when using the mid-plane or top inlets compared with divertor valves. An increase in the scrape-off layer (SOL) density was measured when switching gas injection from divertor to outer mid-plane or top. On JET and DIII-D, the measured SOL density increase when using main chamber puffing is consistent with the antenna coupling resistance increase provided that the distance between the measurement lines of sight and the injection location is taken into account. Optimized gas injection was also found to be beneficial for reducing tungsten (W) sputtering at the AUG antenna limiters, and also to reduce slightly the W and nickel (Ni) content in JET plasmas. Modeling the specific effects of divertor/top/mid-plane injection on the outer mid-plane density was carried out using both the EDGE2D-EIRENE and EMC3-EIRENE plasma boundary code packages; simulations indeed indicate that outer mid-plane gas injection maximizes the density in the mid-plane close to the injection point with qualitative agreement with the AUG SOL density measurements for EMC3-EIRENE. Field line tracing for ITER in the 15 MA Q(DT) = 10 reference scenario indicates that the planned gas injection system could be used to tailor the density in front the antennas. Lastly, benchmarking of EMC3-EIRENE against AUG and JET data is planned as a first step towards the ITER SOL modelling required to quantify the effect of gas injection on the SOL density in front of the antennas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Density limits as disruption forecasters for spherical tokamaks

Fusion power output from spherical tokamaks would benefit from increased confined plasma density, but there exists a limit on the density before confinement is lost and the plasma current is disrupted. This density limit has long been characterized by a simple, global Greenwald limit proportional to the plasma current and inversely proportional to the cross sectional area of the plasma. It is shown that in the database of discharges from the National Spherical Tokamak Experiment (NSTX) and Mega Ampere Spherical Tokamak (MAST) spherical tokamaks, the likelihood of disruption does increase above the Greenwald limit, and especially in the plasma current rampdown phase. The physics of the density limit has been recently theoretically explored through local criteria. Several of these are tested using the disruption event characterization and forecasting (DECAF TM ) code for their potential effectiveness as disruption warning signals. For a limited set of NSTX discharges, a local island power balance criteria was found to be less reliable, presently, than the Greenwald limit. For this work, an empirical critical edge line density and a boundary turbulent transport limit were both tested for MAST-U, which has an electron density profile measurement with high spatial resolution in the outer part of the plasma. Both were found to have similar dependencies on key plasma parameters. In a limited set of MAST-U discharges that appear to disrupt due to rising density at values under the Greenwald limit, crossing of the boundary turbulent transport limit occurred close to the time of disruption. Finally, these limits were evaluated for their potential use in real-time, and it was found that with the necessary real-time inputs and with refinement through further testing, these limits could be implemented in a real-time disruption forecasting system.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Effect of resistivity on poloidal asymmetries in electron density in the edge and scrape off layer in 3D full-F gyro-fluid simulations with FELTOR

In this contribution, we analyze the poloidal asymmetries in electron density in the edge and scrape-off layer (SOL) in a COMPASS-sized, diverted tokamak with the 3D full-F, isothermal, electromagnetic, and gyro-fluid model FELTOR. The study is performed for different simulations that span over 2 orders of magnitude in resistivity. The poloidal asymmetries of density are evaluated in the edge and the SOL relative to the outer midplane (OMP), where the highest densities are usually found. In the closed magnetic surfaces, the relative poloidal asymmetry with respect to the OMP is not larger than 20% independently of the plasma resistivity. For the open field lines in the SOL, the relative density asymmetry can range from 55% for the highest resistivity to around 40% for the lowest. The lowest densities inside the separatrix are found between the inner midplane and the top of the magnetic configuration, away from the X-point. In the SOL it is usually close to the X-point in the high field side. The observations in the closed field lines are consistent with ballooning transport but in the SOL oppose experimental evidence for high-density plasmas. In conclusion, this indicates the necessity for more complex physics to reproduce the experimental observations in the SOL for higher density plasmas, such as neutral-plasma dynamics and realistic divertor conditions.

3D full-f gyrofluid↗

DOE OSTI2021

Enhanced particle transport events approaching the density limit of the J-TEXT tokamak

Enhanced particle transport events are discovered and analyzed as the density limit of the J-TEXT tokamak is approached. Edge shear layer collapse is observed and the ratio of Reynolds power to turbulence production decreases. Simultaneously, the divergence of turbulence internal energy flux (i.e. turbulence spreading) increases, indicating that shear layer collapse triggers an outward spreading event. Studies of correlations show that the enhanced particle transport events are quasi-coherent, and manifested primarily in density fluctuations which exhibit positive skewness. Furthermore, electron adiabaticity emerges as the critical parameter which signals transport event onset. For α < 0.35 as density approaches the Greenwald density, both turbulence spreading and density fluctuations rise rapidly. Taken together, these results elucidate the connections between edge shear layer, density fluctuations, particle transport events, turbulence spreading and plasma edge cooling as the density limit is approached.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Observation and analysis of lower-hybrid-current-drive density limit in EAST

Lower hybrid current drive (LHCD) experiments with line-averaged density up to ~5.1 × 10 19 m –3 were performed in EAST L-mode plasmas. When the line-averaged density rises above a critical value, the hard x-ray (HXR) emission falls to the noise level, indicating that the LHCD density limit is encountered. The experimental results show that the LHCD density limit can be increased with higher wave source frequency (ƒ 0 ) and higher magnetic field (B t ). Although a higher LHCD density limit is obtained by a higher magnetic field for both 2.45 GHz and 4.6 GHz waves, the results show a stronger dependence on the magnetic field for the 4.6 GHz case. Analysis suggests that, for normal operation with a relatively low magnetic field (1.6 T $\leqslant$ B t $\leqslant$ 2.5 T) on EAST, the dominant mechanisms responsible for the LHCD density limit are different between the 2.45 GHz and 4.6 GHz waves. The wave accessibility plays a more significant role during 4.6 GHz LHCD experiments, while parasitic losses due to parametric decay instability (PDIs) dominate the accessibility issue in the 2.45 GHz case. Collisional loss in the scrape-off layer (SOL) may explain the 4.6 GHz result when combined with the accessibility limit at high density and low temperature.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

The role of isotope mass on neutral fueling and density pedestal structure in the DIII-D tokamak

Abstract Experimental measurements on DIII-D of hydrogen neutral penetration lengths ( λ n 0 ) on the high field side (HFS) are longer by a factor of 2 than for deuterium consistent with the thermal velocity ratio for neutrals at the same temperature ( v t h H / v t h D = 2 ) . This ratio is constant for both low and high pedestal electron density. At low pedestal density ( n e ∼ 4 × 10 19 m − 3 ) , the neutral penetration length is greater than the density pedestal width for both isotopes, and the additional 40% increase of neutral penetration in hydrogen widens the pedestal by the same amount. As the density pedestal height increases ( n e ∼ 6 × 10 19 m − 3 ) , the neutral penetration lengths drop below the density pedestal widths for both isotopes, and the increased penetration of hydrogen has no increased effect on the pedestal width compared to deuterium. Extrapolating to future reactor-relevant high electron density pedestals, the isotope-mass change in neutral fueling on the HFS from the deepest neutral penetration of hydrogen, to the shortest neutral penetration of tritium will be negligible (0.2–0.4 cm) in comparison to estimates of the density pedestal width (6–8.5 cm).

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2026

Density limit in peeling-limited pedestals at and above the Greenwald value in DIII-D high poloidal beta plasmas

High pressure, peeling limited pedestals with pedestal normalized beta β N,ped >2 and pedestal top density n ped at or above the Greenwald density nG have been achieved in DIII-D high poloidal beta plasmas, with high global normalized beta β N >3 and energy confinement H 98 ~1.2-1.7. Higher β N allows higher pedestal density above the Greenwald value and higher pedestal pressure, even with a low injected torque. MHD modeling confirms that the experimental profiles lie near the peeling-mode unstable boundary with high normalized pressure gradient βMHD and high edge current density. Experimental analysis and stability calculations indicate that the high poloidal beta with strong Shafranov shift, high βMHD and weak/negative magnetic shear improves the pedestal stability by decoupling the peeling and ballooning modes and stabilizing the ballooning modes, thus facilitating access to the second stable region of peeling-ballooning mode. The access to the second stable peeling-ballooning stability region opens Super-H-like channels without extremely strong shaping or strong torque injection. The high-pressure peeling pedestal allows the pedestal density to go beyond the Greenwald limit with strong ExB shear maintained: pedestal pressure increases with pedestal density even when n ped >n G , until reaching the ideal MHD instability boundary, where giant ELMs occur. The giant ELMs are dominated by a strong n=1 component and cause a large reduction of the edge pressure, but a negligible change of the core pressure, consistent with kink/peeling-mode induced instability. The pedestal recovers from the collapse and typically sustains a high baseline density, around the Greenwald limit, during the whole discharge duration. Experiments also found that internal transport barriers and n ped ~0.9nG, peeling limited pedestals could be simultaneously achieved in high β N plasmas, while an internal feedback between ITB strength and pedestal performance is found.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2016

Generalization of the Kohn-Sham system that can represent arbitrary one-electron density matrices

Density functional theory is currently the most widely applied method in electronic structure theory. The Kohn-Sham method, based on a fictitious system of noninteracting particles, is the workhorse of the theory. The particular form of the Kohn-Sham wave function admits only idempotent one-electron density matrices whereas wave functions of correlated electrons in post-Hartree-Fock methods invariably have fractional occupation numbers. Here we show that by generalizing the orbital concept and introducing a suitable dot product as well as a probability density, a noninteracting system can be chosen that can represent the one-electron density matrix of any system, even one with fractional occupation numbers. This fictitious system ensures that the exact electron density is accessible within density functional theory. It can also serve as the basis for reduced density matrix functional theory. Moreover, to aid the analysis of the results the orbitals may be assigned energies from a mean-field Hamiltonian. This produces energy levels that are akin to Hartree-Fock orbital energies such that conventional analyses based on Koopmans' theorem are available. Lastly, this system is convenient in formalisms that depend on creation and annihilation operators as they are trivially applied to single-determinant wave functions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Ab initio electronic density in solids by many-body plane-wave auxiliary-field quantum Monte Carlo calculations

We present accurate many-body results of the electronic densities in several solid materials, including Si, NaCl, and Cu. These results are obtained using the ab initio auxiliary-field quantum Monte Carlo (AFQMC) method working in a plane-wave basis with norm-conserving, multiple-projector pseudopotentials. AFQMC has been shown to be an excellent many-body total energy method. Computation of observables and correlation functions other than the ground-state energy requires back-propagation, whose adaption and implementation in the plane-wave basis AFQMC framework are discussed in the present paper. This development allows us to compute correlation functions, electronic densities, and interatomic forces, paving the way for geometry optimizations and calculations of thermodynamic properties in solids. Finite supercell size effects are considerably more subtle in the many-body framework than in independent-electron calculations. We analyze the convergence of the electronic density, and obtain best estimates for the thermodynamic limit. The densities from several typical density functionals are benchmarked against our near-exact results. The electronic densities we obtained can also be used to help construct improved density functionals.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Imposing correct jellium response is key to predict the density response by orbital-free DFT

Orbital-free density functional theory constitutes a computationally highly effective tool for modeling electronic structures of systems ranging from room-temperature materials to warm dense matter. Its accuracy critically depends on the employed kinetic energy (KE) density functional, which has to be supplied as an external input. In this work we consider several nonlocal and Laplacian-level KE functionals and use an external harmonic perturbation to compute the static density response at T = 0 K in the linear and beyond-linear response regimes. We test for the satisfaction of exact conditions in the limit of uniform densities and for how approximate KE functionals reproduce the density response of realistic materials (e.g., Al and Si) against the Kohn-Sham DFT reference, which employs the exact KE. The results illustrate that several functionals violate exact conditions in the uniform electron gas (UEG) limit. We find a strong correlation between the accuracy of the KE functionals in the UEG limit and in the strongly inhomogeneous case. This empirically demonstrates the importance of imposing the limit of UEG response for uniform densities and validates the use of the Lindhard function in the formulation of kernels for nonlocal functionals. This conclusion is substantiated by additional calculations for bulk aluminum (Al) with a face-centered cubic (fcc) lattice and silicon (Si) with an fcc lattice, body-centered cubic (bcc) lattice, and semiconducting crystal diamond state. The analysis of fcc Al, and fcc as well as bcc Si data follows closely the conclusions drawn for the UEG, allowing us to extend our conclusions to realistic systems that are subject to density inhomogeneities induced by ions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Skyrme pseudopotentials at next-to-next-to-leading order: Construction of local densities and first symmetry-breaking calculations

There is an ongoing quest to improve on the spectroscopic quality of nuclear energy density functionals (EDFs) of the Skyrme type through extensions of its traditional form. One direction for such activities is the inclusion of terms of higher order in gradients in the EDF. We report on exploratory symmetry-breaking calculations performed for an extension of the Skyrme EDF that includes central terms with four gradients at next-to-next-to-leading order (N2LO) and for which the high-quality parametrization SN2LO1 has been constructed recently. Up to now, the investigation of such functionals with higher-order terms was limited to infinite matter and spherically symmetric configurations of singly and doubly magic nuclei. We address here nuclei and phenomena that require us to consider axial and nonaxial deformation, both for reflection-symmetric and also reflection-asymmetric shapes, as well as the breaking of time-reversal invariance. Achieving these calculations demanded a number of formal developments. These all resulted from the formulation of the N2LO EDF requiring the introduction of new local densities with additional gradients that are not present in the EDF at NLO. Their choice is not unique, but can differ in the way the gradients are coupled. While designing a numerical implementation of N2LO EDFs in Cartesian three-dimensional coordinate-space representation, we have developed a novel definition and a new unifying notation for normal and pair densities that contain gradients at arbitrary order. Besides having mnemonic advantages, the new notation allows for the easy identification of redundancies and reducibilities in a given set of local densities, and the new definition makes it straightforward to construct densities that automatically adopt the symmetries of the many-body state they are constructed from. The resulting scheme resolves several issues with some of the choices that have been made for local densities in the past, in particular when breaking time-reversal symmetry. Guided by general practical considerations, we propose an alternative form of the N2LO contribution to the Skyrme EDF that is built from a different set of densities. It has exactly the same physics content, but is much more efficient to handle in formal discussions and, compared to the original formulation, leads to a substantial reduction of computational cost and memory requirements in deformed codes. As representative examples for the performance of SN2LO1, we have chosen the ground states of even-even Kr and Nd isotopes, the fission barrier of 240 Pu as well as the superdeformed rotational band of 194 Hg. Overall, for the nuclei and phenomena studied here, the SN2LO1 parametrization does not yet present a systematic improvement over standard NLO parametrizations. This finding calls for improved fit protocols that better discriminate between NLO and N2LO terms and better exploit the unique features of the additional degrees of freedom offered by the latter.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2015

Density- and wavefunction-normalized Cartesian spherical harmonics for l ≤ 20

The widely used pseudoatom formalism in experimental X-ray charge-density studies makes use of real spherical harmonics when describing the angular component of aspherical deformations of the atomic electron density in molecules and crystals. The analytical form of the density-normalized Cartesian spherical harmonic functions for up to l ≤ 7 and the corresponding normalization coefficients were reported previously by Paturle & Coppens. It was shown that the analytical form for normalization coefficients is available primarily for l ≤ 4. Only in very special cases it is possible to derive an analytical representation of the normalization coefficients for 4 < l ≤ 7. In most cases for l > 4 the density normalization coefficients were calculated numerically to within seven significant figures. In this study we review the literature on the density-normalized spherical harmonics, clarify the existing notations, use the Paturle–Coppens method in the Wolfram Mathematica software to derive the Cartesian spherical harmonics for l ≤ 20 and determine the density normalization coefficients to 35 significant figures, and computer-generate a Fortran90 code. The article primarily targets researchers who work in the field of experimental X-ray electron density, but may be of some use to all who are interested in Cartesian spherical harmonics.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

eFESTA: Ensemble Feature Exploration with Surface Density Estimates

We propose surface density estimate (SDE) to model the spatial distribution of surface features-isosurfaces, ridge surfaces, and streamsurfaces-in 3D ensemble simulation data. The inputs of SDE computation are surface features represented as polygon meshes, and no field datasets are required (e.g., scalar fields or vector fields). The SDE is defined as the kernel density estimate of the infinite set of points on the input surfaces and is approximated by accumulating the surface densities of triangular patches. We also propose an algorithm to guide the selection of a proper kernel bandwidth for SDE computation. An ensemble Feature Exploration method based on Surface densiTy EstimAtes (eFESTA) is then proposed to extract and visualize the major trends of ensemble surface features. For an ensemble of surface features, each surface is first transformed into a density field based on its contribution to the SDE, and the resulting density fields are organized into a hierarchical representation based on the pairwise distances between them. The hierarchical representation is then used to guide visual exploration of the density fields as well as the underlying surface features. We demonstrate the application of our method using isosurface in ensemble scalar fields, Lagrangian coherent structures in uncertain unsteady flows, and streamsurfaces in ensemble fluid flows.

Computational modeling↗

DOE OSTI2019

Effects of group size and group density on trade–offs in resource selection by a group–territorial central–place foraging woodpecker

Trade-offs in resource selection by central-place foragers are driven by the need to balance the benefits of selecting resources against the costs of travel from the central place. For group-territorial central-place foraging birds, trade-offs in resource selection are likely to be complicated by a competitive advantage for larger groups at high group density that may limit accessibility of high-quality distant resources to small groups. We used the group-territorial, central-place foraging Red-cockaded Woodpecker Leuconotopicus borealis (RCW) as a case study to test predictions that increases in group density lead to differences in foraging distances and resource selection for groups of different sizes. We used GPS tracking and LiDAR-derived habitat data to model effects of group size on foraging distances and selection for high-quality pines (≥ 35.6 cm diameter at breast height (dbh)) and lower quality pines (25.4–35.6 cm dbh) by RCW groups across low ( n = 14), moderate ( n = 10) and high group density ( n = 10) conditions. At low and moderate group density, all RCW groups selected distant high-quality pines in addition to those near the central place because competition for resources was low. In contrast, at high group density, larger groups travelled further to select high-quality pines, whereas smaller groups selected high-quality pines only when they were close to the central place and, conversely, were more likely to select lower quality pines at greater distances from the central place. Selection for high-quality pines only when close to the cavity tree cluster at high group density is important to long-term fitness of small RCW groups because it allows them to maximize benefits from both territorial defence and selecting high-quality resources while minimizing costs of competition. Furthermore these relationships suggest that intraspecific competition at high group density entails substantive costs to smaller groups of territorial central-place foragers by limiting accessibility of distant high-quality foraging resources.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

MO-F-CAMPUS-J-04: Tissue Segmentation-Based MR Electron Density Mapping Method for MR-Only Radiation Treatment Planning of Brain

Purpose: Automatically derive electron density of tissues using MR images and generate a pseudo-CT for MR-only treatment planning of brain tumours. Methods: 20 stereotactic radiosurgery (SRS) patients’ T1-weighted MR images and CT images were retrospectively acquired. First, a semi-automated tissue segmentation algorithm was developed to differentiate tissues with similar MR intensities and large differences in electron densities. The method started with approximately 12 slices of manually contoured spatial regions containing sinuses and airways, then air, bone, brain, cerebrospinal fluid (CSF) and eyes were automatically segmented using edge detection and anatomical information including location, shape, tissue uniformity and relative intensity distribution. Next, soft tissues - muscle and fat were segmented based on their relative intensity histogram. Finally, intensities of voxels in each segmented tissue were mapped into their electron density range to generate pseudo-CT by linearly fitting their relative intensity histograms. Co-registered CT was used as a ground truth. The bone segmentations of pseudo-CT were compared with those of co-registered CT obtained by using a 300HU threshold. The average distances between voxels on external edges of the skull of pseudo-CT and CT in three axial, coronal and sagittal slices with the largest width of skull were calculated. The mean absolute electron density (in Hounsfield unit) difference of voxels in each segmented tissues was calculated. Results: The average of distances between voxels on external skull from pseudo-CT and CT were 0.6±1.1mm (mean±1SD). The mean absolute electron density differences for bone, brain, CSF, muscle and fat are 78±114 HU, and 21±8 HU, 14±29 HU, 57±37 HU, and 31±63 HU, respectively. Conclusion: The semi-automated MR electron density mapping technique was developed using T1-weighted MR images. The generated pseudo-CT is comparable to that of CT in terms of anatomical position of tissues and similarity of electron density assignment. This method can allow MR-only treatment planning.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Multifactorial genetic control and magnesium levels govern the production of a Streptomyces antibiotic with unusual cell density dependence

Streptomyces bacteria are renowned both for their antibiotic production capabilities and for their cryptic metabolic potential. Their metabolic repertoire is subject to stringent genetic control, with many of the associated biosynthetic gene clusters being repressed by the conserved nucleoid-associated protein Lsr2. In an effort to stimulate new antibiotic production in wild Streptomyces isolates, we leveraged the activity of an Lsr2 knockdown construct and successfully enhanced antibiotic production in the wild Streptomyces isolate WAC07094. We determined that this new activity stemmed from increased levels of the angucycline-like family member saquayamycin. Saquayamycin has both antibiotic and anti-cancer activities, and intriguingly, beyond Lsr2-mediated repression, we found saquayamycin production was also suppressed at high density on solid or in liquid growth media; its levels were greatest in low-density cultures. This density-dependent control was exerted at the level of the cluster-situated regulatory gene sqnR and was mediated in part through the activity of the PhoRP two-component regulatory system, where deleting phoRP led to both constitutive antibiotic production and sqnR expression. This suggests that PhoP functions to repress the expression of sqnR at high cell density. We further discovered that magnesium supplementation could alleviate this density dependence, although its action was independent of PhoP. Finally, we revealed that the nitrogen-responsive regulators GlnR and AfsQ1 could relieve the repression exerted by Lsr2 and PhoP. Intriguingly, we found that this low density-dependent production of saquayamycin was not unique to WAC07094; saquayamycin production by another wild isolate also exhibited low-density activation, suggesting that this spatial control may serve an important ecological function in their native environments.

59 BASIC BIOLOGICAL SCIENCES↗