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At least 739 records · Page 41

Transient knockdown of Anopheles stephensi LRIM1 using RNAi increases Plasmodium falciparum sporozoite salivary gland infections

Abstract Background Plasmodium falciparum (Pf) sporozoites (PfSPZ) can be administered as a highly protective vaccine conferring the highest protection seen to date. Sanaria® PfSPZ vaccines are produced using aseptically reared Anopheles stephensi mosquitoes. The bionomics of sporogonic development of P. falciparum in A. stephensi to fully mature salivary gland PfSPZ is thought to be modulated by several components of the mosquito innate immune system. In order to increase salivary gland PfSPZ infections in A. stephensi and thereby increase vaccine production efficiency, a gene knock down approach was used to investigate the activity of the immune deficiency (IMD) signaling pathway downstream effector leucine-rich repeat immune molecule 1 ( LRIM1 ), an antagonist to Plasmodium development. Methods Expression of LRIM1 in A. stephensi was reduced following injection of double stranded (ds) RNA into mosquitoes. By combining the Gal4/UAS bipartite system with in vivo expression of short hairpin (sh) RNA coding for LRIM1 reduced expression of LRIM1 was targeted in the midgut, fat body, and salivary glands. RT-qPCR was used to demonstrate fold-changes in gene expression in three transgenic crosses and the effects on P. falciparum infections determined in mosquitoes showing the greatest reduction in LRIM1 expression. Results LRIM1 expression could be reduced, but not completely silenced, by expression of LRIM1 dsRNA. Infections of P. falciparum oocysts and PfSPZ were consistently and significantly higher in transgenic mosquitoes than wild type controls, with increases in PfSPZ ranging from 2.5- to tenfold. Conclusions Plasmodium falciparum infections in A. stephensi can be increased following reduced expression of LRIM1. These data provide the springboard for more precise knockout of LRIM1 for the eventual incorporation of immune-compromised A. stephensi into manufacturing of Sanaria’s PfSPZ products.

Billingsley, Peter F. (ORCID:0000000311424813)↗

General relativistic MHD simulations of non-thermal flaring in Sagittarius A*

Sgr A* exhibits regular variability in its multiwavelength emission, including daily X-ray flares and roughly continuous near-infrared (NIR) flickering. The origin of this variability is still ambiguous since both inverse Compton and synchrotron emission are possible radiative mechanisms. The underlying particle distributions are also not well constrained, particularly the non-thermal contribution. In this work, we employ the GPU-accelerated general relativistic magnetohydrodynamics code H-AMR to perform a study of flare flux distributions, including the effect of particle acceleration for the first time in high-resolution 3D simulations of Sgr A*. For the particle acceleration, we use the general relativistic ray-tracing code bhoss to perform the radiative transfer, assuming a hybrid thermal+non-thermal electron energy distribution. We extract ~60 h light curves in the sub-millimetre, NIR and X-ray wavebands, and compare the power spectra and the cumulative flux distributions of the light curves to statistical descriptions for Sgr A* flares. Our results indicate that non-thermal populations of electrons arising from turbulence-driven reconnection in weakly magnetized accretion flows lead to moderate NIR and X-ray flares and reasonably describe the X-ray flux distribution while fulfilling multiwavelength flux constraints. These models exhibit high rms per cent amplitudes, $\gtrsim 150{{\ \rm per\ cent}}$ both in the NIR and the X-rays, with changes in the accretion rate driving the 230 GHz flux variability, in agreement with Sgr A* observations.

79 ASTRONOMY AND ASTROPHYSICS↗

Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs

We report that community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Numerical modeling of impurity powder injection in W7-X

In this work, we present numerical simulation results of powder injection in W7-X using the EMC3-EIRENE and DIS codes. First, we model powder injection experiments performed in W7-X with the Probe Mounted Powder Injector. The simulation results qualitatively agree with visible imaging measurements. Secondly, we perform predictive simulations to guide the installation of an Impurity Powder Dropper in W7-X, allowing to choose in between several available non-vertical ports to maximize the amount of powder penetrating into the plasma, as well as the verticality of the port, to minimize sticking of the powders in the in-vessel stainless steel guiding tube. Port AEM41 is selected as the best candidate for IPD installation. The robustness of the simulation results has been verified for different plasma densities, powder materials and sizes, powder friction coefficient and changes in the plasma flow.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Fluid and gyrokinetic turbulence in open field-line, helical plasmas

Two-fluid Braginskii codes have simulated open-field line turbulence for over a decade, and only recently, it has become possible to study these systems with continuum gyrokinetic codes. This work presents a first-of-its-kind comparison between fluid and (long-wavelength) gyrokinetic models in open field-lines, using the GDB and Gkeyll codes to simulate interchange turbulence in the Helimak device at the University of Texas [T. N. Bernard et al., Phys. Plasmas 26, 042301 (2019)]. Partial agreement is attained in a number of diagnostic channels when the GDB sources and sheath boundary conditions (BCs) are selected carefully, especially the heat-flux BCs that can drastically alter the temperature. The radial profile of the fluctuation levels is qualitatively similar and quantitatively comparable on the low-field side, although statistics such as moments of the probability density function and the high-frequency spectrum show greater differences. This comparison indicates areas for future improvement in both simulations, such as sheath BCs, and improvements in GDB like particle conservation and spatially varying thermal conductivity, in order to achieve better fluid-gyrokinetic agreement and increase fidelity when simulating experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Mass measurement of 27 P to constrain type-I x-ray burst models and validate the isobaric multiplet mass equation for the $A = 27, T = \frac{3}{2}$ isospin quartet

Background: Light curves are the primary observable of type-I x-ray bursts. Computational x-ray burst models must match simulations to observed light curves. Most of the error in simulated curves comes from uncertainties in rp process reaction rates, which can be reduced via precision mass measurements of neutron-deficient isotopes in the rp process path. Purpose: Perform a precise atomic mass measurement of 27 P. Use this new measurement to calculate rp process reaction rates and input these rates into an x-ray burst model to reduce simulated light curve uncertainty. Use the mass measurement of 27 P to validate the isobaric multiplet mass equation (IMME) for the A = 27 T = 3/2 isospin quartet which 27 P belongs to. Method: High-precision Penning trap mass spectrometry utilizing the time-of-flight ion cyclotron resonance technique was used to determine the atomic mass of 27 P. The MESA code (Modules for Experiments in Stellar Astrophysics) was then used to simulate x-ray bursts using a one-dimensional multizone model to produce updated light curves. Results: The mass excess of 27 P was measured to be –670.7(6) keV, a 14-fold precision increase over the mass reported in the 2020 Atomic Mass Evaluation (AME2020). The 26 Si(p, $γ$) 27 P– 27 P($γ$, p) 26 Si rate equilibrium has been determined to a higher precision based on the precision mass measurement of 27 P. x-ray burst light curves were produced with the MESA code using the new reaction rates. Changes in the mass of 27 P seem to have minimal effect on light curves, even in burster systems tailored to maximize impact. Conclusion: The mass of 27 P does not play a significant role in x-ray burst light curves. It is important to understand that more advanced models do not just provide more precise results, but often qualitatively different ones. This result brings us a step closer to being able to extract stellar parameters from individual x-ray burst observations. In addition, the IMME has been validated for the A = 27, T = 3/2 quartet. The normal quadratic form of the IMME using the latest data yields a reduced $χ$ 2 of 2.9. Finally, the cubic term required to generate an exact fit to the latest data matches theoretical attempts to predict this term.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Measurement and Modeling of Electron Temperature in Laboratory Photoionized Plasmas Relevant to Astrophysics

The electron temperature of photoionized plasmas characterizes the thermalization of photoelectrons, impacts the charge-state distribution, emissivity, and opacity through atomic recombination processes, and is needed to perform detailed comparisons with theory predictions. We discuss temperature measurements in laboratory photoionized plasmas and a comparison with model calculations done with several theory approximations and codes. These include a radiation-hydrodynamics simulation and two nonequilibrium heating and ionization models that tracked the evolution of the internal energy of the electrons. Furthermore, for the same physics model and X-ray flux time history, calculations were performed assuming steady-state or time-dependent conditions. The time history of steady-state results correlates with that of the X-ray flux, while that of the time-dependent cases does not, and it is qualitatively and quantitatively different from the steady-state case. Steady-state results significantly overestimated temperature measurements, while time-dependent results produced better approximations, which suggests the importance of transient effects in the experiment and also the need for time-resolved measurements.

Laboratory astrophysics↗

Physics-informed machine learning

Despite great progress in simulating multiphysics problems using the numerical discretization of partial differential equations (PDEs), one still cannot seamlessly incorporate noisy data into existing algorithms, mesh generation remains complex, and high-dimensional problems governed by parameterized PDEs cannot be tackled. Moreover, solving inverse problems with hidden physics is often prohibitively expensive and requires different formulations and elaborate computer codes. Machine learning has emerged as a promising alternative, but training deep neural networks requires big data, not always available for scientific problems. Instead, such networks can be trained from additional information obtained by enforcing the physical laws (for example, at random points in the continuous space-time domain). Such physics-informed learning integrates (noisy) data and mathematical models, and implements them through neural networks or other kernel-based regression networks. Moreover, it may be possible to design specialized network architectures that automatically satisfy some of the physical invariants for better accuracy, faster training and improved generalization. Furthermore, we review some of the prevailing trends in embedding physics into machine learning, present some of the current capabilities and limitations and discuss diverse applications of physics-informed learning both for forward and inverse problems, including discovering hidden physics and tackling high-dimensional problems.

97 MATHEMATICS AND COMPUTING↗

An implicit barotropic mode solver for MPAS-ocean using a modern Fortran solver interface

Here, we demonstrate use of a modern Fortran solver interface to manage solver algorithms for an implicit barotropic mode solver in the Model for Predictions Across Scales-Ocean (MPAS-O). ForTrilinos, a Fortran interface to Trilinos that contains a large collection of solver capabilities written in C++, has been implemented in MPAS-O to provide access to a suite of linear solver options. By virtue of the simplified wrapper and interface generator (SWIG) automation tool that generates modern Fortran interfaces to C++ code, we were able to implement the Fortran solver interface in MPAS-O using a familiar Fortran coding style while minimizing performance degradation. The ForTrilinos solver interface is written within MPAS-O’s time stepping modules as a subroutine in conjunction with MPAS-O code. Applied to an idealized ocean and a high-resolution realistic ocean test case, parallel performance of ForTrilinos solvers is examined. It is found that parallel scalability of the ForTrilinos solvers is highly dependent on the number of global synchronization points per solver iteration in each iterative solver algorithm. ForTrilinos solvers perform best compared to the Fortran hand-crafted (FHC) solver when the amount of work per processor is large enough. However, parallel scalability is better with the FHC solver and so when the work per core is modest FHC outperforms ForTrilinos. The intercomparison between the ForTrilinos and FHC solvers reveals that this performance hit in the ForTrilinos solver mostly comes from the global synchronization process, while suggesting that the matrix-vector multiplication process in the FHC solver needs to be optimized for better performance.

97 MATHEMATICS AND COMPUTING↗

WHONDRS Surface Water Chemistry and Organic Matter Characterization along the St. Lawrence River's Inland to Coastal Gradient, Eastern North America (v2)

This dataset supports a broader study examining the inland (Lake Ontario) to coastal (North Atlantic Ocean) geochemistry gradient along the St. Lawrence River in Canada and the United States. The St. Lawrence River is unique in that it contains the convergence of multiple water masses with distinct water signatures that mix only slightly as the river flows downstream. The dataset provides dissolved organic carbon (DOC) and organic matter characterization data generated from surface water. Samples were collected by researchers on board the Lampsilis research vessel (l’Université du Québec à Trois-Rivières) and small boats (St. Lawrence River Institute of Environmental Sciences, Cornwall) at 94 locations across and along the St. Lawrence River to capture longitudinal and transverse variation. Related data were collected and will be published separately in collaboration with the MicrEAU Laboratory (François Guillemette; l’Université du Québec à Trois-Rivières) and the Exploration of Coastal Hydrobiogeochemistry Across a Network of Gradients and Experiments (EXCHANGE) program. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) data (5) surface water sampling protocol; (6) readme; (7) methods codes; (8) international geo-sample number (IGSN) mapping file; and (9) folder of high resolution characterization of organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). The FTICR folder contains two subfolders, one containing the .xml data files and the other containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml. The data package was originally published in November 202. It was updated in April 2025 (v2; modified files). See the change history section in the readme for details.

54 ENVIRONMENTAL SCIENCES↗

Industry Level Integrated Fire Modeling Using Fire Risk Investigation in 3D (FRI3D)

The software Fire Risk Investigation in 3D (FRI3D) has been developed over the last 2 years to integrate 3D spatial modeling with existing fire probabilistic risk assessment (PRA) models and fire simulation codes. The goal of this research and development is to automate many of the fire analysis manual tasks to reduce industry efforts in the initial fire modeling and operational costs for the model maintenance and evaluations required during normal plant operations. The tasks for Fiscal Year (FY) 2021 include first testing the FRI3D modeling capabilities by importing an industry fire model into FRI3D and making a 3D model of a complex/high-risk significant area. (For this work, the switchgear room was chosen.) Then, the second task of FY 2021 is to develop a dynamic fire PRA process that can help optimize traditional fire PRA models. The switchgear room model will be used for the dynamic fire PRA work. This report describes the work and insights learned when using FRI3D software to model both a Nuclear Regulatory Report (NUREG) example models and a full industry switchgear room.

97 MATHEMATICS AND COMPUTING↗

APOGEE-2S Mg–Al anti-correlation of the metal-poor globular cluster NGC 2298

We present detailed elemental abundances and radial velocities of stars in the metal-poor globular cluster (GC) NGC 2298, based on near-infrared high-resolution ($R$ ~ 22 500) spectra of 12 members obtained during the second phase of the Apache Point Observatory Galactic Evolution Experiment (APOGEE-2) at Las Campanas Observatory as part of the seventeenth Data Release (DR 17) of the Sloan Digital Sky Survey IV (SDSS-IV). We employed the Brussels Automatic Code for Characterizing High accuracy Spectra (BACCHUS) software to investigate abundances for a variety of species including α elements (Mg, Si, and Ca), the odd-Z element Al, and iron-peak elements (Fe and Ni) located in the innermost regions of NGC 2298. We find a mean and median metallicity [Fe/H] = -1.76 and -1.75, respectively, with a star-to-star spread of 0.14 dex, which is compatible with the internal measurement errors. Thus, we find no evidence for an intrinsic [Fe/H] abundance spread in NGC 2298. The typical $α$-element enrichment in NGC 2298 is overabundant relative to the Sun, and it follows the trend of other metal-poor GCs. We confirm the existence of an Al-enhanced population in this cluster, which is clearly anti-correlated with Mg, indicating the prevalence of the multiple-population phenomenon in NGC 2298.

79 ASTRONOMY AND ASTROPHYSICS↗

Electron energy distributions in the extended gas nebulae associated with high-z AGN: Maxwell–Boltzmann versus κ distributions

ABSTRACT Emission line observations together with photoionization models provide important information about the ionization mechanisms, densities, temperatures, and metallicities in active galactic nuclei (AGN)-ionized gas. Photoionization models usually assume Maxwell–Boltzmann (M–B) electron energy distributions (EED), but it has been suggested that using κ distributions may be more appropriate and could potentially solve the discrepancies in temperatures and abundances found in HII regions and planetary nebulae. We consider the impact of the presence of κ distributions in photoionized nebulae associated with AGN and study how this might affect spectral modelling and abundance analyses for such regions. Using the photoionization code MAPPINGS 1e, we compute models adopting M–B and κ distributions of electron energies and compare the behaviour of emission line ratios for different values of κ, gas metallicity, density, ionization parameter, and SED slope. We find that the choice of EED can have a large impact on some UV and optical emission lines emitted by photoionized nebulae associated with AGN, and that the impact of adopting a κ distribution is strongly dependent on gas metallicity and ionization parameter. We compile a sample of line ratios for 143 type 2 AGN and compare our models against the observed line ratios. We find that for 98 objects, κ distributions provide a better fit to the observed line ratios than M–B distributions. In addition, we find that adopting κ-distributed electron energies results in significant changes in the inferred gas metallicity and ionization parameter in a significant fraction of objects.

Morais, S. G. (ORCID:0000000200927813)↗

How to Build a Quantum Supercomputer: Scaling from Hundreds to Millions of Qubits

In the span of four decades, quantum computation has evolved from an intellectual curiosity to a potentially realizable technology. Today, small-scale demonstrations have become possible for quantum algorithmic primitives on hundreds of physical qubits and proof-of-principle error-correction on a single logical qubit. Nevertheless, despite significant progress and excitement, the path toward a full-stack scalable technology is largely unknown. There are significant outstanding quantum hardware, fabrication, software architecture, and algorithmic challenges that are either unresolved or overlooked. These issues could seriously undermine the arrival of utility-scale quantum computers for the foreseeable future. Here, we provide a comprehensive review of these scaling challenges. We show how the road to scaling could be paved by adopting existing semiconductor technology to build much higher-quality qubits, employing system engineering approaches, and performing distributed quantum computation within heterogeneous high-performance computing infrastructures. These opportunities for research and development could unlock certain promising applications, in particular, efficient quantum simulation/learning of quantum data generated by natural or engineered quantum systems. To estimate the true cost of such promises, we provide a detailed resource and sensitivity analysis for classically hard quantum chemistry calculations on surface-code error-corrected quantum computers given current, target, and desired hardware specifications based on superconducting qubits, accounting for a realistic distribution of errors. Furthermore, we argue that, to tackle industry-scale classical optimization and machine learning problems in a cost-effective manner, heterogeneous quantum-probabilistic computing with custom-designed accelerators should be considered as a complementary path toward scalability.

Mohseni, Masoud↗

NCAP: Noncanonical Amino Acid Parameterization Software for CHARMM Potentials

Noncanonical Amino Acids (NCAAs) provide numerous avenues for introduction of novel functionality to peptides and proteins. NCAAs can be incorporated through solid phase synthesis or genetic code expansion in conjugation with heterologous expression of the encoded protein modification. Due to the difficulty of synthesis, wide chemical space and lack of empirically resolved structures modeling the effects of NCAA mutation is critical for rational protein design. To evaluate the structural and functional perturbations NCAAs introduce we utilize molecular potentials that describe the forces in protein structure. Most potentials such as CHARMM are designed to model canonical residues but can be parameterized in include novel NCAAs. Here, in this work, we introduce NCAP a software package to generate CHARMM compatible parameters from quantum chemical calculation. Unlike currently available tools NCAP is designed to recognize NCAA structure and automatically bridge the gap between DFT calculations and potential parameters. For our software we discuss workflow, validation against canonical parameter sets and comparison to published NCAA-protein structures.

59 BASIC BIOLOGICAL SCIENCES↗

BEYONDPLANCK VIII. Efficient sidelobe convolution and corrections through spin harmonics

We introduce a new formulation of the Conviqt convolution algorithm in terms of spin harmonics, and apply this to the problem of sidelobe correction for BEYONDPLANCK, the first end-to-end Bayesian Gibbs sampling framework for CMB analysis. We compare our implementation to the previous Planck LevelS implementation, and find good agreement between the two codes in terms of accuracy, but with a speed-up reaching a factor of 3–10, depending on the frequency bandlimits, l max and m max . The new algorithm is significantly simpler to implement and maintain, since all low-level calculations are handled through an external spherical harmonic transform library. We find that our mean sidelobe estimates for Planck LFI are in good agreement with previous efforts. Additionally, we present novel sidelobe rms maps that quantify the uncertainty in the sidelobe corrections due to variations in the sky model.

79 ASTRONOMY AND ASTROPHYSICS↗

Global gyrokinetic simulations of ASDEX Upgrade up to the transport timescale with GENE–Tango

An accurate description of turbulence up to the transport timescale is essential for predicting core plasma profiles and enabling reliable calculations for designing advanced scenarios and future devices. Here, we exploit the gap separation between turbulence and transport timescales and couple the global gyrokinetic code GENE to the transport-solver Tango, including kinetic electrons, collisions, realistic geometries, toroidal rotation and electromagnetic effects for the first time. This approach overcomes gyrokinetic codes' limitations and enables high-fidelity profile calculations in experimentally relevant plasma conditions, significantly reducing the computational cost. We present numerical results of GENE–Tango for two ASDEX Upgrade discharges, one of which exhibits a pronounced peaking of the ion temperature profile not reproduced by TGLF–ASTRA. We show that GENE–Tango can correctly capture the ion temperature peaking observed in the experiment. By retaining different physical effects in the GENE simulations, e.g., collisions, toroidal rotation and electromagnetic effects, we show that the ion temperature profile's peaking can be linked to electromagnetic effects of submarginal (stable) KBM modes. Furthermore, based on these results, the expected GENE–Tango speedup for the ITER standard scenario is larger than two orders of magnitude compared to a single gyrokinetic simulation up to the transport timescale, possibly making first-principles ITER simulations feasible on current computing resources.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

LLNL Response to the DOE ASCR RFI, "Stewardship of Software for Scientific and High-Performance Computing"

For decades, Lawrence Livermore National Laboratory (LLNL) has been engaged in significant research, development, and support for software to enable scientific computing and, particularly, the use of high performance computing (HPC) in the NNSA mission space. In particular, the move in the mid-1990’s to simulation as a leading component of stockpile stewardship through the ASCI and the successor ASC programs, as well as the need for reliable data acquisition and control software for the National Ignition Facility, have been important drivers in building expertise in production-quality software development at LLNL. LLNL has also been a leader in the DOE SciDAC FASTMath Institute and the DOE Exascale Computing Project (ECP), both of which have striven to make scientific computing software – in particular, the enabling technologies underpinning simulation capabilities – more widely adopted and sustainable. As such, we believe that our experience can inform the broader goal of software stewardship for scientific and high-performance computing. LLNL strongly supports the formation of a new DOE ASCR program element in software stewardship and sustainment. Historically, DOE ASCR has funded applied mathematics and computer science research that has led to the development of important new capabilities and algorithms that are expressed as artifacts in research software. Such frameworks, libraries, and tools have seldom been directly funded to address the important issues of code maintenance, documentation, robustness, and community building. Software engineering and support have typically been done on the side in support of the ASCR-driven research products. DOE funding priorities have been slow to recognize that good software engineering, the kind that ensures research investments have more adoption and longevity, requires significant resources. Based upon our experiences, we have prepared this response to highlight the concerns and issues we believe to be important as DOE ASCR considers its role in scientific software stewardship. We believe that role is important and will require a significant investment of new funding to legitimately support the technologies past and future DOE ASCR investments have and will produce to facilitate their uptake and adoption in the broader scientific computing community. Following a summary of our involvement in scientific software development, the remainder our response is organized around the nine topics specifically identified in the RFI.

97 MATHEMATICS AND COMPUTING↗