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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Conformational heterogeneity in the dGsw purine riboswitch: role of Mg²⁺ and 2’-dG in aptamer folding

Recent advancements in RNA structural biology have focused on unraveling the complexities of non-coding mRNA elements like riboswitches. These cis-acting regulatory regions undergo structural changes in response to specific cellular metabolites, leading to up or downregulation of downstream genes. The purine riboswitch family regulates many prokaryotic genes involved in purine degradation and biosynthesis. They feature an aptamer domain organized around a 3-way helical junction, where ligand encapsulation occurs at the junctional core. In our study, we chemically probed the aptamer domain of the 2’-dG-sensing purine riboswitch from Mesoplasma florum (dGsw) under various solution conditions to understand how Mg²⁺ and 2’-dG influence riboswitch folding. Here, we find that efficient 2’-dG binding strongly depends on Mg²⁺, indicating that Mg²⁺ is essential for priming dGsw for ligand interactions. We identified a previously undescribed sequence in the 5’ tail of dGsw that is complementary to a conserved helix. The inclusion of this region in a construct led to intramolecular competition between the alternate helix, Palt, and P1. Mutational analysis confirmed that 5’ flanking end of the aptamer domain forms an alternate helix in the absence of ligand. Molecular dynamics simulations revealed that this alternative conformation is stable. This helix may, therefore, facilitate the formation of an anti-terminator helix by opening the 3-way junction surrounding the 2’-dG binding site. Our study further establishes the importance of a closed terminal P1 helix conformation for metabolite binding and suggests that the delicate interplay between P1 and Palt may fine-tune downstream gene regulation. These insights offer a new perspective on riboswitch structure and enhance our understanding of the role that a conformational ensemble plays in riboswitch activity and regulation.

Biochemistry & Molecular Biology↗
DOE OSTI2024

DG-IMEX method for a two-moment model for radiation transport in the $\mathscr{O}$($v$/$c$) limit

Here, we consider neutral particle systems described by moments of a phase-space density and propose a realizability-preserving numerical method to evolve a spectral two-moment model for particles interacting with a background fluid moving with nonrelativistic velocities. The system of nonlinear moment equations, with special relativistic corrections to $\mathscr{O}$($v$/$c$), expresses a balance between phase-space advection and collisions and includes velocity-dependent terms that account for spatial advection, Doppler shift, and angular aberration. The model is conservative for the correct $\mathscr{O}$($v$/$c$) Eulerian-frame number density and is consistent, to $\mathscr{O}$($v$/$c$), with Eulerian-frame energy and momentum conservation. This model is closely related to the one promoted by Lowrie et al. and similar to models currently used to study transport phenomena in large-scale simulations of astrophysical environments. The proposed numerical method is designed to preserve moment realizability, which guarantees that the moments correspond to a nonnegative phase-space density. The realizability-preserving scheme consists of the following key components: (i) a strong stability-preserving implicit-explicit (IMEX) time-integration method; (ii) a discontinuous Galerkin (DG) phase-space discretization with carefully constructed numerical uxes; (iii) a realizability-preserving implicit collision update; and(iv) a realizability-enforcing limiter. In time integration, nonlinearity of the moment model necessitates solution of nonlinear equations, which we formulate as fixed-point problems and solve with tailored iterative solvers that preserve moment realizability with guaranteed global convergence. We also analyze the simultaneous Eulerian-frame number and energy conservation properties of the semi-discrete DG scheme and propose a "spectral redistribution" scheme that promotes Eulerian-frame energy conservation. Through numerical experiments, we demonstrate the accuracy and robustness of this DG-IMEX method and investigate its Eulerian-frame energy conservation properties.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1986

Observations of jets from low-luminosity stars - DG Tauri B

Low spectral resolution studies of DG Tau B, the faint system of knots south of the T Tauri star DG Tau, are described. The observations show this object to be bipolar, with the blueshifted lobe having extraordinarily low excitation. Infrared observations of the exciting star show it to be of very low luminosity, with a bolometric luminosity of 0.88 solar luminosity. The visual extinction indicates a highly nonspherical distribution of circumstellar dust around the exciting star. In spite of this lack of embedding within an obvious dark cloud, the system is identified as a young one.

Jones, B. F.↗
NASA NTRS2016

A Very Bright, Very Hot, and Very Long Flaring Event from the M Dwarf Binary System DG CVn

On 2014 April 23, the Swift satellite responded to a hard X-ray transient detected by its Burst Alert Telescope, which turned out to be a stellar flare from a nearby, young M dwarf binary DG CVn. We utilize observations at X-ray, UV, optical, and radio wavelengths to infer the properties of two large flares. The X-ray spectrum of the primary outburst can be described over the 0.3100 kiloelectron volts bandpass by either a single very high-temperature plasma or a nonthermal thick-target bremsstrahlung model, and we rule out the nonthermal model based on energetic grounds. The temperatures were the highest seen spectroscopically in a stellar flare, at T(sub x) of 290 megakelvin. The first event was followed by a comparably energetic event almost a day later. We constrain the photospheric area involved in each of the two flares to be greater than 10(exp 20) sq cm, and find evidence from flux ratios in the second event of contributions to the white light flare emission in addition to the usual hot, T approximately 10(exp 4) K blackbody emission seen in the impulsive phase of flares. The radiated energy in X-rays and white light reveal these events to be the two most energetic X-ray flares observed from an M dwarf, with X-ray radiated energies in the 0.3-10 kiloelectron volts bandpass of 4 x 10(exp 35) and 9 x 10(exp 35) erg, and optical flare energies at E(sub V) of 2.8 x 10(exp 34) and 5.2 x 10(exp 34) erg, respectively. The results presented here should be integrated into updated modeling of the astrophysical impact of large stellar flares on close-in exoplanetary atmospheres.

stars: coronae – stars: flare – stars: individ↗
DOE OSTI2026

An implicit-explicit time splitting strategy for the far SOL plasma fluid model with DG-FEM discretization

We consider a far scrape-off layer (SOL) plasma fluid model of ions that is governed by a Braginskiitype model: a one-dimensional, nonlinear system of advection-diffusion equations coupled with a diffusion equation for neutral particles. Our motivation for studying this system arises from the coupling between the edge plasma and radio-frequency (RF) heating, where solving a far SOL plasma fluid model provides critical insights into edge plasma dynamics. Numerical simulations of plasma fluid models require advanced computational techniques to achieve both efficiency and accuracy, especially when resolving the boundary layer in magnetically confined plasmas. In this work, we propose an implicit-explicit time operator splitting strategy that allows for an efficient solution algorithm, where the diffusive terms are treated semi-implicitly requiring only a linear solve, while the advection part is handled explicitly using a strong-stability-preserving Runge-Kutta (SSP-RK3) scheme. This leads to a fully decoupled system in which the diffusion and advection sub-problems can be solved separately, simplifying the overall solution procedure and allowing for efficient parallelization, which is particularly relevant for exploring the impact of RF heating on the SOL plasma. The main challenge of the discretization is due to the strong coupling between diffusion and advection, particularly through the boundary conditions. This makes implementation of such a scheme in an accurate and stable manner nontrivial. We discuss in detail how to split the equations and manage boundary conditions to maintain stability and well-posedness for each subsystem. We also describe a spatial discretization approach, based on the discontinuous Galerkin finite element method (DG-FEM) and present numerical results for a one-dimensional system.

Burkovska, Olena [ORNL] (ORCID:0000000163101130)↗
NASA NTRS1992

10 AU scale halo structure around DG Tauri

Lunar occultation observations of the active T Tauri star DG Tau show that in the infrared K band it has a core-halo structure: 20-25 percent of the flux comes from a region 10 AU in extent and the rest from an unresolved core smaller than an AU. These results are consistent with those reported by Leinert et al. from a separate observation. The results obtained here and those of Leinert et al., measuring the intensity distribution projected along directions spanning roughly 40 deg, indicate that the resolved structure is not highly elongated. The extended emission is interpreted as star light scattered by optically thin dust located in a halo surrounding the star.

Chen, Wen P.↗
NASA NTRS2005

Coronal Emission from dG Halo Stars

The halo dG star HD 114762 was observed with the XMM-Newton satellite on 28-29 June 2004, during orbit 834, and the data were processed using the XMM-Newton Science Analysis System (SAS), version 6.0.0. Somewhat surprisingly, the target was NOT detected during this approx.30 ks exposure, which yielded instead a count rate upper limit of less than 0.0041 cts/s. We computed an X-ray flux upper limit by assuming a Raymond-Smith thermal spectrum of coronal temperature 1 million degrees K, typical of quiet old stars, a hydrogen column density of 2-10$^{19)$ cm$^{-2)$ and sub-solar abundances of 0.2. Our calculated X-ray luminosity upper limit in the 0.25-7.8 keV band is L$_x < 4.95 $\time$10$^{26)$ erg/s, where we have assumed a stellar distance of 28 pc. This relatively low upper limit has implications for the capability of metal poor stars to host solar-like dynamos, as we will report in a forthcoming paper (now in preparation).

Mushotzky, Richard↗
NASA NTRS2018

Parameterizations of Chromospheric Condensations in dG and dMe Model Flare Atmospheres

The origin of the near-ultraviolet and optical continuum radiation in flares is critical for understanding particle acceleration and impulsive heating in stellar atmospheres. Radiative-hydrodynamic (RHD) simulations in 1D have shown that high energy deposition rates from electron beams produce two flaring layers at T approximately 10 (exp 4) K that develop in the chromosphere: a cooling condensation (downflowing compression) and heated non-moving (stationary) flare layers just below the condensation. These atmospheres reproduce several observed phenomena in flare spectra, such as the red-wing asymmetry of the emission lines in solar flares and a small Balmer jump ratio in M dwarf flares. The high beam flux simulations are computationally expensive in 1D, and the (human) timescales for completing NLTE models with adaptive grids in 3D will likely be unwieldy for some time to come. We have developed a prescription for predicting the approximate evolved states, continuum optical depth, and emergent continuum flux spectra of RHD model flare atmospheres. These approximate prescriptions are based on an important atmospheric parameter: the column mass (m(sub ref)) at which hydrogen becomes nearly completely ionized at the depths that are approximately in steady state with the electron beam heating. Using this new modeling approach, we find that high energy flux density (>F11) electron beams are needed to reproduce the brightest observed continuum intensity in IRIS data of the 2014 March 29 X1 solar flare, and that variation in m(sub ref) from 0.001 to 0.02 g cm (exp -2) reproduces most of the observed range of the optical continuum flux ratios at the peak of M dwarf flares.

Kowalski, Adam F.↗
NASA NTRS1994

Inhibition of murine splenic T lymphocyte proliferation by 2-deoxy-D-glucose-induced metabolic stress

Female Swiss-Webster mice were injected with the glucose analogue 2-deoxy-D-glucose (2-DG), which when administered to rodents induces acute periods of metabolic stress. A single or multiple injections of 2-DG invoked a stress response, as evidenced by increases in serum corticosterone levels. The influence of this metabolic stressor on the blastogenic potential of splenic T lymphocytes was then examined. It was found that one, two, or three injections of 2-DG resulted in depressed T cell proliferative responses, with an attenuation of the effect occurring by the fifth injection. The 2-DG-induced inhibition of T cell proliferation was not attributable to 2-DG-induced cytolysis, as in vitro incubation of naive T cells with varying concentrations of 2-DG did not result in a reduction in cell number or viability, and flow cytometric analysis demonstrated that percentages of CD3, CD4, and CD8 splenic T cells were not altered as a result of 2-DG-induced stress. Incubating naive T cells in varying concentrations of 2-DG resulted in a dose-dependent inhibition of T cell blastogenic potential. Following in vivo exposure to 2-DG, T cell proliferation did not return to normal levels until 3 days after the cessation of 2-DG injections. Administering the beta-adrenergic receptor antagonist propranolol did not reverse the inhibited lymphoproliferation in 2-DG-treated mice. The inhibition in T cell proliferation was not observed, however, in mice that had been adrenalectomized or hypophysectomized and injected with 2-DG.(ABSTRACT TRUNCATED AT 250 WORDS).

Non-NASA Center↗
NASA NTRSDate not supplied

Discontinuous Galerkin and Related Methods for ODE

A defining feature of the discontinuous Galerkin (DG) method for ODE is that the piecewise polynomial solution can have a jump discontinuity at the beginning of each step. Starting from the standard integral formulation, the DG method is derived here in differential form. The key ingredient is a polynomial called the correction function, which helps ‘correct’ the discontinuous solution by approximating the jump and yields a continuous one. Under the right Radau quadrature, this continuous solution is identical to the solutions by the right Radau collocation and the continuous Galerkin (CG) methods. Next, the correction function facilitates the construction of the associated implicit Runge-Kutta schemes (IRK-DG). Different quadratures for DG result in different IRK-DG methods: left Radau quadrature in Radau IA, right Radau quadrature in Radau IIA or right Radau collocation, and Gauss quadrature in a method called DG-Gauss. The construction of IRK-DG clarifies the meaning and facilitates the proofs of various 𝐵(𝑝), 𝐶(𝜂), and 𝐷(𝜁) conditions for accuracy. The two consequences of these conditions are that all 𝑠-stage IRK-DG methods are accurate to order 2𝑠 − 1, and the IRK-DG methods of Radau type are unique. Numerical examples showing the behavior of the DG solutions are provided. In all, the correction function plays a key role and helps establish the relations among the DG, IRK-DG, collocation, and CG schemes.

numerical methods↗
NASA NTRSDate not supplied

Discontinuous Galerkin and Related Methods for ODE

Starting from the standard integral formulation, the DG method is derived here in differential form. The key ingredient is a polynomial called the correction function, which helps ‘correct’ the discontinuous solution by approximating the jump and yields a continuous one. Under the right Radau quadrature, this continuous solution is identical to the solutions by the right Radau collocation and the continuous Galerkin (CG) methods. Next, the correction function facilitates the construction of the associated implicit Runge-Kutta schemes (IRK-DG). Different quadratures for DG result in different IRK-DG methods: left Radau quadrature in Radau IA, right Radau quadrature in Radau IIA or right Radau collocation, and Gauss quadrature in a method called DG-Gauss. The construction of IRK-DG clarifies the meaning and facilitates the proofs of various 𝐵(𝑝), 𝐶(𝜂), and 𝐷(𝜁) conditions for accuracy. The two consequences of these conditions are that all 𝑠-stage IRK-DG methods are accurate to order 2𝑠− 1, and the IRK-DG methods of Radau type are unique. Numerical examples showing the behavior of the DG solutions are provided. In all, the correction function plays a key role and helps establish the relations among the DG, IRK DG, collocation, and CG methods.

Numerical Methods for Ordinary Differential Equati↗
NASA NTRS1998

2-deoxy-D-glucose-induced metabolic stress enhances resistance to Listeria monocytogenes infection in mice

Exposure to different forms of psychological and physiological stress can elicit a host stress response, which alters normal parameters of neuroendocrine homeostasis. The present study evaluated the influence of the metabolic stressor 2-deoxy-D-glucose (2-DG; a glucose analog, which when administered to rodents, induces acute periods of metabolic stress) on the capacity of mice to resist infection with the facultative intracellular bacterial pathogen Listeria monocytogenes. Female BDF1 mice were injected with 2-DG (500 mg/kg b. wt.) once every 48 h prior to, concurrent with, or after the onset of a sublethal dose of virulent L. monocytogenes. Kinetics of bacterial growth in mice were not altered if 2-DG was applied concurrently or after the start of the infection. In contrast, mice exposed to 2-DG prior to infection demonstrated an enhanced resistance to the listeria challenge. The enhanced bacterial clearance in vivo could not be explained by 2-DG exerting a toxic effect on the listeria, based on the results of two experiments. First, 2-DG did not inhibit listeria replication in trypticase soy broth. Second, replication of L. monocytogenes was not inhibited in bone marrow-derived macrophage cultures exposed to 2-DG. Production of neopterin and lysozyme, indicators of macrophage activation, were enhanced following exposure to 2-DG, which correlated with the increased resistance to L. monocytogenes. These results support the contention that the host response to 2-DG-induced metabolic stress can influence the capacity of the immune system to resist infection by certain classes of microbial pathogens.

Non-NASA Center↗
DOE OSTI2024

Towards dynamical low-rank approximation for neutrino kinetic equations. Part I: Analysis of an idealized relaxation model

Dynamical low-rank approximation (DLRA) is an emerging tool for reducing computational costs and provides memory savings when solving high-dimensional problems. Here, in this work, we propose and analyze a semi-implicit dynamical low-rank discontinuous Galerkin (DLR-DG) method for the space homogeneous kinetic equation with a relaxation operator, modeling the emission and absorption of particles by a background medium. Both DLRA and the discontinuous Galerkin (DG) scheme can be formulated as Galerkin equations. To ensure their consistency, a weighted DLRA is introduced so that the resulting DLR-DG solution is a solution to the fully discrete DG scheme in a subspace of the standard DG solution space. Similar to the standard DG method, we show that the proposed DLR-DG method is well-posed. We also identify conditions such that the DLR-DG solution converges to the equilibrium. Numerical results are presented to demonstrate the theoretical findings.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1998

Effects of 2-deoxy-D-glucose administration on immune parameters in mice

Physical exercise and diet alterations have been shown to affect immune parameters. Similar effects are also induced by the administration of the non-metabolizable glucose analog, 2-deoxy-D-glucose (2-DG). The current study was designed to characterize the effects of glucoprivation induced by 2-DG administration on leukocyte subset distribution and function. BDF1 mice (n = 8 per group) were injected intraperitoneally one or three times with 0, 500, 750, 1000 or 1500 mg/kg of 2-DG. Two hours after the last injection of 2-DG, immunological parameters were analyzed. A dose-dependent increase in plasma glucose concentrations of mice injected once with up to 1500 mg/kg of 2-DG was observed (p < 0.001). After either one or three injections of up to 1500 mg/kg of 2-DG, corticosterone levels, leukocyte counts in the spleen, and CD3+ cells in the thymus increased. In vitro proliferation of partially purified lymphocytes from the spleen in the presence of both concanavalin-A and lipopolysaccharide decreased in a dose dependent manner (p < 0.05). In addition, after three injections, the proportion of both thymocytes and splenocytes bearing alphabeta-TCR increased as the concentration of 2-DG increased (p < 0.01). These results demonstrate that 2-DG administration induced dose-dependent changes in both thymus and spleen cell distribution and function.

NASA Discipline Regulatory Physiology↗