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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Conservative discontinuous Galerkin interpolation: Sheared boundary conditions

Local studies of accretion disks and laboratory magnetized plasmas employ analytical coordinate mappings that introduce sheared boundary conditions (BCs). Here, we present a discontinuous Galerkin (DG) algorithm to apply such BCs based on projections and quadrature-free integration. The procedure is high-order accurate, preserves moments exactly and works in multiple dimensions. Tests of increasing complexity are provided, beginning with translations of one and two dimensional fields, followed by 3D and 5D simulations with sheared (twist-shift) BCs. Results show that the algorithm is (p + 1)-order accurate in the DG representation and (p + 2) -order accurate in the cell averages, with p being the order of the polynomial basis. Quantification of the algorithm's hyperdiffusion and discussion of aliasing errors are given. This technique enables conservative local simulations of plasma turbulence with DG, not possible until now.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Breast Conservation in Women with Autoimmune Disease: The Role of Active Autoimmune Disease and Hypofractionation on Acute and Late Toxicity in a Case-Controlled Series

Autoimmune connective tissue disease (CTD) has historically represented a relative contraindication to breast conservation (BC) among patients with early-stage breast cancer. Controversy exists regarding the use of hypofractionated radiation therapy (RT) among patients with CTDs. We evaluated acute and late toxicity in patients with breast cancer and CTD treated with BC.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

Potent transmission-blocking monoclonal antibodies from naturally exposed individuals target a conserved epitope on Plasmodium falciparum Pfs230

Pfs230 is essential for Plasmodium falciparum transmission to mosquitoes and is the protein targeted by the most advanced malaria-transmission-blocking vaccine candidate. Prior understanding of functional epitopes on Pfs230 is based on two monoclonal antibodies (mAbs) with moderate transmission-reducing activity (TRA), elicited from subunit immunization. Here, we screened the B cell repertoire of two naturally exposed individuals possessing serum TRA and identified five potent mAbs from sixteen Pfs230 domain-1-specific mAbs. Structures of three potent and three low-activity antibodies bound to Pfs230 domain 1 revealed four distinct epitopes. Highly potent mAbs from natural infection recognized a common conformational epitope that is highly conserved across P. falciparum field isolates, while antibodies with negligible TRA derived from natural infection or immunization recognized three distinct sites. Our study provides molecular blueprints describing P. falciparum TRA, informed by contrasting potent and non-functional epitopes elicited by natural exposure and vaccination.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

A conserved chaperone protein is required for the formation of a noncanonical type VI secretion system spike tip complex

Type VI secretion systems (T6SSs) are dynamic protein nanomachines found in Gram-negative bacteria that deliver toxic effector proteins into target cells in a contact-dependent manner. Prior to secretion, many T6SS effector proteins require chaperones and/or accessory proteins for proper loading onto the structural components of the T6SS apparatus. However, despite their established importance, the precise molecular function of several T6SS accessory protein families remains unclear. In this study, we set out to characterize the DUF2169 family of T6SS accessory proteins. Using gene co-occurrence analyses, we find that DUF2169-encoding genes strictly co-occur with genes encoding T6SS spike complexes formed by valine-glycine repeat protein G (VgrG) and DUF4150 domains. Although structurally similar to Pro-Ala-Ala-Arg (PAAR) domains, “PAAR-like” DUF4150 domains lack PAAR motifs and instead contain a conserved PIPY motif, leading us to designate them PIPY domains. Next, we present both genetic and biochemical evidence that PIPY domains require a cognate DUF2169 protein to form a functional T6SS spike complex with VgrG. This contrasts with canonical PAAR proteins, which bind VgrG on their own to form functional spike complexes. By solving the first crystal structure of a DUF2169 protein, we show that this T6SS accessory protein adopts a novel protein fold. Furthermore, biophysical and structural modeling data suggest that DUF2169 contains a dynamic loop that physically interacts with a hydrophobic patch on the surface of its cognate PIPY domain. Based on these findings, we propose a model whereby DUF2169 proteins function as molecular chaperones that maintain VgrG–PIPY spike complexes in a secretion-competent state prior to their export by the T6SS apparatus.

DUF2169↗
DOE OSTI2020

Energy conservative SBP discretizations of the acoustic wave equation in covariant form on staggered curvilinear grids

In this work, we develop a numerical method for solving the acoustic wave equation in covariant form on staggered curvilinear grids in an energy conserving manner. The use of a covariant basis decomposition leads to a rotationally invariant scheme that outperforms a Cartesian basis decomposition on rotated grids. The discretization is based on high order Summation-By-Parts (SBP) operators and preserves both symmetry and positive definiteness of the contravariant metric tensor. To improve accuracy and decrease computational cost, we also derive a modified discretization of the metric tensor that leads to a conditionally stable discretization. Bounds are derived that yield a point-wise condition that can be evaluated to check for stability of the modified discretization. This condition shows that the interpolation operators should be constructed such that their norm is close to one.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

On numerical energy conservation for an implicit particle-in-cell method coupled with a binary Monte-Carlo algorithm for Coulomb collisions

We report conventional particle-in-cell (PIC) methods suffer from enhanced numerical heating (explicit PIC) or cooling (semi-implicit PIC) when coupled with a binary Monte-Carlo algorithm for Coulomb collisions. In this work, a fully-implicit θ-PIC scheme (with adjustable time-biasing parameter 1/2 ≤ θ ≤) is considered. The discrete change in energy of a closed system after a time step for this scheme scales with (1/2 - θ)C θ , where C θ is a positive definite quantity that depends on the frequency spectrum of the energy in the fields. Collisions lead to additional energy in the field fluctuations associated with high-frequency light waves produced by a numerical Bremsstrahlung process, which can result in a large increase in the numerical cooling rate for θ > 1/2. However, for θ = 1/2, energy is exactly conserved. The energy in the field fluctuations on long time scales agrees with that calculated using the equipartition theorem for a classical system in thermodynamic equilibrium.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Conservative velocity mappings for discontinuous Galerkin kinetics

Continuum computational kinetic plasma models evolve the distribution function of a plasma species f s on a phase-space grid over time. In many problems of interest the distribution function has limited extent in velocity space; hence, using a uniform, highly refined mesh would be costly and slow. Nonuniform velocity grids can reduce the computational cost by placing more degrees of freedom where f s is appreciable and fewer where it is not. In this work we introduce a first-of-its kind discontinuous Galerkin approach to nonuniform velocity-space discretization using mapped velocity coordinates. This new method is presented in the context of a gyrokinetic model used to study magnetized plasmas. We create discretizations of collisionless and collisional terms using mappings in a way that exactly conserves particles and energy. Numerical tests of such properties are presented, and we show that this new discretization can reproduce earlier gyrokinetic simulations using grids with up to 6–60 times fewer cells and 22X-60X speed-ups depending on dimensionality, geometry and plasma parameters.

Discontinuous Galerkin↗
DOE OSTI2020

A new soil mixing layer model for simulating conservative solute loss from initially saturated soil to surface runoff

Surface water pollution due to solute loss from soil to surface runoff is a serious threat to the environment, and it is of great significance to predict the solute loss. While soil mixing layer theory has been widely used to predict the solute loss, it has been observed that the conventional soil mixing layer models with constant mixing layer depth underestimate solute concentration in surface runoff, and thus underestimate the solute loss after surface runoff starts. This study introduced a new soil mixing layer model with a new concept that the mixing layer depth increases downward with time after surface runoff occurs. This new concept was implemented by adding a mixing front between the soil mixing layer and its underlying soil layer, which is conceptually similar to the wetting front of soil infiltration given by the Green-Ampt equation. This is equivalent to treating the soil mixing layer as a deforming control volume. A mechanistic explanation for the new model was presented. This study also developed a closed form solution of the new model. The new model was evaluated by simulating five laboratory experiments conducted by two groups of researchers. The first two experiments have ponding water, and consider different drainage and runoff conditions at both early and late runoff times. The other three experiments do not have ponding water, and consider different infiltration conditions at the bottom of soil boxes. Simulation results of the five experiments show that the new model resolves the underestimation problem of conventional soil mixing layer models. The new model is subject to a total of six limits such as that the new model only considers conservative solute. Three limits are related to the assumptions used to derive the closed form solution, and they may be alleviated in a future research as briefly discussed at the end of the paper.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Verification of Bison fission product species conservation under TRISO reactor conditions

When assessing the reliability and predictive capabilities of a simulation tool, code verification is used to ensure that the implemented numerical algorithm is a faithful representation of its underlying mathematical model, including partial differential or integral equations, initial and boundary conditions, and auxiliary relationships. During this process, numerical results in a discrete solution are compared to the analytical solution of the mathematical model. Here, in this paper, the code verification process is applied to one-dimensional spatiotemporal problems that exercise partial differential equation governing the conservation of fission product species (or mass diffusion). Numerical experiments were performed in the Bison fuel performance code to evaluate its predictive capability under various TRISO reactor conditions such as base irradiation and safety heating test conditions for either short- or long-lived fission product species, as well as a case concerning evaporation from the outer surface of a particle. The code predictions were compared with the expected exact results obtained from the analytical expressions, and the fact that they demonstrate the correct analytical behavior provides strong evidence of proper numerical algorithm implementation.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2021

Effect of epitope variant co-delivery on the depth of CD8 T cell responses induced by HIV-1 conserved mosaic vaccines

To stop the HIV-1 pandemic, vaccines must induce responses capable of controlling vast HIV-1 variants circulating in the population as well as those evolved in each individual following transmission. Numerous strategies have been proposed, of which the most promising include focusing responses on the vulnerable sites of HIV-1 displaying the least entropy among global isolates and using algorithms that maximize vaccine match to circulating HIV-1 variants by vaccine cocktails of optimized complementing sequences. In this study, we investigated CD8 T cell responses induced by a bi-valent mosaic of highly conserved HIVconsvX regions delivered by a combination of simian adenovirus ChAdOx1 and poxvirus MVA. We compared partially and fully mono- and bi-valent prime-boost regimens and their ability to elicit T cells recognizing natural epitope variants using an interferon-g enzyme-linked immunospot (ELISPOT) assay. We used 11 well-defined CD8 T cell epitopes in two mouse haplotypes and, for each epitope, assessed recognition of the two vaccine forms together with the other most frequent epitope variants in the HIV-1 database. We conclude that for the magnitude and depth of epitope recognition, CD8 T cell responses benefitted in most comparisons from the combined bi-valent mosaic and envisage the main advantage of the bi-valent vaccine during its deployment to diverse populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A coupled polygonal DEM-LBM technique based on an immersed boundary method and energy-conserving contact algorithm

Here we present a framework of coupling polygonal discrete elements and the lattice Boltzmann method using a direct forcing immersed boundary scheme. In this technique, an energy-conserving contact algorithm is utilized to handle the interactions between convex and concave polygonal particles. The surface of a polygon is represented by discrete boundary points which includes vertices of polygonal particles and/or points interpolated from vertices. The fluid-particle coupling is obtained through the interactions of the boundary points and the imaginary fluid particles using a direct-forcing immersed boundary method. Validations of the proposed technique are made by single particle and multiple arbitrarily-shaped particle sedimentation tests, and the effect of particle shape is illustrated using a drafting-kissing-tumbling benchmark.

42 ENGINEERING↗
DOE OSTI2026

Conserving asphalt resources: Rethinking rejuvenator performance evaluation through peptizing efficiency

Timely rejuvenation and restoration of asphalt are essential conservation practices that help preserve and extend the service life of roads, bridges, driveways, and parking lots. The performance of asphalt rejuvenators is often assessed based on their diffusion rates and softening power, yet these metrics alone fail to capture true rejuvenation potential. Here, this study integrates density functional theory (DFT) modeling with experimental analysis to show that rejuvenation effectiveness is primarily governed by molecular interactions with oxidized asphaltene nanoaggregates. DFT results revealed that amide- and unsaturated-chain compounds, such as hexadecanamide, oleic acid, and 9,17-octadecadienal, act cooperatively to disrupt π–π stacking and exfoliate asphaltene layers, reducing binding strength and enhancing dispersion. Unlike bulky, rigid molecules that remain trapped, these components remain mobile and repeatedly interact with multiple aggregation sites. Experimental validation using rheometry and FTIR confirmed that such molecularly compatible rejuvenators restore the binder flexibility and polydispersity, even when diffusion is relatively slow. Building on this mechanistic foundation, six rejuvenators (A2, A5, A7, A8, A9, and A10) were evaluated using a three-metric performance framework encompassing cracking resistance (Glover–Rowe parameter), UV stability, and surface hydrophobicity. Among the six rejuvenators evaluated, A9 exhibited the highest overall performance, reducing the Glover–Rowe cracking parameter by 85% (from 351 kPa to 53 kPa), demonstrating the greatest resistance to UV-induced aging with a stability index of 4.17 h·kPa⁻¹, and increasing surface hydrophobicity to a contact angle of 103.6°. Its superior performance is primarily attributed to its amide- and unsaturated-chain components, which act cooperatively to disrupt π–π stacking interactions and exfoliate asphaltene layers, thereby promoting molecular deagglomeration and enhancing long-term durability. These results shift the criteria for selecting rejuvenators: effective candidates must pair the electronic capability to unlock aged asphaltenes with sufficient structural stability to resist secondary aging and restore hydrophobicity. Restoring hydrophobicity is critical, as aging reduces the asphalt’s water repellency and increases water diffusion, which in turn accelerates moisture-related damage; consequently, a high-performing rejuvenator must effectively restore the binder’s hydrophobic characteristic. Collectively, these findings provide a framework for the rational design of next-generation of bio-based rejuvenators that enhance pavement longevity and promote long-term sustainability.

Aging↗
DOE OSTI2021

Cross-reactive immunogenicity of group A streptococcal vaccines designed using a recurrent neural network to identify conserved M protein linear epitopes

The M protein of group A streptococci (Strep A) is a major virulence determinant and protective antigen. The N-terminal sequence of the protein defines the more than 200 M types of Strep A and also contains epitopes that elicit opsonic antibodies, some of which cross-react with heterologous M types. Current efforts to develop broadly protective M protein-based vaccines are directed at identifying potential cross-protective epitopes located in the N-terminal regions of cluster-related M proteins for use as vaccine antigens. In this study, we have used a comprehensive approach using the recurrent neural network ABCpred and IEDB epitope conservancy analysis tools to predict 16 residue linear B-cell epitopes from 117 clinically relevant M types of Strep A (~88% of global Strep A infections). Furthermore, to examine the immunogenicity of these epitope-based vaccines, nine peptides that together shared ≥60% sequence identity with 37 heterologous M proteins were incorporated into two recombinant hybrid protein vaccines, in which the epitopes were repeated 2 or 3 times, respectively. The combined immune responses of immunized rabbits showed that the vaccines elicited significant levels of antibodies against all nine vaccine epitopes present in homologous N-terminal 1–50 amino acid synthetic M peptides, as well as cross-reactive antibodies against 16 of 37 heterologous M peptides predicted to contain similar epitopes. The epitope-specificity of the cross-reactive antibodies was confirmed by ELISA inhibition assays and functional opsonic activity was assayed in HL-60-based bactericidal assays. The results provide important information for the future design of broadly protective M protein-based Strep A vaccines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Evidence for Plant-Conserved Region Mediated Trimeric CESAs in Plant Cellulose Synthase Complexes

Higher plants synthesize cellulose using membrane-bound, six-lobed cellulose synthase complexes, each lobe containing trimeric cellulose synthases (CESAs). Although molecular biology reports support heteromeric trimers composed of different isoforms, a homomeric trimer was reported for in vitro studies of the catalytic domain of CESA1 of Arabidopsis (AtCESA1CatD) and confirmed in cryoEM structures of full-length CESA8 and CESA7 of poplar and cotton, respectively. In both structures, a small portion of the plant-conserved region (P-CR) forms the only contacts between catalytic domains of the monomers. Here, we report inter-subunit lysine-crosslinks that localize to the small P-CR, negative-stain EM structure, and modeling data for homotrimers of AtCESA1CatD. Molecular dynamics simulations for AtCESA1CatD trimers based on the CESA8 cryoEM structure were stable and dependent upon a small set of residue contacts. The results suggest that homomeric CESA trimers may be important for the synthesis of primary and secondary cell walls and identify key residues for future mutagenic studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Assessing the Returns to Land and Greenhouse Gas Savings from Producing Energy Crops on Conservation Reserve Program Land

Using land already enrolled in the Conservation Reserve Program (CRP) in the eastern region of the U.S. for producing energy crops for bioenergy while reducing land rental payments offers the potential for lowering the program costs, increasing returns to CRP landowners, and displacing greenhouse gas (GHG) emissions from fossil fuels. We develop an integrated modeling approach to analyze the combination of biomass prices and CRP land rental payment reductions that can incentivize energy crop production on CRP land and its potential to increase soil carbon stocks and displace fossil fuel emissions. Here, we find that conversion of 3.4 million ha in the CRP can be economically viable at a minimum biomass price of 75 Mg –1 with full CRP land rental payment or at 100 Mg –1 with 75% of this land rental payment; this conversion can result in savings of 0.52 and 1.25 billion Mg CO 2 -eq in life-cycle emissions through the displacement of energy-equivalent fossil fuels and coal-based electricity, respectively, and an additional 0.11 billion Mg CO 2 -eq soil carbon sequestration relative to the status quo, with CRP left unharvested over the 2016–2030 period. The soil carbon debt due to the transition from unharvested CRP land to energy crops is short-lived and more than offset by the reduction in fossil fuel emissions. The net discounted benefits from producing energy crops on CRP land through a reduced need for government payments to maintain existing enrollment, higher returns to CRP landowners, and the value of the reduction in GHG emissions could be as high as 16–30 billion by using them for cellulosic biofuels to displace gasoline and 35–68 billion by displacing coal-based electricity over the 2016–2030 period if biomass prices are 75–125 Mg –1 and land rental payments are reduced by 25%.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

U 4+/5+/6+ in a Conserved Pseudotetrahedral Imidophosphorane Coordination Sphere

While several ligand systems support uranium across a range of oxidation states, spanning more than two oxidation states in a conserved coordination geometry is uncommon among structurally authenticated complexes. Imidophosphorane ligands significantly stabilize high-valent lanthanide and actinide complexes. Here, we report a series of homoleptic uranium imidophosphorane complexes, spanning the +4, +5 and +6 oxidation states in a four-coordinate pseudotetrahedral ligand field. The +6 oxidation state is accessible using a mild ferrocenium oxidant, yielding a rare example of U6+ in a pseudotetrahedral coordination environment. As the formal oxidation state increases, the U–N distances gradually contract, consistent with the Shannon ionic radii of U 4+/5+/6+ . Compared to reported complexes, the short U–N distances observed in the U 6+ complex are more comparable to dianionic imido ligands than monoanionic amido ligands.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗