SEARCH · Search NASA

Results for “CONSERVATION”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 739 records · Page 41

All sources NASA NTRS DOE OSTI

DOE OSTI2015

Mesh-free data transfer algorithms for partitioned multiphysics problems: Conservation, accuracy, and parallelism

In this study we analyze and extend mesh-free algorithms for three-dimensional data transfer problems in partitioned multiphysics simulations. We first provide a direct comparison between a mesh-based weighted residual method using the common-refinement scheme and two mesh-free algorithms leveraging compactly supported radial basis functions: one using a spline interpolation and one using a moving least square reconstruction. Through the comparison we assess both the conservation and accuracy of the data transfer obtained from each of the methods. We do so for a varying set of geometries with and without curvature and sharp features and for functions with and without smoothness and with varying gradients. Our results show that the mesh-based and mesh-free algorithms are complementary with cases where each was demonstrated to perform better than the other. We then focus on the mesh-free methods by developing a set of algorithms to parallelize them based on sparse linear algebra techniques. This includes a discussion of fast parallel radius searching in point clouds and restructuring the interpolation algorithms to leverage data structures and linear algebra services designed for large distributed computing environments. The scalability of our new algorithms is demonstrated on a leadership class computing facility using a set of basic scaling studies. Finally, these scaling studies show that for problems with reasonable load balance, our new algorithms for both spline interpolation and moving least square reconstruction demonstrate both strong and weak scalability using more than 100,000 MPI processes with billions of degrees of freedom in the data transfer operation.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Conservative tightly-coupled simulations of stochastic multiscale systems

Multiphysics problems often involve components whose macroscopic dynamics is driven by microscopic random fluctuations. The fidelity of simulations of such systems depends on their ability to propagate these random fluctuations throughout a computational domain, including subdomains represented by deterministic solvers. When the constituent processes take place in nonoverlapping subdomains, system behavior can be modeled via a domain-decomposition approach that couples separate components at the interfaces between these subdomains. Its coupling algorithm has to maintain a stable and efficient numerical time integration even at high noise strength. We propose a conservative domain-decomposition algorithm in which tight coupling is achieved by employing either Picard's or Newton's iterative method. Coupled diffusion equations, one of which has a Gaussian white-noise source term, provide a computational testbed for analysis of these two coupling strategies. Fully-converged (“implicit”) coupling with Newton's method typically outperforms its Picard counterpart, especially at high noise levels. This is because the number of Newton iterations scales linearly with the amplitude of the Gaussian noise, while the number of Picard iterations can scale superlinearly. At large time intervals between two subsequent inter-solver communications, the solution error for single-iteration (“explicit”) Picard's coupling can be several orders of magnitude higher than that for implicit coupling. Increasing the explicit coupling's communication frequency reduces this difference, but the resulting increase in computational cost can make it less efficient than implicit coupling at similar levels of solution error, depending on the communication frequency of the latter and the noise strength. This trend carries over into higher dimensions, although at high noise strength explicit coupling may be the only computationally viable option.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2017

Stable schemes for dissipative particle dynamics with conserved energy

This article presents a new numerical scheme for the discretization of dissipative particle dynamics with conserved energy. The key idea is to reduce elementary pairwise stochastic dynamics (either fluctuation/dissipation or thermal conduction) to effective single-variable dynamics, and to approximate the solution of these dynamics with one step of a Metropolis–Hastings algorithm. This ensures by construction that no negative internal energies are encountered during the simulation, and hence allows to increase the admissible timesteps to integrate the dynamics, even for systems with small heat capacities. Stability is only limited by the Hamiltonian part of the dynamics, which suggests resorting to multiple timestep strategies where the stochastic part is integrated less frequently than the Hamiltonian one.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

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 OSTI2015

Nuclear Protein-Only Ribonuclease P2 Structure and Biochemical Characterization Provide Insight into the Conserved Properties of tRNA 5' End Processing Enzymes

Protein-only RNase Ps (PRORPs) are a recently discovered class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. PRORPs are found in the nucleus and/or organelles of most eukaryotic organisms. Arabidopsis thaliana is a representative organism that contains PRORP enzymes (PRORP1, PRORP2 and PRORP3) in both its nucleus and its organelles; PRORP2 and PRORP3 localize to the nucleus and PRORP1 localizes to the chloroplast and the mitochondria. Apart from their identification, almost nothing is known about the structure and function of PRORPs that act in the nucleus. Here, we use a combination of biochemical assays and X-ray crystallography to characterize A. thaliana PRORP2. We solved the crystal structure of PRORP2 (3.2 Å) revealing an overall V-shaped protein and conserved metallonuclease active-site structure. Our biochemical studies indicate that PRORP2 requires Mg 2+ for catalysis and catalyzes the maturation of nuclear encoded substrates up to 10-fold faster than mitochondrial encoded precursor nad6 t-element under single-turnover conditions. We also demonstrate that PRORP2 preferentially binds precursor tRNAs containing short 5' leaders and 3' trailers; however, leader and trailer lengths do not significantly alter the observed rate constants of PRORP2 in single-turnover cleavage assays. In conclusion, our data provide a biochemical and structural framework to begin understanding how nuclear localized PRORPs recognize and cleave their substrates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

HnRNP A1 Alters the Structure of a Conserved Enterovirus IRES Domain to Stimulate Viral Translation

Enteroviruses use a type I Internal Ribosome Entry Site (IRES) structure to facilitate protein synthesis and promote genome replication. Type I IRES elements require auxiliary host proteins to organize RNA structure for 40S ribosomal subunit assembly. Heterogeneous nuclear ribonucleoprotein A1 stimulates enterovirus 71 (EV71) translation in part through specific interactions with its stem loop II (SLII) IRES domain. Here, we determined a conjoined NMR-small angle x-ray scattering structure of the EV71 SLII domain and a mutant that significantly attenuates viral replication by abrogating hnRNP A1 interactions. Native SLII adopts a locally compact structure wherein stacking interactions in a conserved 5'-AUAGC-3' bulge preorganize the adjacent helices at nearly orthogonal orientations. Mutating the bulge sequence to 5'-ACCCC-3' ablates base stacking in the loop and globally reorients the SLII structure. Biophysical titrations reveal that the 5'-AUAGC-3' bulge undergoes a conformational change to assemble a functional hnRNP A1–RNA complex. Importantly, IRES mutations that delete the bulge impair viral translation and completely inhibit replication. Furthermore, this work provides key details into how an EV71 IRES structure adapts to hijack a cellular protein, and it suggests that the SLII domain is a potential target for antiviral therapy.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Diverse Antibody Responses to Conserved Structural Motifs in Plasmodium falciparum Circumsporozoite Protein

Malaria vaccine candidate RTS,S/AS01 is based on the central and C-terminal regions of the circumsporozoite protein (CSP) of P. falciparum. mAb397 was isolated from a volunteer in an RTS,S/AS01 clinical trial, and it protects mice from infection by malaria sporozoites. However, mAb397 originates from the less commonly used VH3-15 germline gene compared to the VH3-30/33 antibodies generally elicited by RTS,S to the central NANP repeat region of CSP. The crystal structure of mAb397 with an NPNA4 peptide shows that the central NPNA forms a type I β-turn and is the main recognition motif. In most anti-NANP antibodies studied to date, a germline-encoded Trp is used to engage the Pro in NPNA β-turns, but here the Trp interacts with the first Asn. This “conserved” Trp, however, can arise from different germline genes and be located in the heavy or the light chain. Variation in the terminal ψ angles of the NPNA β-turns results in different dispositions of the subsequent NPNA and, hence, different stoichiometries and modes of antibody binding to rsCSP. Diverse protective antibodies against NANP repeats are therefore not limited to a single germline gene response or mode of binding.

59 BASIC BIOLOGICAL 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 OSTI2019

Freeway Loop Detector Data Reconciliation Based on Vehicle Conservation

Loop detector is the most common source of traffic flow measurements on freeways. Though being a mature technology, loop detector is prone to miscounts even when it is properly deployed and adjusted. If a loop detectors systematically over- or under-counts, the estimation based on vehicle conservation leads to results that are not physically plausible such as negative density or density higher than the jam-density. Here we propose an optimization-based method in which plausible values of accumulation is guaranteed through explicit constraints. Compared to similar methods, the proposed method distinct in the following: (i) the optimization problem is convex therefore leads to shorter computational time; (ii) occupancy is also taken into account in order to estimate upper and lower bounds in the accumulation between stations; (iii) no modifications are required when data from one or multiple lanes are missing. The method is first validated using micro-simulation by disturbing the loop-detector from micro-simulation, applying the method and then comparing the results with the ground truth data. The results show the method is able to capture the average counts almost exactly while providing estimate of density with satisfactory accuracy. The method is also successfully applied in a scenario in which field-data is available.

data reconciliation↗

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 OSTI2014

Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain

CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the “HK97-fold” shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain (“I-domain”), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphology of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently. - Highlights: • Asymmetric and symmetric three-dimensional reconstructions of phage CUS-3 are presented. • CUS-3 major capsid protein has a conserved I-domain, which is found in all three categories of “P22-like phage”. • CUS-3 has very different tailspike receptor binding domain from those of P22 and Sf6. • The CUS-3 tailspike likely was acquired by horizontal gene transfer.

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↗