Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Expression systems”

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.

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

At least 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Dynamic security assessment of systems powered only by grid-forming power plants with uncertain dispatch using polynomial vectors

A modern challenge in power engineering is to perform the dynamic security assessment (DSA) of grids that are 100% powered by inverter-based resources (IBRs). Addressing this challenge is difficult because: (i) the dispatch of IBRs can be uncertain as a result of the variability of renewable resources and (ii) they have hard current control limits that cannot be neglected, contrasting synchronous machines. To address this problem, this paper sets forth a framework to conduct DSA of bulk power systems that are 100% powered by grid-forming IBRs. Furthermore, the framework considers that IBR operational conditions are unknown but bounded by a zonotope which is also expressed as a polynomial vector for uncertainty propagation via Dormand–Prince integration. The framework is applied to modified versions of the WSCC 9-bus and IEEE 39-bus grids.

14 SOLAR ENERGY↗
DOE OSTI2022

Space-Split Algorithm for Sensitivity Analysis of Discrete Chaotic Systems With Multidimensional Unstable Manifolds

Accurate approximations of the change of a system's output and its statistics with respect to the input are highly desired in computational dynamics. Ruelle's linear response theory provides breakthrough mathematical machinery for computing the linear response of chaotic dynamical systems. In this paper, we propose an algorithm for sensitivity analysis of discrete chaos with an arbitrary number of positive Lyapunov exponents. We combine the concept of perturbation space-splitting, which regularizes Ruelle's original expression, together with measure-based parameterization of the expanding subspace. We use these tools to rigorously derive trajectory-following recursive relations that converge exponentially fast, and construct a memory-efficient Monte Carlo scheme for derivatives of the output statistics. Thanks to the regularization and lack of simplifying assumptions on the system's behavior, our method is immune to the common problems of other popular methods such as the exploding tangent solutions and unphysical shadowing directions. Here, we provide a ready-to-use algorithm, analyze its complexity, and demonstrate several numerical examples of sensitivity computation using physically-inspired low-dimensional systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Three-state harmonic models for photoinduced charge transfer

A widely used strategy for simulating the charge transfer between donor and acceptor electronic states in an all-atom anharmonic condensedphase system is based on invoking linear response theory to describe the system in terms of an effective spin-boson model Hamiltonian. Extending this strategy to photoinduced charge transfer processes requires also taking into consideration the ground electronic state in addition to the excited donor and acceptor electronic states. In this paper, we revisit the problem of describing such nonequilibrium processes in terms of an effective three-state harmonic model. We do so within the framework of nonequilibrium Fermi’s golden rule (NE-FGR) in the context of photoinduced charge transfer in the carotenoid–porphyrin–C 60 (CPC 60 ) molecular triad dissolved in explicit tetrahydrofuran (THF). To this end, we consider different ways for obtaining a three-state harmonic model from the equilibrium autocorrelation functions of the donor–acceptor, donor–ground, and acceptor–ground energy gaps, as obtained from all-atom molecular dynamics simulations of the CPC 60 /THF system. The quantum-mechanically exact time-dependent NE-FGR rate coefficients for two different charge transfer processes in two different triad conformations are then calculated using the effective three-state model Hamiltonians as well as a hierarchy of more approximate expressions that lead to the instantaneous Marcus theory limit. Our results show that the photoinduced charge transfer in CPC 60 /THF can be described accurately by the effective harmonic three-state models and that nuclear quantum effects are small in this system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Plant Nutrition Influences Resistant Maize Defense Responses to the Fall Armyworm ( Spodoptera frugiperda )

Plants are often confronted by different groups of herbivores, which threaten their growth and reproduction. However, they are capable of mounting defenses against would-be attackers which may be heightened upon attack. Resistance to insects often varies among plant species, with different genotypes exhibiting unique patterns of chemical and physical defenses. Within this framework, plant access to nutrients may be critical for maximal functioning of resistance mechanisms and are likely to differ among plant genotypes. In this study, we aimed to test the hypothesis that access to nutrition would alter the expression of plant resistance to insects and alter insect performance in a manner consistent with fertilization regime. We used two maize (Zea mays) genotypes possessing different levels of resistance and the fall armyworm (Spodoptera frugiperda) as model systems. Plants were subjected to three fertilization regimes prior to assessing insect-mediated responses. Upon reaching V4 stage, maize plants were separated into two groups, one of which was infested with fall armyworm larvae to induce plant defenses. Plant tissue was collected and used in insect bioassays and to measure the expression of defense-related genes and proteins. Insect performance differed between the two plant genotypes substantially. For each genotype, fertilization altered larval performance, where lower fertilization rates hindered larval growth. Induction of plant defenses by prior herbivory substantially reduced naïve fall armyworm growth in both genotypes. The effects between fertilization and induced defenses were complex, with low fertilization reducing induced defenses in the resistant maize. Gene and protein expression patterns differed between the genotypes, with herbivory often increasing expression, but differing between fertilization levels. The soluble protein concentrations did not change across fertilization levels but was higher in the susceptible maize genotype. These results demonstrate the malleability of plant defenses and the cascading effects of plant nutrition on insect herbivory.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Synchronization-Based Guaranteed-Performance Formation Design for Swarm Systems

Guaranteed-performance formation control for swarm systems with the second-order dynamics is investigated based on the synchronization control strategy. Firstly, a new formation protocol is presented, where the weights of connected edges are adaptively regulated and the performance constraint is imposed. Then, on the basis of the Riccati inequality, sufficient conditions for synchronization-based guaranteed-performance formation are proposed, and an explicit expression of the guaranteed-performance cost is shown, where it is fully distributed to design gain matrices of the formation protocol in the sense that it is independent of global information of swarm systems. Moreover, the whole motion of a swarm system is determined, which is associated with initial states of all agents and formation control vectors. Finally, two numerical examples are shown to demonstrate theoretical conclusions, where the static whole motion and the dynamic whole motion are considered, respectively.

Dang, Hongtao↗
DOE OSTI2021

Kinetics of Carbon Condensation in Detonation of High Explosives: First-Order Phase Transition Theory Perspective

We report the kinetics of carbon condensation, or carbon clustering, in detonation of carbon-rich high explosives is modeled by solving a system of rate equations for concentrations of carbon particles. Unlike previous efforts, the rate equations account not only for the aggregation of particles but also for their fragmentation in a thermodynamically consistent manner. Numerical simulations are performed, yielding the distribution of particle concentrations as a function of time. In addition to that, analytical expressions are obtained for all the distinct steps and regimes of the condensation kinetics, which facilitates the analysis of the numerical results and allows one to study the sensitivity of the kinetic behavior to the variation of system parameters. The latter is important because the numerical values of many parameters are not reliably known at present. The theory of the kinetics of first-order phase transitions is found adequate to describe the general kinetic trends of carbon condensation, as described by the rate equations. Such physical phenomena and processes as the coagulation, nucleation, growth, and Ostwald ripening are observed, and their dependence on various system parameters is studied and reported. It is believed that the present work will become useful when analyzing the present and future results for the kinetics of carbon condensation, obtained from experiments or atomistic simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Factorization for jet production in heavy-ion collisions

We develop an Effective Field Theory approach for jet observables in heavy-ion collisions, where the jet is treated as an open quantum system interacting with a hot and dense QCD medium. Within this framework, we derive a novel factorization formula for inclusive jet production, expressed as a series expansion with an increasing number of radiating subjet functions that encode forward scattering with the Quark-Gluon Plasma, convolved with perturbative matching coefficients. This work provides a systematic framework for computing jet observables at higher order and understanding their non-perturbative aspects, paving the way for future applications in heavy-ion phenomenology.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Dynamics of skyrmion contraction and expansion in a magnetic film

Contraction and expansion of skyrmions in ferromagnetic films are investigated. In centrosymmetric systems, the dynamics of a collapsing skyrmion is driven by dissipation. The collapse time has a minimum on the damping constant. In systems with broken inversion symmetry, the evolution of skyrmions toward equilibrium size is driven by the Dzyaloshinskii–Moriya interaction. As a result, expressions describing the time dependence of the skyrmion size are derived and their implications for skyrmion-based information processing are discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Experimental and computational studies of the kinetics of the reaction of hydrogen peroxide with the amidogen radical

In this work, the pulsed-laser photolysis/laser-induced fluorescence method is used to study the kinetics of the reaction of NH 2 with H 2 O 2 to yield a second-order rate constant of (2.42 ± 0.55) × 10 –14 cm 3 molecule –1 s –1 at 412 K in 10–22 mbar of Ar bath gas. There are no prior measurements for comparison. To check this value and enable reliable extrapolation to other temperatures, we also compute thermal rate constants for this process over the temperature range 298–3000 K via multi-structural canonical variational transition-state theory with small-curvature multidimensional tunneling (MS-CVT/SCT). The CVT/SCT rate constants are derived using a dual-level direct dynamics approach utilizing single-point CCSD(T)-F12b/cc-pVQZ-F12 energies—corrected for core-valence and scalar relativistic effects—and M06-2X/MG3S geometries, gradients, and Hessians—for all stationary and non-stationary points along the reaction path. The multistructural method with torsional anharmonicity, based on a coupled torsional potential, is then employed to calculate correction factors for the rate constants, accounting for the comprehensive effects of torsional anharmonicity on the kinetics of this reaction system. The final MS-CVT/SCT rate constants are found to be in good agreement with our measurements and can be expressed in modified Arrhenius form as 2.13 × 10 –15 (T/298 K) 4.02 exp(–513 K/T) cm 3 molecule –1 s –1 over the temperature range of 298–3000 K.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Towards quantum simulations in particle physics and beyond on noisy intermediate-scale quantum devices

We review two algorithmic advances that bring us closer to reliable quantum simulations of model systems in high-energy physics and beyond on noisy intermediate-scale quantum (NISQ) devices. The first method is the dimensional expressivity analysis of quantum circuits, which allows for constructing minimal but maximally expressive quantum circuits. The second method is an efficient mitigation of readout errors on quantum devices. Both methods can lead to significant improvements in quantum simulations, e.g. when variational quantum eigensolvers are used. This article is part of the theme issue ‘Quantum technologies in particle physics’.

Science & Technology - Other Topics↗
DOE OSTI2022

PioABC-Dependent Fe(II) Oxidation during Photoheterotrophic Growth on an Oxidized Carbon Substrate Increases Growth Yield

Microorganisms that carry out Fe(II) oxidation play a major role in biogeochemical cycling of iron in environments with low oxygen. Fe(II) oxidation has been largely studied in the context of autotrophy. Here, we show that the anoxygenic phototroph, Rhodopseudomonas palustris CGA010, carries out Fe(II) oxidation during photoheterotrophic growth with an oxidized carbon source, malate, leading to an increase in cell yield and allowing more carbon to be directed to cell biomass. We probed the regulatory basis for this by transcriptome sequencing (RNA-seq) and found that the expression levels of the known pioABC Fe(II) oxidation genes in R. palustris depended on the redox-sensing two-component system, RegSR, and the oxidation state of the carbon source provided to cells. This provides the first mechanistic demonstration of mixotrophic growth involving reducing power generated from both Fe(II) oxidation and carbon assimilation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Hybridization History and Repetitive Element Content in the Genome of a Homoploid Hybrid, Yucca gloriosa (Asparagaceae)

Hybridization in plants results in phenotypic and genotypic perturbations that can have dramatic effects on hybrid physiology, ecology, and overall fitness. Hybridization can also perturb epigenetic control of transposable elements, resulting in their proliferation. Understanding the mechanisms that maintain genomic integrity after hybridization is often confounded by changes in ploidy that occur in hybrid plant species. Homoploid hybrid species, which have no change in chromosome number relative to their parents, offer an opportunity to study the genomic consequences of hybridization in the absence of change in ploidy. Yucca gloriosa (Asparagaceae) is a young homoploid hybrid species, resulting from a cross between Yucca aloifolia and Yucca filamentosa. Previous analyses of ~11 kb of the chloroplast genome and nuclear-encoded microsatellites implicated a single Y. aloifolia genotype as the maternal parent of Y. gloriosa. Using whole genome resequencing, we assembled chloroplast genomes from 41 accessions of all three species to re-assess the hybrid origins of Y. gloriosa. We further used re-sequencing data to annotate transposon abundance in the three species and mRNA-seq to analyze transcription of transposons. The chloroplast phylogeny and haplotype analysis suggest multiple hybridization events contributing to the origin of Y. gloriosa, with both parental species acting as the maternal donor. Transposon abundance at the superfamily level was significantly different between the three species; the hybrid was frequently intermediate to the parental species in TE superfamily abundance or appeared more similar to one or the other parent. In only one case—Copia LTR transposons—did Y. gloriosa have a significantly higher abundance relative to either parent. Expression patterns across the three species showed little increased transcriptional activity of transposons, suggesting that either no transposon release occurred in Y. gloriosa upon hybridization, or that any transposons that were activated via hybridization were rapidly silenced. The identification and quantification of transposon families paired with expression evidence paves the way for additional work seeking to link epigenetics with the important trait variation seen in this homoploid hybrid system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Arabinogalactan Structures of Repetitive Serine-Hydroxyproline Glycomodule Expressed by Arabidopsis Cell Suspension Cultures

Arabinogalactan-proteins (AGPs) are members of the hydroxyproline-rich glycoprotein (HRGP) superfamily. They are heavily glycosylated with arabinogalactans, which are usually composed of a β-1,3-linked galactan backbone with 6-O-linked galactosyl, oligo-1,6-galactosyl, or 1,6-galactan side chains that are further decorated with arabinosyl, glucuronosyl, rhamnosyl, and/or fucosyl residues. Here, our work with Hyp-O-polysaccharides isolated from (Ser-Hyp)32-EGFP (enhanced green fluorescent protein) fusion glycoproteins overexpressed in transgenic Arabidopsis suspension culture is consistent with the common structural features of AGPs isolated from tobacco. In addition, this work confirms the presence of β-1,6-linkage on the galactan backbone identified previously in AGP fusion glycoproteins expressed in tobacco suspension culture. Furthermore, the AGPs expressed in Arabidopsis suspension culture lack terminal-rhamnosyl residues and have a much lower level of glucuronosylation compared with those expressed in tobacco suspension culture. These differences not only suggest the presence of distinct glycosyl transferases for AGP glycosylation in the two systems, but also indicate the existence of minimum AG structures for type II AG functional features.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Information-incorporated gene network construction with FDR control

Abstract Motivation Large-scale gene expression studies allow gene network construction to uncover associations among genes. To study direct associations among genes, partial correlation-based networks are preferred over marginal correlations. However, FDR control for partial correlation-based network construction is not well-studied. In addition, currently available partial correlation-based methods cannot take existing biological knowledge to help network construction while controlling FDR. Results In this paper, we propose a method called Partial Correlation Graph with Information Incorporation (PCGII). PCGII estimates partial correlations between each pair of genes by regularized node-wise regression that can incorporate prior knowledge while controlling the effects of all other genes. It handles high-dimensional data where the number of genes can be much larger than the sample size and controls FDR at the same time. We compare PCGII with several existing approaches through extensive simulation studies and demonstrate that PCGII has better FDR control and higher power. We apply PCGII to a plant gene expression dataset where it recovers confirmed regulatory relationships and a hub node, as well as several direct associations that shed light on potential functional relationships in the system. We also introduce a method to supplement observed data with a pseudogene to apply PCGII when no prior information is available, which also allows checking FDR control and power for real data analysis. Availability and implementation R package is freely available for download at https://cran.r-project.org/package=PCGII.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Early Holocene cold snaps and their expression in the moraine record of the eastern European Alps

Glaciers preserve climate variations in their geological and geomorphological records, which makes them prime candidates for climate reconstructions. Investigating the glacier–climate system over the past millennia is particularly relevant first because the amplitude and frequency of natural climate variability during the Holocene provides the climatic context against which modern, human-induced climate change must be assessed. Second, the transition from the last glacial to the current interglacial promises important insights into the climate system during warming, which is of particular interest with respect to ongoing climate change. Evidence of stable ice margin positions that record cooling during the past 12 kyr are preserved in two glaciated valleys of the Silvretta Massif in the eastern European Alps, the Jamtal (JAM) and the Laraintal (LAR). We mapped and dated moraines in these catchments including historical ridges using beryllium-10 surface exposure dating (10Be SED) techniques and correlate resulting moraine formation intervals with climate proxy records to evaluate the spatial and temporal scale of these cold phases. The new geochronologies indicate the formation of moraines during the early Holocene (EH), ca. 11.0 ± 0.7 ka (n = 19). Boulder ages along historical moraines (n = 6) suggest at least two glacier advances during the Little Ice Age (LIA; ca. 1250–1850 CE) around 1300 CE and in the second half of the 18th century. An earlier advance to the same position may have occurred around 500 CE. The Jamtal and Laraintal moraine chronologies provide evidence that millennial-scale EH warming was superimposed by centennial-scale cooling. The timing of EH moraine formation coincides with brief temperature drops identified in local and regional paleoproxy records, most prominently with the Preboreal Oscillation (PBO) and is consistent with moraine deposition in other catchments in the European Alps and in the Arctic region. This consistency points to cooling beyond the local scale and therefore a regional or even hemispheric climate driver. Freshwater input sourced from the Laurentide Ice Sheet (LIS), which changed circulation patterns in the North Atlantic, is a plausible explanation for EH cooling and moraine formation in the Nordic region and in Europe.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Genomics of sorghum local adaptation to a parasitic plant

Host–parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential trade-offs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and below-ground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with trade-offs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR–Cas9-edited sorghum further indicate that the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

scRNA seq of an F1 cross of Marek’s disease resistant and susceptible chickens identifies allele specific expression signatures enriched in transcription modulators

Abstract Marek’s disease (MD), a T cell lymphoma disease in chickens, is caused by the Marek’s disease virus (MDV) found ubiquitously in the poultry industry. Genetically resistant Line 6 3 (L6) and susceptible Line 7 2 (L7) chickens have been instrumental to research on avian immune system response to MDV infection. In this study we characterized molecular signatures unique to splenic immune cell types across different genetic backgrounds 6 days after infection. Using three populations, L6, L7, and an F1 cross between L6xL7, we evaluated the immune cell transcriptome of responding cell types using single cell RNA sequencing. Several MDV genes were found expressed mainly in cytotoxic T cells while ICP4 and MEQ MDV genes were expressed across infected cell types. Using the F1 we quantified allele specific expression (ASE) of biallelic SNPs and found biased expression of parental alleles specific to immune cell subtypes. We identified 22 SNPs with ASE in response to MDV infection mapped to gene rich regions surrounding 59 genes of critical importance for chromatin remodeling and transcriptional regulation. Histone deacetylase genes (HDAC1 and HDAC8) had increased expression of L6 alleles, while small nuclear RNA genes (SNORA68 and SNORA72) expressed higher levels of L7 alleles with infection in T cell subsets. SNPs with ASE also mapped genes important for an adequate immune response including GNLY (cytotoxic activity) and PDIA3 (component of MHC class I peptide loading complex), and genes known to promote viral replication (MCM5 and EIF3M). These results show that functional variants associated with susceptibility to MD may have a bigger impact in subsets of immune cell types, and by characterizing the transcriptomes of these subtypes we can unravel molecular signatures specific to MD genomic resistance.

Science & Technology - Other Topics↗