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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.

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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
NASA NTRS1994

Expression and purification of recombinant polyomavirus VP2 protein and its interactions with polyomavirus proteins

Recombinant polyomavirus VP2 protein was expressed in Escherichia coli (RK1448), using the recombinant expression system pFPYV2. Recombinant VP2 was purified to near homogeneity by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, electroelution, and Extracti-Gel chromatography. Polyclonal serum to this protein which reacted specifically with recombinant VP2 as well as polyomavirus virion VP2 and VP3 on Western blots (immunoblots) was produced. Purified VP2 was used to establish an in vitro protein-protein interaction assay with polyomavirus structural proteins and purified recombinant VP1. Recombinant VP2 interacted with recombinant VP1, virion VP1, and the four virion histones. Recombinant VP1 coimmunoprecipitated with recombinant VP2 or truncated VP2 (delta C12VP2), which lacked the carboxy-terminal 12 amino acids. These experiments confirmed the interaction between VP1 and VP2 and revealed that the carboxyterminal 12 amino acids of VP2 and VP3 were not necessary for formation of this interaction. In vivo VP1-VP2 interaction study accomplished by cotransfection of COS-7 cells with VP2 and truncated VP1 (delta N11VP1) lacking the nuclear localization signal demonstrated that VP2 was capable of translocating delta N11VP1 into the nucleus. These studies suggest that complexes of VP1 and VP2 may be formed in the cytoplasm and cotransported to the nucleus for virion assembly to occur.

Non-NASA Center↗
DOE OSTI2024

Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish

Despite deep evolutionary conservation, recombination rates vary greatly across the genome and among individuals, sexes and populations. Yet the impact of this variation on adaptively diverging populations is not well understood. Here we characterized fine-scale recombination landscapes in an adaptively divergent pair of marine and freshwater populations of threespine stickleback from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic locations of almost 50,000 crossovers and built recombination maps for marine, freshwater and hybrid individuals at a resolution of 3.8 kb. We used these maps to quantify the factors driving variation in recombination rates. We found strong heterochiasmy between sexes but also differences in recombination rates among ecotypes. Hybrids showed evidence of significant recombination suppression in overall map length and in individual loci. Recombination rates were lower not only within individual marine–freshwater-adaptive loci, but also between loci on the same chromosome, suggesting selection on linked gene ‘cassettes’. Through temporal sampling along a natural hybrid zone, we found that recombinants showed traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers, whose functions are disrupted in hybrids, may play an important role in maintaining differences among adaptively diverging populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Recombination smooths the time-signal disrupted by latency in within-host HIV phylogenies

Within-host HIV evolution involves several features that may disrupt standard phylogenetic reconstruction. One important feature is re-activation of latently integrated provirus, which has the potential to disrupt the temporal signal, leading to variation in the branch lengths and apparent evolutionary rates in a tree. Yet, real within-host HIV phylogenies tend to show clear, ladder-like trees structured by the time of sampling. Another important feature is recombination, which violates the fundamental assumption that evolutionary history can be represented by a single bifurcating tree. Thus, recombination complicates the within-host HIV dynamic by mixing genomes and creating evolutionary loop structures that cannot be represented in bifurcating trees. In this paper, we develop a coalescent-based simulator of within-host HIV evolution that includes latency, recombination, and effective population size dynamics that allows us to study the relationship between the true, complex genealogy of within-host HIV evolution, encoded as an Ancestral Recombination Graph (ARG), and the observed phylogenetic tree. To compare our ARG results to the familiar phylogeny format, we calculate the expected bifurcating tree after decomposing the ARG into all unique site trees, their combined distance matrix, and the overall corresponding bifurcating tree. While latency and recombination separately disrupt the phylogenetic signal, remarkably, we find that recombination recovers the temporal signal of within-host HIV evolution caused by latency by mixing fragments of old, latent genomes into the contemporary population. In effect, recombination averages over extant heterogeneity, whether it stems from mixed time-signals or population bottlenecks. Further, we establish that the signals of latency and recombination can be observed in phylogenetic trees despite being an incorrect representation of the true evolutionary history. Using an Approximate Bayesian Computation method, we develop a set of statistical probes to tune our simulation model to nine longitudinally-sampled within-host HIV phylogenies. Because ARGs are exceedingly difficult to infer from real HIV data, our simulation system allows investigating effects of latency, recombination, and population size bottlenecks by matching decomposed ARGs to real data as observed in standard phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Carbon in GaN as a nonradiative recombination center

Trap-assisted nonradiative recombination has been shown to limit the efficiency of optoelectronic devices. While substitutional carbon (⁠C N ) has been suggested to be a nonradiative recombination center in GaN devices, a complete recombination cycle including the two charge-state transition levels has not been previously described. In this work, we investigate the trap-assisted recombination process due to C N in GaN, including multiphonon emission, radiative recombination, trap-assisted Auger–Meitner (TAAM) recombination as well as thermal emission of holes. Our study shows the key role of TAAM processes at the high carrier densities relevant for devices. We also reveal the carrier-density regimes where thermal emission and radiative recombination are expected to play an observable role. Our results highlight that carbon concentrations exceeding ~10 17 cm −3 can have a noticeable impact on device efficiency, not just in GaN active layers but also in InGaN and AlGaN. Furthermore, our comprehensive formalism not only offers detailed results for carbon but also provides a general framework for assessing the multiple processes that participate in trap-assisted recombination in semiconductors.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Cosmic recombination in the presence of primordial magnetic fields

Primordial magnetic fields (PMFs) may explain observations of magnetic fields on extragalactic scales. They are most cleanly constrained by measurements of cosmic microwave background radiation (CMB) anisotropies. Their effects on cosmic recombination may even be at the heart of the resolution of the Hubble tension. We present the most detailed analysis of the effects of PMFs on cosmic recombination to date. To this end we extend the public magneto-hydrodynamic code ENZO with a new cosmic recombination routine, Monte-Carlo simulations of Lyman-α photon transport, and a Compton drag term in the baryon momentum equation. The resulting code allows us, for the first time, to realistically predict the impact of PMFs on the cosmic ionization history and the clumping of baryons during cosmic recombination. Our results identify the importance of mixing of Lyman-α photons between overdense- and underdense- regions for small PMF strength. This mixing speeds up recombination beyond the speed-up due to clumping. We also investigate the effects of pecuilar flows on the recombination rate and find it to be small for small PMF strengths. For non-helical PMFs with a Batchelor spectrum we find a surprising dependency of results on ultra-violet magnetic modes. We further show that the increase in the ionization fraction at low redshift by hydrodynamic baryon heating due to PMF dissipation is completely compensated by the faster recombination from baryon clumping. In conclusion, the present study shall serve as a theoretical foundation for a future precise comparison of recombination with PMFs to CMB data.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Evaluation of Potential In Vitro Recombination Events in Codon Deoptimized FMDV Strains

Codon deoptimization (CD) has been recently used as a possible strategy to derive foot-and-mouth disease (FMD) live-attenuated vaccine (LAV) candidates containing DIVA markers. However, reversion to virulence, or loss of DIVA, from possible recombination with wild-type (WT) strains has yet to be analyzed. An in vitro assay was developed to quantitate the levels of recombination between WT and a prospective A24-P2P3 partially deoptimized LAV candidate. By using two genetically engineered non-infectious RNA templates, we demonstrate that recombination can occur within non-deoptimized viral genomic regions (i.e., 3'end of P3 region). The sequencing of single plaque recombinants revealed a variety of genome compositions, including full-length WT sequences at the consensus level and deoptimized sequences at the sub-consensus/consensus level within the 3'end of the P3 region. Notably, after further passage, two recombinants that contained deoptimized sequences evolved to WT. Overall, recombinants featuring large stretches of CD or DIVA markers were less fit than WT viruses. Our results indicate that the developed assay is a powerful tool to evaluate the recombination of FMDV genomes in vitro and should contribute to the improved design of FMDV codon deoptimized LAV candidates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Trap-Assisted Auger-Meitner Recombination from First Principles

Trap-assisted nonradiative recombination is known to limit the efficiency of optoelectronic devices, but the conventional multiphonon emission (MPE) process fails to explain the observed loss in wide-band-gap materials. Here, we highlight the role of trap-assisted Auger-Meitner (TAAM) recombination and present a first-principles methodology to determine TAAM rates due to defects or impurities in semiconductors or insulators. We assess the impact on efficiency of light emitters in a recombination cycle that may include both TAAM and carrier capture via MPE. We apply the formalism to the technologically relevant case study of a calcium impurity in InGaN, where a Shockley-Read-Hall recombination cycle involving MPE alone cannot explain the experimentally observed nonradiative loss. We find that, for band gaps larger than 2.5 eV, the inclusion of TAAM results in recombination rates that are orders of magnitude larger than recombination rates based on MPE alone, demonstrating that TAAM can be a dominant nonradiative process in wide-band-gap materials. Furthermore, our computational formalism is general and can be applied to the calculation of TAAM rates in any semiconducting or insulating material.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Recombination of Autodissociated Water Ions in a Nanoscale Pure Water Droplet

The recombination of water ions has diverse scientific and practical implications, ranging from acid-base chemistry and biological systems to planetary environments and applications in fuel cell and carbon conversion technologies. While spatial confinement affects the physicochemical properties of water dynamics, its impact on the recombination process has rarely been studied. In this work, we investigate the dynamics of water, the water ion distribution, and the ion recombination process in water droplets as a function of droplet size through molecular dynamics simulations and adaptive quantum mechanical/molecular mechanical calculations. We compare the dynamics of recombination in water droplet sizes ranging from 100 to 18 000 waters, both in their interiors and on their surfaces. We found that the self-diffusion of water dramatically decreases in droplets with a diameter below 2.2 nm. Using a classical RexPoN force-field, we found that the ions in 1000 H2O's spend almost 50% of the time on the surface and 0.5 nm beneath it with a slight preference for OH- ion to reside longer on the surface. We estimate that, on average, recombination in these drops occurs at 400 ps in 1000 H2O's and 1 ns in 3000 H2O's. We also found that recombination is not limited by the local structure of the surface or the size of the droplet but can be influenced by the geometry of the water wire connecting the ions as they approach each other, which can often prevent recombination. Our results provide insights to the reaction microenvironments presented by nanoscopic water droplets.

Kwon, Soonho↗
DOE OSTI2023

Trends in runaway electron plateau partial recombination by massive H 2 or D 2 injection in DIII-D and JET and first extrapolations to ITER and SPARC

Abstract Experimental trends in thermal plasma partial recombination resulting from massive D 2 injection into high-Z (Ar) containing runaway electron (RE) plateaus in DIII-D and JET are studied for the purpose of achieving sufficiently low electron density ( n e ≈ 10 18 m − 3 ) to increase RE final loss MHD levels. In both DIII-D and JET, thermal electron density n e is found to drop by ∼100 × when the thermal plasma partially recombines, with a minimum at a vacuum vessel-averaged D 2 density in the range 10 20 − 10 21 m − 3 . RE effective resistivity also drops after partial recombination, indicating expulsion of the Ar content. The n e level after partial recombination is found to increase as RE current is increased. The amount of initial Ar in the RE plateau is not observed to have a strong effect on partial recombination. Partial recombination timescales of order 5 ms in DIII-D and 15 ms in JET are observed. These basic trends and timescales are matched with a 1D diffusion model, which is then used to extrapolate to ITER and SPARC tokamaks. Within the approximations of this model, it is predicted that ITER will be able to achieve sufficiently low n e values on time scales faster than expected RE plateau vertical drift timescales (of order 100 ms), provided sufficient D 2 or H 2 is injected. In SPARC, it is predicted that achieving significant n e recombination will be challenging, due to the very high RE current density. In both ITER and SPARC, it is predicted that achieving low n e will be easier with Ar as a background impurity (rather than Ne).

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Stepwise recombination suppression around the mating-type locus in an ascomycete fungus with self-fertile spores

Recombination is often suppressed at sex-determining loci in plants and animals, and at self-incompatibility or mating-type loci in plants and fungi. In fungal ascomycetes, recombination suppression around the mating-type locus is associated with pseudo-homothallism, i.e. the production of self-fertile dikaryotic sexual spores carrying the two opposite mating types. This has been well studied in two species complexes from different families of Sordariales: Podospora anserina and Neurospora tetrasperma. However, it is unclear whether this intriguing association holds in other species. We show here that Schizothecium tetrasporum, a fungus from a third family in the order Sordariales, also produces mostly self-fertile dikaryotic spores carrying the two opposite mating types. This was due to a high frequency of second meiotic division segregation at the mating-type locus, indicating the occurrence of a single and systematic crossing-over event between the mating-type locus and the centromere, as in P. anserina. The mating-type locus has the typical Sordariales organization, plus a MAT1-1-1 pseudogene in the MAT1-2 haplotype. High-quality genome assemblies of opposite mating types and segregation analyses revealed a suppression of recombination in a region of 1.47 Mb around the mating-type locus. We detected three evolutionary strata, indicating a stepwise extension of recombination suppression. The three strata displayed no rearrangement or transposable element accumulation but gene losses and gene disruptions were present, and precisely at the strata margins. Our findings indicate a convergent evolution of self-fertile dikaryotic sexual spores across multiple ascomycete fungi. The particular pattern of meiotic segregation at the mating-type locus was associated with recombination suppression around this locus, that had extended stepwise. This association between pseudo-homothallism and recombination suppression across lineages and the presence of gene disruption at the strata limits are consistent with a recently proposed mechanism of sheltering deleterious alleles to explain stepwise recombination suppression.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1977

The influence of autoionization accompanied by excitation on dielectronic recombination and ionization equilibrium

In the process of dielectronic recombination, the doubly excited state formed by radiationless capture may autoionize preferentially into an excited state of the recombining ion. This additional autoionization process has not been discussed in previous treatments of dielectronic recombination. The dielectronic recombination rates for certain nonhydrogenic Fe ions, although still larger than the direct radiative recombination rates, are found to be substantially reduced by the inclusion of the additional autoionization rate in the branching ratio for the stabilizing radiative transition. Consequently, the temperatures of maximum equilibrium abundance are significantly lower than those predicted by recent calculations. Finally, the radiative energy loss rate coefficients are calculated for radiation processes involving electron Fe-ion collisions in high-temperature plasmas. Electron impact excitation of resonance line radiation is the dominant radiative cooling mechanism in steady-state plasmas at temperatures where ions with bound electrons are abundant. However, it is found that the radiation emitted during dielectronic recombination can be more important than direct recombination radiation and bremsstrahlung.

Jacobs, V. L.↗
NASA NTRS1980

'Bottleneck' calculation of ion-electron recombination coefficients for lithium-like ions

The ion-electron recombination coefficients for the lithium-like ions C IV, O VI, Ne VIII, Si XII and Ar XVI are computed by the bottleneck method of Byron et al. (1962). In this method, the minimum rate of transitions down the ladder of energy level is taken as the limiting recombination rate, and the particular energy level corresponding to the minimum transition rate is found. The partial collisional radiative recombination coefficient is obtained in terms of the equilibrium population, the rate of collisional de-excitation, the mean radiative transition probability from the bottleneck level and the total transition probability from a level above the bottleneck level to all levels below it. The full collisional-radiative recombination is then obtained by the addition of the values of the radiative recombination coefficient and the three-body recombination coefficient to the ground level. Results of the calculation are shown to be in good agreement with those of Drawin and Emard (1975) for the case of hydrogen. It is also noted that the process of dielectronic recombination, which is not accounted for here, may be significant at lower densities.

Kastner, S. O.↗
DOE OSTI2024

Excitonic Shockley-Read-Hall recombination in organic semiconductors

Trap-mediated recombination influences the performance of a wide range of electronic devices. The well-known Shockley-Read-Hall (SRH) expression for inorganic semiconductors is often invoked to describe the recombination rate in organic materials, although without a clear understanding of how its parameters relate to the underlying material properties or how it should be modified to account for the finite lifetime of exciton intermediates in, for example, the doped emissive layer of an organic light-emitting diode (OLED). Here, we formalize SRH recombination for organic semiconductors based on diffusive trapping and Langevin recombination. We show that including the exciton state suppresses the recombination rate in host-guest systems with type II energy level alignment whenever the interfacial gap between the host and guest molecular orbitals is comparable to the exciton energy. Furthermore, these results quantify the balance between bimolecular and trap-mediated recombination in doped OLED emissive layers, and indicate that devices with type II host-guest pairings can, in principle, beat the thermodynamic limit of their neat guest counterparts.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Bias‐Dependent Quantum Efficiency Reveals Recombination Pathways in Thin Film Solar Cells

Identifying where recombination predominantly occurs—whether at the front interface, back interface, or throughout the bulk—is crucial for optimizing CdSeTe solar cells and many other photovoltaic device architectures. Here, a simple and effective diagnostic is demonstrated: measuring external quantum efficiency (QE) under varying forward biases. The drift–diffusion simulations reveal that each recombination pathway leaves a distinct bias-induced signature in the normalized QE: a progressive drop at long wavelengths for back-limited devices, a short-wavelength decline for front-limited devices, and a relatively uniform decrease across all wavelengths for bulk-limited devices. These predictions are validated with experiments on As-doped and Cu-doped CdSeTe devices, with and without passivation layers or different front buffers. In each case, the observed bias-dependent QE spectral changes align with the simulated recombination map. Because this method uses standard QE instrumentation, it offers a broadly accessible and cost-efficient means to diagnose recombination pathways—extending beyond CdSeTe to other thin-film and emerging solar cell technologies. By pinpointing recombination bottlenecks, researchers and manufacturers can strategically refine doping profiles, passivation schemes, and interface designs to further improve device performance.

CdTe↗
DOE OSTI2023

Previous exposure to Spike-providing parental strains confers neutralizing immunity to XBB lineage and other SARS-CoV-2 recombinants in the context of vaccination

The emergence of SARS-CoV-2 recombinants is of particular concern as they can result in a sudden increase in immune evasion due to antigenic shift. Recent recombinants XBB and XBB.1.5 have higher transmissibility than previous recombinants such as “Deltacron.” We hypothesized that immunity to a SARS-CoV-2 recombinant depends on prior exposure to its parental strains. To test this hypothesis, we examined whether Delta or Omicron (BA.1 or BA.2) immunity conferred through infection, vaccination, or breakthrough infection could neutralize Deltacron and XBB/XBB.1.5 recombinants. We found that Delta, BA.1, or BA.2 breakthrough infections provided better immune protection against Deltacron and its parental strains than did the vaccine booster. None of the sera were effective at neutralizing the XBB lineage or its parent BA.2.75.2, except for the sera from the BA.2 breakthrough group. These results support our hypothesis. In turn, our findings underscore the importance of multivalent vaccines that correspond to the antigenic profile of circulating variants of concern and of variant-specific diagnostics that may guide public health and individual decisions in response to emerging SARS-CoV-2 recombinants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Scalable production of recombinant three-finger proteins: from inclusion bodies to high quality molecular probes

The three-finger proteins are a collection of disulfide bond rich proteins of great biomedical interests. Scalable recombinant expression and purification of bioactive three-finger proteins is quite difficult. We introduce a working pipeline for expression, purification and validation of disulfide-bond rich three-finger proteins using E. coli as the expression host. With this pipeline, we have successfully obtained highly purified and bioactive recombinant α-Βungarotoxin, k-Bungarotoxin, Hannalgesin, Mambalgin-1, α-Cobratoxin, MTα, Slurp1, Pate B etc. Milligrams to hundreds of milligrams of recombinant three finger proteins were obtained within weeks in the lab. The recombinant proteins showed specificity in binding assay and six of them were crystallized and structurally validated using X-ray diffraction protein crystallography. Our pipeline allows refolding and purifying recombinant three finger proteins under optimized conditions and can be scaled up for massive production of three finger proteins. As many three finger proteins have attractive therapeutic or research interests and due to the extremely high quality of the recombinant three finger proteins we obtained, our method provides a competitive alternative to either their native counterparts or chemically synthetic ones and should facilitate related research and applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Engineering the green algae Chlamydomonas incerta for recombinant protein production

Chlamydomonas incerta , a genetically close relative of the model green alga Chlamydomonas reinhardtii , shows significant potential as a host for recombinant protein expression. Because of the close genetic relationship between C. incerta and C. reinhardtii , this species offers an additional reference point for advancing our understanding of photosynthetic organisms, and also provides a potential new candidate for biotechnological applications. This study investigates C. incerta ’s capacity to express three recombinant proteins: the fluorescent protein mCherry, the hemicellulose-degrading enzyme xylanase, and the plastic-degrading enzyme PHL7. We have also examined the capacity to target protein expression to various cellular compartments in this alga, including the cytosol, secretory pathway, cytoplasmic membrane, and cell wall. When compared directly with C. reinhardtii , C. incerta exhibited a distinct but notable capacity for recombinant protein production. Cellular transformation with a vector encoding mCherry revealed that C. incerta produced approximately 3.5 times higher fluorescence levels and a 3.7-fold increase in immunoblot intensity compared to C. reinhardtii . For xylanase expression and secretion, both C. incerta and C. reinhardtii showed similar secretion capacities and enzymatic activities, with comparable xylan degradation rates, highlighting the industrial applicability of xylanase expression in microalgae. Finally, C. incerta showed comparable PHL7 activity levels to C. reinhardtii , as demonstrated by the in vitro degradation of a polyester polyurethane suspension, Impranil® DLN. Finally, we also explored the potential of cellular fusion for the generation of genetic hybrids between C. incerta and C. reinhardtii as a means to enhance phenotypic diversity and augment genetic variation. We were able to generate genetic fusion that could exchange both the recombinant protein genes, as well as associated selectable marker genes into recombinant offspring. These findings emphasize C. incerta ’s potential as a robust platform for recombinant protein production, and as a powerful tool for gaining a better understanding of microalgal biology.

cell membranes↗
DOE OSTI2023

Spin selective charge recombination in chiral donor-bridge-acceptor triads

In this paper, we outline a physically motivated framework for describing spin-selective recombination processes in chiral systems, from which we derive spin-selective reaction operators for recombination reactions of donor–bridge–acceptor molecules, where the electron transfer is mediated by chirality and spin–orbit coupling. In general, the recombination process is selective only for spin-coherence between singlet and triplet states, and it is not, in general, selective for spin polarization. We find that spin polarization selectivity only arises in hopping-mediated electron transfer. We describe how this effective spin-polarization selectivity is a consequence of spin-polarization generated transiently in the intermediate state. Furthermore, the recombination process also augments the coherent spin dynamics of the charge separated state, which is found to have a significant effect on the recombination dynamics and to destroy any long-lived spin polarization. Although we only consider a simple donor–bridge–acceptor system, the framework we present here can be straightforwardly extended to describe spin-selective recombination processes in more complex systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗