Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Recombinant”

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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Characterization of novel recombinant mycobacteriophages derived from homologous recombination between two temperate phages

Comparative analyses of mycobacteriophage genomes reveals extensive genetic diversity in genome organization and gene content, contributing to widespread mosaicism. We previously reported that the prophage of mycobacteriophage Butters (cluster N) provides defense against infection by Island3 (subcluster I1). To explore the anti-Island3 defense mechanism, we attempted to isolate Island3 defense escape mutants on a Butters lysogen, but only uncovered phages with recombinant genomes comprised of regions of Butters and Island3 arranged from left arm to right arm as Butters-Island3-Butters (BIBs). Recombination occurs within two distinct homologous regions that encompass lysin A, lysin B, and holin genes in one segment, and RecE and RecT genes in the other. Structural genes of mosaic BIB genomes are contributed by Butters while the immunity cassette is derived from Island3. Consequently, BIBs are morphologically identical to Butters (as shown by transmission electron microscopy) but are homoimmune with Island3. Recombinant phages overcome antiphage defense and silencing of the lytic cycle. We leverage this observation to propose a stratagem to generate novel phages for potential therapeutic use.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Over 31% efficient indoor organic photovoltaics enabled by simultaneously reduced trap-assisted recombination and non-radiative recombination voltage loss

Indoor organic photovoltaics (OPVs) have shown great potential application in driving low-energy-consumption electronics for the Internet of Things. There is still great room for further improving the power conversion efficiency (PCE) of indoor OPVs, considering that the desired morphology of the active layer to reduce trap-assisted recombination and voltage losses and thus simultaneously enhance the fill factor (FF) and open-circuit voltage for efficient indoor OPVs remains obscure. Herein, by optimizing the bulk and interface morphology via a layer-by-layer (LBL) processing strategy, low leakage current and low non-radiative recombination loss can be synergistically achieved in PM6:Y6-O based devices. Detailed characterizations reveal the stronger crystallinity, purer domains and ideal interfacial contacts in the LBL devices compared to their bulk-heterojunction (BHJ) counterparts. The optimized morphology yields a reduced voltage loss and an impressive FF of 81.5%, and thus contributes to a high PCE of 31.2% under a 1000 lux light-emitting diode (LED) illumination in the LBL devices, which is the best reported efficiency for indoor OPVs. Additionally, this LBL strategy exhibits great universality in promoting the performance of indoor OPVs, as exemplified by three other non-fullerene acceptor systems. Finally, this work provides guidelines for morphology optimization and synergistically promotes the fast development of efficient indoor OPVs.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Reduced recombination via tunable surface fields in perovskite thin films

Here, the ability to reduce energy loss at semiconductor surfaces through passivation or surface field engineering is an essential step in the manufacturing of efficient photovoltaic (PV) and optoelectronic devices. Similarly, surface modification of emerging halide perovskites with quasi-two-dimensional (2D) heterostructures is now ubiquitous to achieve PV power conversion efficiencies (PCEs) >25%, yet a fundamental understanding to how these treatments function is still generally lacking. Here we use a unique combination of depth-sensitive nanoscale characterization techniques to uncover a tunable passivation strategy and mechanism found in perovskite PV devices that were the first to reach the >25% PCE milestone. Namely, treatment with hexylammonium bromide leads to the simultaneous formation of an iodide-rich 2D layer along with a Br halide gradient that extends from defective surfaces and grain boundaries into the bulk three-dimensional (3D) layer. This interface can be optimized to extend the charge carrier lifetime to record values >30 μs and to reduce interfacial recombination velocities to values as low as <7 cm s −1 .

Devices for energy harvesting↗
DOE OSTI2026

Dynamics of iodine geminate recombination in supercritical xenon solvent: Caging effect

Understanding the dynamics of chemical reactions in solutions is vital, as their rates and kinetics are significantly affected by the solvent environment. Supercritical solvents offer extensive applications in chemical reactions by enabling the manipulation of the solution environment. Here, in this study, we investigate the geminate recombination of iodine in a supercritical xenon solvent by using ReaxFF-based molecular dynamics simulations. Our findings reveal that the highest iodine recombination rate occurs near supercritical conditions, while lower-pressure conditions lead to reduced collision rates and unstable recombination, and higher-pressure conditions hinder iodine diffusion, resulting in a lower recombination rate. Our analysis shows that the xenon local density at the time of recombination is at least 2.5 times higher than the global density, confirming the presence of xenon clusters surrounding the Iodine atoms. This observation is further supported by coordination number analysis, which confirms an elevated xenon local density during recombination. In addition, the correlation between the total energy of xenon atoms within a cluster and recombined iodine atoms underscores the kinetic energy transfer process, validating the occurrence of geminate recombination. The excess kinetic energy from the recombining iodine atoms is transferred to the surrounding xenon atoms. Our examination of geminate recombination demonstrates that iodine atoms confined within xenon clusters—whether through manual insertion of atoms or the fast dissociation of an iodine molecule within xenon clusters—are more likely to recombine as primary geminate recombination. However, extending the iodine molecule dissociation time allows iodine atoms to diffuse out of the cluster, and the recombination to shift toward secondary geminate recombination.

Cage effect↗
DOE OSTI2023

Comprehensive Genetic Characterization of Four Novel HIV-1 Circulating Recombinant Forms (CRF129_56G, CRF130_A1B, CRF131_A1B, and CRF138_cpx): Insights from Molecular Epidemiology in Cyprus

Molecular investigations of the HIV-1 pol region (2253–5250 in the HXB2 genome) were conducted on sequences obtained from 331 individuals infected with HIV-1 in Cyprus between 2017 and 2021. This study unveiled four distinct HIV-1 putative transmission clusters, encompassing 19 previously unidentified HIV-1 recombinants. These recombinants, each comprising eight, three, four, and four sequences, respectively, did not align with previously established Circulating Recombinant Forms (CRFs). To characterize these novel HIV-1 recombinants, near-full-length genome sequences were successfully obtained for 16 of the 19 recombinants (790–8795 in the HXB2 genome) using an in-house-developed RT-PCR assay. Phylogenetic analyses, employing MEGAX and Cluster-Picker, along with confirmatory neighbor-joining tree analyses of subregions, were conducted to identify distinct clusters and determine subtypes. The uniqueness of the HIV-1 recombinants was evident in their exclusive clustering within generated maximum likelihood trees. Recombination analyses highlighted the distinct chimeric nature of these recombinants, with consistent mosaic patterns observed across all sequences within each of the four putative transmission clusters. Conclusive genetic characterization identified four novel HIV-1 CRFs: CRF129_56G, CRF130_A1B, CRF131_A1B, and CRF138_cpx. CRF129_56G exhibited two recombination breakpoints and three fragments of subtypes CRF56_cpx and G. Both CRF130_A1B and CRF131_A1B featured seven recombination breakpoints and eight fragments of subtypes A1 and B. CRF138_cpx displayed five recombination breakpoints and six fragments of subtypes CRF22_01A1 and F2, along with an unclassified fragment. Additional BLAST analyses identified a Unique Recombinant Form (URF) of CRF138_cpx with three additional recombination sites, involving subtype F2, a fragment of unknown subtype origin, and CRF138_cpx. Post-identification, all putative transmission clusters remained active, with CRF130_A1B, CRF131_A1B, and CRF138_cpx clusters exhibiting further growth. Furthermore, international connections were identified through BLAST analyses, linking one sequence from the USA to the CRF130_A1B strain, and three sequences from Belgium and Cameroon to the CRF138_cpx strain. This study contributes valuable insights into the dynamic landscape of HIV-1 diversity and transmission patterns, emphasizing the need for ongoing molecular surveillance and global collaboration in tracking emerging viral variants.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Evolution of homologous recombination rates across bacteria

Bacteria are nonsexual organisms but are capable of exchanging DNA at diverse degrees through homologous recombination. Intriguingly, the rates of recombination vary immensely across lineages where some species have been described as purely clonal and others as “quasi-sexual.” However, estimating recombination rates has proven a difficult endeavor and estimates often vary substantially across studies. It is unclear whether these variations reflect natural variations across populations or are due to differences in methodologies. Consequently, the impact of recombination on bacterial evolution has not been extensively evaluated and the evolution of recombination rate—as a trait—remains to be accurately described. Here, we developed an approach based on Approximate Bayesian Computation that integrates multiple signals of recombination to estimate recombination rates. We inferred the rate of recombination of 162 bacterial species and one archaeon and tested the robustness of our approach. Our results confirm that recombination rates vary drastically across bacteria; however, we found that recombination rate—as a trait—is conserved in several lineages but evolves rapidly in others. Although some traits are thought to be associated with recombination rate (e.g., GC-content), we found no clear association between genomic or phenotypic traits and recombination rate. Overall, our results provide an overview of recombination rate, its evolution, and its impact on bacterial evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Homologous recombination shapes the architecture and evolution of bacterial genomes

Homologous recombination is a key evolutionary force that varies considerably across bacterial species. However, how the landscape of homologous recombination varies across genes and within individual genomes has only been studied in a few species. Here, we used Approximate Bayesian Computation to estimate the recombination rate along the genomes of 145 bacterial species. Our results show that homologous recombination varies greatly along bacterial genomes and shapes many aspects of genome architecture and evolution. The genomic landscape of recombination presents several key signatures: rates are highest near the origin of replication in most species, patterns of recombination generally appear symmetrical in both replichores (i.e. replicational halves of circular chromosomes) and most species have genomic hotspots of recombination. Furthermore, many closely related species share conserved landscapes of recombination across orthologs indicating that recombination landscapes are conserved over significant evolutionary distances. We show evidence that recombination drives the evolution of GC-content through increasing the effectiveness of selection and not through biased gene conversion, thereby contributing to an ongoing debate. Finally, we demonstrate that the rate of recombination varies across gene function and that many hotspots of recombination are associated with adaptive and mobile regions often encoding genes involved in pathogenicity.

Torrance, Ellis L [University of North Carolina, G↗
DOE OSTI2023

Influence of trap-assisted and intrinsic Auger–Meitner recombination on efficiency droop in green InGaN/GaN LEDs

Here, we study the impact of deep-level defects on trap-assisted Auger–Meitner recombination in c-plane InGaN/GaN LEDs using a small-signal electroluminescence (SSEL) method and deep-level optical spectroscopy (DLOS). Carrier dynamics information, including carrier lifetime, recombination rate, and carrier density, is obtained from SSEL, while DLOS is used to obtain the deep-level defect density. Through fitting the nonradiative recombination rates of wafers with different deep-level defect densities, we obtain the Shockley–Read–Hall (SRH) and trap-assisted Auger–Meitner recombination (TAAR) coefficients. We show that defect-related nonradiative recombination, including both SRH and TAAR, accounts for a relatively small fraction of the total nonradiative recombination, which is dominated by intrinsic Auger–Meitner recombination. The interplay between carrier localization and Coulomb enhancement has a different impact on radiative and intrinsic Auger–Meitner recombination. Evidence is presented that the imbalance between the change of radiative and intrinsic Auger–Meitner recombination is the primary cause of the efficiency droop at high carrier densities in the samples studied.

36 MATERIALS SCIENCE↗
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↗