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DOE OSTI2022

Protoplast fusion in Bacillus species produces frequent, unbiased, genome-wide homologous recombination

Abstract In eukaryotes, fine-scale maps of meiotic recombination events have greatly advanced our understanding of the factors that affect genomic variation patterns and evolution of traits. However, in bacteria that lack natural systems for sexual reproduction, unbiased characterization of recombination landscapes has remained challenging due to variable rates of genetic exchange and influence of natural selection. Here, to overcome these limitations and to gain a genome-wide view on recombination, we crossed Bacillus strains with different genetic distances using protoplast fusion. The offspring displayed complex inheritance patterns with one of the parents consistently contributing the major part of the chromosome backbone and multiple unselected fragments originating from the second parent. Our results demonstrate that this bias was in part due to the action of restriction–modification systems, whereas genome features like GC content and local nucleotide identity did not affect distribution of recombination events around the chromosome. Furthermore, we found that recombination occurred uniformly across the genome without concentration into hotspots. Notably, our results show that species-level genetic distance did not affect genome-wide recombination. This study provides a new insight into the dynamics of recombination in bacteria and a platform for studying recombination patterns in diverse bacterial species.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

An all optical approach for comprehensive in-operando analysis of radiative and nonradiative recombination processes in GaAs double heterostructures

We demonstrate an all optical approach that can surprisingly offer the possibility of yielding much more information than one would expect, pertinent to the carrier recombination dynamics via both radiative and nonradiative processes when only one dominant deep defect level is present in a semiconductor material. By applying a band-defect state coupling model that explicitly treats the inter-band radiative recombination and Shockley–Read–Hall (SRH) recombination via the deep defect states on an equal footing for any defect center occupation fraction, and analyzing photoluminescence (PL) as a function of excitation density over a wide range of the excitation density (e.g., 5–6 orders in magnitude), in conjunction with Raman measurements of the LO-phonon plasmon (LOPP) coupled mode, nearly all of the key parameters relevant to the recombination processes can be obtained. They include internal quantum efficiency (IQE), minority and majority carrier density, inter-band radiative recombination rate (W r ), minority carrier nonradiative recombination rate (W nr ), defect center occupation fraction (f), defect center density (N t ), and minority and majority carrier capture cross-sections (σ t and σ tM ). While some of this information is thought to be obtainable optically, such as IQE and the W r /W nr ratio, most of the other parameters are generally considered to be attainable only through electrical techniques, such as current-voltage (I-V) characteristics and deep level transient spectroscopy (DLTS). Following a procedure developed herein, this approach has been successfully applied to three GaAs double-heterostructures that exhibit two distinctly different nonradiative recombination characteristics. The method greatly enhances the usefulness of the simple PL technique to an unprecedented level, facilitating comprehensive material and device characterization without the need for any device processing.

14 SOLAR ENERGY↗

DOE OSTI2021

Distinguishing bulk and surface recombination in CdTe thin films and solar cells using time-resolved terahertz and photoluminescence spectroscopies

Understanding the nature of recombination and its dependence on defects and interfaces is essential for engineering materials and contacts for higher open circuit voltage (V oc ) and power conversion efficiency in photovoltaic (PV) devices. Time-resolved photoluminescence (TRPL) has conventionally been used to evaluate recombination, but carrier redistribution often dominates the response at short times. In this work, we report on the quantification of carrier dynamics and recombination mechanisms by complementary use of both time-resolved terahertz spectroscopy (TRTS) and TRPL combined with numerical modeling of the continuity equations and Poisson’s equation. We have demonstrated this approach using CdTe thin films. A thin film stack with CdTe fabricated by vapor transport deposition and treated with CdCl 2 exhibited a bulk lifetime of 1.7 ± 0.1 ns, negligible CdTe/CdS interface recombination velocity, and back surface recombination velocity of 6.3 ± 1.3 x10 4 cm/s. In contrast, a film stack without CdCl 2 treatment had a bulk lifetime of only 68 ± 12 ps and a higher interface recombination velocity of 4 ± 2 x10 8 cm/s. By determining the locus and mechanisms of performance-limiting recombination, we can accelerate the development of thin-film PVs with higher V oc and efficiency. While the method has been demonstrated here using CdTe, it is also applicable to perovskites, Cu(InGa)Se 2 , Cu2ZnSn(S,Se) 4, and emerging technologies.

14 SOLAR ENERGY↗

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 OSTI2020

The charge reduction rate for multiply charged polymer ions via ion–ion recombination at atmospheric pressure

The charge reduction of multiply charged macromolecular ions via recombination with small ions in the gas phase is commonly employed to modulate the charge on macromolecules prior to mass spectrometric and mobility analyses. We employ a recently developed continuum-Molecular Dynamics (MD) calculation approach to determine the recombination rate coefficient of multiply charged (1 to 7 excess positive charged) polyethylene glycol ions (mass of 4600 Da) with smaller singly charged anions, modeled as NO 2 – ions. The continuum-MD approach accounts explicitly for the influence of the background gas on the recombination process, accounts explicitly for ion translational, vibrational, and rotational motion, and enables recombination rate coefficient calculation in nitrogen near atmospheric pressure, wherein neither low pressure nor high pressure recombination theories are strictly applicable. Continuum-MD simulations yield recombination rate coefficients near 3.9 × 10 –14 m 3 s –1 for singly charged ions, increasing to 3.0 × 10 –11 m 3 s –1 for the +7 ion. Pre-existing collision rate coefficient expressions for rigid ions are found to be within a factor of 2–5 of calculations for all charge states, but their use requires knowledge of an appropriate collision distance, which is not well-defined for flexible polymer ions. Continuum-MD-inferred rate coefficients are incorporated into a model of charge reduction, and the charge state distribution versus anion concentration determined with it is compared to charge reduction measurements made via atmospheric pressure differential mobility analysis. Furthermore, good agreement is observed between simulations and experiments; although results are extremely sensitive to the recombination rate coefficients, experimental results are bound by models utilizing rates within a factor of 2 (0.5–2.0×) of the continuum-MD rates.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2020

Model for photothermal ionization and molecular recombination during pulsed ablation of polyethylene

The surface erosion of polyethylene is studied under conditions characteristic of extremely high-rate heating expected in laser-driven and high energy density experiments. A coupled model for photoionization and volumetric photothermal degradation of polyethylene is developed that includes finite rate chemistry and molecular recombination of radicals. First, the model is used to explore the evolution of radicals and hydrocarbons during isochoric heating, for which it is found that polyethylene is not in chemical equilibrium for rates >108K/s. Then, the model is used to explore the cooperativity between photoionization and photothermal ionization during one-dimensional ablation from a pulsed heating source, accounting for coupled energy deposition, thermokinetics, thermochemistry, hydrodynamics, mechanics, and thermal conduction in the ALEGRA multi-physics code. The ablation depth per energy pulse is found to agree with an analytical model for instantaneous energy deposition and absent molecular recombination or photoionization. Otherwise, molecular recombination of radicals reduces the depth of ablation per pulse, owing to thermal stabilization on forming branched molecules. Radical formation through photoionization can be compensated for by recombination, but it accelerates ablation at high enough photoionization rates. Finally, the influence of molecular recombination on the ablation depth is found to decrease for long pulses, owing to decreased recombination reaction rates at lower vapor densities near the ablated surface. These and other findings highlight competition between the processes of scission, recombination, and photoionization during pulsed ablation of polyethylene.

Moore, N. W. (ORCID:0000000272259674)↗

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↗