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DOE OSTI2020

Improved bacterial recombineering by parallelized protein discovery

Exploiting bacteriophage-derived homologous recombination processes has offered precise, multiplex editing of microbial genomes and the construction of billions of customized genetic variants in a single day. The techniques that enable this, multiplex automated genome engineering (MAGE) and directed evolution with random genomic mutations (DIvERGE), are however, currently limited to a handful of microorganisms for which single-stranded DNA-annealing proteins (SSAPs) that promote efficient recombineering have been identified. Thus, to enable genome-scale engineering in new hosts, efficient SSAPs must first be found. Here we present a high-throughput method for SSAP discovery that we call “serial enrichment for efficient recombineering” (SEER). By performing SEER in Escherichia coli to screen hundreds of putative SSAPs, we identify highly active variants PapRecT and CspRecT. CspRecT increases the efficiency of single-locus editing to as high as 50% and improves multiplex editing by 5- to 10-fold in E. coli , while PapRecT enables efficient recombineering in Pseudomonas aeruginosa , a concerning human pathogen. CspRecT and PapRecT are also active in other, clinically and biotechnologically relevant enterobacteria. We envision that the deployment of SEER in new species will pave the way toward pooled interrogation of genotype-to-phenotype relationships in previously intractable bacteria.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Optimization of InGaN quantum well interfaces for fast interwell carrier transport and low nonradiative recombination

Efficient high-power operation of light emitting diodes based on InGaN quantum wells (QWs) requires rapid interwell hole transport and low nonradiative recombination. The transport rate can be increased by replacing GaN barriers with that of InGaN. Introduction of InGaN barriers, however, increases the rate of the nonradiative recombination. In this work, we have attempted to reduce the negative impact of the nonradiative recombination by introducing thin GaN or AlGaN interlayers at the QW/barrier interfaces. The interlayers, indeed, reduce the nonradiative recombination rate and increase the internal quantum efficiency by about 10%. Here, the interlayers do not substantially slow down the interwell hole transport; for 0.5 nm Al 0.10 Ga 0.90 N interlayers the transport rate has even been found to increase. Another positive feature of the interlayers is narrowing of the QW PL linewidth, which is attributed to smoother QW interfaces and reduced fluctuations of the QW width.

carrier transport↗

DOE OSTI2020

The Frequency of Sex: Population Genomics Reveals Differences in Recombination and Population Structure of the Aflatoxin-Producing Fungus Aspergillus flavus

The apparent rarity of sex in many fungal species has raised questions about how much sex is needed to purge deleterious mutations and how differences in frequency of sex impact fungal evolution. We sought to determine how differences in the extent of recombination between populations of Aspergillus flavus impact the evolution of genes associated with the synthesis of aflatoxin, a notoriously potent carcinogen. We sequenced the genomes of, and quantified aflatoxin production in, 94 isolates of A. flavus sampled from seven states in eastern and central latitudinal transects of the United States. The overall population is subdivided into three genetically differentiated populations (A, B, and C) that differ greatly in their extent of recombination, diversity, and aflatoxin-producing ability. Estimates of the number of recombination events and linkage disequilibrium decay suggest relatively frequent sex only in population A. Population B is sympatric with population A but produces significantly less aflatoxin and is the only population where the inability of nonaflatoxigenic isolates to produce aflatoxin was explained by multiple gene deletions. Population expansion evident in population B suggests a recent introduction or range expansion. Population C is largely nonaflatoxigenic and restricted mainly to northern sampling locations through restricted migration and/or selection. Despite differences in the number and type of mutations in the aflatoxin gene cluster, codon optimization and site frequency differences in synonymous and nonsynonymous mutations suggest that low levels of recombination in some A. flavus populations are sufficient to purge deleterious mutations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Heterogeneity and Recombination of Foot-and-Mouth Disease Virus during Multi-Strain Coinfection of Cattle

Superinfection of cattle persistently infected with foot-and-mouth disease virus (FMDV), with a heterologous FMDV strain has been shown to generate novel recombinant viruses. In this study, we investigated the pathogenesis events within specific tissues associated with FMDV coinfections in cattle subjected to either simultaneous or serial exposure to two distinct strains of FMDV. Both strains of FMDV (one each of serotypes O and A) were similarly localized to the nasopharyngeal mucosa during the early stages of infection. However, while no recombinant FMDV genomes were recovered from simultaneously coinfected cattle, interserotypic recombinants were isolated from nasopharyngeal tissue samples obtained at 48 h after heterologous superinfection of a persistently infected FMDV carrier. Additionally, analysis of FMDV genomes obtained from replicate nasopharyngeal tissue samples demonstrated that adjacent segments of the mucosa were sometimes infected by distinct viruses, demonstrating a multifocal and heterogeneous distribution of FMDV infection during primary and persistent phases of infection. Furthermore, this work indicates that superinfection of FMDV carriers may be an important source of emergent recombinant strains of FMDV in areas where multiple strains are co-circulating.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Promising approaches for the assembly of the catalytically active, recombinant Desulfomicrobium baculatum hydrogenase with substitutions at the active site

Background: Hydrogenases (H2ases) are metalloenzymes capable of the reversible conversion of protons and electrons to molecular hydrogen. Exploiting the unique enzymatic activity of H2ases can lead to advancements in the process of biohydrogen evolution and green energy production. Results: Here we created of a functional, optimized operon for rapid and robust production of recombinant [NiFe] Desulfomicrobium baculatum hydrogenase (Dmb H2ase). The conversion of the [NiFeSe] Dmb H2ase to [NiFe] type was performed on genetic level by site-directed mutagenesis. The native dmb operon includes two structural H2ase genes, coding for large and small subunits, and an additional gene, encoding a specific maturase (protease) that is essential for the proper maturation of the enzyme. Dmb, like all H2ases, needs intricate bio-production machinery to incorporate its crucial inorganic ligands and cofactors. Strictly anaerobic, sulfate reducer D. baculatum bacteria are distinct, in terms of their biology, from E. coli. Thus, we introduced a series of alterations within the native dmb genes. As a result, more than 100 elements, further compiled into 32 operon variants, were constructed. The initial requirement for a specific maturase was omitted by the artificial truncation of the large Dmb subunit. The assembly of the produced H2ase subunit variants was investigated both, in vitro and in vivo. This approach resulted in 4 recombinant [NiFe] Dmb enzyme variants, capable of H 2 evolution. The aim of this study was to overcome the gene expression, protein biosynthesis, maturation and ligand loading bottlenecks for the easy, fast, and cost-effective delivery of recombinant [NiFe] H2ase, using a commonly available E. coli strains. Conclusion: The optimized genetic constructs together with the developed growth and purification procedures appear to be a promising platform for further studies toward fully-active and O 2 tolerant, recombinant [NiFeSe] Dmb H2ase, resembling the native Dmb enzyme. It could likely be achieved by selective cysteine to selenocysteine substitution within the active site of the [NiFe] Dmb variant.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Two-step conversion of polyethylene into recombinant proteins using a microbial platform

Background: The increasing prevalence of plastic waste combined with the inefficiencies of mechanical recycling has inspired interest in processes that can convert these waste streams into value-added biomaterials. To date, the microbial conversion of plastic substrates into biomaterials has been predominantly limited to polyhydroxyalkanoates production. Expanding the capabilities of these microbial conversion platforms to include a greater diversity of products generated from plastic waste streams can serve to promote the adoption of these technologies at a larger scale and encourage a more sustainable materials economy. Results: Herein, we report the development of a new strain of Pseudomonas bacteria capable of converting depolymerized polyethylene into high value bespoke recombinant protein products. Using hexadecane, a proxy for depolymerized polyethylene, as a sole carbon nutrient source, we optimized media compositions that facilitate robust biomass growth above 1 × 10 9 cfu/ml, with results suggesting the benefits of lower hydrocarbon concentrations and the use of NH 4 Cl as a nitrogen source. We genomically integrated recombinant genes for green fluorescent protein and spider dragline-inspired silk protein, and we showed their expression in Pseudomonas aeruginosa, reaching titers of approximately 10 mg/L when hexadecane was used as the sole carbon source. Lastly, we demonstrated that chemically depolymerized polyethylene, comprised of a mixture of branched and unbranched alkanes, could be converted into silk protein by Pseudomonas aeruginosa at titers of 11.3 ± 1.1 mg/L. Conclusion: This work demonstrates a microbial platform for the conversion of a both alkanes and plastic-derived substrates to recombinant, protein-based materials. The findings in this work can serve as a basis for future endeavors seeking to upcycle recalcitrant plastic wastes into value-added recombinant proteins.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Effect of Palladium‐Tetrakis(Triphenylphosphine) Catalyst Traces on Charge Recombination and Extraction in Non‐Fullerene‐based Organic Solar Cells

Abstract The effect of the cross‐coupling catalyst tetrakis(triphenylphosphine)palladium(0) (Pd(PPh 3 ) 4 ) on the performance of a model organic bulk‐heterojunction solar cell composed of a blend of poly([2,6′‐4,8‐di(5‐ethylhexylthienyl)benzo[1,2‐b;3,3‐b]dithiophene]{3‐fluoro‐2[(2‐ethylhexyl)carbonyl]thieno[3,4‐b]thiophenediyl}) (PTB7‐Th) donor and 3,9‐bis(2‐methylene‐((3‐(1,1‐dicyanomethylene)‐6,7‐difluoro)‐indanone))‐5,5,11,11‐tetrakis(4‐hexylphenyl)‐dithieno[2,3‐d:2′,3′‐d′]‐s‐indaceno[1,2‐b:5,6‐b′]dithiophene (IOTIC‐4F) non‐fullerene acceptor is investigated. The effect of intentional addition of different amounts of Pd(PPh 3 ) 4 on morphology, free charge carrier generation, non‐geminate bulk trap‐ and surface trap‐assisted recombination as well as bimolecular recombination and charge extraction is quantified. This work shows that free charge carrier generation is affected significantly, while the impact of Pd(PPh 3 ) 4 on non‐geminate recombination processes is limited because the catalyst does not facilitate efficient trap‐assisted recombination. The studied system shows substantial robustness towards the addition of Pd(PPh 3 ) 4 in small amounts.

Schopp, Nora↗

DOE OSTI2022

Nonradiative Recombination via Charge-Transfer-Exciton to Polaron Energy Transfer Limits Photocurrent in Organic Solar Cells

Here, a recombination and exciton loss mechanism is reported in organic solar cells involving energy transfer between charge transfer (CT) excitons and polarons, impacting photocurrent generation, particularly in the near-infrared where polaronic transitions typically reside. This process sets a low-energy cut-off in the external quantum efficiency spectrum of an excitonic donor/acceptor interface, determined by the low-energy polaron absorption peak and the CT state reorganization energy. Furthermore, this process explains the deviation from unity and bias dependence of the CT state's internal quantum efficiency at low photon energies. This process is demonstrated in a variety of systems and it is hypothesized that CT state to polaron energy transfer recombination may be responsible for a share of nonradiative recombination in all organic photovoltaics and can explain numerous experimentally observed device trends regarding photocurrent generation and energy losses. Overall, this work enhances the understanding of photophysical processes in organic materials and allows the design of systems that can avoid this recombination pathway.

14 SOLAR ENERGY↗

DOE OSTI2020

Auger Recombination Lifetime Scaling for Type I and Quasi-Type II Core/Shell Quantum Dots

Having already achieved near-unity quantum yields, with promising properties for light-emitting diode, lasing, and charge separation applications, colloidal core/shell quantum dots have great technological potential. The shell thickness and band alignment of the shell and core materials are known to influence the efficiency of these devices. In many such applications, improving the efficiency requires a deep understanding of multiexcitonic states. In this paper, we elucidate the shell thickness and band alignment dependencies of the biexciton Auger recombination lifetime for quasi-type II CdSe/CdS and type I CdSe/ZnS core/shell quantum dots. We find that the biexciton Auger recombination lifetime increases with the total nanocrystal volume for quasi-type II CdSe/CdS core/shell quantum dots and is independent of the shell thickness for type I CdSe/ZnS core/shell quantum dots. To perform these calculations and compute Auger recombination lifetimes, we developed a low-scaling approach based on the stochastic resolution of identity. The numerical approach provided a framework for studying the scaling of the biexciton Auger recombination lifetimes in terms of the shell thickness dependencies of the exciton radii, Coulomb couplings, and density of final states in quasi-type II CdSe/CdS and type I CdSe/ZnS core/shell quantum dots.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Local Background Hole Density Drives Nonradiative Recombination in Tin Halide Perovskites

In this study, we use multimodal microscopy to study carrier recombination in semiconducting tin halide perovskite films based on PEA 0.2 FA 0.8 SnI 3 (PEA = phenethylammonium; FA = formamidinium). We use the observation of pseudo-first-order photoluminescence (PL) decay kinetics to establish a method for quantifying the hole dopant level and nonradiative recombination rate constant. We find that untreated PEA 0.2 FA 0.8 SnI 3 films exhibit large hole doping concentrations of p 0 ≈ 10 19 cm –3 , which is reduced to p 0 ≈ 10 16 cm –3 after SnF 2 treatment. While it is well-known that the radiative recombination rates are increased with p 0 , we reveal that the nonradiative rate is also increased. We find that p-type regions in untreated PEA 0.2 FA 0.8 SnI 3 films are centers for nonradiative recombination, which are diminished in films with p 0 ≈ 10 16 cm –3 . We discover significant PL heterogeneity even in PEA 0.2 FA 0.8 SnI 3 films with moderate dopant levels, suggesting that new strategies to eliminate deleterious defects in PEA 0.2 FA 0.8 SnI 3 must be developed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

19.31% binary organic solar cell and low non-radiative recombination enabled by non-monotonic intermediate state transition

Non-fullerene acceptors based organic solar cells represent the frontier of the field, owing to both the materials and morphology manipulation innovations. Non-radiative recombination loss suppression and performance boosting are in the center of organic solar cell research. Here, we developed a non-monotonic intermediate state manipulation strategy for state-of-the-art organic solar cells by employing 1,3,5-trichlorobenzene as crystallization regulator, which optimizes the film crystallization process, regulates the self-organization of bulk-heterojunction in a non-monotonic manner, i.e., first enhancing and then relaxing the molecular aggregation. As a result, the excessive aggregation of non-fullerene acceptors is avoided and we have achieved efficient organic solar cells with reduced non-radiative recombination loss. In PM6:BTP-eC9 organic solar cell, our strategy successfully offers a record binary organic solar cell efficiency of 19.31% (18.93% certified) with very low non-radiative recombination loss of 0.190 eV. And lower non-radiative recombination loss of 0.168 eV is further achieved in PM1:BTP-eC9 organic solar cell (19.10% efficiency), giving great promise to future organic solar cell research.

14 SOLAR ENERGY↗

DOE OSTI2024

Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination

Abstract Recent genomic analyses have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars), but the mechanisms that create and maintain these units remain unclear. By analyzing closely-related isolate genomes from the same or related samples and identifying recent recombination events using a novel bioinformatics methodology, we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection-driven) horizontal gene flow, mediated by homologous recombination, often underlie these diversity patterns. Ecological cohesiveness was inferred based on greater similarity in temporal abundance patterns of genomes of the same vs. different units, and recombination was shown to affect all sizable segments of the genome (i.e., be genome-wide) and have two times or greater impact on sequence evolution than point mutations. These results were observed in bothSalinibacter ruber, an environmental halophilic organism, andEscherichia coli, the model gut-associated organism and an opportunistic pathogen, indicating that they may be more broadly applicable to the microbial world. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or recombination, but not necessarily their synergistic effect, and answer an important question for microbiology: what a species and a subspecies are.

Science & Technology - Other Topics↗

DOE OSTI2025

Hints of primordial magnetic fields at recombination and implications for the Hubble tension

Primordial Magnetic Fields (PMFs), long studied as relics of the early Universe, accelerate recombination and have been proposed as a way to relieve the Hubble tension. However, previous studies relied on simplified toy models. Here, in this study, we use recent evaluations of recombination with PMFs, incorporating full magnetohydrodynamic (MHD) simulations and detailed Lyman-alpha radiative transfer, to test PMF-enhanced recombination (bΛCDM) against observational data from the cosmic microwave background (CMB), baryon acoustic oscillations (BAO), and Type Ia supernovae (SN). Focusing on non-helical PMFs with a Batchelor spectrum, we find a preference for presentday total field strengths of approximately 5-10 pico-Gauss. Depending on the dataset combination, this preference ranges from mild (∼ 1.8σ with Planck + DESI) to moderate (∼ 3σ with Planck + DESI + SH0ES-calibrated SN) significance. The bΛCDM has Planck + DESI χ 2 values equal to or better than ΛCDM while predicting a higher Hubble constant. Future high-resolution CMB temperature and polarization measurements will be crucial for confirming or further constraining PMFs at recombination. Field strengths of 5-10 pico-Gauss align closely with those required for cluster magnetic fields to originate entirely from primordial sources, without the need for additional dynamo amplification.

Jedamzik, Karsten [Centre National de la Recherche↗

DOE OSTI2021

Singlet fission and triplet pair recombination in bipentacenes with a twist

We investigate triplet pair dynamics in pentacene dimers that have varying degrees of coplanarity (pentacene–pentacene twist angle). The fine-tuning of the twist angle was achieved by alternating connectivity at the 1-position or 2-positions of pentacene. This mix-and-match connectivity leads to tunable twist angles between the two covalently linked pentacenes. These twisted dimers allow us to investigate the subtle effects that the dihedral angle between the covalently linked pentacenes imparts on singlet fission and triplet pair recombination dynamics. We observe that as the dihedral angle between the two bonded pentacenes is increased, the rates of singlet fission decrease, while the accompanying decrease in triplet recombination rates is stark. Temperature-dependent transient optical studies combined with theoretical calculations show that the triplet pair recombination proceeds primarily through a direct multiexciton internal conversion process. Calculations further show that the significant decrease in recombination rates can be directly attributed to a corresponding decrease in the magnitude of the nonadiabatic coupling between the singlet multiexcitonic state and the ground state. Furthermore, these results highlight the importance of the twist angle in designing systems that exhibit rapid singlet fission, while maintaining long triplet pair lifetimes in pentacene dimers.

14 SOLAR ENERGY↗

DOE OSTI2022

Spontaneous carrier generation and low recombination in high-efficiency non-fullerene solar cells

The current research reveals the unique photo physical properties and carrier generation mechanisms of high efficiency non-fullerene acceptor-based organic photovoltaic blends. The analysis of device performance, morphology, and photo physics reveals that the interface carrier generation cannot support the device's current output. It is seen that primary photon excitons can dissociate into charge carriers in Y6, which displays a time scale of ∼0.3 ps with polaron yields above 28% in neat and blended thin films. This characteristic in combination with a large exciton diffusion length enables high morphology tolerance in Y6-overloaded blends. The carrier generation process is also combined with recombination studies. The recombination rate quantified by flux-dependent transient absorption measurements yields less than 5% total recombination and nearly 0% geminate recombination. Furthermore, these results define the advantages of the Y6 non-fullerene acceptor (NFA) and reveal the fundamental importance of developing new NFA materials with superior photo physical properties.

14 SOLAR ENERGY↗

DOE OSTI2023

Interface property–functionality interplay suppresses bimolecular recombination facilitating above 18% efficiency organic solar cells embracing simplistic fabrication

Efficient exciton-to-charge generation from the introduction of non-fullerene acceptors (NFAs) has been an important breakthrough in organic solar cell (OSC) developments. However, low device fill factors (FFs) following significant free charge carrier recombination loss continue to undermine their marketplace potential. Previous studies have successfully uncovered the importance of donor and acceptor domains in promoting charge transport. However, the functionality of donor/acceptor (D/A) interfaces relevant to free charge recombination remains unclear despite such interfaces being present throughout the material. In this work, the disorder-induced uphill bulk-to-D/A interface transport energy landscape is unveiled to enhance the polaron recombination resistance thereby also mitigating the triplet state formation from back charge transfer. In simple words, increasing the interface disorder while keeping the purer domains highly ordered will impart greater bulk-to-interface differential energy which then serves as a recombination energy barrier. Herein, these are made possible by varying the NFA outer side chains from linear alkyls to bulkier 2D phenylalkyls which influence the donor–acceptor interaction and define the interfacial disorder. Meanwhile, the extent of interface disorder without tradeoff in geminate losses is dependent on electrostatics and nanomorphology driving efficient exciton dissociation. By understanding these interplays, remarkable FFs over 80% and power conversion efficiencies (PCEs) above 18% are revealed to remain accessible even with simple binary component device fabrication without additional components/treatments thereby maintaining the scalability. Consequently, the principles uncovered here will serve as the foundation to reach the optimum potential of binary and simple systems, a prerequisite to ultimately realize the most cost-effective OSC design strategies for practical applications.

14 SOLAR ENERGY↗

DOE OSTI2024

Laser-assisted radiative recombination in a cold hydrogen plasma

Abstract We study the process of laser-assisted radiative recombination of an electron with a proton in a cold hydrogen plasma employing the semiclassical Kramers’ approach which involves calculation of classical trajectories in combined laser and Coulomb fields and the use of the correspondence principle. Due to the Coulomb focusing effect, recombination is the most effective when the initial electron momentum is parallel to the laser polarization. Orders of magnitude enhancement of the cross section, as compared to the laser-free case, is observed in this case. With increasing angle between the electron momentum and polarization, the recombination cross section drops. However, even after averaging over Maxwellian velocity distribution we obtain a substantial enhancement of the recombination rate constant, as compared to the zero-field case. For the field intensities in the range 30–350 MW cm −2 , the enhancement occurs in the region of the radiation wavelength from 5 to 20 µ m and for the plasma temperature from 20 to 300 K.

Fabrikant, I. I. (ORCID:0000000293849454)↗

DOE OSTI2025

Angular dependent measurement of electron-ion recombination in liquid argon for ionization calorimetry in the ICARUS liquid argon time projection chamber

This paper reports on a measurement of electron-ion recombination in liquid argon in the ICARUS liquid argon time projection chamber (LArTPC). A clear dependence of recombination on the angle of the ionizing particle track relative to the drift electric field is observed. An ellipsoid modified box (EMB) model of recombination describes the data across all measured angles. These measurements are used for the calorimetric energy scale calibration of the ICARUS TPC, which is also presented. The impact of the EMB model is studied on calorimetric particle identification, as well as muon and proton energy measurements. Accounting for the angular dependence in EMB recombination improves the accuracy and precision of these measurements.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗