Enhancement Of Recombination Research Articles

Lasing action and extraordinary reduction in long radiative lifetime of type-II GaSb/GaAs quantum dots using circular photonic crystal nanocavity

We demonstrated the lasing action and remarkable reduction in long radiative lifetimes of type-II GaSb/GaAs quantum dots using a circular photonic-crystal nano-cavity with high Purcell factors. The associated enhancement in carrier recombination was surprisingly high and could even surpass type-I counterparts in similar conditions. These phenomena reveal that the type-II sample exhibited extremely low nonradiative recombination so that weak radiative transitions were more dominant than expected. The results indicate that type-II nanostructures may be advantageous for applications which require controllable radiative transitions but low nonradiative depletions.

Effect of Different Graphene Oxide Contents on Dye-Sensitized Solar Cells

Graphene/TiO2 composite films were deposited on fluorine-doped SnO2-coated conductive substrates by spin coating acting as photoelectrodes of dye-sensitized solar cells. The graphene/TiO2 composite films were characterized by scanning electronic microscopy, an X-ray diffractometer, a UV–visible spectrometer, and electrochemical impedance spectroscopy. Nyquist plots showed the decrease of impedance, in which electron transport rate was promoted. The photovoltaic properties showed that the incorporation of graphene could increase the short-circuit current density and photoelectric conversion efficiency. However, an excessive incorporation of graphene led to the enhancement of charge recombination and the reduction of photoelectric conversion efficiency. The graphene/TiO2 composite film with 1.5-mL graphene oxide solution obtained the optimal photoelectric conversion efficiency of 5.26%.

Differential chromosome conformations as hallmarks of cellular identity revealed by mathematical polymer modeling.

Inherently dynamic, chromosomes adopt many different conformations in response to DNA metabolism. Models of chromosome organization in the yeast nucleus obtained from genome-wide chromosome conformation data or biophysical simulations provide important insights into the average behavior but fail to reveal features from dynamic or transient events that are only visible in a fraction of cells at any given moment. We developed a method to determine chromosome conformation from relative positions of three fluorescently tagged DNA in living cells imaged in 3D. Cell type specific chromosome folding properties could be assigned based on positional combinations between three loci on yeast chromosome 3. We determined that the shorter left arm of chromosome 3 is extended in MATα cells, but can be crumpled in MAT a cells. Furthermore, we implemented a new mathematical model that provides for the first time an estimate of the relative physical constraint of three linked loci related to cellular identity. Variations in this estimate allowed us to predict functional consequences from chromatin structural alterations in asf1 and recombination enhancer deletion mutant cells. The computational method is applicable to identify and characterize dynamic chromosome conformations in any cell type.

Mating-type Gene Switching in Saccharomyces cerevisiae.

The budding yeast Saccharomyces cerevisiae has two alternative mating types designated MATa and MATα. These are distinguished by about 700 bp of unique sequences, Ya or Yα, including divergent promoter sequences and part of the open reading frames of genes that regulate mating phenotype. Homothallic budding yeast, carrying an active HO endonuclease gene, HO, can switch mating type through a recombination process known as gene conversion, in which a site-specific double-strand break (DSB) created immediately adjacent to the Y region results in replacement of the Y sequences with a copy of the opposite mating type information, which is harbored in one of two heterochromatic donor loci, HMLα or HMRa. HO gene expression is tightly regulated to ensure that only half of the cells in a lineage switch to the opposite MAT allele, thus promoting conjugation and diploid formation. Study of the silencing of these loci has provided a great deal of information about the role of the Sir2 histone deacetylase and its associated Sir3 and Sir4 proteins in creating heterochromatic regions. MAT switching has been examined in great detail to learn about the steps in homologous recombination. MAT switching is remarkably directional, with MATa recombining preferentially with HMLα and MATα using HMRa. Donor preference is controlled by a cis-acting recombination enhancer located near HML. RE is turned off in MATα cells but in MATa binds multiple copies of the Fkh1 transcription factor whose forkhead-associated phosphothreonine binding domain localizes at the DSB, bringing HML into conjunction with MATa.

Function of the N‐terminal segment of the RecA‐dependent nuclease Ref

The bacteriophage P1 Ref (recombination enhancement function) protein is a RecA-dependent, HNH endonuclease. It can be directed to create targeted double-strand breaks within a displacement loop formed by RecA. The 76 amino acid N-terminal region of Ref is positively charged (25/76 amino acid residues) and inherently unstructured in solution. Our investigation of N-terminal truncation variants shows this region is required for DNA binding, contains a Cys involved in incidental dimerization, and is necessary for efficient Ref-mediated DNA cleavage. Specifically, Ref N-terminal truncation variants lacking between 21 and 47 amino acids are more effective RecA-mediated targeting nucleases. We propose a Ref cleavage model, in which the N-terminal region acts as an anchor and allows rearrangement of the nuclease domain for sequential cleavage of strands in double-stranded DNA.

Effect of the Quantum-Well Shape on the Performance of InGaN-Based Light-Emitting Diodes Emitting in the 400–500-nm Range

The electrical and optical properties of InGaN–GaN light-emitting diodes (LEDs) emitting in the 400–500-nm range and having a v-shaped quantum well (VSQW) and a u-shaped quantum well (USQW) are numerically investigated using APSYS simulation program. The simulation results showed that the devices containing VSQW have superior performance in terms of optical power and internal quantum efficiency droop compared to those with USQW. The optical power of the LEDs containing USQW increases gradually and reaches a maximum at 460 nm; however, the optical power of the LEDs with VSQW improves gradually, and the maximum is obtained in a window from 420 to 436 nm as a result of radiative recombination enhancement. The simulation results suggest that the higher performance of the VSQW is due to piezoelectric field reduction and an enhancement of electron and hole wave functions overlap.

Prospects and merits of metal-clad semiconductor lasers from nearly UV to far IR.

Using metal-clad (or plasmonic) waveguide structures in semiconductor lasers carries a promise of reduced size, threshold, and power consumption. This promise is put to a rigorous theoretical test, that takes into account increased waveguide loss, Auger recombination, and Purcell enhancement of spontaneous recombination. The conclusion is that purported benefits of metal waveguides are small to nonexistent for all the band-to-band and intersubband lasers operating from UV to Mid-IR range, with a prominent exception of far-IR and THz quantum cascade lasers. For these devices, however, metal waveguides already represent the state of the art, and the guiding mechanism in them has far more in common with a ubiquitous transmission line than with plasmonics.

Function of the N-terminal segment of the RecA-dependent nuclease Ref.

The bacteriophage P1 Ref (recombination enhancement function) protein is a RecA-dependent, HNH endonuclease. It can be directed to create targeted double-strand breaks within a displacement loop formed by RecA. The 76 amino acid N-terminal region of Ref is positively charged (25/76 amino acid residues) and inherently unstructured in solution. Our investigation of N-terminal truncation variants shows this region is required for DNA binding, contains a Cys involved in incidental dimerization and is necessary for efficient Ref-mediated DNA cleavage. Specifically, Ref N-terminal truncation variants lacking between 21 and 47 amino acids are more effective RecA-mediated targeting nucleases. We propose a more refined set of options for the Ref-mediated cleavage mechanism, featuring the N-terminal region as an anchor for at least one of the DNA strand cleavage events.

Effect of silicon delta-doping density on optical properties of type-II InAs/GaAsSb quantum dots

We have investigated the optical properties of type-II InAs/GaAs0.83Sb0.17 quantum dots (QDs) with different silicon delta-doping densities of 5×1010, 5×1011, and 2×1012cm−2 using photoluminescence (PL). The PL spectra of the QD ground state (GS) emission peaks for the samples are blueshifted at a slower rate with increasing the doping density due to the enhanced radiative recombination rate of the carriers. The PL intensity ratio of the GS emission to the first excited state emission increases with the doping density, which is indicative of the faster radiative recombination at the GS subbands with the doping density. The redshift rate of the GS emissions becomes faster at a high temperature (>130K) as the doping density increases up to 5×1011cm−2 resulting from the quantum confined Stark effect by the electric field of the ionized dopants, and decreases at an increased doping density of 2×1012cm−2 due to the enhanced QD size uniformity. Time-resolved PL exhibits that the QD sample doped at 5×1010cm−2 has a longer total radiative lifetime than the undoped sample, and a further increase in the doping density to 2×1012cm−2 decreases the lifetime due to the enhancement of the radiative recombination through fast carrier relaxation.

Endonuclease G initiates DNA rearrangements at the MLL breakpoint cluster upon replication stress.

MLL (myeloid/lymphoid or mixed-lineage leukemia) rearrangements are frequent in therapy-related and childhood acute leukemia, and are associated with poor prognosis. The majority of the rearrangements fall within a 7.3-kb MLL breakpoint cluster region (MLLbcr), particularly in a 0.4-kb hotspot at the intron11-exon12 boundary. The underlying mechanisms are poorly understood, though multiple pathways including early apoptotic signaling, accompanied by high-order DNA fragmentation, have been implicated. We introduced the MLLbcr hotspot in an EGFP-based recombination reporter system and demonstrated enhancement of both spontaneous and genotoxic treatment-induced DNA recombination by the MLLbcr in various human cell types. We identified Endonuclease G (EndoG), an apoptotic nuclease, as an essential factor for MLLbcr-specific DNA recombination after induction of replication stress. We provide evidence for replication stress-induced nuclear accumulation of EndoG, DNA binding by EndoG as well as cleavage of the chromosomal MLLbcr locus in a manner requiring EndoG. We demonstrate additional dependency of MLLbcr breakage on ATM signaling to histone H2B monoubiquitinase RNF20, involved in chromatin relaxation. Altogether our findings provide a novel mechanism underlying MLLbcr destabilization in the cells of origin of leukemogenesis, with replication stress-activated, EndoG-mediated cleavage at the MLLbcr, which may serve resolution of the stalled forks via recombination repair, however, also permits MLL rearrangements.

Double-graded bandgap in Cu(In,Ga)Se2 thin film solar cells by low toxicity selenization process

A low-toxic selenization with post gallium diffusion (PGD) treatment has been demonstrated to increase the bandgap in the surface Cu(In,Ga)Se2 (CIGSe) absorbers and to form double-graded bandgap profiles to improve the cell efficiency. The CIGSe absorber with PGD for 5 min increased open-circuit voltage from 0.49 to 0.66 V and efficiency from 9.2% to 13.2%, contributed by the enhancement of carrier recombination in the space-charge region. The reduction in short-circuit current from 30.8 to 29.9 mA/cm2, attributed to the absorption loss in long-wavelength regions, can be potentially improved by further optimization of the minimum bandgap value in gradient valley.

Enhanced specialized transduction using recombineering in Mycobacterium tuberculosis.

ABSTRACTGenetic engineering has contributed greatly to our understanding of Mycobacterium tuberculosis biology and has facilitated antimycobacterial and vaccine development. However, methods to generate M. tuberculosis deletion mutants remain labor-intensive and relatively inefficient. Here, methods are described that significantly enhance the efficiency (greater than 100-fold) of recovering deletion mutants by the expression of mycobacteriophage recombineering functions during the course of infection with specialized transducing phages delivering allelic exchange substrates. This system has been successfully applied to the CDC1551 strain of M. tuberculosis, as well as to a ΔrecD mutant generated in the CDC1551 parental strain. The latter studies were undertaken as there were precedents in both the Escherichia coli literature and mycobacterial literature for enhancement of homologous recombination in strains lacking RecD. In combination, these measures yielded a dramatic increase in the recovery of deletion mutants and are expected to facilitate construction of a comprehensive library of mutants with every nonessential gene of M. tuberculosis deleted. The findings also open up the potential for sophisticated genetic screens, such as synthetic lethal analyses, which have so far not been feasible for the slow-growing mycobacteria.

Monte-Carlo simulations of the radiative recombination of ions with electrons in cold magnetized plasma

We report here on the results of Monte-Carlo simulations of the radiative recombination of highly charged ions with low-energy electrons in the presence of a guiding magnetic field. The simulations are based on a semi-classical geometrical model, recently proposed by our group, which has been developed in order to explain systematic discrepancies, the so-called ‘enhancement effect’, of the radiative recombination rates measured in the guiding magnetic field of electron coolers with respect to theoretical calculations. With the simulations, we demonstrate that the enhancement of radiative recombination rates in the magnetic field could be caused by ‘transverse’ collisions with the impact parameter in the μm range and the impact parameter cut-off value depending on the strength of the guiding B-field in magnetized plasma. In this paper, the methodology of the simulations, the obtained B-field dependence of the radiative recombination enhancement and the observed impact parameter cut-off will be discussed.

Creating targeted double‐stranded breaks in vitro and in vivo using RecA‐dependent endonucleases P1 and φW39 Ref (552.1)

P1 bacteriophage recombination enhancement function (Ref) protein is an HNH class and RecA‐dependent endonuclease. RecA‐bound oligonucleotides homologous to a specific region on circular dsDNA will catalyze RecA strand‐invasion, creating a displacement loop (D‐loop). Upon Ref addition, double‐stranded breaks (DSBs) are created within the D‐loop. Thus, the Ref protein, in concert with RecA, is a programmable endonuclease. The closely related φW39 Ref protein exhibits increased RecA‐dependent endonuclease activity compared to P1 Ref. P1 Ref protein missing the disordered 76 N‐terminus residues is incapable of DNA binding and exhibits decreased nuclease activity, which indicates the importance of the N‐terminal region for these functions. Characterization of N‐terminal truncations based on charge distribution for φW39 Refs ΔN21, ΔN47, ΔN59, ΔN66, and ΔN74 revealed modulated activity for DSB formation and DNA binding. In addition to these in vitro studies, cells transformed with a plasmid containing P1 Ref and introduced to an oligo homologous to a region in the rpsL gene demonstrate recombination events with the oligo. The Ref/RecA/oligo system acts as an oligo‐targeting inducer of DSBs operating both in vitro and in vivo with potential for genome editing functions and in vitro targeting.Grant Funding Source: NIH GM32335

Effects of different doubly excited states on the ionization balance and M-emissivity in high-Z plasmas

2-Electron processes play important roles in the ionization balance both in high and low temperature plasmas, so it is necessary to take into account doubly excited states in the population calculations, either explicitly or implicitly. In order to make clear what kinds of doubly excited states are most important, the effects of three types of doubly excited states on ionization balance and M-emissivity are investigated for gold plasmas within the condition of indirect drive experiments. The present results show that doubly excited states with an inner M-shell electron excited are most important. Omitting such states may decrease the ionization more than 10% and results in more than a magnitude lower M-emissivity. The reason is that including such doubly excited states enhances the ionization significantly while the enhancement in recombination is much weaker for charge states 37–48 when electron temperature is higher than 1.0 keV. We suggest that for gold, at temperature larger than 1.0 keV, M-shell excitation should be taken into account when ion charge is larger than 37. Effects on the ionization balance of the other two types of doubly excited states are not as strong as the one mentioned above, but the largest difference in M-emissivity would be 30% if neglecting one of the two types of doubly excited states with electron density no more than 1021 cm−3. At higher electron density (1022 cm−3), omitting triply excited states may decrease M-emissivity nearly 50% when temperature is around 1.0 keV.

Ultrafast all-optical switching and error-free 10 Gbit/s wavelength conversion in hybrid InP-silicon on insulator nanocavities using surface quantum wells

Ultrafast switching with low energies is demonstrated using InP photonic crystal nanocavities embedding InGaAs surface quantum wells heterogeneously integrated to a silicon on insulator waveguide circuitry. Thanks to the engineered enhancement of surface non radiative recombination of carriers, switching time is obtained to be as fast as 10 ps. These hybrid nanostructures are shown to be capable of achieving systems level performance by demonstrating error free wavelength conversion at 10 Gbit/s with 6 mW switching powers.

RecA-dependent programmable endonuclease Ref cleaves DNA in two distinct steps

The bacteriophage P1 recombination enhancement function (Ref) protein is a RecA-dependent programmable endonuclease. Ref targets displacement loops formed when an oligonucleotide is bound by a RecA filament and invades homologous double-stranded DNA sequences. Mechanistic details of this reaction have been explored, revealing that (i) Ref is nickase, cleaving the two target strands of a displacement loop sequentially, (ii) the two strands are cleaved in a prescribed order, with the paired strand cut first and (iii) the two cleavage events have different requirements. Cutting the paired strand is rapid, does not require RecA-mediated ATP hydrolysis and is promoted even by Ref active site variant H153A. The displaced strand is cleaved much more slowly, requires RecA-mediated ATP hydrolysis and does not occur with Ref H153A. The two cleavage events are also affected differently by solution conditions. We postulate that the second cleavage (displaced strand) is limited by some activity of RecA protein.

Photoluminescence efficiency in AlGaN quantum wells

Photoluminescence spectroscopy of AlGaN/AlGaN multiple quantum wells under quasi-steady-state conditions in the temperature range from 8 to 300K revealed a strong dependence of droop onset threshold on temperature that was explained by the influence of carrier delocalization. The delocalization at room temperature results predominantly in enhancement of bimolecular radiative recombination, while being favorable for enhancement of nonradiative recombination at low temperatures. Studies of stimulated emission confirmed the strong influence of carrier localization on droop.

Mono- and bi-metallic plasmonic photocatalysts for degradation of organic compounds under UV and visible light irradiation

Titania powders were surface modified with gold and/or silver nanoparticles (NPs) by photodeposition method. Gold modified titania exhibited much higher photocatalytic activity during methanol dehydrogenation under UV irradiation than titania modified with monometallic silver and bimetallic Au–Ag NPs. Bimetallic photocatalysts exhibited either enhanced or reduced visible light activity, depending on properties of noble metal NPs, sequence of their deposition on titania, and properties of host titania. Though numerical simulation (3D-FDTD) showed strong plasmonic field enhancement at the interface between titania and bimetallic core(Au)–shell(Ag) NP, it is thought that co-deposition caused an enhancement of charge carriers recombination (by electron sinking in nearby second metal) inhibiting photoactivity under visible light irradiation. The highest level of photoactivity showed large rutile NPs with successively deposited metals, mainly in the form of individual monometallic NPs, due to size/shape polydispersity of deposited NPs, and thus with ability of light absorption in a broad wavelength range.

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