Effective Recombination Rate Research Articles

Band Alignment at Heterointerface with Rapid Charge Transfer Supporting Excellent Photocatalytic Degradation of Methylene Blue under Sunlight

AbstractEngineering 2D heterostructure using proximitized interfaces is an effective approach to attain high efficiency photocatalytic performance toward dye degradation. Strong interfacial interaction and abundant coupled interfaces and 2D/2D face‐to‐face contact heterostructure facilitate efficient charge separation contributing to high photocatalytic activity. In this aspect, for the first time the authors have analyzed the band alignment of the 2D/2D heterojunction, using Perdew–Burke–Ernzerhof semilocal meta‐generalized‐gradient approximation case and Heyd–Scuseria–Ernzerhof hybrid functional approach in density functional theory stimulation. Close proximity of CuSe nanoflakes with carbon nitride sheets facilitate electron transfer process leading to more proficient photocatalytic degradation, which is confirmed from the inverse participation ratio of individual atoms on the proximitized hetero interface and electrostatic potential line‐ups. The results demonstrate that this 2D/2D heterostructure has desired type‐II band alignment, which is facilitating rapid separation of photogenerated carriers in support of experimental findings. The face‐to‐face contact heterostructure with effective separation and low recombination rate of photogenerated electron–hole pairs helps in complete degradation of dye within 15 min. Further, the brilliance in photocatalytic performance of the developed type II heterostructure correlating with experimental results has introduced this system as a new class of material for wastewater treatment.

Advanced photocatalytic degradation of acetaminophen using Cu2O/WO3/TiO2 ternary composite under solar irradiation

Acetaminophen (ATM) is an emerging persistent organic pollutant, which has come to the forefront of environmental issues. Herein, a solar responsive cuprous oxide (Cu2O)/tungsten oxide (WO3)/titanium dioxide (TiO2) ternary composite was successfully synthesized. The prepared composite displayed a 92.50% ATM photodegradation % towards 1 mg.L−1 of ATM under 60 min of solar irradiation, which is about a 12.94% improvement compared to the bare TiO2 particles. The main reason is attributed to the effective separation and low recombination rate of the charge carriers. The produced composite exhibited high reusability photodegradation % with 83.00% at the fifth cycle of ATM photodegradation.

植物交配系统与分子进化理论及其应用研究

<p indent="0mm">With the transition of plant mating system from outcrossing to selfing, both the flower traits and genomic structure develop into selfing syndromes. Here we systematically discussed the theoretical basis and the molecular mechanisms that form these characteristics, and analyzed the basic theory of the interactions between mating system and different evolutionary processes. Selfing results in decrease in the effective population size, mutation rate, recombination rate and selection efficacy, but increase in genetic drift effects and linkage disequilibrium. These theories are effective in explaining the patterns of the relative rate of nonsynonymous to synonymous mutations, the change of the number of transposable elements, the genetic correlation between multigene family members and the pattern of genomic structure. Although molecular markers are often employed to score mating system, studies of mating system and molecular evolution have been mainly in different research fields. Some questions of biological significance could arise from an integration of these two research fields, such as the mode of driving or reinforcing molecular mechanism of speciation that the mating system operates, the different models of molecular evolution between populations of selfing versus outcrossing system, and the distinct genomic structure between populations of the same species with different mating systems. Clarification of these questions aids in our understanding of the role that mating system plays in affecting molecular evolution within and between species.

Domestication Shapes Recombination Patterns in Tomato.

Meiotic recombination is a biological process of key importance in breeding, to generate genetic diversity and develop novel or agronomically relevant haplotypes. In crop tomato, recombination is curtailed as manifested by linkage disequilibrium decay over a longer distance and reduced diversity compared with wild relatives. Here, we compared domesticated and wild populations of tomato and found an overall conserved recombination landscape, with local changes in effective recombination rate in specific genomic regions. We also studied the dynamics of recombination hotspots resulting from domestication and found that loss of such hotspots is associated with selective sweeps, most notably in the pericentromeric heterochromatin. We detected footprints of genetic changes and structural variants, among them associated with transposable elements, linked with hotspot divergence during domestication, likely causing fine-scale alterations to recombination patterns and resulting in linkage drag.

Balancing selection maintains hyper-divergent haplotypes in Caenorhabditis elegans.

Across diverse taxa, selfing species have evolved independently from outcrossing species thousands of times. The transition from outcrossing to selfing significantly decreases the effective population size, effective recombination rate, and heterozygosity within a species. These changes lead to a reduction in genetic diversity, and therefore adaptive potential, by intensifying the effects of random genetic drift and linked selection. Within the nematode genus Caenorhabditis, selfing has evolved at least three times and all three species, including in the model organism Caenorhabditis elegans, show substantially reduced genetic diversity relative to outcrossing species. Selfing and outcrossing Caenorhabditis species are often found in the same niches, but we still do not know how selfing species with limited genetic diversity can adapt to these environments. Here, we examine the whole-genome sequences from 609 wild C. elegans strains isolated worldwide and show that genetic variation is concentrated in punctuated hyper-divergent regions that cover 20% of the C. elegans reference genome. These regions are enriched in environmental response genes that mediate sensory perception, pathogen response, and xenobiotic stress response. Population genomic evidence suggests that genetic diversity in these regions has been maintained by long-term balancing selection. Using long- read genome assemblies for 15 wild strains, we show that hyper-divergent haplotypes contain unique sets of genes and show levels of divergence comparable to levels found between Caenorhabditis species that diverged millions of years ago. These results provide an example for how species can avoid the evolutionary “dead end” associated with selfing.

Genomic divergence landscape in recurrently hybridizing Chironomus sister taxa suggests stable steady state between mutual gene flow and isolation.

Divergence is mostly viewed as a progressive process often initiated by selection targeting individual loci, ultimately resulting in ever increasing genomic isolation due to linkage. However, recent studies show that this process may stall at intermediate stable equilibrium states without achieving complete genomic isolation. We tested the extent of genomic isolation between two recurrently hybridizing nonbiting midge sister taxa, Chironomus riparius and Chironomus piger, by analyzing the divergence landscape. Using a principal component‐based method, we estimated that only about 28.44% of the genomes were mutually isolated, whereas the rest was still exchanged. The divergence landscape was fragmented into isolated regions of on average 30 kb, distributed throughout the genome. Selection and divergence time strongly influenced lengths of isolated regions, whereas local recombination rate only had minor impact. Comparison of divergence time distributions obtained from several coalescence‐simulated divergence scenarios with the observed divergence time estimates in an approximate Bayesian computation framework favored a short and concluded divergence event in the past. Most divergence happened during a short time span about 4.5 million generations ago, followed by a stable equilibrium between mutual gene flow through ongoing hybridization for the larger part of the genome and isolation in some regions due to rapid purifying selection of introgression, supported by high effective population sizes and recombination rates.

Enhanced trap-assisted recombination in organic semiconductors

An analytical model to describe the interaction of excitons and charge transfer states with deep traps is formulated for the case of molecular materials. Here, we have considered the influence of a trap-assisted recombination on this phenomenon. The final expression for the effective recombination rate has been derived from the Shockley–Read–Hall theory and kinetic equations which characterize different photophysical processes. The presented model can be applied in modeling of organic photovoltaic devices.

Quantifying Photon Recycling in Solar Cells and Light-Emitting Diodes: Absorption and Emission Are Always Key.

Photon recycling has received increased attention in recent years following its observation in halide perovskites. It has been shown to lower the effective bimolecular recombination rate and thus increase excitation densities within a material. Here we introduce a general framework to quantify photon recycling which can be applied to any material. We apply our model to idealized solar cells and light-emitting diodes based on halide perovskites. By varying controllable parameters which affect photon recycling, namely, thickness, charge trapping rate, nonideal transmission at interfaces, and absorptance, we quantify the effect of each on photon recycling. In both device types, we demonstrate that maximizing absorption and emission processes remains paramount for optimizing devices, even if this is at the expense of photon recycling. Our results provide new insight into quantifying photon recycling in optoelectronic devices and demonstrate that photon recycling cannot always be seen as a beneficial process.

Hidden genetic variance contributes to increase the short-term adaptive potential of selfing populations.

Standing genetic variation is considered a major contributor to the adaptive potential of species. The low heritable genetic variation observed in self-fertilizing populations has led to the hypothesis that species with this mating system would be less likely to adapt. However, a non-negligible amount of cryptic genetic variation for polygenic traits, accumulated through negative linkage disequilibrium, could prove to be an important source of standing variation in self-fertilizing species. To test this hypothesis, we simulated populations under stabilizing selection subjected to an environmental change. We demonstrate that, when the mutation rate is high (but realistic), selfing populations are better able to store genetic variance than outcrossing populations through genetic associations, notably due to the reduced effective recombination rate associated with predominant selfing. Following an environmental shift, this diversity can be partially remobilized, which increases the additive variance and adaptive potential of predominantly (but not completely) selfing populations. In such conditions, despite initially lower observed genetic variance, selfing populations adapt as readily as outcrossing ones within a few generations. For low mutation rates, purifying selection impedes the storage of diversity through genetic associations, in which case, as previously predicted, the lower genetic variance of selfing populations results in lower adaptability compared to their outcrossing counterparts. The population size and the mutation rate are the main parameters to consider, as they are the best predictors of the amount of stored diversity in selfing populations. Our results and their impact on our knowledge of adaptation under high selfing rates are discussed.

Efficiency improvement of AlGaN-based deep ultraviolet LEDs with gradual Al-composition AlGaN conduction layer

The low internal quantum efficiency (IQE) of AlGaN-based deep ultraviolet light emitting diode (DUV-LED) limits its wider application. The main reasons for low IQE include low carrier concentration, poor carrier location and large defects. The bending of energy band between AlGaN electron blocking layer and conduction layer obstructs transport of holes to multiple quantum wells. In this paper, we propose a gradual Al-composition p-type AlGaN (p-AlGaN) conduction layer to improve the light emitting properties of AlGaN-based DUV-LED. Increased carrier concentration in the active region enhances the effective radiative recombination rate of the LED. Consequently, the IQE of our optimazited DUV-LED is increased by 162% in comparison with conventional DUV-LEDs.

A coarse-graining, ultrametric approach to resolve the phylogeny of prokaryotic strains with frequent homologous recombination

BackgroundA frequent event in the evolution of prokaryotic genomes is homologous recombination, where a foreign DNA stretch replaces a genomic region similar in sequence. Recombination can affect the relative position of two genomes in a phylogenetic reconstruction in two different ways: (i) one genome can recombine with a DNA stretch that is similar to the other genome, thereby reducing their pairwise sequence divergence; (ii) one genome can recombine with a DNA stretch from an outgroup genome, increasing the pairwise divergence. While several recombination-aware phylogenetic algorithms exist, many of these cannot account for both types of recombination; some algorithms can, but do so inefficiently. Moreover, many of them reconstruct the ancestral recombination graph (ARG) to help infer the genome tree, and require that a substantial portion of each genome has not been affected by recombination, a sometimes unrealistic assumption.MethodsHere, we propose a Coarse-Graining approach for Phylogenetic reconstruction (CGP), which is recombination-aware but forgoes ARG reconstruction. It accounts for the tendency of a higher effective recombination rate between genomes with a lower phylogenetic distance. It is applicable even if all genomic regions have experienced substantial amounts of recombination, and can be used on both nucleotide and amino acid sequences. CGP considers the local density of substitutions along pairwise genome alignments, fitting a model to the empirical distribution of substitution density to infer the pairwise coalescent time. Given all pairwise coalescent times, CGP reconstructs an ultrametric tree representing vertical inheritance.ResultsBased on simulations, we show that the proposed approach can reconstruct ultrametric trees with accurate topology, branch lengths, and root positioning. Applied to a set of E. coli strains, the reconstructed trees are most consistent with gene distributions when inferred from amino acid sequences, a data type that cannot be utilized by many alternative approaches.ConclusionsThe CGP algorithm is more accurate than alternative recombination-aware methods for ultrametric phylogenetic reconstructions.

MOFs-derived Cu3P@CoP p-n heterojunction for enhanced photocatalytic hydrogen evolution

In this study, we developed a novel in situ growth scheme to construct the Cu-MOFs@ZIF-9(Co) core-shell precursor material. The Cu-MOFs@ZIF-9(Co) core-shell precursor was treated by low-temperature phosphorization to obtain a Cu3P@CoP composite catalyst with a self-supporting structure. Cu3P@CoP composite catalyst not only had a hierarchical structure, but also built a p-n heterojunction at the interface. The unique structure and composition of Cu3P@CoP could promote charge migration and provide large surface area and rich active sites to drive water photolysis. In addition, by controlling the degree of phosphation of Cu-MOFs@ZIF-9(Co) material and adjusting the ratio of Cu and Co, it was found that the maximum hydrogen-producing activity of the composite photocatalyst reached 469.95 μmol (9399 μmol h−1 g−1), and it had a very excellent cycle stability. The results of photoelectrochemical and fluorescence tests showed that the proper conduction and valence band positions of Cu3P and CoP formed a more effective path way for the thermodynamic charge transfer. The construction of p-n type heterojunction provided a fast electron transfer channel in the Cu-P@Co-P interface. The formed special structrue and the existence of the bult-in electric filed in the p-n heterojunction made the photogenerated carriers in the composite have more effective separation and lower recombination rate, which significantly enhanced H2 production activity. At the same time, our work will provide a new strategy for the rational design of efficient catalysts of MOFs derivatives and a new direction for the design of transition metal phosphide photocatalysts.

Recombination Rate Variation and Infrequent Sex Influence Genetic Diversity in Chlamydomonas reinhardtii.

Recombination confers a major evolutionary advantage by breaking up linkage disequilibrium between harmful and beneficial mutations, thereby facilitating selection. However, in species that are only periodically sexual, such as many microbial eukaryotes, the realized rate of recombination is also affected by the frequency of sex, meaning that infrequent sex can increase the effects of selection at linked sites despite high recombination rates. Despite this, the rate of sex of most facultatively sexual species is unknown. Here, we use genomewide patterns of linkage disequilibrium to infer fine-scale recombination rate variation in the genome of the facultatively sexual green alga Chlamydomonas reinhardtii. We observe recombination rate variation of up to two orders of magnitude and find evidence of recombination hotspots across the genome. Recombination rate is highest flanking genes, consistent with trends observed in other nonmammalian organisms, though intergenic recombination rates vary by intergenic tract length. We also find a positive relationship between nucleotide diversity and physical recombination rate, suggesting a widespread influence of selection at linked sites in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations, estimating a sexual cycle roughly every 840 generations. We argue that the relatively infrequent rate of sex and large effective population size creates a population genetic environment that increases the influence of selection on linked sites across the genome.

Pervasive within-host recombination and epistasis as major determinants of the molecular evolution of the foot-and-mouth disease virus capsid.

Although recombination is known to occur in foot-and-mouth disease virus (FMDV), it is considered only a minor determinant of virus sequence diversity. Analysis at phylogenetic scales shows inter-serotypic recombination events are rare, whereby recombination occurs almost exclusively in non-structural proteins. In this study we have estimated recombination rates within a natural host in an experimental setting. African buffaloes were inoculated with a SAT-1 FMDV strain containing two major viral sub-populations differing in their capsid sequence. This population structure enabled the detection of extensive within-host recombination in the genomic region coding for structural proteins and allowed recombination rates between the two sub-populations to be estimated. Quite surprisingly, the effective recombination rate in VP1 during the acute infection phase turns out to be about 0.1 per base per year, i.e. comparable to the mutation/substitution rate. Using a high-resolution map of effective within-host recombination in the capsid-coding region, we identified a linkage disequilibrium pattern in VP1 that is consistent with a mosaic structure with two main genetic blocks. Positive epistatic interactions between co-evolved variants appear to be present both within and between blocks. These interactions are due to intra-host selection both at the RNA and protein level. Overall our findings show that during FMDV co-infections by closely related strains, capsid-coding genes recombine within the host at a much higher rate than expected, despite the presence of strong constraints dictated by the capsid structure. Although these intra-host results are not immediately translatable to a phylogenetic setting, recombination and epistasis must play a major and so far underappreciated role in the molecular evolution of the virus at all scales.

The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns

Within the siphonous green algal order Bryopsidales, the size and gene arrangement of chloroplast genomes has been examined extensively, while mitochondrial genomes have been mostly overlooked. The recently published mitochondrial genome of Caulerpa lentillifera is large with expanded noncoding DNA, but it remains unclear if this is characteristic of the entire order. Our study aims to evaluate the evolutionary forces shaping organelle genome dynamics in the Bryopsidales based on the C. lentillifera and Ostreobium quekettii mitochondrial genomes. In this study, the mitochondrial genome of O. quekettii was characterised using a combination of long and short read sequencing, and bioinformatic tools for annotation and sequence analyses. We compared the mitochondrial and chloroplast genomes of O. quekettii and C. lentillifera to examine hypotheses related to genome evolution. The O. quekettii mitochondrial genome is the largest green algal mitochondrial genome sequenced (241,739 bp), considerably larger than its chloroplast genome. As with the mtDNA of C. lentillifera, most of this excess size is from the expansion of intergenic DNA and proliferation of introns. Inflated mitochondrial genomes in the Bryopsidales suggest effective population size, recombination and/or mutation rate, influenced by nuclear-encoded proteins, differ between the genomes of mitochondria and chloroplasts, reducing the strength of selection to influence evolution of their mitochondrial genomes.

A simple model of the trap-assisted recombination with the excitonic Auger mechanism

We present a simple model of the trap-assisted recombination combined with the excitonic Auger mechanism. It has been shown that only six independent transitions of electrons and holes should be taken into account to describe a combination of the Shockley–Read–Hall (SRH) recombination with this excitonic process. This is in opposition to a well-known model of the SRH mechanism with the free carriers Auger effect via deep states, where eight separated transitions take place. The derived equation for the effective recombination rate can be useful for modeling the excitonic processes in semiconductors, especially in photovoltaic and optoelectronic devices.

Earth-abundant nontoxic direct band gap semiconductors for photovoltaic applications by ab-initio simulations

Direct band gap semiconductors with high optical absorption, high electrical conductivity, high carrier mobility, low reflectance and low recombination rate of charge carriers are needed for a variety of applications in solar energy conversion and optoelectronics. We have identified three ternary semiconductors Ca3PN, NaBaP and ZrOS which have direct-band gap and other promising properties for solar energy applications. The prime novelty of this work mainly projects a detailed information on the electronic structure and optical properties for the three materials. From the first principles computational work and analysis, we have found that all the three materials with optimum band gap (~1.52 eV) value are having suitable absorption coefficient, extinction coefficient, optical conductivity and low reflectance in the visible region. Moreover, these materials are found to have low charge carrier effective masses and low recombination rates which can enhance carrier mobility and electrical conductivity. As a result, we will have three best non-silicon based direct band gap materials consisting of earth-abundant and non-toxic elements in the photovoltaic (PV) industry.

Effects of surface processes on hydrogen outgassing from metal in desorption experiments

Effects of surface processes on hydrogen outgassing during desorption experiments are investigated using a standard reaction–diffusion model describing hydrogen transport, retention and desorption in material. Three mechanisms for hydrogen migration and desorption on material surface are considered: hydrogen migration from material bulk to material surface (readsorption), hydrogen migration from material surface to material bulk (reabsorption) and hydrogen desorption from material surface by molecular recombination. Three hydrogen outgassing regimes are identified: (i) recombination-limited outgassing when hydrogen recombination and desorption is fast compared to hydrogen reabsorption and slow compared to hydrogen transport from material bulk onto material surface (ii) reabsorption-limited outgassing when hydrogen recombination and desorption is slow compared to hydrogen reabsorption and when the effective hydrogen recombination and desorption is slow compared to hydrogen transport from material bulk onto material surface (iii) bulk-limited outgassing otherwise. Regimes of hydrogen outgassing from tungsten and beryllium are estimated for various experimental conditions. Analytical expressions of the outgassing flux are then derived for each outgassing regime, and used to characterize TDS spectra obtained in thermal desorption spectroscopy (TDS) experiments. It is shown that TDS spectra in recombination-limited regime are skewed toward high temperature, while TDS spectra in reabsorption-limited and bulk-limited regimes are skewed toward low temperature. Furthermore, the temperature of the desorption peak in TDS spectra is shown to decrease in recombination-limited regime and to increase in reabsorption-limited and bulk-limited regimes as the total amount of hydrogen stored in material increases. Finally, it is observed that the effective hydrogen recombination rate measured in reabsorption-limited permeation experiments may be not be reliably used to model and predict hydrogen retention and recycling from tungsten during plasma operations in tokamak.

A whole genome scan of SNP data suggests a lack of abundant hard selective sweeps in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum.

The pathogenic fungus Sclerotinia sclerotiorum infects over 600 species of plant. It is present in numerous environments throughout the world and causes significant damage to many agricultural crops. Fragmentation and lack of gene flow between populations may lead to population sub-structure. Within discrete recombining populations, positive selection may lead to a ‘selective sweep’. This is characterised by an increase in frequency of a favourable allele leading to reduction in genotypic diversity in a localised genomic region due to the phenomenon of genetic hitchhiking. We aimed to assess whether isolates of S. sclerotiorum from around the world formed genotypic clusters associated with geographical origin and to determine whether signatures of population-specific positive selection could be detected. To do this, we sequenced the genomes of 25 isolates of S. sclerotiorum collected from four different continents–Australia, Africa (north and south), Europe and North America (Canada and the northen United States) and conducted SNP based analyses of population structure and selective sweeps. Among the 25 isolates, there was evidence for two major population clusters. One of these consisted of 11 isolates from Canada, the USA and France (population 1), and the other consisted of nine isolates from Australia and one from Morocco (population 2). The rest of the isolates were genotypic outliers. We found that there was evidence of outcrossing in these two populations based on linkage disequilibrium decay. However, only a single candidate selective sweep was observed, and it was present in population 2. This sweep was close to a Major Facilitator Superfamily transporter gene, and we speculate that this gene may have a role in nutrient uptake from the host. The low abundance of selective sweeps in the S. sclerotiorum genome contrasts the numerous examples in the genomes of other fungal pathogens. This may be a result of its slow rate of evolution and low effective recombination rate due to self-fertilisation and vegetative reproduction.

Efficient Visible‐Light‐Driven Hydrogen Generation on g‐C3N4 Coupled with Iron Phosphide

AbstractTransition metal phosphides as promising noble metal free cocatalysts are gaining increasing interest for hydrogen generation and other energy conversion reactions. The present study reports a new Fe2P/g‐C3N4 hybrid for efficient photocatalytic hydrogen generation by water splitting under visible light irradiation. The H2 production rate obtained using this system is approximately 15 times higher than that obtained using pure g‐C3N4, and is comparable with that of Pt/g‐C3N4 under the same conditions. According to detailed studies using UV/Vis diffuse reflectance and photoluminescence spectroscopies as well as photoelectrochemical measurements, the reason for the high efficiency of the Fe2P/g‐C3N4 hybrid is due to a highly effective separation and low recombination rate of photogenerated electrons and holes rather than absorption under visible light. The present study reports a promising non‐toxic photocatalyst with low cost and high natural abundance for improving photocatalytic H2 generation.