Mechanism that dictates pore width and <111>a pore propagation in InP

We report a mechanism for pore growth and propagation based on a three-step charge transfer model. The study is supported by electron microscopy analysis of highly doped n-InP samples anodised in aqueous KOH. The model and experimental data are used to explain propagation of pores of characteristic diameter preferentially along the A directions. We also show evidence for deviation of pore growth from the A directions and explain why such deviations should occur. The model is self-consistent and predicts how carrier concentration affects the internal dimensions of the porous structures

Preferential <111>A pore propagation mechanism in n-InP anodized in KOH

This paper describes the formation of pores during the anodization of n-InP in aqueous KOH. The pores propagate preferentially along the A crystallographic directions and form truncated tetrahedral domains. A model is presented that explains preferential A pore propagation and the uniform diameters of pores. The model outlines how pores can deviate from the A directions and from their characteristic diameters. It also details the effect of variation of carrier concentration on the dimensions of the porous structures

Propagation of nanopores during anodic etching of n-InP in KOH

We propose a three-step model of electrochemical nanopore formation in n-InP in KOH that explains how crystallographically oriented etching can occur even though the rate-determining process (hole generation) occurs only at pore tips. The model shows that competition in kinetics between hole diffusion and electrochemical reaction determines the average diffusion distance of holes along the semiconductor surface and this, in turn, determines whether etching is crystallographic. If the kinetics of reaction are slow relative to diffusion, etching can occur at preferred crystallographic sites within a zone in the vicinity of the pore tip, leading to pore propagation in preferential directions. Symmetrical etching of three {111}A faces forming the pore tip causes it to propagate in the (remaining) 〈111〉A direction. As a pore etches, propagating atomic ledges can meet to form sites that can become new pore tips and this enables branching of pores along any of the 〈111〉A directions. The model explains the observed uniform width of pores and its variation with temperature, carrier concentration and electrolyte concentration. It also explains pore wall thickness, and deviations of pore propagation from the 〈111〉A directions. We believe that the model is generally applicable to electrochemical pore formation in III–V semiconductors

Pore propagation directions and nanoporous domain shape in n-InP anodized in KOH

Pore propagation during anodization of (100) n-InP electrodes in aqueous KOH was studied in detail by scanning and transmission electron microscopy (SEM and TEM). Pores emanating from surface pits propagate along the 〈111〉A crystallographic directions to form, in the early stages of anodization, porous domains with the shape of a tetrahedron truncated symmetrically through its center by a plane parallel to the surface of the electrode. This was confirmed by comparing the predictions of a detailed model of pore propagation with SEM and TEM observations. The model showed in detail how 〈111〉A pore propagation leads to domains with the shape of a tetrahedron truncated by a (100) plane. Observed cross sections corresponded in detail and with good precision to those predicted by the model. SEM and TEM showed that cross sections were trapezoidal and triangular, respectively, in the two cleavage planes of the wafer, and TEM showed that they were rectangular parallel to the surface plane, as predicted. Aspect ratios and angles calculated from observed cross sections were in good agreement with predicted values. The pore patterns observed were also in good agreement with those predicted and SEM observations of the surface further confirmed details of the model

Process of formation of porous layers in n-InP

This paper describes variations in current density observed in linear sweep voltammetry curves during the anodization of n-InP in aqueous KOH electrolyte and how these variations arise. The analysis is performed by stopping the anodization after different durations of etching and observing via scanning electron microscopy and other techniques the porous structures that have formed. A mathematical model for the expansion and merging of domains of pores that propagate preferentially along the A directions is also presented and used to explain the previously mentioned variations in current density

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism