H3 Sites Research Articles

Histone Acetyltransferase GCN5 Regulates Rice Growth and Development and Enhances Salt Tolerance

Histone acetylation, is indispensable in the process of crops resisting abiotic stress, which is jointly catalyzed by histone acetyltransferase and deacetylase. However, the mechanism of regulating salt tolerance through histone acetyltransferase GCN5 is still unclear. We reveal that OsGCN5 can catalyze the acetylation of canonical H3 and H4 lysine sites in vivo and in vitro in rice. The knockout mutants and RNAi lines of OsGCN5 exhibited severe growth inhibition and defects in salt tolerance, while the overexpression of OsGCN5 enhanced the salt tolerance of rice seedlings, indicating that OsGCN5 positively regulates the response process of rice to salt stress. The RNA-seq analysis suggest OsGCN5 may positively regulate the salt tolerance of rice by inhibiting the expression of OsHKT2;1, or other salt-responsive genes. Taken together, our study indicates that GCN5 plays a key role in the preservation of salt tolerance in rice.

Quantitative Pattern of hPTMs by Mass Spectrometry-Based Proteomics with Implications for Triple-Negative Breast Cancer.

Triple-negative breast cancer (TNBC) is known for its aggressive nature, and TNBC management is currently challenging due to the lack of effective targets. Despite the importance of histone post-translational modifications (hPTMs) in breast cancer, their associations with molecular subtypes of breast cancer, especially TNBC, are poorly understood. In this study, a combination of untargeted and targeted proteomics approaches, supplemented by a derivatization method, was applied to breast cancer cells and tissue samples. Untargeted proteomics of eight breast cancer cell lines belonging to different molecular subtypes revealed 36 modified peptides with 12 lysine modification sites in histone H3, and the most frequently reported top 5 histone H3 methylation and acetylation sites were covered. Then, targeted proteomics was carried out to quantify the total 20 target hPTMs at the covered modification sites (i.e., mono-, di-, trimethylation, and acetylation for each site), indicating the difficulty in distinguishing TNBC cells from normal cells. Subsequently, the analysis in TNBC patients revealed significant expression differences in 4 specific hPTMs (H3K14ac, H3K27me1, H3K36me2, and H3K36me3) between TNBC and adjacent normal tissue samples. These unique hPTM patterns allowed for the differentiation of TNBC from normal cases. This finding provides promising implications for advancing targeted treatment strategies for TNBC in the future.

Spin Coupling in the Initial Stages of the Zinc‐Blende MnN Growth on the CrN (111) Surface

AbstractSpin‐polarized first‐principles calculations are carried out to study the structural, electronic, and magnetic properties of the MnN growth on the CrN (111) surface. Different magnetic configurations between Mn‐deposited atoms and the substrate are considered. The H3 site is the most favorable site for the adoption and incorporation cases and the Mn spins switch from paramagnetic to antiferromagnetic arrangement. The minimum energy pathway for the Mn diffusion is calculated, showing magnetic modifications in the substrate. A structural transition from tetragonal rock‐salt to zinc‐blende (ZB) structure as the number of MnN deposited layers increases is noticed. Thermodynamic analysis demonstrates that the growth of MnN on CrN is feasible. The density of states for an MnN layer with an extra nitrogen layer shows a half‐metallic behavior and the remaining structures exhibit a metallic character. The ZB‐MnN structures have an antiferromagnetic behavior with a metallic character. Magnetic anisotropy energies reveal a switching of easy magnetization axis, from in‐plane to out‐of‐plane with the formation of MnN on the surface. These results suggest that the CrN/ZB‐MnN system may be employed in antiferromagnetic spintronics applications as the fabrication of perpendicular magnetic tunnel junctions.

Elucidation of the CadA Protein 3D Structure and Affinity for Metals.

The mitigation of cadmium (Cd) pollution, a significant ecological threat, is of paramount importance. Pseudomonas aeruginosa harbors 2 Cd resistance genes, namely, cadR and cadA. Presently, our focus is on the identification and characterization of the cation-transporting P-type ATPase (cadA) in Pseudomonas aeruginosa BC15 through in silico methods. The CadA protein and its binding capacities remain poorly understood, with no available structural elucidation. The presence of the cadA gene in P aeruginosa was confirmed, showing a striking 99% sequence similarity with both P aeruginosa and P putida. Phylogenetic analysis unveiled the evolutionary relationship between CadA protein sequences from various Pseudomonas species. Physicochemical analysis demonstrated the stability of CadA, revealing a composition of 690 amino acids, a molecular weight of 73 352.85, and a predicted isoelectric point (PI) of 5.39. Swiss-Model homology modelling unveiled a 33.73% sequence homology with CopA (3J09), and the projected structure indicated that 89.3% of amino acid residues were situated favourably within the Ramachandran plot, signifying energetic stability. Notably, the study identified metal-binding sites in CadA, namely, H3, C30, C32, C35, H48, C89, and C106. Docking studies revealed a higher efficiency of Cd binding with CadA compared to other heavy metals. This underscores the crucial role of N-terminal cysteine residues in Cd removal. It is evident that CadA of P aeruginosa BC15 plays a crucial role in Cd tolerance, rendering it a potential microorganism for Cd toxicity bioremediation. The structural and functional elucidation of CadA, facilitated by this study, holds promise for advancing cost-effective strategies in the remediation of cadmium-contaminated environments.

Effects of chemisorption impurities on hydrogen diffusion mechanism from Pd(100) surface into subsurface

The impurities exhibit a remarkable impact on adsorption, absorption, and diffusion behavior of hydrogen on catalyst surface, and prompt an essential ongoing challenge on security and development strategy in hydrogen production, separation, purification, and utilization. Given this, S and CO impurities accompanied with or without atomic hydrogen, i.e. S, S + H, CO, and CO + H, were focused to discreetly elucidate their influences on microscopic mechanism for hydrogen travelling into Pd(100) subsurface in terms of spatial orientations and distinct coverages. All viable minimum energy pathways were thoroughly explored by climbing image nudged elastic band method, in which substrate relaxation and reconstruction effects were considered. Quantum results manifest that S or CO overwhelmingly changes structural and electrical properties of metal surface, and thus facilitates hydrogen diffusion, except for ones on H3 site at 0.25 ML coverage. Whereas, H in both S + H and CO + H shows inhibition effect by increasing barrier and blocking active surface site.

Structural Basis of Sirtuin 6-Catalyzed Nucleosome Deacetylation.

The reversible acetylation of histone lysine residues is controlled by the action of acetyltransferases and deacetylases (HDACs), which regulate chromatin structure and gene expression. The sirtuins are a family of NAD-dependent HDAC enzymes, and one member, sirtuin 6 (Sirt6), influences DNA repair, transcription, and aging. Here, we demonstrate that Sirt6 is efficient at deacetylating several histone H3 acetylation sites, including its canonical site Lys9, in the context of nucleosomes but not free acetylated histone H3 protein substrates. By installing a chemical warhead at the Lys9 position of histone H3, we trap a catalytically poised Sirt6 in complex with a nucleosome and employ this in cryo-EM structural analysis. The structure of Sirt6 bound to a nucleosome reveals extensive interactions between distinct segments of Sirt6 and the H2A/H2B acidic patch and nucleosomal DNA, which accounts for the rapid deacetylation of nucleosomal H3 sites and the disfavoring of histone H2B acetylation sites. These findings provide a new framework for understanding how HDACs target and regulate chromatin.

Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl.

Avian influenza A virus (AIV) is ubiquitous in waterfowl and is detected annually at high prevalence in waterfowl during the Northern Hemisphere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at a high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002–9) from mallards (Anas platyrhynchos) sampled in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into three distinct lineages, structured by year of isolation. Specifically, across the 8 years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigenic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly amplify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2–3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.

Understanding the catalytic abilities of class IV sirtuin OsSRT1 and its linkage to the DNA repair system under stress conditions

The roles of sirtuins in plants are slowly unraveling. Regarding OsSRT1, there are only reports of its H3K9Ac deacetylation. Here we detect the other lysine deacetylation sites in histones, H3 and H4. Further, our studies shed light on its dual enzyme capability with preference for mono ADP ribosylation over deacetylation. OsSRT1 can specifically transfer the single ADP ribose group on its substrates in an enzymatic manner. This mono ADPr effect is not well known in plants, more so for deacetylases. The products of this reaction (NAM and ADP ribose) have a negative effect on this enzyme’s action suggesting a tighter regulation. Resveratrol, a natural plant polyphenol proves to be a good activator of this enzyme at 150 ± 40 µM concentration. Under different abiotic stress conditions, we could link this ADP ribosylase activity to the DNA damage repair (DDR) pathway by activating the enzyme PARP1. There is also evidence of OsSRT1′s interaction with the components of DDR machinery. Changes in the extent of different histone deacetylation by OsSRT1 is also related with these stress conditions. Metal stress in plants also influences these enzyme activities. Structurally there is a long C-terminal domain in OsSRT1 in comparison to other classes of plant sirtuins, which is required for its catalysis.

Distinct Histone Post-translational Modifications during Plasmodium falciparum Gametocyte Development.

Histones are the building units of nucleosomes, which constitute chromatin. Histone post-translational modifications (PTMs) play an essential role in epigenetic gene regulation. The Plasmodium falciparum genome encodes canonical and variant histones and a collection of conserved enzymes for histone PTMs and chromatin remodeling. Herein, we profiled the P. falciparum histone PTMs during the development of gametocytes, the obligatory stage for parasite transmission. Mass spectrometric analysis of histones extracted from the early, middle, and late stages of gametocytes identified 457 unique histone peptides with 90 PTMs, of which 50% were novel. The gametocyte histone PTMs display distinct patterns from asexual stages, with many new methylation sites in histones H3 and H3.3 (e.g., K14, K18, and K37). Quantitative analyses revealed a high abundance of acetylation in H3 and H4, mono-methylation of H3/H3.3 K37, and ubiquitination of H3BK112, suggesting that these PTMs play critical roles in gametocytes. Gametocyte histones also showed extensive and unique combinations of PTMs. These data indicate that the parasite harbors distinct transcription regulation mechanisms during gametocyte development and lay the foundation for further characterization of epigenetic regulation in the life cycle of the malaria parasite.

Incorporation of a histone mutant with H3K56 site substitution perturbs the replication machinery in mouse embryonic stem cells.

Sense mutations in several conserved modifiable sites of histone H3 have been found to be strongly correlated with multiple tissue-specific clinical cancers. These clinical site mutants acquire a distinctively new epigenetic role and mediate cancer evolution. In this study, we mimicked histone H3 at the 56th lysine (H3K56) mutant incorporation in mouse embryonic stem cells (mESCs) by lentivirus-mediated ectopic expression and analyzed the effects on replication and epigenetic regulation. The data show that two types of H3K56 mutants, namely H3 lysine 56-to-methionine (H3K56M) and H3 lysine 56-to-alanine (H3K56A), promote replication by recruiting more minichromosome maintenance complex component 3 and checkpoint kinase 1 onto chromatin compared with wild-type histone H3 and other site substitution mutants. Under this condition, the frequency of genomic copy number gain in H3K56M and H3K56A cells globally increases, especially in the Mycl1 region, a known molecular marker frequently occurring in multiple malignant cancers. Additionally, we found the disruption of H3K56 acetylation distribution in the copy-gain regions, which indicates a probable epigenetic mechanism of H3K56M and H3K56A. We then identified that H3K56M and H3K56A can trigger a potential adaptation to transcription; genes involved in the mitogen-activated protein kinase pathway are partially upregulated, whereas genes associated with intrinsic apoptotic function show obvious downregulation. The final outcome of ectopic H3K56M and H3K56A incorporation in mESCs is an enhanced ability to form carcinomas. This work indicates that H3K56 site conservation and proper modification play important roles in harmonizing the function of the replication machinery in mESCs.

First principles study of IIIA atoms adsorbed on ZnO (0001) surface and the applications in optoelectronic devices

First principles method is used to study the adsorption behavior, formation energy and electronic structure of IIIA (B, Al, Ga, In) atoms adsorbed on Top, T4 and H3 sites of ZnO (0001) surface. The date shows that the formation energy of B, Al, Ga and In atoms adsorbed on Top site is highest, then followed by T4 site, and H3 is a more stable adsorption site. With the periodic increase of B, Al, Ga and In atoms, the formation energy of corresponding models decreases gradually, and the binding ability with O atoms also decreases gradually. The electronic structure of ZnO (0001) surface is sensitive to the adsorption sites. When these atoms are adsorbed on Top sites, the electronic structures of B-Top, Al-Top, Ga-Top and In-Top models have a little change compared with ZnO (0001) surface. However, when these atoms are adsorbed on T4 and H3 sites, the impurity states appear on the VBM, which narrowing the band gap of the corresponding models.

Oxygen Coverage Effect on the Magnetic Properties of the Cr2NOx (0 ≤ x ≤ 2) MXene

Using DFT calculations, we investigated the structural, electronic, and magnetic properties of the Cr2N MXene functionalized with different oxygen concentrations. Our calculations show that pristine Cr2N shows an antiferromagnetic (AFM) behavior; also, according to the density of states, the MXene is metallic, in agreement with previous reports. We study the changes in the magnetic and electronic properties of the functionalized Cr2NOx MXene with 1 < x ≤ 2; in all cases, O occupies the H3 site; in the range 0.25 < x ≤ 0.75, the system acquires half-metallic properties with ferrimagnetic alignments. In the range 1 < x ≤ 1.75, the MXene returns to be metallic; also, the FiM characteristic remains. Finally, for full oxygen coverage, the functionalized MXene switches to the ferromagnetic state with half-metallic properties, which match with the results previously reported by Wang and Kumar et al. Pristine CrN exhibits an energy difference of ∼1.5 eV between AFM and FM, and this energy difference starts to decrease as the oxygen concentration increases. For the Cr2NO MXene, the difference is ∼0.75 eV, and for a fully oxidized MXene, the most stable configuration is FM. Our results suggest that the AFM to FM transition is a gradual process, where the oxygen concentration plays an essential role in the magnetic properties of the MXene. Our calculations demonstrate that the Cr2NOx MXene at different oxygen coverages is suitable for spintronic applications as by varying the oxygen coverages, we can modulate the spin polarization around the Fermi level.

A new family of copper-based MXenes

In this work, we demonstrate, through first-principles calculations, the existence of a new family of copper-based MXenes. These add up new structures to the previously reported universe and span the interest of such 2D materials for applications in heterogeneous catalysis, ion-based batteries, sensors, biomedical applications, and so on. First, we propose the MXene-like structures: Cu2N, Cu2C, and Cu2O. Phonon spectra calculations confirmed their dynamical stability by showing just positive frequencies all through the 2D Brillouin zone. The new MXenes family displays metallic characteristics, mainly induced by the Cu-3d orbitals. Bader charge analysis and charge density differences depict bonds with ionic character in which Cu is positively charged, and the non-metal atom gets an anionic character. Also, we investigate the functionalization of the proposed structures with Cl, F, O, and OH groups. Results show that the H3 site is the most favorable for functionalization. In all cases, the non-magnetic nature and metallic properties of the pristine MXenes remain. Our results lay the foundations for the experimental realization of a new MXenes family.

Density functional theory study on surface adsorptions in AlN metalorganic vapor phase epitaxy process

By the density functional theory (DFT) study, the adsorptions of the main surface precursors, MMAl and DMAlNH2, on the ideal and NH2-covered AlN(0001)-Al surfaces were investigated for AlN MOVPE process. By comparing the adsorption energies, the Mulliken Populations and the partial density of states (PDOS) for adsorbed atoms at different surface sites, it is found that on the ideal AlN surface, MMAl can be stably adsorbed at T4, H3 or Br sites with similar probabilities; DMAlNH2 can be stably adsorbed at Top-Top or 3Top sites, with dissociative adsorption occurring at the latter site. On the NH2-covered surface, MMAl can be stably adsorbed at T4 and H3 sites with similar probabilities; while DMAlNH2 can be stably adsorbed at only Top site. On the Al-terminated ideal AlN surface, the adsorption of DMAlNH2 is more stable than that of MMAl; while on the N-terminated (NH2-covered) AlN surface, the adsorption of MMAl is much more stable than that of DMAlNH2.

Theoretical investigation of the AlN (0 0 0 1)-(2 × 2) surface doped with nickel: Structural, electronic and magnetic properties

Structural, electronic and magnetic properties of the nickel doped AlN (0 0 0 1)-(2 × 2) surfaces are investigated by spin-polarized first-principle total-energy calculations. The exchange–correlation potential energies are treated within the generalized gradient approximation (GGA) with the Perdew, Burke and Enzernof (PBE) functional. Electron-ion interactions are dealt with the pseudopotential approach. According to results the H3 site is the most favorable structure in the adsorption of Ni at different coverage from ¼ to 1 monolayer (ML). When coverage is in the range from ½ to 1 ML, we found ferromagnetic (FM) behavior as a consequence of the Ni presence with magnetic moment (>0.7 μB/atom). Also, we found the formation of dimers, trimers and atomic chains in the ½, ¾ and 1ML coverage, respectively. The minimum energy pathways in the Ni adsorption and incorporation show activation energies of 1.53 and 1.26 eV, respectively. The deposit of Ni into substitutional sites suggests the possibility of growing NiN epitaxially. We employed the surface formation energy formalism to investigate the different structures stability. Results indicate that the Ni doping is favorable under Ni-rich conditions in all the range of chemical potential ΔμAlN, finding four AlN surfaces with different magnetic properties: the 1Ni ads and 4Ni subs models are non-magnetic, however the 1Ni subs model is FM and the 2Ni subs model is antiferromagnetic (AFM) with magnetic moments of the order of 0.8 μB/atom. Therefore, we can conclude that high concentrations of Ni induce a non-magnetic behavior, and low concentrations favor the magnetic properties, provided that the Ni atoms occupy substitutional sites. The density of states shows that only the 1st ML of surfaces is metallic, in contrast layers beneath the first layer are semiconductor, where the valence and conductions bands are mainly formed by the N-p and Al-p orbitals, respectively.

Synergetic effects of metals in graphyne 2D carbon structure for high promotion of CO2 capturing

Structural and electronic properties of co-decorated graphyne (GY) by Sc and Cr atoms toward CO2 capture are investigated by DFT-D3 method. First, different configurations of Sc-Cr co-decorated GY (SCGY) are considered to find the best site and side of GY for SC and Cr atoms and structural, magnetic, and electronic properties of them are investigated. Then, the adsorption behavior of the best configurations toward CO2 capture is followed. Results show that in single Sc or Cr decorated GY, the best site for metals is the center of the 12-membered ring (H1) and Eads are −4.856 and −2.414 eV, respectively. In SCGY, the best site for Cr and Sc are H1 and H3 sites, but they lie in the opposite sides and Eads improves about 0.505 eV. In brief, Edas of CO2 for pristine GY (PGY), Sc-GY, Cr-GY, Sc-Cr-GY, Sc-Sc-GY, and Cr-Cr-GY are about −0.242, −0.717, −1.502, −0.795, −2.970 and −1.754 eV, respectively. Increasing of Eads due to the insertion of one or two metal atoms for some systems is about 3 to 12 times more than PGY, surprisingly. The best system can capture up to 19 CO2 molecules with Eads- of −0.516 eV/CO2 that is CO2 storage capacity of 55.66 wt%. These results show that co-decorated GYs with various metals, due to having synergistic effects, can be used as promising candidates for the CO2 capture, storage, detection, and removal applications in the future.

Ab initio and thermodynamic picture of Al adsorption of AlN(0001) surface – Role of bond creation and electron transition contributions

The role of bond creation and electron transition contribution were investigated in thermodynamic picture of adsorption obtained from intensive ab initio density functional theory (DFT) calculations. It was shown that electron transitions may reduce the overall energy gain from Al adsorption at AlN(0001) surface by 50%. Accordingly properties of AlN polar N-terminated AlN(0001) surface such as crystallographic structure, the type and energy of the surface states, the band profiles close to the surface were obtained. At the clean surface Al is adsorbed with the energy gain of 9.6 eV at H3 site creating bonds using two Al3p states by the overlap with the neighboring surface N atoms. The excess electrons are transferred to surface N broken bond states. At the critical coverage θAl-cr=14ML all these states are occupied, therefore for higher Al coverage the electrons are transferred to Al3pz states. As their energy is higher by 2.5 eV, the adsorption energy gain is dropped to 4.089 eV, i.e. about 50%. For higher coverage Al adatoms are shifted to bridge and on-top configurations reducing the electron transfer and increasing energy gain by 2.5 eV for full coverage of Al adatoms located in the on-top positions. The temperature dependent pressure-coverage diagram was obtained showing the two stable regions. The first, up to 0.25 ML Al (θAl≤14ML) with Al adatoms located in H3 positions, correspond to extremely low Al pressure, below 10−13 bar at 2500 K. The second region, at pAl>2.18×10-5bar, is stable for high coverage, i.e. for θAl>0.999ML (at 2500 K) with Al adatoms located in the on-top positions. For the pressures between, i.e. 1.80×10-12bar<pAl<2.18×10-5bar, nonuniform coverage is stable, composed to these two phases. Finally at the coverage close to 1 ML, Langmuir entropic singularity in chemical potential was detected, corresponding to dramatic increase of the pressure over single Al layer which leads to transition to multiple Al layers and bulk Al.

Quantum chemical study of the Co-adsorption of NH3 and MMAl on ideal AlN(0 0 0 1)-Al surfaces

By employing the density functional theory, the co-adsorption of surface reaction precursors NH3 and MMAl on ideal AlN(0 0 0 1)-Al surfaces was investigated during the growth of AlN MOVPE. The adsorption mechanism of the particles on the surface was determined by analyzing the adsorption energy, molecular interaction energy, population of chemical bonds, and partial density of states. The study found that when comparing the co-adsorption reactions of NH3 and MMAl at different adsorption positions with an individual adsorption of particles on the surface: ① the co-adsorption and single adsorption of NH3 and MMA on the surface concluded similarly, that is, the stable adsorption of NH3 was at the Top site; while the stable adsorption of MMAl was at the T4 and H3 sites, but the co-adsorption structure was more stable. ② A chemical reaction took place between NH3, MMAl and the surface atoms with the reaction equation: 3Al(s) + NH3(ads) + AlCH3(ads) → Al(s)–NH2(ads)-Al(ads)-2Al(s) + CH4. Here, Al in MMAl was adsorbed on the Br site, and the N in NH3 was adsorbed on the Top site.

Estabilidad estructural y electrónica para la adsorción de Nb sobre la superficie polar del AlN

&#x0D; &#x0D; &#x0D; &#x0D; Se reportan cálculos de primeros principios con el fin de analizar la adsorción y la difusión de un átomo de Nb en la superficie AlN (0001) con una geometría 2 × 2, la cual se construye con el modelo de supercelda. En los cálculos se resuelven las ecuaciones de Konh-Sham con una base de ondas planas y pseudopontenciales atómicos, para lo cual se utiliza la aproximación del gradiente generalizado (GGA) para describir la interacción electrón-electrón, dentro del marco de la teoría del funcional de la densidad (DFT). Con el propósito de estudiar el modelo de adsorción más favorable, se consideran los sitios de alta simetría T1, T4 y H3. Se encuentra que las estructuras energéticamente más favorables corresponden a la de un átomo de Nb localizado en los sitos H3 y T4, mientras que la adsorción del Nb sobre un átomo de aluminio (sitio T1) es desfavorable. La difusión del Nb sobre la superficie muestra una energía de activación de 0.453 eV de T4 hacia H3. Los resultados de las reconstrucciones adsorbato-superficie en los diferentes puntos de alta simetría presentan una relajación lateral de unas centésimas de angstrom con relación a su configuración más estable. Finalmente, se comparan la densidad de estados de la superficie limpia AlN(0001) y las reconstrucciones que presentan mayor favorabilidad energética.&#x0D; &#x0D; &#x0D; &#x0D;

Study on the initial growth mechanism of (ZnO)1−x(InN)x using first-principles calculation

We investigated the initial growth mechanism of a novel complex semiconductor alloy, (ZnO)1-x(InN)x (=ZION) theoretically using first-principles calculation. We evaluated the adsorption energies of adatoms on the ZnO substrate with several adsorption patterns. It was found that the most favorable first step in the growth is that an In atom is adsorbed on the H3 site of an O-polar ZnO(0001) substrate, although the H3 site is not a proper site for epitaxial growth. We also calculated self-surfactant energies that cause the adsorbed In atom to migrate to a top site. It is revealed that the migration will be caused by a concurrent adsorption of O and N atoms on the nearest neighbor sites of the H3 site. We conclude that these processes will promote the epitaxial growth of ZION.