Atom-by-Atom and Sheet-by-Sheet Chemical Mechanical Polishing of Diamond Assisted by OH Radicals: A Tight-Binding Quantum Chemical Molecular Dynamics Simulation Study.

Ultraflat and damage-free single-crystal diamond is a promising material for use in electronic devices such as field-effect transistors. Diamond surfaces are conventionally prepared by the chemical mechanical polishing (CMP) method, although the CMP efficiency remains a critical issue owing to the extremely high hardness of diamond. Recently, OH radicals have been demonstrated to be potentially useful for improving the CMP efficiency for diamond; however, the underlying mechanisms are still elusive. In this work, we applied our previously developed CMP-specialized tight-binding quantum chemical molecular dynamics simulator to comprehensively elucidate the CMP mechanisms of diamond assisted by OH radicals. Our simulation results indicate that the diamond surface is oxidized by reactions with OH radicals and then a concomitant surface reconstruction takes place due to the distorted and unstable nature of the oxidized diamond surface structure. Furthermore, we interestingly reveal that the reconstruction of the diamond surface ultimately leads to two distinct removal mechanisms: (i) gradual atom-by-atom removal through the desorption of gaseous molecules (e.g., CO2 and H2CO3) and (ii) drastic sheet-by-sheet removal through the exfoliation of graphitic ring structures. Hence, we propose that promoting the oxidation-induced graphitization of the diamond surface may provide a route to further improving the CMP efficiency.

Cooperative roles of chemical reactions and mechanical friction in chemical mechanical polishing of gallium nitride assisted by OH radicals: tight-binding quantum chemical molecular dynamics simulations.

Chemical mechanical polishing (CMP) is a key manufacturing process for applying gallium nitride (GaN), especially the Ga-face GaN, to semiconductor devices such as laser diodes. However, the CMP efficiency for GaN is very low due to its high hardness and chemical stability. Experimentally, OH radicals appear able to improve the CMP efficiency of GaN polished by a SiO2 abrasive grain, whereas the mechanisms of the OH-radical-assisted CMP process remain unclear because experimental elucidation of the complex chemical reactions occurring among GaN substrate, abrasive grain, and OH radicals is difficult. In this work, we used our previously developed tight-binding quantum chemical molecular dynamics simulator to study the OH-radical-assisted CMP process of the widely employed Ga-face GaN substrate polished by an amorphous SiO2 abrasive grain in an effort to understand how OH radicals assist the CMP process and then aid the development of next-generation CMP techniques. Our simulations revealed that the OH-radical-assisted CMP process of GaN occurs via the following three basic reaction steps: (i) first, all hydrogen terminations on the GaN surface are replaced by OH terminations through continuous reactions with OH radicals; (ii) after the substrate is fully terminated by OH, the hydrogen atoms of these OH terminations are removed by reacting with newly added OH radicals, which forms H2O molecules and leaves energetic oxygen atoms with dangling bonds on the surface; and (iii) finally, these energetic oxygen atoms intrude inside the substrate with concomitant dissociation of Ga-N bonds and the generation of N2 and gallium hydroxide molecules, which accumulatively lead to the removal of N and Ga atoms from the substrate.

Pulmonary Hyalinizing Granuloma Mimicking Primary Lung Cancer.

We herein report a case of pulmonary hyalinizing granuloma (PHG), which is a rare pulmonary mass. A 69-year-old man with no symptoms presented to our hospital because of the appearance of an abnormal shadow on chest X-ray. Computed tomography revealed a right middle-lobe mass with spicula and infiltration into the upper lobe. Since a bronchofiberscopic examination showed no malignant cells in the specimen, the patient underwent thoracoscopic surgery, which revealed PHG. Spiculation and interlobar infiltration, which comprise the characteristic features of primary lung cancer, are uncommon presentations of this rare entity.

Diagnosis of cystic fibrosis in an adult Japanese male.

Chest computed tomography image of a 23-year-old man. Image shows right-sided middle and lower lobe consolidation and multiple cystic bronchiectasis.

Atomistic Mechanisms of Chemical Mechanical Polishing of a Cu Surface in Aqueous H2O2: Tight-Binding Quantum Chemical Molecular Dynamics Simulations.

We applied our original chemical mechanical polishing (CMP) simulator based on the tight-binding quantum chemical molecular dynamics (TB-QCMD) method to clarify the atomistic mechanism of CMP processes on a Cu(111) surface polished with a SiO2 abrasive grain in aqueous H2O2. We reveal that the oxidation of the Cu(111) surface mechanically induced at the friction interface is a key process in CMP. In aqueous H2O2, in the first step, OH groups and O atoms adsorbed on a nascent Cu surface are generated by the chemical reactions of H2O2 molecules. In the second step, at the friction interface between the Cu surface and the abrasive grain, the surface-adsorbed O atom intrudes into the Cu bulk and dissociates the Cu-Cu bonds. The dissociation of the Cu-Cu back-bonds raises a Cu atom from the surface that is mechanically sheared by the abrasive grain. In the third step, the raised Cu atom bound to the surface-adsorbed OH groups is removed from the surface by the generation and desorption of a Cu(OH)2 molecule. In contrast, in pure water, there are no geometrical changes in the Cu surface because the H2O molecules do not react with the Cu surface, and the abrasive grain slides smoothly on the planar Cu surface. The comparison between the CMP simulations in aqueous H2O2 and pure water indicates that the intrusion of a surface-adsorbed O atom into the Cu bulk is the most important process for the efficient polishing of the Cu surface because it induces the dissociation of the Cu-Cu bonds and generates raised Cu atoms that are sheared off by the abrasive grain. Furthermore, density functional theory calculations show that the intrusion of the surface-adsorbed O atoms into the Cu bulk has a high activation energy of 28.2 kcal/mol, which is difficult to overcome at 300 K. Thus, we suggest that the intrusion of surface-adsorbed O atoms into the Cu bulk induced by abrasive grains at the friction interface is a rate-determining step in the Cu CMP process.

Tight-binding quantum chemical molecular dynamics simulations for the elucidation of chemical reaction dynamics in SiC etching with SF6/O2 plasma.

We used our etching simulator [H. Ito et al., J. Phys. Chem. C, 2014, 118, 21580-21588] based on tight-binding quantum chemical molecular dynamics (TB-QCMD) to elucidate SiC etching mechanisms. First, the SiC surface is irradiated with SF5 radicals, which are the dominant etchant species in experiments, with the irradiation energy of 300 eV. After SF5 radicals bombard the SiC surface, Si-C bonds dissociate, generating Si-F, C-F, Si-S, and C-S bonds. Then, etching products, such as SiS, CS, SiFx, and CFx (x = 1-4) molecules, are generated and evaporated. In particular, SiFx is the main generated species, and Si atoms are more likely to vaporize than C atoms. The remaining C atoms on SiC generate C-C bonds that may decrease the etching rate. Interestingly, far fewer Si-Si bonds than C-C bonds are generated. We also simulated SiC etching with SF3 radicals. Although the chemical reaction dynamics are similar to etching with SF5 radicals, the etching rate is lower. Next, to clarify the effect of O atom addition on the etching mechanism, we also simulated SiC etching with SF5 and O radicals/atoms. After bombardment with SF5 radicals, Si-C bonds dissociate in a similar way to the etching without O atoms. In addition, O atoms generate many C-O bonds and COy (y = 1-2) molecules, inhibiting the generation of C-C bonds. This indicates that O atom addition improves the removal of C atoms from SiC. However, for a high O concentration, many C-C and Si-Si bonds are generated. When the O atoms dissociate the Si-C bonds and generate dangling bonds, the O atoms terminate only one or two dangling bonds. Moreover, at high O concentrations there are fewer S and F atoms to terminate the dangling bonds than at low O concentration. Therefore, few dangling bonds of dissociated Si and C atoms are terminated, and they form many Si-Si and C-C bonds. Furthermore, we propose that the optimal O concentration is 50-60% because both Si and C atoms generate many etching products producing fewer C-C and Si-Si bonds are generated. Finally, we conclude that our TB-QCMD etching simulator is effective for designing the optimal conditions for etching processes in which chemical reactions play a significant role.

The reason why thin-film silicon grows layer by layer in plasma-enhanced chemical vapor deposition.

Thin-film Si grows layer by layer on Si(001)-(2 × 1):H in plasma-enhanced chemical vapor deposition. Here we investigate the reason why this occurs by using quantum chemical molecular dynamics and density functional theory calculations. We propose a dangling bond (DB) diffusion model as an alternative to the SiH3 diffusion model, which is in conflict with first-principles calculation results and does not match the experimental evidence. In our model, DBs diffuse rapidly along an upper layer consisting of Si-H3 sites, and then migrate from the upper layer to a lower layer consisting of Si-H sites. The subsequently incident SiH3 radical is then adsorbed onto the DB in the lower layer, producing two-dimensional growth. We find that DB diffusion appears analogous to H diffusion and can explain the reason why the layer-by-layer growth occurs.

Characterization of a wheat pathogenesis-related protein, TaBWPR-1.2, in seminal roots in response to waterlogging stress.

We examined the role of pathogenesis-related protein TaBWPR-1.2 in the context of molecular and physiological responses of wheat (Triticum aestivum) seminal roots under waterlogging stress. Two cDNAs corresponding to the TaBWPR-1.2 gene, TaBWPR-1.2#2 and TaBWPR-1.2#13 were cloned from seminal roots. These cDNAs were predicted to encode proteins of 173 and 172 amino acids, respectively. In a time-course experiment, TaBWPR-1.2 gene expression was highest in whole seminal roots after 1 day of waterlogging treatment and higher than the control for at least 10 days; significantly increased protein abundance was observed after 7 days of waterlogging. Drought, another abiotic stress, did not influence TaBWPR-1.2 gene expression in wheat seminal roots at 5-d-old seedlings. Tissue-specific studies revealed that the highest TaBWPR-1.2 gene expression and protein levels were in the aerenchymatous root zone. TaBWPR-1.2 expression in seminal roots was also increased by the signalling molecules 1-aminocyclopropane-1-carboxylic acid (ACC; an ethylene precursor), H2O2, jasmonic acid (JA), and nitric oxide (NO); however, treatment with abscisic acid (ABA), salicylic acid (SA), and ethanol did not alter its expression. Interestingly, aerenchyma formation in the seminal root cortex was induced only by ACC and H2O2. Taken together, these results indicate that TaBWPR-1.2 is a waterlogging-responsive gene that might be associated with root cortex tissue alteration in wheat plants through ACC and/or H2O2 regulatory mechanisms.

Adventitious roots of wheat seedlings that emerge in oxygen-deficient conditions have increased root diameters with highly developed lysigenous aerenchyma.

Exposing roots of plants to hypoxic conditions is known to greatly improve their anoxic stress tolerance. We previously showed that pre-treatment of wheat seedlings with an ethylene precursor, 1-aminocyclopropanecarboxylic acid (ACC), enhanced their tolerance of oxygen-deficient conditions. Although ACC-pretreated seminal roots of wheat seedlings grown under oxygen-deficient conditions avoided root tip death, they elongated very little. In the present study, we assessed the effects of ethylene on the responses of adventitious roots of wheat seedlings to oxygen-deficient conditions. Lysigenous aerenchyma formation in the adventitious roots of wheat seedlings pretreated with ACC appeared to reduce tip death under oxygen-deficient conditions, but the adventitious roots, like the seminal roots, hardly elongated. We also found that adventitious roots that emerge in oxygen-deficient conditions continued to elongate even under such conditions. The adventitious roots emerged in oxygen-deficient conditions were found to have thicker root diameters than those emerged in aerated conditions. These results suggest that the adventitious roots with thicker root diameters can better cope with oxygen-deficient conditions. Measurements of the area of the lysigenous aerenchyma confirmed that the increased root diameters have a greater amount of air space generated by lysigenous aerenchyma formation.

Ethylene and reactive oxygen species are involved in root aerenchyma formation and adaptation of wheat seedlings to oxygen-deficient conditions.

Exposing plants to hypoxic conditions greatly improves their anoxic stress tolerance by enhancing the activities of glycolysis and fermentation in roots. Ethylene may also be involved in these adaptive responses because its synthesis is increased in roots under hypoxic conditions. Here it is reported that pre-treatment of wheat seedlings with an ethylene precursor, 1-aminocyclopropanecarboxylic acid (ACC), enhanced accumulation of ethylene in the roots of wheat seedlings, and enhanced their tolerance of oxygen-deficient conditions through increasing the expression of genes encoding ethanol fermentation enzymes, alcohol dehydrogenase and pyruvate decarboxylase, in the roots. Lysigenous aerenchyma formation in root was induced by ACC pre-treatment and was further induced by growth under oxygen-deficient conditions. ACC pre-treatment increased the expression of three genes encoding respiratory burst oxidase homologue (a plant homologue of gp91(phox) in NADPH oxidase), which has a role in the generation of reactive oxygen species (ROS), in roots of seedlings. Co-treatment with ACC and an NADPH oxidase inhibitor, diphenyleneiodonium, partly suppressed the ACC-induced responses. These results suggest that ethylene and ROS are involved in adaptation of wheat seedlings to oxygen-deficient conditions through controlling lysigenous aerenchyma formation and the expression of genes encoding ethanol fermentation enzymes.

Quantitative Proteomics of the Root of Transgenic Wheat Expressing TaBWPR-1.2 Genes in Response to Waterlogging.

Once candidate genes are available, the application of genetic transformation plays a major part to study their function in plants for adaptation to respective environmental stresses, including waterlogging (WL). The introduction of stress-inducible genes into wheat remains difficult because of low transformation and plant regeneration efficiencies and expression variability and instability. Earlier, we found two cDNAs encoding WL stress-responsive wheat pathogenesis-related proteins 1.2 (TaBWPR-1.2), TaBWPR-1.2#2 and TaBWPR-1.2#13. Using microprojectile bombardment, both cDNAs were introduced into "Bobwhite". Despite low transformation efficiency, four independent T2 homozygous lines for each gene were isolated, where transgenes were ubiquitously and variously expressed. The highest transgene expression was obtained in Ubi:TaBWPR-1.2#2 L#11a and Ubi:TaBWPR-1.2#13 L#4a. Using quantitative proteomics, the root proteins of L#11a were analyzed to explore possible physiological pathways regulated by TaBWPR-1.2 under normal and waterlogged conditions. In L#11a, the abundance of proteasome subunit alpha type-3 decreased under normal conditions, whereas that of ferredoxin precursor and elongation factor-2 increased under waterlogged conditions in comparison with normal plants. Proteomic results suggest that L#11a is one of the engineered wheat plants where TaBWPR-1.2#2 is most probably involved in proteolysis, protein synthesis and alteration in the energy pathway in root tissues via the above proteins in order to gain metabolic adjustment to WL.

Expression analyses of beta-tubulin isotype genes in rice.

Microtubules play important roles in many cellular processes, such as cell division and cell elongation in plants. beta-tubulins, which are the basic components of microtubules, are encoded by multigene family in eukaryotes and their nucleotide sequences are highly conserved in protein coding regions. A homology search within the rice expressed sequence tag database identified at least eight beta-tubulin (OsTUB) isotypes including three novel OsTUB genes. Northern analysis using specific probes to 3'-UTR of OsTUB isotypes showed differential and tissue-specific expression. Seven out of eight OsTUB genes dominantly expressed in leaf sheath, while OsTUB8 was preferentially expressed in anther including mature pollens. The existence of anther-specific beta-tubulin suggests its unique role in the formation of microtubules during the anther and pollen development or pollen tube growth. Furthermore, transcripts of OsTUB5, 6 and 7 genes were significantly enhanced by gibberellin but all eight OsTUB genes were repressed by abscisic acid. Our results imply that OsTUB genes are differentially regulated by developmental and hormonal signals and different OsTUB isotypes might play special role in the growth and development of specific organs in rice.