Polar Faces Research Articles

Identification of 6H-SiC polar faces with pull-off force of atomic force microscopy

Distinguishing SiC (0001) Si-face from SiC (000-1) C-face without any damages is extremely important because the two polar faces have different physical and chemical properties which seriously influence the quality of a homoepitaxy or heteroepitaxy thin film on it. Here, a convenient and nondestructive detection method is developed to distinguish the Si-face and C-face of a (0001) oriented SiC wafer by employing a pull-off force measurement using atomic force microscopy. It is found that the pull-off force from a Si-face of 6H-SiC is about two times of that from a C-face, no matter it is a two-face chemical mechanical polishing or etched 6H-SiC wafer. The method developed here is suitable to identify polar faces of materials only if the two polar faces having different surface energy.

(Invited) Periodically Oriented Gallium Nitride for Frequency Conversion

Gallium nitride is a semiconductor widely used in both optical and electronic devices. The polarity of GaN (+/- c-direction) influences many properties of the resultant material, including chemical reactivity and electric field in these ‘spontaneously polarized’ materials. By engineering inversion layers, we have demonstrated control of GaN polarity on both polar faces of GaN. By employing a selective growth method to deposit the IL, the lateral polarity of the GaN can be alternated, thus enabling structures referred to as periodically oriented (PO) GaN. We have shown such structures on both N-polar and Ga-polar native substrates by changing the IL material. On N-polar substrates, we demonstrated that optimization of the MOCVD growth rates resulted in sharp, vertical interfaces and smooth surfaces. This work has moved the technology substantially closer to practical non-linear optic emitters by using HVPE to extend the PO GaN templates on N-polar substrates to total thicknesses of up to 500 μm, while faithfully maintaining the pattern of alternating polarity. Additionally, cross-sectional cathode-luminescence (CL) imaging of such an extension shows that the large initial dislocation densities occurring in the original inversion layers greatly decreased after about 25 μm of regrowth. The results of phase matching experiments with these structures will be presented, with discussion on fabrication issues. These methods of GaN polarity inversion offer the promise of engineered materials with custom lateral and vertical polarity variations for applications in novel electronic and optoelectronic devices, a subset of which are expected to be suitable for non-linear optics.

Atomic-Scale Origin of Long-Term Stability and High Performance of p-GaN Nanowire Arrays for Photocatalytic Overall Pure Water Splitting.

The atomic-scale origin of the unusually high performance and long-term stability of wurtzite p-GaN oriented nanowire arrays is revealed. Nitrogen termination of both the polar (0001¯) top face and the nonpolar (101¯0) side faces of the nanowires is essential for long-term stability and high efficiency. Such a distinct atomic configuration ensures not only stability against (photo) oxidation in air and in water/electrolyte but, as importantly, also provides the necessary overall reverse crystal polarization needed for efficient hole extraction in p-GaN.

Design of an α-helical antimicrobial peptide with improved cell-selective and potent anti-biofilm activity.

AR-23 is a melittin-related peptide with 23 residues. Like melittin, its high α-helical amphipathic structure results in strong bactericidal activity and cytotoxicity. In this study, a series of AR-23 analogues with low amphipathicity were designed by substitution of Ala1, Ala8 and Ile17 with positively charged residues (Arg or Lys) to study the effect of positively charged residue distribution on the biological viability of the antimicrobial peptide. Substitution of Ile17 on the nonpolar face with positively charged Lys dramatically altered the hydrophobicity, amphipathicity, helicity and the membrane-penetrating activity against human cells as well as the haemolytic activity of the peptide. However, substitution on the polar face only slightly affected the peptide biophysical properties and biological activity. The results indicate that the position rather than the number of positively charged residue affects the biophysical properties and selectivity of the peptide. Of all the analogues, A(A1R, A8R, I17K), a peptide with Ala1-Arg, Ala8-Arg and Ile17-Lys substitutions, exhibited similar bactericidal activity and anti-biofilm activity to AR-23 but had much lower haemolytic activity and cytotoxicity against mammalian cells compared with AR-23. Therefore, the findings reported here provide a rationalization for peptide design and optimization, which will be useful for the future development of antimicrobial agents.

Interaction between Nonstructural Proteins NS4B and NS5A Is Essential for Proper NS5A Localization and Hepatitis C Virus RNA Replication.

The hepatitis C virus NS5A protein is tethered to cellular membranes via an amphipathic amino-terminal helix that is inserted in-plane into the outer endoplasmic reticulum (ER)-derived membrane leaflet. The charged face of the helix faces the cytoplasm and may contribute to interactions involved in replicase assembly and function. Using an aggressive charge flip mutagenesis strategy, we identified a number of essential residues for replication on the charged face of the NS5A anchor and identified a double charge face mutant that is lethal for RNA replication but generates suppressor mutations in the carboxy-terminal helix of the NS4B protein. This suppressor restores RNA replication of the NS5A helix double flip mutant (D1979K/D1982K) and, interestingly, seems to function by restoring the proper localization of NS5A to the viral replicase. These data add to our understanding of the complex organization and assembly of the viral replicase via NS4B-NS5A interactions. Information about the functional role of the cytosolic face of the NS5A anchoring helix remains obscure. In this study, we show that while the hydrophobic face of the NS5A anchor helix mediates membrane association, the polar cytosolic face of the helix plays a key role during hepatitis C virus (HCV) replication by mediating the interaction of NS5A with other HCV nonstructural proteins via NS4B. Such an interaction determines the subcellular localization of NS5A by engaging NS5A in the HCV replication process during the formation of a functional HCV replication complex. Thus, collectively, it can be stated that the findings in the present study provide further information about the interactions between the HCV nonstructural proteins during HCV RNA replication and provide a platform to gain more insights about the molecular architecture of HCV replication complexes.

Highly-defective nanocrystals of ZnS formed via dissimilatory bacterial sulfate reduction: A comparative study with their abiogenic analogues

The physicochemical properties of a (nano)mineral are strongly affected by its formation processes, and thus, may indicate the (nano)mineral’s formation environment and mechanism. This correlation, although relevant to a myriad of geological, environmental, and material-science processes, has not yet been fully appreciated and systematically explored. Here, using the Zn–S system, we demonstrate that biological and abiotic processes at similar experimental conditions can produce distinctive particle size, morphology, and crystal structure in the formed ZnS. Specifically, bacterial sulfate reduction led to the formation of highly-defective nanocrystals of mixed sphalerite and wurtzite in a range of ∼4–12nm. By comparison, the abiotic procedures of titration- or diffusion-controlled precipitation resulted in the formation of polycrystalline aggregates that contained randomly-oriented, ultrafine crystals below ∼2–3nm. The poor crystallinity in the abiogenic samples, regardless of the sulfide addition rates, reveals an overall nucleation-dominated, crystal growth-restricted pathway for the formation of ZnS from low-temperature aqueous solutions. The difficulty in the ZnS crystallization likely stems from the intrinsic surface instability of the ZnS growth units (i.e., in the form of nanoclusters) resulting from the dipole–dipole interactions of the unit with surrounding water molecules. In the biogenic samples, the ZnS crystallinity was significantly improved, indicating that the presence of bacterial metabolites somehow promoted the crystallization process. With evidence for the enlarged {111} planes in the biogenic nanocrystals, we attribute this enhancement mainly to the selective interaction of the bacterial metabolites with polar faces of the ZnS growth units, which might have effectively screened the dipole moments in the growth units and enabled their crystallographic assembly. By revealing the intrinsic difficulty and specific pathways for the ZnS crystallization, we also present viable explanations for the exclusive occurrence of structural defects in {111} planes of the biogenic nanocrystals. The findings of our study provide insight into the origin and fate of metal sulfide nanoparticles in the environment, and have implications for biomineralization, bioremediation of metal-contaminated sites, and bacterial production of functional nanomaterials.

Design of pH Triggered, Macromolecular Pore Forming Peptides for Endosomal Escape

The plasma membrane insulates a cell from its outside environment, serving as an selectively impermeable barrier across which only small or hydrophobic molecules can pass. Although the membrane is protective and necessary for life, it is also problematic when useful macromolecules such as antibodies, peptides, polysaccharides, and imaging agents are blocked from entry. Most macromolecules can easily be uptaken by the cell through endocytosis, but remain trapped and eventually degraded within endosomes, which mature into lysosomes. To promote the escape of macromolecules from endosomes prior to their maturation into lysosomes, we have designed pH triggered, pore-forming peptides. The peptides were selected from a high-throughput screen of a 18,432 member combinatorial library based on the sequence of the pH insensitive pore-forming peptide, MelP5. We identified that 5 acidic residues along the polar face of an amphipatic helix mediates a structural change from a charged, soluble state at pH 7 to an uncharged, membrane bound, and pore-forming helix at pH 5. The peptides have been shown to deliver fluorescently labeled 10 kDa dextrans in CHO cells. The discovery of the pHD peptides illustrates the power of combinatorial chemistry and high throughput screening for engineering membrane active peptides with specific capabilities despite the lack of structural information about the pore.

Epitaxial growth of atomically flat KBr(111) films via a thin film ionic liquid in a vacuum

The NaCl-type crystal (111) polar face is electrostatically so unstable that its atomically flat (111) surface has been difficult to obtain so far. In this work, based on our preliminary results on flat KBr(111) microcrystals on an α-Al2O3(0001) substrate grown via ionic liquid droplets by vacuum deposition, we have achieved atomically flat, epitaxial KBr(111) films grown all over an α-Al2O3(0001) substrate. The key point to this success is the great improvement in the wettability of the ionic liquid on the substrate by introducing an amorphous-like “wetting layer”. Furthermore, in situ growth monitoring by means of an optical microscope with a long-distance focus lens reveals the growth process in the ionic liquid: random nucleation occurs directly on the substrate, but not in the ionic liquid, and subsequently, the nucleated KBr islands grow more rapidly in the in-plane direction rather than in the out-of-plane direction to coalesce with each other, forming a continuous KBr film over the substrate. The lateral overgrowth mechanism is proposed to explain the epitaxial growth of KBr(111) films even on the amorphous-like wetting layer/α-Al2O3(0001) substrate on the basis of a cross-sectional TEM observation.

Influence of Crystal Habit on the Dissolution of Simvastatin Single Crystals.

In order to achieve better in-vivo performance of the final dosage form comprising a poorly soluble drug the physicochemical properties of the active pharmaceutical ingredient can be altered not only by changing the solid state form but also through the conversion of their crystal habits. To elucidate this approach in the case of simvastatin, the dissolution behaviour of large crystals with the same internal structure but expressing different crystal habits was studied using atomic force microscope. The obtained differences in the dissolution were explained through the determination of crystal morphology its orientation and assignation of the molecular functional groups that were emerging on the surface of the dissolving crystal face. The dissolution rates of the particular crystal faces were found to be distinctly higher than others. The dissolution rate of single crystals differed as a consequence of higher incidence of more polar faces in case of rod shaped crystals isolated from more hydrophilic solvent mixture which we have established through a thorough research of the single crystal morphology, orientation and the assignation of specific functional groups for each of evolved crystal faces.

Designing potent antimicrobial peptides by disulphide linked dimerization and N-terminal lipidation to increase antimicrobial activity and membrane perturbation: Structural insights into lipopolysaccharide binding

HypothesisThe remarkable rise in multi-drug resistant Gram-negative bacterial pathogens is a major concern to the well being of humans as well as susceptible plants. In recent years, diseases associated with inflammation and septicemia have already become a global health issue. Therefore, there is a rising demand for the development of novel “super” antibiotics. In this context, antimicrobial peptides offer an attractive, alternate therapeutic solution to conventional antibiotics. ExperimentsMicrobroth dilution assay was performed to investigate the antimicrobial activities of the two designed peptides against Gram negative bacterial pathogens. Fluorescence studies including NPN dye uptake assay, Calcein entrapped vesicle leakage assay, quenching and anisotropy in presence of lipopolysaccharide (LPS) were performed to elucidate binding interactions and enhanced membrane permeabilisation. Hemolytic assay and endotoxin/LPS neutralisation assay were performed to study the hemolytic effects and LPS scavenging abilities of the peptides. High resolution NMR studies were performed to obtain insights into LPS-peptide interaction at the molecular level. FindingsHere, we report more potent analogues of previously designed peptide VG16KRKP, designed through dimerization via Cys–Cys disulphide linkage and N-terminal lipidation. Similar to the parent peptide, VG16KRKP, the modified analogue peptides are non hemolytic in nature, but possessed, 2–10-fold increase in antibacterial activities against E. coli, human pathogen Pseudomonas aeruginosa and the devastating plant pathogen, Xanthomonas campestris pv. campestris as well as membrane permeabilization, and endotoxin neutralization. LPS bound solution structure of both analogues, as determined by NMR spectroscopy, reveal that the conserved hydrophobic triad motif, formed by Trp5, Leu11 and Phe12 is compactly organized and stabilized either by the acyl chain or disulphide bond. This structural constraint accounts for the separation of polar face from the hydrophobic face of the peptides. Our novel peptides designed through Cys–Cys dimerization and N-terminal lipidation, will serve as a template to develop more potent antimicrobials in future, to control plant and human diseases.

Effect of Growth Pressure on Epitaxial Graphene Grown on 4H-SiC Substrates by Using Ethene Chemical Vapor Deposition.

The Si(0001) face and C(000-1) face dependences on growth pressure of epitaxial graphene (EG) grown on 4H-SiC substrates by ethene chemical vapor deposition (CVD) was studied using atomic force microscopy (AFM) and micro-Raman spectroscopy (μ-Raman). AFM revealed that EGs on Si-faced substrates had clear stepped morphologies due to surface step bunching. However, This EG formation did not occur on C-faced substrates. It was shown by μ-Raman that the properties of EG on both polar faces were different. EGs on Si-faced substrates were relatively thinner and more uniform than on C-faced substrates at low growth pressure. On the other hand, D band related defects always appeared in EGs on Si-faced substrates, but they did not appear in EG on C-faced substrate at an appropriate growth pressure. This was due to the μ-Raman covering the step edges when measurements were performed on Si-faced substrates. The results of this study are useful for optimized growth of EG on polar surfaces of SiC substrates.

Steroidal Surfactants: Detection of Premicellar Aggregation, Secondary Aggregation Changes in Micelles, and Hosting of a Highly Charged Negative Substance.

CHAPSO and CHAPS are zwitterionic surfactants derived from bile salts which are usually employed in protein purification and for the preparation of liposomes and bicelles. Despite their spread use, there are significant discrepancies on the critical concentrations that determine their aggregation behavior. In this work, we study the interaction between these surfactants with the negative fluorescent dye pyranine (HPTS) by absorbance, fluorescence, and infrared spectrometry to establish their concentration-dependent aggregation. For the studied surfactants, we detect three critical concentrations showing their concentration-dependent presence as a monomeric form, premicellar aggregates, micelles, and a second type of micelle in aqueous medium. The nature of the interaction of HPTS with the surfactants was studied using analogues of their tails and the negative bile salt taurocholate (TC) as reference for the sterol ring. The results indicate that the chemical groups involved are the hydroxyl groups of the polar face of the sterol ring and the sulfonate groups of the dye. This interaction causes not only the incorporation of the negative dye in CHAPSO and CHAPS micelles but also its association with their premicellar aggregates. Surprisingly, this hosting behavior for a negative charged molecule was also detected for the negative bile salt TC, bypassing, in this way, the electrostatic repulsion between the guest and the host.

On the radially symmetric vibrations of circular sandwich plates with polar orthotropic facings and isotropic core of quadratically varying thickness by harmonic differential quadrature method

In the present paper, analysis and numerical results are presented for free axisymmetric vibrations of circular sandwich plate with isotropic core and polar orthotropic face sheets employing harmonic differential quadrature (HDQ) method. The thickness of the core is assumed to vary quadratically in the radial direction and the face sheets are treated as membranes of constant thickness. The effect of shear deformation and rotatory inertia in the core has been taken into account and the mathematical analysis is based upon Mindlin’s theory/first-order shear deformation theory. The governing differential equations of motion of the model have been obtained by using Hamilton’s energy principle. In the resulting equation HDQ method is employed to obtain the frequency equations for the three edges, namely; clamped, simply supported and free. The lowest three roots of these equations have been reported as the frequencies for the first three modes of vibration for all the three plates. The effect of various plate parameters such as taper parameter, core thickness at the centre and facing thickness on the natural frequencies has been studied. Three-dimensional mode shapes for the specified plates have been illustrated. To check the validity of the present considerations and the technique, frequency parameter has been compared in particular cases.

Nitrogen Incorporation during Seeded Sublimation Growth of 4H-SiC and 6H-SiC

We address the problem of nitrogen incorporation during bulk crystal growth of 4H-SiC and 6H-SiC by seeded sublimation method. The partial pressure of nitrogen and temperature dependence were considered in bulk SiC crystals. Free carrier concentration and incorporated nitrogen were determined using Raman spectroscopy and Secondary Ion Mass Spectrometry, respectively. The incorporated nitrogen at the (000-1) C-face of 4H-SiC and 6H-SiC is found to be independent of the polytype of the crystal. Higher desorption rate at Si-face compared to C-face is found, using a Langmuir equation, which is attributed to the difference in bond density between the two polar faces. The increased nitrogen desorption when growth temperature increases is believed to be the most contributing factor, based on the temperature dependent trends.

Controlling Planar Defects in 3C-SiC: Ways to Wake it up as a Practical Semiconductor

Eelectrically active defects in 3C–SiC are investigated by considering the structures and interactions of planar defects. An anti-phase boundary (APB) largely degrades the blocking property of semiconductor devices due to its semimetallic nature. Although APBs can be eliminated by orienting the specific polar face of 3C-SiC along a particular direction, stacking faults (SFs) cannot be eliminated due to Shockley-type partial dislocation glide. SFs with Shockley-type partial dislocations form a trapezoidal plate which expands the Si-terminated surface with increasing 3C-SiC thickness. Although the density of SFs can be reduced by counter termination, specific cross-junctions between a pair of counter SFs forms a forest dislocation, and this is regarded as an electrically active defect. This paper proposes an effective way to suppress the forest dislocations and APBs which nucleate during 3C-SiC growth.

Identification of amino acid changes in the envelope glycoproteins of bovine viral diarrhea viruses isolated from alpaca that may be involved in host adaptation

Bovine viral diarrhea viruses (BVDV) are most commonly associated with infections of cattle. However, BVDV are often isolated from closely related ruminants with a number of BVDV-1b viruses being isolated from alpacas that were both acutely and persistently infected. The complete nucleotide sequence of the open reading frame of eleven alpaca-adapted BVDV isolates and the region encoding the envelope glycoproteins of an additional three isolates were determined. With the exception of one, all alpaca isolates were >99.2% similar at the nucleotide level. The Hercules isolate was more divergent, with 95.7% sequence identity to the other viruses. Sequence similarity of the 14 viruses indicated they were isolates of a single BVDV strain that had adapted to and were circulating through alpaca herds. Hercules was a more distantly related strain that has been isolated only once in Canada and represented a separate adaptation event that possessed the same adaptive changes. Comparison of amino acid sequences of alpaca and bovine-derived BVDV strains revealed three regions with amino acid sequences unique to all alpaca isolates. The first contained two small in-frame deletions near the N-terminus of the E2 glycoprotein. The second was found near the C-terminus of the E2 protein where four altered amino acids were located within a 30 amino acid domain that participates in E2 homodimerization. The third region contained three variable amino acids in the C-terminus of the Erns within the amphipathic helix membrane anchor. These changes were found in the polar side of the amphipathic helix and resulted in an increased charge within the polar face. Titration of bovine and alpaca viruses in both bovine and alpaca cells indicated that with increased charge in the amphipathic helix, the ability to infect alpaca cells also increased.

ReaxFF molecular dynamics study on oxidation behavior of 3C-SiC: Polar face effects**Project supported by the 111 Project (Grant No. B07050) and the National Natural Science Foundation of China (Grant No. 11402206).

The oxidation of nanoscale 3C-SiC involving four polar faces (, Si(100), , and Si(111)) is studied by means of a reactive force field molecular dynamics (ReaxFF MD) simulation. It is shown that the consistency of 3C-SiC structure is broken over 2000 K and the low-density carbon chains are formed within SiC slab. By analyzing the oxygen concentration and fitting to rate theory, activation barriers for , Si(100), , and Si(111) are found to be 30.1, 35.6, 29.9, and 33.4 kJ·mol−1. These results reflect lower oxidative stability of C-terminated face, especially along [111] direction. Compared with hexagonal polytypes of SiC, cubic phase may be more energy-favorable to be oxidized under high temperature, indicating polytype effect on SiC oxidation behavior.

(Invited) Developing Periodically Oriented Gallium Nitride for Frequency Conversion

Gallium nitride is a semiconductor widely used in both optical and electronic devices. The polarity of GaN (+/- c-direction) influences many properties of the resultant material, including chemical reactivity and electric field in these ‘spontaneously polarized’ materials. By engineering inversion layers, we have demonstrated control of GaN polarity on both polar faces of GaN. By employing a selective growth method to deposit the IL, the lateral polarity of the GaN can be alternated, thus enabling structures referred to as periodically oriented (PO) GaN. On N-polar substrates, we demonstrated that optimization of the MOCVD growth rates resulted in sharp, vertical interfaces and smooth surfaces. This work has moved the technology substantially closer to practical non-linear optic emitters by using HVPE to extend the PO GaN templates on N-polar substrates to total thicknesses of up to 500 mm, while faithfully maintaining the pattern of alternating polarity. Additionally, cross-sectional cathode-luminescence (CL) imaging of such an extension shows that the large initial dislocation densities occurring in the original inversion layers greatly decreased after about 25 mm of regrowth. For growth on Ga-polar substrates, we have demonstrated that inversion layers can be created using atomic layer deposition (ALD) of Al2O3. This new capability is especially relevant because Ga-polar films are more prominent in devices, as they result in lower impurities, higher quality and smoother films. In this case, GaN grown over the inversion layer is N-polar. This inversion layer was used to form laterally-patterned stripes of alternating Ga- and N-polar films. We find that annealing the ALD films crystallizes the Al2O3, thereby allowing N-polar GaN to be grown over the new sapphire-like surface. Transmission electron microscopy shows that the inversion layer in a PO GaN structure is crystalline, a-plane oriented, and a-phase. TEM characterization further indicates that the GaN layers, both above and below the Al2O3 inversion layer, are c-oriented without any rotation between them. The optimization of this process has enhanced the surface smoothness. These methods of GaN polarity inversion offer the promise of engineered materials with custom lateral and vertical polarity variations for applications in novel electronic and optoelectronic devices, a subset of which are expected to be suitable for non-linear optics.

Highly Unusual Triangular Crystals of Theophylline: The Influence of Solvent on the Growth Rates of Polar Crystal Faces

A noteworthy feature of the compound theophylline is that it forms crystals with a triangular habit, an extremely rare phenomenon for an organic molecule. Here, we investigate the formation of these crystals, comprised of the polymorph Form II (Pna21), and demonstrate that the triangles are obtained from solvents which are highly hydrophobic, or which have a hydrogen bond acceptor group and no hydrogen bond donor group. The formation of the triangular crystal habit is rationalized on the basis of the way such solvents interact with the inequivalent (001) and (001) polar crystal faces of Form II. Interactions are significantly stronger at one face than the other, inhibiting growth in one direction and limiting crystal growth to a single, triangle-shaped, growth sector. This rationalization also enabled interesting surface features observed by atomic force microscopy to be interpreted. Furthermore, we report a second, previously unreported, type of triangular crystal of theophylline for which the angle at ...

(Invited) Developing Periodically Oriented Gallium Nitride for Frequency Conversion

The development of GaN as a quasi-phase matched material for high power frequency conversion by periodically orienting the crystal orientation is presented. For high power applications, thick material on native substrates is required. Recent work has produced periodically oriented (PO) GaN with thicknesses reaching 500μm on N-polar GaN substrates. Work on Ga-polar substrates has progressed, with demonstrations of PO structures. The ability to create PO structures on both polar faces of GaN substrates offers the promise of engineered materials with custom lateral and vertical polarity variations for applications in novel electronic and optoelectronic devices, a subset of which are expected to be suitable for non-linear optics.