Hyperstable Synthetic Mini-Proteins as Effective Ligand Scaffolds.

Small, single-domain protein scaffolds are compelling sources of molecular binding ligands with the potential for efficient physiological transport, modularity, and manufacturing. Yet, mini-proteins require a balance between biophysical robustness and diversity to enable new functions. We tested the developability and evolvability of millions of variants of 43 designed libraries of synthetic 40-amino acid ßαßß proteins with diversified sheet, loop, or helix paratopes. We discovered a scaffold library that yielded hundreds of binders to seven targets while exhibiting high stability and soluble expression. Binder discovery yielded 6-122 nM affinities without affinity maturation and Tms averaging ≥78 °C. Broader ßαßß libraries exhibited varied developability and evolvability. Sheet paratopes were the most consistently developable, and framework 1 was the most evolvable. Paratope evolvability was dependent on target, though several libraries were evolvable across many targets while exhibiting high stability and soluble expression. Select ßαßß proteins are strong starting points for engineering performant binders.

Fabrication of Specimens for Atom Probe Tomography Using a Combined Gallium and Neon Focused Ion Beam Milling Approach.

We demonstrate a new focused ion beam sample preparation method for atom probe tomography. The key aspect of the new method is that we use a neon ion beam for the final tip-shaping after conventional annulus milling using gallium ions. This dual-ion approach combines the benefits of the faster milling capability of the higher current gallium ion beam with the chemically inert and higher precision milling capability of the noble gas neon ion beam. Using a titanium-aluminum alloy and a layered aluminum/aluminum-oxide tunnel junction sample as test cases, we show that atom probe tips prepared using the combined gallium and neon ion approach are free from the gallium contamination that typically frustrates composition analysis of these materials due to implantation, diffusion, and embrittlement effects. We propose that by using a focused ion beam from a noble gas species, such as the neon ions demonstrated here, atom probe tomography can be more reliably performed on a larger range of materials than is currently possible using conventional techniques.

Crosstalk between ERK and MRTF-A signaling regulates TGFß1-induced epithelial-mesenchymal transition.

Epithelial-mesenchymal transition (EMT) is a physiological process that is essential during embryogenesis and wound healing and also contributes to pathologies including fibrosis and cancer. EMT is characterized by marked gene expression changes, loss of cell-cell contacts, remodeling of the cytoskeleton, and acquisition of enhanced motility. In the late stages of EMT, cells can exhibit myofibroblast-like properties with enhanced expression of the mesenchymal protein marker α-smooth muscle actin and contractile activity. Transforming growth factor (TGF)-ß1 is a well-known inducer of EMT and it activates a plethora of signaling cascades including extracellular signal-regulated kinase (ERK). Previous reports have demonstrated a role for ERK signaling in the early stages of EMT, but the molecular impacts of ERK signaling on the late stages of EMT are still unknown. Here, we found that inhibition of the phosphorylation of ERK enhances focal adhesions, stress fiber formation, cell contractility, and gene expression changes associated with TGFß1-induced EMT in mammary epithelial cells. These effects are mediated in part by the phosphorylation state and subcellular localization of myocardin-related transcription factor-A. These findings indicate that the intricate crosstalk between signaling cascades plays an important role in regulating the progression of EMT and suggests new approaches to control EMT processes.

Crystallographic polarity measurements in two-terminal GaN nanowire devices by lateral piezoresponse force microscopy.

Lateral piezoresponse force microscopy (L-PFM) is demonstrated as a reliable method for determining the crystallographic polarity of individual, dispersed GaN nanowires that were functional components in electrical test structures. In contrast to PFM measurements of vertically oriented (as-grown) nanowires, where a biased probe tip couples to out-of-plane deformations through the d33 piezoelectic coefficient, the L-PFM measurements in this study were implemented on horizontally oriented nanowires that coupled to shear deformations through the d15 coefficient. L-PFM phase-polarity relationships were determined experimentally using a bulk m-plane GaN sample with a known [0001] direction and further indicated that the sign of the d15 piezoelectric coefficient was negative. L-PFM phase images successfully revealed the in-plane [0001] orientation of self-assembed GaN nanowires as part of a growth polarity study and results were validated against scanning transmission electron microscopy lattice images. Combined characterization of electrical properties and crystallographic polarity was also implemented for two-terminal GaN/Al0.1Ga0.9N/GaN nanowires devices, demonstrating L-PFM measurements as a viable tool for assessing correlations between device rectification and polarization-induced band bending.

An algorithm for correcting systematic energy deficits in the atom probe mass spectra of insulating samples.

Improvements in the mass resolution of a mass spectrometer directly correlate to improvements in peak identification and quantification. Here, we describe a post-processing technique developed to increase the quality of mass spectra of strongly insulating samples in laser-pulsed atom probe microscopy. The technique leverages the self-similarity of atom probe mass spectra collected at different times during an experimental run to correct for electrostatic artifacts that present as systematic energy deficits. We demonstrate the method on fused silica (SiO2) and neodymium-doped ceria (CeO2) samples which highlight the improvements that can be made to the mass spectrum of strongly insulating samples.

Field Ion Emission in an Atom Probe Microscope Triggered by Femtosecond-Pulsed Coherent Extreme Ultraviolet Light.

This paper describes initial experimental results from an extreme ultraviolet (EUV) radiation-pulsed atom probe microscope. Femtosecond-pulsed coherent EUV radiation of 29.6 nm wavelength (41.85 eV photon energy), obtained through high harmonic generation in an Ar-filled hollow capillary waveguide, successfully triggered controlled field ion emission from the apex of amorphous SiO2 specimens. The calculated composition is stoichiometric within the error of the measurement and effectively invariant of the specimen base temperature in the range of 25 K to 150 K. Photon energies available in the EUV band are significantly higher than those currently used in the state-of-the-art near-ultraviolet laser-pulsed atom probe, which enables the possibility of additional ionization and desorption pathways. Pulsed coherent EUV light is a new and potential alternative to near-ultraviolet radiation for atom probe tomography.

The role of Si in GaN/AlN/Si(111) plasma assisted molecular beam epitaxy: polarity and inversion.

The microstructure, polarity and Si distribution in AlN/GaN layers grown by plasma assisted molecular beam epitaxy (PAMBE) on Si(111) was assessed by scanning transmission electron microscopy (STEM). Samples grown under both metal- and nitrogen-rich conditions contained defects at the AlN/Si interface which suggest formation of an Al-Si eutectic. Correlated with this, interfacial segregation of Si was found in the samples. It is proposed that Si is dissolved in a eutectic layer floating on the AlN surface under metal-rich conditions. This Si is then incorporated into the film if the growth becomes nitrogen-rich, either intentionally or due to plasma source transients. These Si-rich layers appear to induce inversion of the nitride from nitrogen- to metal-polarity, and uncontrolled variations in the Si concentration cause occasional nonuniformity in the resulting inversion.

UV LEDs based on p-i-n core-shell AlGaN/GaN nanowire heterostructures grown by N-polar selective area epitaxy.

Ultraviolet light-emitting diodes fabricated from N-polar AlGaN/GaN core-shell nanowires (NWs) with p-i-n structure produced electroluminescence at 365 nm with ∼5× higher intensities than similar GaN homojunction LEDs. The improved characteristics were attributed to localization of spontaneous recombination to the NW core, reduction of carrier overflow losses through the NW shell, and elimination of current shunting. Poisson-drift-diffusion modeling indicated that a shell Al mole fraction of x = 0.1 in Al x Ga1-x N effectively confines electrons and injected holes to the GaN core region. AlGaN overcoat layers targeting this approximate Al mole fraction were found to possess a low-Al-content tip and high-Al-content shell, as determined by scanning transmission electron microscopy. Photoluminescence spectroscopy further revealed the actual Al mole fraction to be NW diameter-dependent, where the tip and shell compositions converged towards the nominal flux ratio for large diameter NWs.

A Three-Dimensional Atom Probe Microscope Incorporating a Wavelength-Tuneable Femtosecond-Pulsed Coherent Extreme Ultraviolet Light Source.

Pulsed coherent extreme ultraviolet (EUV) radiation is a potential alternative to pulsed near-ultraviolet (NUV) wavelengths for atom probe tomography. EUV radiation has the benefit of high absorption within the first few nm of the sample surface for elements across the entire periodic table. In addition, EUV radiation may also offer athermal field ion emission pathways through direct photoionization or core-hole Auger decay processes, which are not possible with the (much lower) photon energies used in conventional NUV laser-pulsed atom probe. We report preliminary results from what we believe to be the world's first EUV radiation-pulsed atom probe microscope. The instrument consists of a femtosecond-pulsed, coherent EUV radiation source interfaced to a local electrode atom probe tomograph by means of a vacuum manifold beamline. EUV photon-assisted field ion emission (of substrate atoms) has been demonstrated on various insulating, semiconducting, and metallic specimens. Select examples are shown.

Eutectic Formation, V/III Ratio and Controlled Polarity Inversion in Nitrides on Silicon[1].

The crystallographic polarity of AlN grown on Si(111) by plasma assisted molecular beam epitaxy is intentionally inverted from N-polar to Al-polar at a planar boundary. The position of the inversion boundary is controlled by a two-step growth process that abruptly changes from Al-rich to N-rich growth conditions. The polarity inversion is induced by the presence of Si, which is incorporated from an Al-Si eutectic layer that forms during the initial stages of AlN growth and floats on the AlN surface under Al-rich growth conditions. When the growth conditions change to N-rich the Al and Si in the eutectic react with the additional N-flux and are incorporated into the solid AlN film. Relatively low levels of Al-Si eutectic formation combined with lateral variations in the Si incorporation lead to nonuniformity in the polarity inversion and formation of surprisingly narrow, vertical inversion domains. The results suggest that intentional incorporation of uniform layers of Si may provide a method for producing polarity engineered nitride structures.

Electron-Enhanced Atomic Layer Deposition of Boron Nitride Thin Films at Room Temperature and 100 °C.

Electron-enhanced atomic layer deposition (EE-ALD) was used to deposit boron nitride (BN) thin films at room temperature and 100 °C using sequential exposures of borazine (B3N3H6) and electrons. Electron-stimulated desorption (ESD) of hydrogen surface species and the corresponding creation of reactive dangling bonds are believed to facilitate borazine adsorption and reduce the temperature required for BN film deposition. In situ ellipsometry measurements showed that the BN film thickness increased linearly versus the number of EE-ALD cycles at room temperature. Maximum growth rates of ~3.2 Å/cycle were measured at electron energies of 80-160 eV. BN film growth was self-limiting versus borazine and electron exposures, as expected for an ALD process. The calculated average hydrogen ESD cross section was σ = 4.2 × 10-17 cm2. Ex situ spectroscopic ellipsometry measurements across the ~1 cm2 area of the BN film defined by the electron beam displayed good uniformity in thickness. Ex situ X-ray photoelectron spectroscopy and in situ Auger spectroscopy revealed high purity, slightly boron-rich BN films with C and O impurity levels <3 at. %. High-resolution transmission electron microscopy (HR-TEM) imaging revealed polycrystalline hexagonal and turbostratic BN with the basal planes approximately parallel to the substrate surface. Ex situ grazing incidence X-ray diffraction measurements observed peaks consistent with hexagonal BN with domain sizes of 1-2 nm. The BN EE-ALD growth rate of ~3.2 Å/cycle is close to the distance of 3.3 Å between BN planes in hexagonal BN. The growth rate and HR-TEM images suggest that approximately one monolayer of BN is deposited for every BN EE-ALD cycle. TEM and scanning TEM/electron energy loss spectroscopy measurements of BN EE-ALD on trenched wafers also showed preferential BN EE-ALD on the horizontal surfaces. This selective deposition on the horizontal surfaces suggests that EE-ALD may enable bottom-up filling of vias and trenches.

Selective Area Growth and Structural Characterization of GaN Nanostructures on Si(111) Substrates.

Selective area growth (SAG) of GaN nanowires and nanowalls on Si(111) substrates with AlN and GaN buffer layers grown by plasma-assisted molecular beam epitaxy was studied. For N-polar samples filling of SAG features increased with decreasing lattice mismatch between the SAG and buffer. Defects related to Al-Si eutectic formation were observed in all samples, irrespective of lattice mismatch and buffer layer polarity. Eutectic related defects in the Si surface caused voids in N-polar samples, but not in metal-polar samples. Likewise, inversion domains were present in N-polar, but not metal-polar samples. The morphology of Ga-polar GaN SAG on nitride buffered Si(111) was similar to that of homoepitaxial GaN SAG.

Core-shell p-i-n GaN nanowire LEDs by N-polar selective area growth.

GaN nanowire LEDs with radial p-i-n junctions were grown by molecular beam epitaxy using N-polar selective area growth on Si(111) substrates. The N-polar selective area growth process facilitated the growth of isolated and high-aspect-ratio n-type NW cores that were not subject to self-shadowing effects during the subsequent growth of a conformal low-temperature Mg:GaN shell. LED devices were fabricated from single-NW and multiple-NW arrays in their as-grown configuration by contacting the n-type core through an underlying conductive GaN layer and the p-type NW shell via a metallization layer. The NW LEDs exhibited rectifying I-V characteristics with a sharp turn-on voltage near the GaN bandgap and low reverse bias leakage current. Under forward bias, the NW LEDs produced electroluminescence with a peak emission wavelength near 380 nm and exhibited a small spectral blueshift with increasing current injection, both of which are consistent with electron recombination in the p-type shell layer through donor-acceptor-pair recombination. These core-shell NW devices demonstrate N-polar selective area growth as an effective technique for producing on-chip nanoscale light sources.

Comparison of convergent beam electron diffraction and annular bright field atomic imaging for GaN polarity determination.

A comparison of two electron microscopy techniques used to determine the polarity of GaN nanowires is presented. The techniques are convergent beam electron diffraction (CBED) in TEM mode and annular bright field (ABF) imaging in aberration corrected STEM mode. Both measurements were made at nominally the same locations on a variety of GaN nanowires. In all cases the two techniques gave the same polarity result. An important aspect of the study was the calibration of the CBED pattern rotation relative to the TEM image. Three different microscopes were used for CBED measurements. For all three instruments there was a substantial rotation of the diffraction pattern (120 or 180°) relative to the image, which, if unaccounted for, would have resulted in incorrect polarity determination. The study also shows that structural defects such as inversion domains can be readily identified by ABF imaging, but may escape identification by CBED. The relative advantages of the two techniques are discussed.

Near-Field Control and Imaging of Free Charge Carrier Variations in GaN Nanowires.

Despite their uniform crystallinity, the shape and faceting of semiconducting nanowires (NWs) can give rise to variations in structure and associated electronic properties. Here we develop a hybrid scanning probe-based methodology to investigate local variations in electronic structure across individual n-doped GaN NWs integrated into a transistor device. We perform scanning microwave microscopy (SMM), which we combine with scanning gate microscopy (SGM) to determine the free-carrier SMM signal contribution and image local charge carrier density variations. In particular, we find significant variations in free carriers across NWs, with a higher carrier density at the wire facets. By increasing the local carrier density through tip-gating, we find that the tip injects current into the NW with strongly localized current when positioned over the wire vertices. These results suggest that the strong variations in electronic properties observed within NWs have significant implications for device design and may lead to new paths to optimization.

Long-term agroecosystem research in the central Mississippi river basin: hydrogeologic controls and crop management influence on nitrates in loess and fractured glacial till.

Nitrogen from agriculture is known to be a primary source of groundwater NO-N. Research was conducted in a northeastern Missouri watershed to assess the impact of cropping systems on NO-N for a loess and fractured glacial till aquifer underlying claypan soils. Three cropped fields with 10 yr of similar management were each instrumented with 20 to 25 monitoring wells, 3 to 15 m in depth, in 1991 to 1992. Wells were sampled and analyzed for NO-N at least annually from 1991 to 2004. Initial NO-N concentrations were variable, ranging from undetectable to >24 mg L but averaged 7.0 mg L. Groundwater NO-N was significantly higher in Field 3, probably the result of concurrent applications of manure and N fertilizer before 1980. Overall changes in NO-N levels in Fields 1 and 2 were generally small; however, NO-N levels for Field 3 have decreased an average of 0.28 mg L yr. Excessive loading of N into the matrix of the glacial till may have had a long-term impact on NO-N for this field. Despite the presence of dissolved O in the aquifer, evidence of denitrification in some upper-landscape groundwater wells was found. The greatest decreases in NO-N concentration occurred as groundwater moved through an in-field tree line or through a riparian zone. While overall conclusions were complicated by the long-term impact of past management, the capacity of the till to buffer changes, hydrogeologic variability found among wells, and the activity of biological processes, we conclude that cropping practices during this study did not increase glacial till NO-N.

GaN nanowire coated with atomic layer deposition of tungsten: a probe for near-field scanning microwave microscopy.

GaN nanowires were coated with tungsten by means of atomic layer deposition. These structures were then adapted as probe tips for near-field scanning microwave microscopy. These probes displayed a capacitive resolution of ~0.03 fF, which surpasses that of a commercial Pt tip. Upon imaging of MoS2 sheets with both the Pt and GaN nanowire tips, we found that the nanowire tips were comparatively immune to surface contamination and far more durable than their Pt counterparts.

Analysis of contact interfaces for single GaN nanowire devices.

Single GaN nanowire (NW) devices fabricated on SiO2 can exhibit a strong degradation after annealing due to the occurrence of void formation at the contact/SiO2 interface. This void formation can cause cracking and delamination of the metal film, which can increase the resistance or lead to a complete failure of the NW device. In order to address issues associated with void formation, a technique was developed that removes Ni/Au contact metal films from the substrates to allow for the examination and characterization of the contact/substrate and contact/NW interfaces of single GaN NW devices. This procedure determines the degree of adhesion of the contact films to the substrate and NWs and allows for the characterization of the morphology and composition of the contact interface with the substrate and nanowires. This technique is also useful for assessing the amount of residual contamination that remains from the NW suspension and from photolithographic processes on the NW-SiO2 surface prior to metal deposition. The detailed steps of this procedure are presented for the removal of annealed Ni/Au contacts to Mg-doped GaN NWs on a SiO2 substrate.

On-chip optical interconnects made with gallium nitride nanowires.

In this Letter we report on the fabrication, device characteristics, and optical coupling of a two-nanowire device comprising GaN nanowires with light-emitting and photoconductive capabilities. Axial p-n junction GaN nanowires were grown by molecular beam epitaxy, transferred to a non-native substrate, and selectively contacted to form discrete optical source or detector nanowire components. The optical coupling demonstrated for this device may provide new opportunities for integration of optical interconnects between on-chip electrical subsystems.