Strain and Bond Length Dynamics upon Growth and Transfer of Graphene by NEXAFS Spectroscopy from First-Principles and Experiment.

As the quest toward novel materials proceeds, improved characterization technologies are needed. In particular, the atomic thickness in graphene and other 2D materials renders some conventional technologies obsolete. Characterization technologies at wafer level are needed with enough sensitivity to detect strain in order to inform fabrication. In this work, NEXAFS spectroscopy was combined with simulations to predict lattice parameters of graphene grown on copper and further transferred to a variety of substrates. The strains associated with the predicted lattice parameters are in agreement with experimental findings. The approach presented here holds promise to effectively measure strain in graphene and other 2D systems at wafer levels to inform manufacturing environments.

A tumor deconstruction platform identifies definitive end points in the evaluation of drug responses.

Tumor heterogeneity and the presence of drug-sensitive and refractory populations within the same tumor are almost never assessed in the drug discovery pipeline. Such incomplete assessment of drugs arising from spatial and temporal tumor cell heterogeneity reflects on their failure in the clinic and considerable wasted costs in the drug discovery pipeline. Here we report the derivation of a flow cytometry-based tumor deconstruction platform for resolution of at least 18 discrete tumor cell fractions. This is achieved through concurrent identification, quantification and analysis of components of cancer stem cell hierarchies, genetically instable clones and differentially cycling populations within a tumor. We also demonstrate such resolution of the tumor cytotype to be a potential value addition in drug screening through definitive cell target identification. Additionally, this real-time definition of intra-tumor heterogeneity provides a convenient, incisive and analytical tool for predicting drug efficacies through profiling perturbations within discrete tumor cell subsets in response to different drugs and candidates. Consequently, possible applications in informed therapeutic monitoring and drug repositioning in personalized cancer therapy would complement rational design of new candidates besides achieving a re-evaluation of existing drugs to derive non-obvious combinations that hold better chances of achieving remission.

Dynamic modulation of electronic properties of graphene by localized carbon doping using focused electron beam induced deposition.

We report on the first demonstration of controllable carbon doping of graphene to engineer local electronic properties of a graphene conduction channel using focused electron beam induced deposition (FEBID). Electrical measurements indicate that an "n-p-n" junction on graphene conduction channel is formed by partial carbon deposition near the source and drain metal contacts by low energy (<50 eV) secondary electrons due to inelastic collisions of long range backscattered primary electrons generated from a low dose of high energy (25 keV) electron beam (1 × 10(18) e(-) per cm(2)). Detailed AFM imaging provides direct evidence of the new mechanism responsible for dynamic evolution of the locally varying graphene doping. The FEBID carbon atoms, which are physisorbed and weakly bound to graphene, diffuse towards the middle of graphene conduction channel due to their surface chemical potential gradient, resulting in negative shift of Dirac voltage. Increasing a primary electron dose to 1 × 10(19) e(-) per cm(2) results in a significant increase of carbon deposition, such that it covers the entire graphene conduction channel at high surface density, leading to n-doping of graphene channel. Collectively, these findings establish a unique capability of FEBID technique to dynamically modulate the doping state of graphene, thus enabling a new route to resist-free, "direct-write" functional patterning of graphene-based electronic devices with potential for on-demand re-configurability.

Stick-slip water penetration into capillaries coated with swelling hydrogel.

We have observed intriguing stick-slip behavior during capillary pressure driven filling of borosilicate microtubes coated with hydrogel on their inner wall. Swelling of hydrogel upon exposure to a translating waterfront is accompanied by "stick-and-slip" motion. This results in the macroscopic filling velocity for water penetration into glass capillaries coated with poly(N-isopropylacrylamide) (PNIPAM) being constant throughout the filling process, and reduced by three orders of magnitude when compared to filling of uncoated capillaries. A simple scaling analysis is used to introduce a possible explanation by considering the mechanisms responsible for pinning and unpinning of the contact line. The explanation assumes that the time scale for water diffusion into a hydrogel film and the resulting swelling/change of the local meniscus contact angle define the duration of each "stick" event. The "slip" length scale is in turn established by the elastocapillary deformation of dry hydrogel at the pinning point of the contact line. The sequential dynamics of these processes then determine the rate of water filling into a swelling capillary. Collectively, these experimental and theoretical results provide a new conceptual framework for liquid motion confined by soft, dynamically evolving polymer interfaces, in which the system creates an energy barrier to further motion through elasto-capillary deformation, and then lowers the barrier through diffusive softening. This insight has implications for optimal design of microfluidic and lab-on-a-chip devices based on stimuli-responsive smart polymers.

Bidirectional rescue of extreme genetic predispositions to anxiety: impact of CRH receptor 1 as epigenetic plasticity gene in the amygdala.

The continuum of physiological anxiety up to psychopathology is not merely dependent on genes, but is orchestrated by the interplay of genetic predisposition, gene x environment and epigenetic interactions. Accordingly, inborn anxiety is considered a polygenic, multifactorial trait, likely to be shaped by environmentally driven plasticity at the genomic level. We here took advantage of the extreme genetic predisposition of the selectively bred high (HAB) and low anxiety (LAB) mouse model exhibiting high vs low anxiety-related behavior and tested whether and how beneficial (enriched environment) vs detrimental (chronic mild stress) environmental manipulations are capable of rescuing phenotypes from both ends of the anxiety continuum. We provide evidence that (i) even inborn and seemingly rigid behavioral and neuroendocrine phenotypes can bidirectionally be rescued by appropriate environmental stimuli, (ii) corticotropin-releasing hormone receptor 1 (Crhr1), critically involved in trait anxiety, shows bidirectional alterations in its expression in the basolateral amygdala (BLA) upon environmental stimulation, (iii) these alterations are linked to an increased methylation status of its promoter and, finally, (iv) binding of the transcription factor Yin Yang 1 (YY1) to the Crhr1 promoter contributes to its gene expression in a methylation-sensitive manner. Thus, Crhr1 in the BLA is critically involved as plasticity gene in the bidirectional epigenetic rescue of extremes in trait anxiety.

On modeling biomolecular-surface nonbonded interactions: application to nucleobase adsorption on single-wall carbon nanotube surfaces.

In this work we explored the selectivity of single nucleobases towards adsorption on chiral single-wall carbon nanotubes (SWCNTs) by density functional theory calculations. Specifically, the adsorption of molecular models of guanine (G), adenine (A), thymine (T), and cytosine (C), as well as of AT and GC Watson-Crick (WC) base pairs on chiral SWCNT C(6, 5), C(9, 1) and C(8, 3) model structures, was analyzed in detail. The importance of correcting the exchange-correlation functional for London dispersion was clearly demonstrated, yet limitations in modeling such interactions by considering the SWCNT as a molecular model may mask subtle effects in a molecular-macroscopic material system. The trend in the calculated adsorption energies of the nucleobases on same diameter C(6, 5) and C(9, 1) SWCNT surfaces, i.e., G > A > T > C, was consistent with related computations and experimental work on graphitic surfaces, however contradicting experimental data on the adsorption of single-strand short homo-oligonucleotides on SWCNTs that demonstrated a trend of G > C > A > T (Albertorio et al 2009 Nanotechnology 20 395101). A possible role of electrostatic interactions in this case was partially captured by applying the effective fragment potential method, emphasizing that the interplay of the various contributions in modeling nonbonded interactions is complicated by theoretical limitations. Finally, because the calculated adsorption energies for Watson-Crick base pairs have shown little effect upon adsorption of the base pair farther from the surface, the results on SWCNT sorting by salmon genomic DNA could be indicative of partial unfolding of the double helix upon adsorption on the SWCNT surface.

Understanding effects of molecular adsorption at a single-wall boron nitride nanotube interface from density functional theory calculations.

In this paper, we explored computationally the feasibility of modulating the bandgap in a single-wall BN nanotube (BNNT) upon noncovalent adsorption of organic molecules, combined with the application of a transverse electric field. Effects of analytes' physisorption on the surface of BNNTs regarding structural and electronic properties were delineated. Relatively large binding energies were calculated, however, with minimal perturbation of the structural framework. Electronic structure calculations indicated that the bandgap of BNNTs can be modified by weak adsorption due to the presence of adsorbate states in the gap of the host system. Furthermore, we have shown that the application of a transverse electric field can tune the bandgap by shifting adsorbate states, consistent with calculated current-voltage characteristics.

Bio-based approaches to inorganic material synthesis.

Nature is an exquisite designer of inorganic materials using biomolecules as templates. Diatoms create intricate silica wall structures with fine features using the protein family of silaffins as templates. Marine sponges create silica spicules also using proteins, termed silicateins. In recent years, our group and others have used biomolecules as templates for the deposition of inorganic materials. In contrast with the traditional materials science approach, which requires high heat, extreme pH and non-aqueous solutions, the bio-based approaches allow the reactions to proceed usually at near ambient conditions. Additionally, the biological templates allow for the control of the inorganic nanoparticle morphology. The use of peptides and biomolecules for templating and assembling inorganics will be discussed here.

Ceramic nanoparticle assemblies with tailored shapes and tailored chemistries via biosculpting and shape-preserving inorganic conversion.

A novel biosynthetic paradigm is introduced for fabricating three-dimensional (3-D) ceramic nanoparticle assemblies with tailored shapes and tailored chemistries: biosculpting and shape-preserving inorganic conversion (BaSIC). Biosculpting refers to the use of biomolecules that direct the precipitation of ceramic nanoparticles to form a continuous 3-D structure with a tailored shape. We used a peptide derived from a diatom (a type of unicellular algae) to biosculpt silica nanoparticle based assemblies that, in turn, were converted into a new (nonsilica) composition via a shape-preserving gas/silica displacement reaction. Interwoven, microfilamentary silica structures were prepared by exposing a peptide, derived from the silaffin-1A protein of the diatom Cylindrotheca fusiformis, to a tetramethylorthosilicate solution under a linear shear flow condition. Subsequent exposure of the silica microfilaments to magnesium gas at 900 degrees C resulted in conversion into nanocrystalline magnesium oxide microfilaments with a retention of fine (submicrometer) features. Fluid(gas or liquid)/silica displacement reactions leading to a variety of other oxides have also been identified. This hybrid (biogenic/synthetic) approach opens the door to biosculpted ceramic microcomponents with multifarious tailored shapes and compositions for a wide range of environmental, aerospace, biomedical, chemical, telecommunications, automotive, manufacturing, and defense applications.

The thermostability of an alpha-helical coiled-coil protein and its potential use in sensor applications.

Coiled-coil proteins are assemblies of two to four alpha-helices that pack together in a parallel or anti-parallel fashion. Coiled-coil structures can confer a variety of functional capabilities, which include enabling proteins, such as myosin, to function in the contractile apparatus of muscle and non-muscle cells. The TlpA protein encoded by the virulence plasmid of Salmonella is an alpha-helical protein that forms an elongated coiled-coil homodimer. A number of studies have clearly established the role of TlpA as a temperature-sensing gene regulator, however the potential use of a TlpA in a thermo-sensor application outside of the organism has not been exploited. In this paper, we demonstrate that TlpA has several characteristics that are common with alpha-helical coiled-coils and its thermal folding and unfolding is reversible and rapid. TlpA is extremely sensitive to changes in temperature. We have also compared the heat-stability of TlpA with other structurally similar proteins. Using a folding reporter, in which TlpA is expressed as a C-terminal fusion with green fluorescent protein (GFP), we were able to use fluorescence as an indicator of folding and unfolding of the fusion protein. Our results on the rapid conformational changes inherent in TlpA support the previous findings and we present here preliminary data on the use of a GFP-TlpA fusion protein as temperature sensor.

Ultrafast holographic nanopatterning of biocatalytically formed silica.

Diatoms are of interest to the materials research community because of their ability to create highly complex and intricate silica structures under physiological conditions: what these single-cell organisms accomplish so elegantly in nature requires extreme laboratory conditions to duplicate-this is true for even the simplest of structures. Following the identification of polycationic peptides from the diatom Cylindrotheca fusiformis, simple silica nanospheres can now be synthesized in vitro from silanes at nearly neutral pH and at ambient temperatures and pressures. Here we describe a method for creating a hybrid organic/inorganic ordered nanostructure of silica spheres through the incorporation of a polycationic peptide (derived from the C. fusiformis silaffin-1 protein) into a polymer hologram created by two-photon-induced photopolymerization. When these peptide nanopatterned holographic structures are exposed to a silicic acid, an ordered array of silica nanospheres is deposited onto the clear polymer substrate. These structures exhibit a nearly fifty-fold increase in diffraction efficiency over a comparable polymer hologram without silica. This approach, combining the ease of processability of an organic polymer with the improved mechanical and optical properties of an inorganic material, could be of practical use for the fabrication of photonic devices.

Use of small fluorescent molecules to monitor channel activity.

The Mechanosensitive channel of Large conductance (MscL) allows bacteria to rapidly adapt to changing environmental conditions such as osmolarity. The MscL channel opens in response to increases in membrane tension, which allows for the efflux of cytoplasmic constituents. Here we describe the cloning and expression of Salmonella typhimurium MscL (St-MscL). The amino acid sequence encoding for this MscL exhibits a high degree of similarity to Escherichia coli MscL (Eco-MscL). Using a fluorescence efflux assay, we demonstrate that efflux through the MscL channel during hypoosmotic shock can be monitored using endogenously produced fluorophores. These fluorophores are synthesized by a cotransformed gene, cobA. In addition, we observe that thermal stimulation, i.e., heat shock, can induce efflux through MscL.

The PBN1 gene of Saccharomyces cerevisiae: an essential gene that is required for the post-translational processing of the protease B precursor.

The vacuolar hydrolase protease B in Saccharomyces cerevisiae is synthesized as an inactive precursor (Prb1p). The precursor undergoes post-translational modifications while transiting the secretory pathway. In addition to N- and O-linked glycosylations, four proteolytic cleavages occur during the maturation of Prb1p. Removal of the signal peptide by signal peptidase and the autocatalytic cleavage of the large amino-terminal propeptide occur in the endoplasmic reticulum (ER). Two carboxy-terminal cleavages of the post regions occur in the vacuole: the first cleavage is catalyzed by protease A and the second results from autocatalysis. We have isolated a mutant, pbn1-1, that exhibits a defect in the ER processing of Prb1p. The autocatalytic cleavage of the propeptide from Prb1p does not occur and Prb1p is rapidly degraded in the cytosol. PBN1 was cloned and is identical to YCL052c on chromosome III. PBN1 is an essential gene that encodes a novel protein. Pbn1p is predicted to contain a sub-C-terminal transmembrane domain but no signal sequence. A functional HA epitope-tagged Pbn1p fusion localizes to the ER. Pbn1p is N-glycosylated in its amino-terminal domain, indicating a lumenal orientation despite the lack of a signal sequence. Based on these results, we propose that one of the functions of Pbn1p is to aid in the autocatalytic processing of Prb1p.

Regulation of the proteinase B structural gene PRB1 in Saccharomyces cerevisiae.

The expression of PRB1, the gene that encodes the precursor to the soluble vacuolar proteinase B (PrB) in Saccharomyces cerevisiae, is regulated by carbon and nitrogen sources and by growth phase. Little or no PRB1 mRNA is detectable during exponential growth on glucose as the carbon source; it begins to accumulate as cells exhaust the glucose. Previous work has shown that glucose repression of PRB1 transcription is not mediated by HXK2 or by the SNF1, SNF4, and SNF6 genes (C. M. Moehle and E. W. Jones, Genetics 124:39-55, 1990). We analyzed the effects of mutations in the MIG1, TUP1, and GRR1 genes on glucose repression of PRB1 and found that mutations in each partially alleviate glucose repression. tup1 and mig1 mutants fail to translocate all of the Prb1p into the lumen of the endoplasmic reticulum. A screen for new mutants revealed mutations in MIG1 and REG1, genes already known to regulate glucose repression, as well as in three new genes that we have named PBD1 to PBD3; all cause derepressed expression. Mutations that result in failure to completely derepress PRB1 were also identified in two new genes, named PND1 and PND2. Good nitrogen sources, like ammonia, repress PRB1 transcription; mutations in URE2 do not affect this response. Derepression upon transfer to a poor nitrogen source is dependent upon GLN3.