Time- and momentum-resolved photoemission studies using time-of-flight momentum microscopy at a free-electron laser.

Time-resolved photoemission with ultrafast pump and probe pulses is an emerging technique with wide application potential. Real-time recording of nonequilibrium electronic processes, transient states in chemical reactions, or the interplay of electronic and structural dynamics offers fascinating opportunities for future research. Combining valence-band and core-level spectroscopy with photoelectron diffraction for electronic, chemical, and structural analyses requires few 10 fs soft X-ray pulses with some 10 meV spectral resolution, which are currently available at high repetition rate free-electron lasers. We have constructed and optimized a versatile setup commissioned at FLASH/PG2 that combines free-electron laser capabilities together with a multidimensional recording scheme for photoemission studies. We use a full-field imaging momentum microscope with time-of-flight energy recording as the detector for mapping of 3D band structures in (kx, ky, E) parameter space with unprecedented efficiency. Our instrument can image full surface Brillouin zones with up to 7 Å-1 diameter in a binding-energy range of several eV, resolving about 2.5 × 105 data voxels simultaneously. Using the ultrafast excited state dynamics in the van der Waals semiconductor WSe2 measured at photon energies of 36.5 eV and 109.5 eV, we demonstrate an experimental energy resolution of 130 meV, a momentum resolution of 0.06 Å-1, and a system response function of 150 fs.

The occupied electronic structure of ultrathin boron doped diamond.

Using angle-resolved photoelectron spectroscopy, we compare the electronic band structure of an ultrathin (1.8 nm) δ-layer of boron-doped diamond with a bulk-like boron doped diamond film (3 µm). Surprisingly, the measurements indicate that except for a small change in the effective mass, there is no significant difference between the electronic structure of these samples, irrespective of their physical dimensionality, except for a small modification of the effective mass. While this suggests that, at the current time, it is not possible to fabricate boron-doped diamond structures with quantum properties, it also means that nanoscale boron doped diamond structures can be fabricated which retain the classical electronic properties of bulk-doped diamond, without a need to consider the influence of quantum confinement.

Simultaneous Conduction and Valence Band Quantization in Ultrashallow High-Density Doping Profiles in Semiconductors.

We demonstrate simultaneous quantization of conduction band (CB) and valence band (VB) states in silicon using ultrashallow, high-density, phosphorus doping profiles (so-called Si:P δ layers). We show that, in addition to the well-known quantization of CB states within the dopant plane, the confinement of VB-derived states between the subsurface P dopant layer and the Si surface gives rise to a simultaneous quantization of VB states in this narrow region. We also show that the VB quantization can be explained using a simple particle-in-a-box model, and that the number and energy separation of the quantized VB states depend on the depth of the P dopant layer beneath the Si surface. Since the quantized CB states do not show a strong dependence on the dopant depth (but rather on the dopant density), it is straightforward to exhibit control over the properties of the quantized CB and VB states independently of each other by choosing the dopant density and depth accordingly, thus offering new possibilities for engineering quantum matter.

Reaction pathways for pyridine adsorption on silicon (0 0 1).

Density functional theory is used to describe the reactions of chemisorption of pyridine on the silicon (0 0 1) surface. Adsorption energies of six relevant structures, and the activation energies between them are reported. We consider in detail the dative to tight-bridge transition for which conflicting results have been reported in the literature, and provide a description of the formation of inter-row chains observed in high-coverage experiments. We demonstrate that the choice of DFT functional has a considerable effect on the relative energetics and of the four DFT functionals considered, we find that the range-separated hybrid ωB97X-D functional with empirical dispersion provides the most consistent description of the experiment data.

Binding geometry of hydrogen-bonded chain motif in self-assembled gratings and layers on Ag(111).

Upon adsorption on the (111) facet of Ag, 4-[trans-2-(pyrid-4-yl-vinyl)] benzoic acid (PVBA) self-assembles into a highly ordered, chiral twin chain structure at submonolayer coverages with domains that can extend for micrometers in one dimension. Using polarization-dependent measurements of C and N K-shell excitations in near-edge X-ray absorption fine structure (NEXAFS) spectra, we determine the binding geometry of single PVBA molecules within this unique ensemble for both low and high coverage regimes. At submonolayer coverage, the molecule is twisted to facilitate the formation of hydrogen bonds. The gas-phase planarity is gradually recovered as the coverage is increased, with complete planarity coinciding with loss of order in the overlayer. Thermal treatment of the PVBA film results in deprotonation of the carboxyl tail of the molecule, but despite the suppression of the stabilizing hydrogen-bonds, the overlayer remains ordered.

A complete fabrication route for atomic-scale, donor-based devices in single-crystal germanium.

Despite the rapidly growing interest in Ge for ultrascaled classical transistors and innovative quantum devices, the field of Ge nanoelectronics is still in its infancy. One major hurdle has been electron confinement since fast dopant diffusion occurs when traditional Si CMOS fabrication processes are applied to Ge. We demonstrate a complete fabrication route for atomic-scale, donor-based devices in single-crystal Ge using a combination of scanning tunneling microscope lithography and high-quality crystal growth. The cornerstone of this fabrication process is an innovative lithographic procedure based on direct laser patterning of the semiconductor surface, allowing the gap between atomic-scale STM-patterned structures and the outside world to be bridged. Using this fabrication process, we show electron confinement in a 5 nm wide phosphorus-doped nanowire in single-crystal Ge. At cryogenic temperatures, Ohmic behavior is observed and a low planar resistivity of 8.3 kΩ/□ is measured.

Step-by-step growth of epitaxially aligned polythiophene by surface-confined reaction.

One of the great challenges in surface chemistry is to assemble aromatic building blocks into ordered structures that are mechanically robust and electronically interlinked--i.e., are held together by covalent bonds. We demonstrate the surface-confined growth of ordered arrays of poly(3,4-ethylenedioxythiophene) (PEDOT) chains, by using the substrate (the 110 facet of copper) simultaneously as template and catalyst for polymerization. Copper acts as promoter for the Ullmann coupling reaction, whereas the inherent anisotropy of the fcc 110 facet confines growth to a single dimension. High resolution scanning tunneling microscopy performed under ultrahigh vacuum conditions allows us to simultaneously image PEDOT oligomers and the copper lattice with atomic resolution. Density functional theory calculations confirm an unexpected adsorption geometry of the PEDOT oligomers, which stand on the sulfur atom of the thiophene ring rather than lying flat. This polymerization approach can be extended to many other halogen-terminated molecules to produce epitaxially aligned conjugated polymers. Such systems might be of central importance to develop future electronic and optoelectronic devices with high quality active materials, besides representing model systems for basic science investigations.

Self-assembly of rubrene on Cu(111).

We performed an ultra-high vacuum scanning tunneling microscopy (STM) investigation of the self-assembly of rubrene at room temperature on Cu(111), a metal surface with threefold symmetry. Rubrene self-assembles into two different structures called row and trimer. Both are different than the structures already observed on Cu(110) and Cu(100). Row and trimer structures have comparable molecular packing densities and are equally distributed across the surface. In the row structure the molecules are oriented with their backbone along the same high symmetry directions of the surface: [[Formula: see text]], [[Formula: see text]] or [[Formula: see text]]. The trimer structure is composed of units of three rubrene molecules, oriented along the high symmetry surface directions. These units are chiral, as revealed by height profile measurements by STM, and self-assemble in domains containing only one type of enantiomer.

Rattling modes and the intrinsic vibrational spectrum of beetle-type scanning tunneling microscopes.

It is known that the vibrational spectra of beetle-type scanning tunneling microscopes with a total mass of approximately 3-4 g contain extrinsic 'rattling' modes in the frequency range extending from 500 to 1700 Hz that interfere with image acquisition. These modes lie below the lowest calculated eigenfrequency of the beetle and it has been suggested that they arise from the inertial sliding of the beetle between surface asperities on the raceway. In this paper we describe some cross-coupling measurements that were performed on three home-built beetle-type STMs of two different designs. We provide evidence that suggests that for beetles with total masses of 12-15 g all the modes in the rattling range are intrinsic. This provides additional support for the notion that the vibrational properties of beetle-type scanning tunneling microscopes can be improved by increasing the contact pressure between the feet of the beetle and the raceway.

Compatibility of the thioamide functional group with beta-sheet secondary structure: incorporation of a thioamide linkage into a beta-hairpin peptide.

[structure: see text]. We report the incorporation of a thioamide linkage between the i + 2 and i + 3 residues of the type II' beta-turn of a peptide known to fold into a beta-hairpin conformation. Two-dimensional NMR spectroscopy and circular dichroism spectroscopy indicate that the thioxo peptide adopts a hairpin conformation similar to that of the oxo peptide and that the hairpin conformation persists at elevated temperatures. The results show that a thioamide linkage is compatible with beta-sheet secondary structure.

Patients with constipation-predominant irritable bowel syndrome (IBS) may have elevated serotonin concentrations in colonic mucosa as compared with diarrhea-predominant patients and subjects with normal bowel habits.

BACKGROUND: Serotonin (5-HT) may play an important role in the regulation of colonic motility in humans. However, it is not known whether alterations in the colonic 5-HT system are involved in the pathophysiology of irritable bowel syndrome (IBS). METHODS: Colonic mucosal specimens ranging from the ascending colon to the rectum were obtained from patients with diarrhea- or constipation-predominant IBS (n = 7 and n = 8, respectively) and from subjects with normal bowel habits (n = 7) by endoscopic biopsy in order to determine whether patients with different clinical manifestations of IBS have different mucosal disposition of 5-HT. The tissue concentrations of 5-HT and its major metabolite, 5-hydroxyindoleacetic acid, were determined by reversed-phase high-performance liquid chromatography with fluorescence detection. RESULTS: In all study groups, the mean mucosal 5-HT concentrations obtained from the rectum were significantly (p < 0.05) higher than those obtained from more cephalic regions of the colon. In addition, the overall mean mucosal 5-HT concentrations obtained from patients with constipation-predominant IBS were significantly (p < 0.05) higher than those obtained from the control subjects and patients with diarrhea-predominant IBS. No significant differences were observed in 5-hydroxyindoleacetic acid concentrations among the three groups. CONCLUSIONS: The mucosal 5-HT concentrations in the colon showed an ascending cephalocaudal gradient in all study groups. Although the mucosal 5-HT concentrations were elevated in patients with constipation-predominant IBS as compared with those with diarrhea-predominant IBS and the control subjects, further studies are necessary to determine whether the elevated mucosal 5-HT is a cause or a result of abnormal colonic motility.

Long-term nicotine adaptation in Caenorhabditis elegans involves PKC-dependent changes in nicotinic receptor abundance.

Chronic exposure to nicotine leads to long-term changes in both the abundance and activity of nicotinic acetylcholine receptors, processes thought to contribute to nicotine addiction. We have found that in Caenorhabditis elegans, prolonged nicotine treatment results in a long-lasting decrease in the abundance of nicotinic receptors that control egg-laying. In naive animals, acute exposure to cholinergic agonists led to the efficient stimulation of egg-laying, a response mediated by a nicotinic receptor functionally expressed in the vulval muscle cells. Overnight exposure to nicotine led to a specific and long-lasting change in egg-laying behavior, which rendered the nicotine-adapted animals insensitive to simulation of egg-laying by the nicotinic agonist and was accompanied by a promoter-independent reduction in receptor protein levels. Mutants defective in the gene tpa-1, which encodes a homolog of protein kinase C (PKC), failed to undergo adaptation to nicotine; after chronic nicotine exposure they remained sensitive to cholinergic agonists and retained high levels of receptor protein in the vulval muscles. These results suggest that PKC-dependent signaling pathways may promote nicotine adaptation via regulation of nicotinic receptor synthesis or degradation.

lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the mammalian CNS.

Elapid snake venom neurotoxins exert their effects through high-affinity interactions with specific neurotransmitter receptors. A novel murine gene, lynx1, is highly expressed in the brain and contains the cysteine-rich motif characteristic of this class of neurotoxins. Primary sequence and gene structure analyses reveal an evolutionary relationship between lynx1 and the Ly-6/neurotoxin gene family. lynx1 is expressed in large projection neurons in the hippocampus, cortex, and cerebellum. In cerebellar neurons, lynx1 protein is localized to a specific subdomain including the soma and proximal dendrites. lynx1 binding to brain sections correlates with the distribution of nAChRs, and application of lynx1 to Xenopus oocytes expressing nAChRs results in an increase in acetylcholine-evoked macroscopic currents. These results identify lynx1 as a novel protein modulator for nAChRs in vitro, which could have important implications in the regulation of cholinergic function in vivo.

Mutations in genes encoding extracellular matrix proteins suppress the emb-5 gastrulation defect in Caenorhabditis elegans.

The second division of the gut precursor E cells is lethally accelerated during Caenorhabditis elegans gastrulation by mutations in the emb-5 gene, which encodes a presumed nuclear protein. We have isolated suppressor mutations of the temperature-sensitive allele emb-5(hc61), screened for them among dpy and other mutations routinely used as genetic markers, and identified eight emb-5 suppressor genes. Of these eight suppressor genes, at least four encode extracellular matrix proteins, i.e., three collagens and one proteoglycan. The suppression of the emb-5 gastrulation defect seemed to require the maternal expression of the suppressors. Phenotypically, the suppressors by themselves slowed down early embryonic cell divisions and corrected the abnormal cell-division sequence of emb-5 mutant embryos. We propose an indirect stress-response mechanism to be the main cause of the suppression because: (1) none of these suppressors is specific, either to particular temperature-sensitive emb-5 alleles or to the emb-5 gene; (2) suppressible alleles of genes, reported here or elsewhere, are temperature sensitive or weak; (3) the suppression is not strong but marginal; (4) the suppression itself shows some degree of temperature dependency; and (5) none of the extracellular matrix proteins identified here is known to be expressed in oocytes or early embryos, despite the present observation that the suppression is maternal.

Atypical protein kinase C cooperates with PAR-3 to establish embryonic polarity in Caenorhabditis elegans.

Asymmetric cell divisions, critically important to specify cell types in the development of multicellular organisms, require polarized distribution of cytoplasmic components and the proper alignment of the mitotic apparatus. In Caenorhabditis elegans, the maternally expressed protein, PAR-3, is localized to one pole of asymmetrically dividing blastomeres and is required for these asymmetric divisions. In this paper, we report that an atypical protein kinase C (PKC-3) is essential for proper asymmetric cell divisions and co-localizes with PAR-3. Embryos depleted of PKC-3 by RNA interference die showing Par-like phenotypes including defects in early asymmetric divisions and mislocalized germline-specific granules (P granules). The defective phenotypes of PKC-3-depleted embryos are similar to those exhibited by mutants for par-3 and another par gene, par-6. Direct interaction of PKC-3 with PAR-3 is shown by in vitro binding analysis. This result is reinforced by the observation that PKC-3 and PAR-3 co-localize in vivo. Furthermore, PKC-3 and PAR-3 show mutual dependence on each other and on three of the other par genes for their localization. We conclude that PKC-3 plays an indispensable role in establishing embryonic polarity through interaction with PAR-3.

Molecular evidence for the direct involvement of a protein kinase C in developmental and behavioural susceptibility to tumour-promoting phorbol esters in Caenorhabditis elegans.

The nematode Caenorhabditis elegans displays developmental and behavioural sensitivity to tumour-promoting phorbol esters. This sensitivity involves the gene tpa-1, which encodes two protein kinase C isoforms, TPA-1A and TPA-1B. Here we report the molecular nature of the sensitivity in this animal. Characterization of transposon Tc1-induced phorbol ester-resistant mutants has revealed that Tc1 was inserted in a region encoding the kinase domain, resulting in the loss of tpa-1 products. Introduction of a genomic DNA containing the entire wild-type tpa-1 locus into a Tc1-inserted mutant restored the sensitivity to tumour promoters, and tpa-1 products were also produced. These results suggest that the function of wild-type TPA-1 is necessary and sufficient for tumour promoters to cause developmental and behavioural sensitivity in C. elegans.

The tpa-1 gene of Caenorhabditis elegans encodes two proteins similar to Ca(2+)-independent protein kinase Cs: evidence by complete genomic and complementary DNA sequences of the tpa-1 gene.

The gene tpa-1 on chromosome IV of the nematode Caenorhabditis elegans plays a major and definitive role in the adversary action of tumour-promoting phorbol esters, which induce growth arrest and locomotory distress in the animal. The gene was deduced to code for a protein kinase C (PKC) homologue by molecular cloning. We have now sequenced the complete genomic and complementary DNAs for tpa-1 and have analysed their structural features in detail: (1) tpa-1 spans over 20 kb consisting of eleven exons and ten introns; (2) two different-sized mRNAs are generated from the tpa-1 locus; (3) both mRNAs are trans-spliced to the trans-spliced leader SL1; (4) both mRNAs encode PKC isoforms, which are most similar to Ca(2+)-independent novel PKC0; (5) the two PKC isoforms differ from each other in that the smaller lacks the amino-terminal region of the larger corresponding to the first four exons and a portion of the fifth exon; and (6) three introns are located at; identical positions in the polypeptide sequences aligned between the C. elegans tpa-1 product and a PKC of the fruit fly Drosophila melanogaster.

The C. elegans unc-18 gene encodes a protein expressed in motor neurons.

The C. elegans unc-18 gene is required to maintain normal acetylcholine levels. We determined the complete structure of an unc-18 cDNA that encodes a protein of 591 highly charged and hydrophilic amino acids. The protein shows sequence similarity with elements of the secretory pathway in the yeast S. cerevisiae. Antibodies raised against a portion of the unc-18-encoded protein (UNC-18) detected a 68 kd soluble antigen on immunoblots and intensely stained all vertical cord motor neurons in situ. These findings suggest that UNC-18 participates in the axonal transport system and influences the acetylcholine flow in motor neurons.