Imaging Valley Excitons in a 2D Semiconductor with Scanning Tunneling Microscope-Induced Luminescence

Valley excitons dominate the optoelectronic response of transition-metal dichalcogenides and are drastically affected by structural and environmental inhomogeneities localized in these materials. Critical to understanding and controlling these nanoscale excitonic changes is the ability to correlate the imaging of excitonic states with crystalline structures on the atomic scale. Here, we apply scanning tunneling microscope-induced luminescence microscopy to image valley excitons in a semiconducting transition-metal dichalcogenide monolayer decoupled by a 10 nanometer-thick hexagonal-boron-nitride flake incorporated in a lateral homojunction on an Au electrode surface. This design enables the observation of chiral excitonic emission arising from neutral and charged valley excitons of the monolayer semiconductor at ambipolar voltages with a quantum efficiency up to ∼10-5 photon/electron. The measured light helicity demonstrates considerable circular polarization dependent on the sample voltage, reaching as much as 40%. The real-space luminescence imaging maps─at subnanometer resolution─of the valley excitons reveal striking spatial variations associated with localized inhomogeneities, including surface impurities and possibly nanoscale dielectric and/or potential disorders in the monolayer. Our study introduces a promising format for 2D materials to explore and tailor their optoelectronic processes at the atomic scale.

Backbone Engineering of Monodisperse Conjugated Polymers via Integrated Iterative Binomial Synthesis

Synthesis of sequence-defined monodisperse π-conjugated polymers with versatile backbones remains a substantial challenge. Here we report the development of an integrated iterative binomial synthesis (IIBS) strategy to enable backbone engineering of conjugated polymers with precisely controlled lengths and sequences as well as high molecular weights. The IIBS strategy capitalizes on the use of phenol as a surrogate for aryl bromide and represents the merge between protecting-group-aided iterative synthesis (PAIS) and iterative binomial synthesis (IBS). Long and monodisperse conjugated polymers with diverse irregular backbones, which are inaccessible by conventional polymerizations, can be efficiently prepared by IIBS. In addition, topology-dependent and chain-length-dependent properties have been investigated.

Low-Frequency Oscillations in Optical Measurements of Metal-Nanoparticle Vibrations

Time-resolved optical measurements of vibrating metal nanoparticles have been used extensively to probe the ultrafast mechanical properties of the nanoparticles and of the surrounding liquid, but nearly all investigations so far have been limited to the linear regime. Here, we report the observation of a low-frequency oscillating signal in transient-absorption measurements of nanoparticles with octahedral gold cores and cubic silver shells; the signal appears at the difference of two mechanical vibrational frequencies in the particles, suggesting a nonlinear mixing process. We tentatively attribute this proposed mixing to a nonlinear coupling between a vibrational mode of the nanoparticle and its optical-frequency plasmon resonance. The optimization of this nonlinear transduction may enable high-efficiency opto-mechanical frequency mixing in the GHz-THz frequency regime.

Ingrained: An Automated Framework for Fusing Atomic-Scale Image Simulations into Experiments

To fully leverage the power of image simulation to corroborate and explain patterns and structures in atomic resolution microscopy, an initial correspondence between the simulation and experimental image must be established at the outset of further high accuracy simulations or calculations. Furthermore, if simulation is to be used in context of highly automated processes or high-throughput optimization, the process of finding this correspondence itself must be automated. In this work, "ingrained," an open-source automation framework which solves for this correspondence and fuses atomic resolution image simulations into the experimental images to which they correspond, is introduced. Herein, the overall "ingrained" workflow, focusing on its application to interface structure approximations, and the development of an experimentally rationalized forward model for scanning tunneling microscopy simulation are described.

Silicon-Phosphorene Nanocavity-Enhanced Optical Emission at Telecommunications Wavelengths

Generating and amplifying light in silicon (Si) continues to attract significant attention due to the possibility of integrating optical and electronic components in a single material platform. Unfortunately, silicon is an indirect band gap material and therefore an inefficient emitter of light. With the rise of integrated photonics, the search for silicon-based light sources has evolved from a scientific quest to a major technological bottleneck for scalable, CMOS-compatible, light sources. Recently, emerging two-dimensional materials have opened the prospect of tailoring material properties based on atomic layers. Few-layer phosphorene, which is isolated through exfoliation from black phosphorus (BP), is a great candidate to partner with silicon due to its layer-tunable direct band gap in the near-infrared where silicon is transparent. Here we demonstrate a hybrid silicon optical emitter composed of few-layer phosphorene nanomaterial flakes coupled to silicon photonic crystal resonators. We show single-mode emission in the telecommunications band of 1.55 μm ( E_g = 0.8 eV) under continuous wave optical excitation at room temperature. The solution-processed few-layer BP flakes enable tunable emission across a broad range of wavelengths and the simultaneous creation of multiple devices. Our work highlights the versatility of the Si-BP material platform for creating optically active devices in integrated silicon chips.

A modular synthetic approach for band-gap engineering of armchair graphene nanoribbons

Despite the great promise of armchair graphene nanoribbons (aGNRs) as high-performance semiconductors, practical band-gap engineering of aGNRs remains an unmet challenge. Given that width and edge structures are the two key factors for modulating band-gaps of aGNRs, a reliable synthetic method that allows control of both factors would be highly desirable. Here we report a simple modular strategy for efficient preparation of N = 6 aGNR, the narrowest member in the N = 3p (p: natural number) aGNR family, and two unsymmetrically edge-functionalized GNRs that contain benzothiadiazole and benzotriazole moieties. The trend of band-gap transitions among these GNRs parallels those in donor–acceptor alternating conjugated polymers. In addition, post-functionalization of the unsymmetrical heterocyclic edge via C–H borylation permits further band-gap tuning. Therefore, this method opens the door for convenient band-gap engineering of aGNRs through modifying the heteroarenes on the edge.

Effective band-gap engineering of armchair graphene nanoribbons calls for control over both width and edge structure. Here, the authors report a modular synthesis of narrow N = 6 armchair graphene nanoribbons whose edges can be unsymmetrically modified with heteroarenes, introducing a simple way to tune band gap.

Imaging Catalytic Activation of CO2 on Cu2O (110): A First-Principles Study

Balancing global energy needs against increasing greenhouse gas emissions requires new methods for efficient CO₂ reduction. While photoreduction of CO₂ is promising, the rational design of photocatalysts hinges on precise characterization of the surface catalytic reactions. Cu₂O is a promising next-generation photocatalyst, but the atomic-scale description of the interaction between CO₂ and the Cu₂O surface is largely unknown, and detailed experimental measures are lacking. In this study, density-functional theory (DFT) calculations have been performed to identify the Cu₂O (110) surface stoichiometry that favors CO₂ reduction. To facilitate interpretation of scanning tunneling microscopy (STM) and X-ray absorption near-edge structures (XANES) measurements, which are useful for characterizing catalytic reactions, we present simulations based on DFT-derived surface morphologies with various adsorbate types. STM and XANES simulations were performed using the Tersoff-Hamann approximation and Bethe-Salpeter equation (BSE) approach, respectively. The results provide guidance for observation of CO₂ reduction reaction on, and rational surface engineering of, Cu₂O (110). They also demonstrate the effectiveness of computational image and spectroscopy modeling as a predictive tool for surface catalysis characterization.

Atomistic determination of the surface structure of Cu2O(111): experiment and theory

Atomic-scale defects on the surface of Cu₂O(111) are characterized through UHV STM measurements, DFT calculations and STM simulations.

Understanding How Acoustic Vibrations Modulate the Optical Response of Plasmonic Metal Nanoparticles

Measurements of acoustic vibrations in nanoparticles provide an opportunity to study mechanical phenomena at nanometer length scales and picosecond time scales. Vibrations in noble-metal nanoparticles have attracted particular attention because they couple to plasmon resonances in the nanoparticles, leading to strong modulation of optical absorption and scattering. There are three mechanisms that transduce the mechanical oscillations into changes in the plasmon resonance: (1) changes in the nanoparticle geometry, (2) changes in electron density due to changes in the nanoparticle volume, and (3) changes in the interband transition energies due to compression/expansion of the nanoparticle (deformation potential). These mechanisms have been studied in the past to explain the origin of the experimental signals; however, a thorough quantitative connection between the coupling of phonon and plasmon modes has not yet been made, and the separate contribution of each coupling mechanism has not yet been quantified. Here, we present a numerical method to quantitatively determine the coupling between vibrational and plasmon modes in noble-metal nanoparticles of arbitrary geometries and apply it to silver and gold spheres, shells, rods, and cubes in the context of time-resolved measurements. We separately determine the parts of the optical response that are due to shape changes, changes in electron density, and changes in deformation potential. We further show that coupling is, in general, strongest when the regions of largest electric field (plasmon mode) and largest displacement (phonon mode) overlap. These results clarify reported experimental results and should help guide future experiments and potential applications.

Self-Sustained Micromechanical Oscillator with Linear Feedback

Autonomous oscillators, such as clocks and lasers, produce periodic signals without any external frequency reference. In order to sustain stable periodic motion, there needs to be an external energy supply as well as nonlinearity built into the oscillator to regulate the amplitude. Usually, nonlinearity is provided by the sustaining feedback mechanism, which also supplies energy, whereas the constituent resonator that determines the output frequency stays linear. Here, we propose a new self-sustaining scheme that relies on the nonlinearity originating from the resonator itself to limit the oscillation amplitude, while the feedback remains linear. We introduce a model for describing the working principle of the self-sustained oscillations and validate it with experiments performed on a nonlinear microelectromechanical oscillator.

Large Spatially Resolved Rectification in a Donor-Acceptor Molecular Heterojunction

We demonstrate that rectification ratios (RR) of ≳250 (≳1000) at biases of 0.5 V (1.2 V) are achievable at the two-molecule limit for donor-acceptor bilayers of pentacene on C60 on Cu using scanning tunneling spectroscopy and microscopy. Using first-principles calculations, we show that the system behaves as a molecular Schottky diode with a tunneling transport mechanism from semiconducting pentacene to Cu-hybridized metallic C60. Low-bias RRs vary by two orders-of-magnitude at the edge of these molecular heterojunctions due to increased Stark shifts and confinement effects.

Visualizing Redox Dynamics of a Single Ag/AgCl Heterogeneous Nanocatalyst at Atomic Resolution

Operando characterization of gas-solid reactions at the atomic scale is of great importance for determining the mechanism of catalysis. This is especially true in the study of heterostructures because of structural correlation between the different parts. However, such experiments are challenging and have rarely been accomplished. In this work, atomic scale redox dynamics of Ag/AgCl heterostructures have been studied using in situ environmental transmission electron microscopy (ETEM) in combination with density function theory (DFT) calculations. The reduction of Ag/AgCl to Ag is likely a result of the formation of Cl vacancies while Ag(+) ions accept electrons. The oxidation process of Ag/AgCl has been observed: rather than direct replacement of Cl by O, the Ag/AgCl nanocatalyst was first reduced to Ag, and then Ag was oxidized to different phases of silver oxide under different O2 partial pressures. Ag2O formed at low O2 partial pressure, whereas AgO formed at atmospheric pressure. By combining in situ ETEM observation and DFT calculations, this structural evolution is characterized in a distinct nanoscale environment.

Environmental factors in the development of autism spectrum disorders

Autism spectrum disorders (ASD) are highly heterogeneous developmental conditions characterized by deficits in social interaction, verbal and nonverbal communication, and obsessive/stereotyped patterns of behavior and repetitive movements. Social interaction impairments are the most characteristic deficits in ASD. There is also evidence of impoverished language and empathy, a profound inability to use standard nonverbal behaviors (eye contact, affective expression) to regulate social interactions with others, difficulties in showing empathy, failure to share enjoyment, interests and achievements with others, and a lack of social and emotional reciprocity. In developed countries, it is now reported that 1%-1.5% of children have ASD, and in the US 2015 CDC reports that approximately one in 45 children suffer from ASD. Despite the intense research focus on ASD in the last decade, the underlying etiology remains unknown. Genetic research involving twins and family studies strongly supports a significant contribution of environmental factors in addition to genetic factors in ASD etiology. A comprehensive literature search has implicated several environmental factors associated with the development of ASD. These include pesticides, phthalates, polychlorinated biphenyls, solvents, air pollutants, fragrances, glyphosate and heavy metals, especially aluminum used in vaccines as adjuvant. Importantly, the majority of these toxicants are some of the most common ingredients in cosmetics and herbicides to which almost all of us are regularly exposed to in the form of fragrances, face makeup, cologne, air fresheners, food flavors, detergents, insecticides and herbicides. In this review we describe various scientific data to show the role of environmental factors in ASD.

Current-Driven Hydrogen Desorption from Graphene: Experiment and Theory

Electron-stimulated desorption of hydrogen from the graphene/SiC(0001) surface at room temperature was investigated with ultrahigh vacuum scanning tunneling microscopy and ab initio calculations in order to elucidate the desorption mechanisms and pathways. Two different desorption processes were observed. In the high electron energy regime (4-8 eV), the desorption yield is independent of both voltage and current, which is attributed to the direct electronic excitation of the C-H bond. In the low electron energy regime (2-4 eV), however, the desorption yield exhibits a threshold dependence on voltage, which is explained by the vibrational excitation of the C-H bond via transient ionization induced by inelastic tunneling electrons. The observed current independence of the desorption yield suggests that the vibrational excitation is a single-electron process. We also observed that the curvature of graphene dramatically affects hydrogen desorption. Desorption from concave regions was measured to be much more probable than desorption from convex regions in the low electron energy regime (∼2 eV), as would be expected from the identified desorption mechanism.

Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs

At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal.

Nonlinearity-induced synchronization enhancement in micromechanical oscillators

An autonomous oscillator synchronizes to an external harmonic force only when the forcing frequency lies within a certain interval-known as the synchronization range-around the oscillator's natural frequency. Under ordinary conditions, the width of the synchronization range decreases when the oscillation amplitude grows, which constrains synchronized motion of micro- and nanomechanical resonators to narrow frequency and amplitude bounds. Here, we show that nonlinearity in the oscillator can be exploited to manifest a regime where the synchronization range increases with increasing oscillation amplitude. Experimental data are provided for self-sustained micromechanical oscillators operating in this regime, and analytical results show that nonlinearities are the key determinants of this effect. Our results provide a new strategy to enhance the synchronization of micromechanical oscillators by capitalizing on their intrinsic nonlinear dynamics.

Self-assembled nanoparticle drumhead resonators

The self-assembly of nanoscale structures from functional nanoparticles has provided a powerful path to developing devices with emergent properties from the bottom-up. Here we demonstrate that freestanding sheets self-assembled from various nanoparticles form versatile nanomechanical resonators in the megahertz frequency range. Using spatially resolved laser-interferometry to measure thermal vibrational spectra and image vibration modes, we show that their dynamic behavior is in excellent agreement with linear elastic response for prestressed drumheads of negligible bending stiffness. Fabricated in a simple one-step drying-mediated process, these resonators are highly robust and their inorganic-organic hybrid nature offers an extremely low mass, low stiffness, and the potential to couple the intrinsic functionality of the nanoparticle building blocks to nanomechanical motion.

Chiral "pinwheel" heterojunctions self-assembled from C60 and pentacene

We demonstrate the self-assembly of C60 and pentacene (Pn) molecules into acceptor-donor heterostructures which are well-ordered and--despite the high degree of symmetry of the constituent molecules--chiral. Pn was deposited on Cu(111) to monolayer coverage, producing the random-tiling (R) phase as previously described. Atop R-phase Pn, postdeposited C60 molecules cause rearrangement of the Pn molecules into domains based on chiral supramolecular "pinwheels". These two molecules are the highest-symmetry achiral molecules so far observed to coalesce into chiral heterostructures. Also, the chiral pinwheels (composed of 1 C60 and 6 Pn each) may share Pn molecules in different ways to produce structures with different lattice parameters and degree of chirality. High-resolution scanning tunneling microscopy results and knowledge of adsorption sites allow the determination of these structures to a high degree of confidence. The measurement of chiral angles identical to those predicted is a further demonstration of the accuracy of the models. van der Waals density functional theory calculations reveal that the Pn molecules around each C60 are torsionally flexed around their long molecular axes and that there is charge transfer from C60 to Pn in each pinwheel.

Structural and electronic decoupling of C₆₀ from epitaxial graphene on SiC

We have investigated the initial stages of growth and the electronic structure of C(60) molecules on graphene grown epitaxially on SiC(0001) at the single-molecule level using cryogenic ultrahigh vacuum scanning tunneling microscopy and spectroscopy. We observe that the first layer of C(60) molecules self-assembles into a well-ordered, close-packed arrangement on graphene upon molecular deposition at room temperature while exhibiting a subtle C(60) superlattice. We measure a highest occupied molecular orbital-lowest unoccupied molecular orbital gap of ∼3.5 eV for the C(60) molecules on graphene in submonolayer regime, indicating a significantly smaller amount of charge transfer from the graphene to C(60) and substrate-induced screening as compared to C(60) adsorbed on metallic substrates. Our results have important implications for the use of graphene for future device applications that require electronic decoupling between functional molecular adsorbates and substrates.

Conduction of topologically protected charged ferroelectric domain walls

We report on the observation of nanoscale conduction at ferroelectric domain walls in hexagonal HoMnO(3) protected by the topology of multiferroic vortices using in situ conductive atomic force microscopy, piezoresponse force microscopy, and Kelvin-probe force microscopy at low temperatures. In addition to previously observed Schottky-like rectification at low bias [Phys. Rev. Lett. 104, 217601 (2010)], conductance spectra reveal that negatively charged tail-to-tail walls exhibit enhanced conduction at high forward bias, while positively charged head-to-head walls exhibit suppressed conduction at high reverse bias. Our results pave the way for understanding the semiconducting properties of the domains and domain walls in small-gap ferroelectrics.

Emergence of excited-state plasmon modes in linear hydrogen chains from time-dependent quantum mechanical methods

Explicitly time-dependent configuration-interaction theory is used to predict a new type of plasmonic behavior in linear hydrogen chains. After an intense ultrashort laser pulse brings the system into a broad superposition of excited states, the electronic dipole of the entire chain oscillates coherently, and the system is predicted to emit radiation at energies significantly lower than the first absorption band. A simple classical model accurately predicts the energy of this plasmon resonance for different hydrogen chain lengths and electron densities, demonstrating that collective, free-electron-like behavior can arise in chains of as few as 20 hydrogen atoms. The excitation mechanism for this plasmonic resonance is a highly nonlinear, multiphoton process, different from the linear excitation of ordinary surface plasmons.

Atomic-scale investigation of graphene grown on Cu foil and the effects of thermal annealing

We have investigated the effects of thermal annealing on ex-situ chemically vapor deposited submonolayer graphene islands on polycrystalline Cu foil at the atomic-scale using ultrahigh vacuum scanning tunneling microscopy. Low-temperature annealed graphene islands on Cu foil (at ∼430 °C) exhibit predominantly striped Moiré patterns, indicating a relatively weak interaction between graphene and the underlying polycrystalline Cu foil. Rapid high-temperature annealing of the sample (at 700-800 °C) gives rise to the removal of Cu oxide and the recovery of crystallographic features of the copper that surrounds the intact graphene. These experimental observations of continuous crystalline features between the underlying copper (beneath the graphene islands) and the surrounding exposed copper areas revealed by high-temperature annealing demonstrates the impenetrable nature of graphene and its potential application as a protective layer against corrosion.

Epitaxial graphene on Cu(111)

The growth of graphene on single crystal Cu(111) has been achieved by thermal decomposition of ethylene in an ultrahigh vacuum chamber for the first time. The structural and electronic properties of graphene on Cu(111) have been investigated by scanning tunneling microscopy and spectroscopy. The nucleation of monolayer islands and two predominant domain orientations have been observed, which lead to the formation of numerous domain boundaries with increasing coverage. These results reveal that reducing the density of domain boundaries is one challenge of growing high-quality graphene on copper.

Polarization-modulated rectification at ferroelectric surfaces

By correlating room temperature conductive atomic force microscopy with low temperature electrostatic force microscopy images of the same sample region, we demonstrate that nanoscale electric conduction between a sharp tip and the surface of ferroelectric HoMnO3 is intrinsically modulated by the polarization of ferroelectric domains. Conductance spectra reveal that the electric conduction is described by polarization-induced Schottky-like rectification at low bias, but dominated by a space-charge limited conduction mechanism at high bias. Our observation demonstrates visualization of ferroelectric domain structure by electric conduction, which may be used for nondestructive readout of nanoscale ferroelectric memories and/or ferroelectric sensors.

Nanometer-scale striped surface terminations on fractured SrTiO(3) surfaces

Using cross-sectional scanning tunneling microscopy on in situ fractured SrTiO(3), one of the most commonly used substrates for the growth of complex oxide thin films and superlattices, atomically smooth terraces have been observed on (001) surfaces. Furthermore, it was discovered that fracturing this material at room temperature results in the formation of stripe patterned domains having characteristic widths ( approximately 10 to approximately 20 nm) of alternating surface terminations that extend over a long range. Spatial characterization utilizing spectroscopy techniques revealed a strong contrast in the electronic structure of the two domains. Combining these results with topographic data, we are able to assign both TiO(2) and SrO terminations to their respective domains. The results of this experiment reveal that fracturing this material leads to reproducibly flat surfaces that can be characterized at the atomic-scale and suggest that this technique can be utilized for the study of technologically relevant complex oxide interfaces.

Patterning graphene at the nanometer scale via hydrogen desorption

We have demonstrated the reversible and local modification of the electronic properties of graphene by hydrogen passivation and subsequent electron-stimulated hydrogen desorption with an scanning tunneling microscope tip. In addition to changing the morphology, we show that the hydrogen passivation is stable at room temperature and modifies the electronic properties of graphene, opening a gap in the local density of states. This insulating state is reversed by local desorption of the hydrogen, and the unaltered electronic properties of graphene are recovered. Using this mechanism, we have "written" graphene patterns on nanometer length scales. For patterned regions that are roughly 20 nm or greater, the inherent electronic properties of graphene are completely recovered. Below 20 nm we observe dramatic variations in the electronic properties of the graphene as a function of pattern size. This reversible and local mechanism for modifying the electronic properties of graphene has far-reaching implications for nanoscale circuitry fabricated from this revolutionary material.

Temperature and size dependence of antiferromagnetism in mn nanostructures

We report on variable-temperature STM investigations of the spontaneous long-range magnetic order of Mn monolayer nanostructures epitaxially grown on stepped W(110). The measurements reveal that the onset of the antiferromagnetic order is closely related to the Mn nanostructure width along the [001] direction, with a decreasing Néel temperature as we move from a 2D toward a quasi-1D system. In contrast, lateral confinement along the [110] direction seems to play a less important role. The results are discussed in terms of anisotropic exchange coupling and of boundary effects, both potentially stabilizing long-range magnetic order in nanostructures confined in the [110] direction.

Electroluminescence from electrolyte-gated carbon nanotube field-effect transistors

We demonstrate near-infrared electroluminescence from ambipolar, electrolyte-gated arrays of highly aligned single-walled carbon nanotubes (SWNT). Using electrolytes instead of traditional oxide dielectrics in carbon nanotube field-effect transistors (FET) facilitates injection and accumulation of high densities of holes and electrons at very low gate voltages with minimal current hysteresis. We observe numerous emission spots, each corresponding to individual nanotubes in the array. The positions of these spots indicate the meeting point of the electron and hole accumulation zones determined by the applied gate and source-drain voltages. The movement of emission spots with gate voltage yields information about relative band gaps, contact resistance, defects, and interaction between carbon nanotubes within the array. Introducing thin layers of HfO(2) and TiO(2) provides a means to modify exciton screening without fundamentally changing the current-voltage characteristics or electroluminescence yield of these devices.

Laser trapping of 225Ra and 226Ra with repumping by room-temperature blackbody radiation

We have demonstrated Zeeman slowing and capture of neutral 225Ra and 226Ra atoms in a magneto-optical trap. The intercombination transition 1S0-->3P1 is the only quasicycling transition in radium and was used for laser-cooling and trapping. Repumping along the 3D1-->1P1 transition extended the lifetime of the trap from milliseconds to seconds. Room-temperature blackbody radiation was demonstrated to provide repumping from the metastable 3P0 level. We measured the isotope shift and hyperfine splittings on the 3D1-->1P1 transition with the laser-cooled atoms, and set a limit on the lifetime of the 3D1 level based on the measured blackbody repumping rate. Laser-cooled and trapped radium is an attractive system for studying fundamental symmetries.

The interaction of folic acid derivatives in the methylation of homocysteine

1. The cobalamin-independent synthesis of methionine from serine and homocysteine by ultrasonic extracts of E. coli with tetrahydropteroyltriglutamate as cofactor was inhibited competitively by tetrahydropteroylmonoglutamate and derivatives which were readily converted into this compound. 2. The potency of these inhibitors was directly related to their ability to function as cofactors or substrates in the alternative, cobalamin- dependent mechanism for homocysteine methylation. 3. The cobalamin-dependent and -independent mechanisms of homocysteine methylation were both inhibited by reduced derivatives of aminopterin in a similar manner. 4. It was tentatively concluded that the inhibition was due to a competitive interaction between the folates for N(5)N(10)-methylenetetrahydrofolate reductase.

Landau quantization and time dependence in the ionization of cold, strongly magnetized Rydberg atoms

The electric-field-ionization and autoionization behavior of cold Rydberg atoms of 85Rb in magnetic fields up to 6 T is investigated. Multiple ionization potentials and field-ionization bands reflecting the Landau energy quantization of the quasifree Rydberg electron are observed. The time-resolved and state-selective field-ionization study provides evidence of mixing and spin flips of the Rydberg electron. Spin-orbit coupling combined with mixing gives rise to a Feshbach-type autoionization of metastable positive-energy atoms.

Magnetic trapping of long-lived cold Rydberg atoms

We report on the trapping of long-lived strongly magnetized Rydberg atoms. 85Rb atoms are laser cooled and collected in a superconducting magnetic trap with a strong bias field (2.9 T) and laser excited to Rydberg states. Collisions scatter a small fraction of the Rydberg atoms into long-lived high-angular momentum "guiding-center" Rydberg states, which are magnetically trapped. The Rydberg atomic cloud is examined using a time-delayed, position-sensitive probe. We observe magnetic trapping of these Rydberg atoms for times up to 200 ms. Oscillations of the Rydberg-atom cloud in the trap reveal an average magnetic moment of the trapped Rydberg atoms of approximately -8microB. These results provide guidance for other Rydberg-atom trapping schemes and illuminate a possible route for trapping antihydrogen.

Laser cooling and magnetic trapping at several tesla

Laser cooling and magnetic trapping of (85)Rb atoms have been performed in extremely strong and tunable magnetic fields, extending these techniques to a new regime and setting the stage for a variety of cold atom and plasma experiments. Using a superconducting Ioffe-Pritchard trap and an optical molasses, 2.4 x 10(7) atoms were laser cooled to the Doppler limit and magnetically trapped at bias fields up to 2.9 T. At magnetic fields up to 6 T, 3 x 10(6) cold atoms were laser cooled in a pulsed loading scheme. These bias fields are well beyond an order of magnitude larger than those in previous experiments. Loading rates, molasses lifetimes, magnetic-trapping times, and temperatures were measured using photoionization and electron detection.

Histopathological methods for the investigation of microbial communities associated with disease lesions in reef corals

AIMS

To determine the spatial structure of microbial communities associated with disease lesions of reef corals (Scleractinia).

METHODS AND RESULTS

Agarose pre-embedding preserved the structure of the disease lesion and surrounding tissues prior to demineralization of the carbonate exoskeleton and embedding in resin. Fluorescence in situ hybridization (FISH) was used to localize bacteria in the lesions of various diseases.

CONCLUSIONS

The techniques successfully preserved the in situ spatial structure of degenerated coral tissues. In one case (white plague disease), significant bacterial populations were found only in fragmented remnants of degenerated coral tissues at the lesion boundary that would not have been detected using conventional histopathological techniques.

SIGNIFICANCE AND IMPACT OF THE STUDY

Determining the composition, spatial structure and dynamics of microbial communities within the disease lesions is necessary to understand the process of disease progression. The methods described may be applicable to a wide range of diseases involving necrotic lesion formation and requiring extensive tissue processing, such as skeleton demineralization.

Tunneling resonances and coherence in an optical lattice

The center-of-mass quantization of atoms trapped in a gray optical lattice is observed to manifest itself in the steady-state properties of the atoms. Modulations in the lifetime and macroscopic magnetization as a function of an applied B field are attributed to quantum mechanical tunneling resonances and are shown to exist only under conditions which afford spatial coherence of the trapped atoms over several lattice wells and coherence times that exceed the tunneling period.

Inhibition of the Escherichia coli pyruvate dehydrogenase complex E1 subunit and its tyrosine 177 variants by thiamin 2-thiazolone and thiamin 2-thiothiazolone diphosphates. Evidence for reversible tight-binding inhibition

Variants of the pyruvate dehydrogenase subunit (E1; EC ) of the Escherichia coli pyruvate dehydrogenase multienzyme complex with Y177A and Y177F substitutions were created. Both variants displayed pyruvate dehydrogenase multienzyme complex activity at levels of 11% (Y177A E1) and 7% (Y177F E1) of the parental enzyme. The K(m) values for thiamin diphosphate (ThDP) were 1.58 microm (parental E1) and 6.65 microm (Y177A E1), whereas the Y177F E1 variant was not saturated at 200 microm. According to fluorescence studies, binding of ThDP was unaffected by the Tyr(177) substitutions. The ThDP analogs thiamin 2-thiazolone diphosphate (ThTDP) and thiamin 2-thiothiazolone diphosphate (ThTTDP) behaved as tight-binding inhibitors of parental E1 (K(i) = 0.003 microm for ThTDP and K(i) = 0.064 microm for ThTTDP) and the Y177A and Y177F variants. This analysis revealed that ThTDP and ThTTDP bound to parental E1 via a two-step mechanism, but that ThTDP bound to the Y177A variant via a one-step mechanism. Binding of ThTDP was affected and that of ThTTDP was unaffected by substitutions at Tyr(177). Addition of ThDP or ThTDP to parental E1 resulted in similar CD spectral changes in the near-UV region. In contrast, binding of ThTTDP to either parental E1 or the Y177A and Y177F variants was accompanied by the appearance of a positive band at 330 nm, indicating that ThTTDP was bound in a chiral environment. In combination with x-ray structural evidence on the location of Tyr(177), the kinetic and spectroscopic data suggest that Tyr(177) has a role in stabilization of some transition state(s) in the reaction pathway, starting with the free enzyme and culminating with the first irreversible step (decarboxylation), as well as in reductive acetylation of the dihydrolipoamide acetyltransferase component.

Functional versatility in the CRP-FNR superfamily of transcription factors: FNR and FLP

The cAMP receptor protein (CRP; sometimes known as CAP, the catabolite gene activator protein) and the fumarate and nitrate reduction regulator (FNR) of Escherichia coli are founder members of an expanding superfamily of structurally related transcription factors. The archetypal CRP structural fold provides a very versatile mechanism for transducing environmental and metabolic signals to the transcription machinery. It allows different functional specificities at the sensory, DNA-recognition and RNA-polymerase-interaction levels to be 'mixed and matched' in order to create a diverse range of transcription factors tailored to respond to particular physiological conditions. This versatility is clearly illustrated by comparing the properties of the CRP, FNR and FLP (FNR-like protein) regulators. At the sensory level, the basic structural fold has been adapted in FNR and FLP by the acquisition in the N-terminal region of different combinations of cysteine or other residues; which bestow oxygen/redox sensing mechanisms that are poised according to the oxidative stress thresholds affecting the metabolism of specific bacteria. At the DNA-recognition level, discrimination between distinct but related DNA targets is mediated by amino acid sequence modifications in the conserved core contact between the DNA-recognition helix and target DNA. And, at the level of RNA-polymerase-interaction, different combinations of three discrete regions contacting the polymerase (the activating regions) are used for polymerase recruitment and promoting transcription.

Near-field coherent spectroscopy and microscopy of a quantum dot system

We combined coherent nonlinear optical spectroscopy with nano-electron volt energy resolution and low-temperature near-field microscopy with subwavelength resolution (<lambda/2) to provide direct and local access to the excitonic dipole in a semiconductor nanostructure quantum system. Our technique allows the ability to address, excite, and probe single eigenstates of solid-state quantum systems with spectral and spatial selectivity while simultaneously providing a measurement of all the various time scales of the excitation including state relaxation and decoherence rates. In analogy to scanning tunneling microscopy measurements, we can now map the optical local density of states of a disordered nanostructure. These measurements lay the groundwork for studying and exploiting spatial and temporal coherence in the nanoscopic regime of solid-state systems.

High-angular-momentum states in cold Rydberg gases

Cold, dense Rydberg gases produced in a cold-atom trap are investigated using spectroscopic methods and time-resolved electron counting. Optical excitation on the discrete Rydberg resonances reveals long-lasting electron emission from the Rydberg gas ( >20 ms). Our observations are explained by lm-mixing collisions between Rydberg atoms and slow electrons that lead to the population of long-lived high-angular-momentum Rydberg states. These atoms thermally ionize slowly and with large probabilities.

The high-resolution X-ray crystallographic structure of the ferritin (EcFtnA) of Escherichia coli; comparison with human H ferritin (HuHF) and the structures of the Fe(3+) and Zn(2+) derivatives

The high-resolution structure of the non-haem ferritin from Escherichia coli (EcFtnA) is presented together with those of its Fe(3+) and Zn(2+) derivatives, this being the first high-resolution X-ray analysis of the iron centres in any ferritin. The binding of both metals is accompanied by small changes in the amino acid ligand positions. Mean Fe(A)(3+)-Fe(B)(3+) and Zn(A)(2+)-Zn(B)(2+) distances are 3.24 A and 3.43 A, respectively. In both derivatives, metal ions at sites A and B are bridged by a glutamate side-chain (Glu50) in a syn-syn conformation. The Fe(3+) derivative alone shows a third metal site (Fe( C)( 3+)) joined to Fe(B)(3+) by a long anti-anti bidentate bridge through Glu130 (mean Fe(B)(3+)-Fe(C)(3+) distance 5.79 A). The third metal site is unique to the non-haem bacterial ferritins. The dinuclear site lies at the inner end of a hydrophobic channel connecting it to the outside surface of the protein shell, which may provide access for dioxygen and possibly for metal ions shielded by water. Models representing the possible binding mode of dioxygen to the dinuclear Fe(3+) pair suggest that a gauche micro-1,2 mode may be preferred stereochemically. Like those of other ferritins, the 24 subunits of EcFtnA are folded as four-helix bundles that assemble into hollow shells and both metals bind at dinuclear centres in the middle of the bundles. The structural similarity of EcFtnA to the human H chain ferritin (HuHF) is remarkable (r.m.s. deviation of main-chain atoms 0.66 A) given the low amino acid sequence identity (22 %). Many of the conserved residues are clustered at the dinuclear centre but there is very little conservation of residues making inter-subunit interactions.

Anaerobic acquisition of [4FE 4S] clusters by the inactive FNR(C20S) variant and restoration of activity by second-site amino acid substitutions

The FNR protein of Escherichia coli controls the transcription of target genes in response to anoxia. The anaerobic incorporation of oxygen-sensitive [4Fe 4S] clusters promotes dimerization, which in turn enhances DNA binding. Four potential iron ligands (C20, C23, C29 and C122) are essential for normal FNR activity in vivo. Three FNR variants (C20S, C23G and C29G) retained the ability to incorporate oxygen-sensitive [4Fe 4S] clusters and to bind target DNA with essentially unimpaired affinity, suggesting that their failure to function normally in vivo resides at a later stage in the signal transduction pathway. The C122 variant failed to assemble iron-sulphur clusters and to bind DNA. Second-site substitutions that partially restore activity to FNR(C20S) were generated by error-prone polymerase chain reaction and were located in the dimer interface, in the activating regions (AR1, 2 or 3) or close to C122. Substitutions at E47, R48, E123, I124, E127 or T128 allowed the extent of the FNR AR2 surface to be defined. Only one revertant, FNR(C20S Y69F G149S), specifically corrected the C20S defect. It was concluded that [4Fe 4S] cluster acquisition, dimerization and DNA binding are not sufficient to confer transcription regulatory activity on FNR: the iron-sulphur cluster must also be correctly liganded in order to establish effective activating contacts between FNR and RNA polymerase.

A novel promoter architecture for microaerobic activation by the anaerobic transcription factor FNR

The yfiD gene of Escherichia coli has an unusual promoter architecture in which an FNR dimer located at -93.5 inhibits transcription activation mediated by another FNR dimer bound at the typical class II position (-40.5). In vitro transcription from the yfiD promoter indicated that FNR alone can downregulate yfiD expression. Analysis of yfiD::lac reporters showed that five turns of the DNA helix between FNR sites was optimal for downregulation. FNR heterodimers, in which one subunit carried a defective repression surface, revealed that the upstream subunit of the -40.5 dimer and the downstream subunit of the -93.5 dimer were most important for downregulating yfiD expression. Deletion of the C-terminal domain of the alpha-subunit of RNA polymerase (RNAP) did not affect FNR-mediated repression, suggesting that repression is mediated through FNR-FNR and not FNR-RNAP interactions. Maximum yfiD::lac expression was observed in cultures exposed to 10 microM oxygen. More or less oxygen reduced expression dramatically. This pattern of response was dependent on the combination of a high-affinity site at the activating class II position and a lower affinity site at the upstream position.

Ponderomotive optical lattice for Rydberg atoms

We propose to use the ponderomotive energy of Rydberg electrons in standing-wave light fields to form an optical lattice for Rydberg atoms. Application of the Born-Oppenheimer approximation shows that, with readily achievable experimental parameters, atoms in any Rydberg state can be trapped. Realization of this scheme would extend the benefits of atom trapping to highly excited atoms.

Zinc uptake, oxidative stress and the FNR-like proteins of Lactococcus lactis

Lactococcus lactis ssp. cremoris MG1363 contains two FNR homologues, FlpA and FlpB, encoded by the distal genes of two paralogous operons (orfX(A/B)-orfY(A/B)-flpA/B). An flpA flpB double mutant strain is hypersensitive to hydrogen peroxide and has a depleted intracellular Zn(II) pool. The phenotypes of the flp mutant strains suggest that FlpA and FlpB control the expression of high and low affinity ATP-dependent Zn(II) uptake systems, respectively. Plate tests revealed that expression from a orfX(B)::lac reporter was activated by Cd(II), consistent with other Zn(II)-regulated systems. The link between a failure to acquire Zn(II) and hypersensitivity to oxidative stress suggests that Zn(II) may be required to protect vulnerable protein thiols from oxidation.

Role of activating region 1 of Escherichia coli FNR protein in transcription activation at class II promoters

FNR is an Escherichia coli transcription factor that activates gene expression in response to anaerobiosis at a large number of promoters by making direct contacts with RNA polymerase. At class II FNR-dependent promoters, where the DNA site for FNR overlaps the -35 element, activating region 1 of FNR is proposed to interact with the C-terminal domain of the RNA polymerase alpha-subunit. Using a model class II FNR-dependent promoter, FF(-41.5), we have performed in vivo and in vitro experiments to investigate the role of this interaction. Our results show that FNR, carrying substitutions in activating region 1, is compromised in its ability to promote open complex formation and thus to activate transcription. Abortive initiation assays were used to assess the contribution of activating region 1 of FNR to open complex formation. A new method for the purification of the FNR protein is also described.

Characterization of the Lactococcus lactis transcription factor FlpA and demonstration of an in vitro switch

The commercially important bacterium Lactococcus lactis contains two FNR-like proteins (FlpA and FlpB) which have a high degree of identity to each other and to the FLP of Lactobacillus casei. FlpA was isolated from a GST-FlpA fusion protein produced in Escherichia coli. Like FLP, isolated FlpA is a homodimeric protein containing both Zn and Cu. However, the properties of FlpA were more like those of the E. coli oxygen-responsive transcription factor FNR than the FLP of L. casei. As prepared FlpA recognized an FNR site (TTGAT-N4-ATCAA) but not an FLP site (CCTGA-N4-TCAGG) in band-shift assays. In contrast to FLP, DNA binding by FlpA did not require the formation of an intramolecular disulphide bond. However, despite containing only two cysteine residues per monomer, FlpA was able to acquire an FNR-like, oxygen-labile [4Fe 4S] cluster. But, whereas the incorporation of a [4Fe 4S] cluster into FNR enhances interaction with target DNA, it abolished DNA binding by FlpA. An FlpA variant (FlpA') with an N-terminal region designed to be more FLP-like failed to incorporate an iron-sulphur cluster but could now form an intramolecular disulphide. This simple example of protein engineering, converting an oxygen-labile [4Fe 4S] containing FNR-like protein into a dithiol-disulphide FLP-like redox sensor demonstrates the versatility of the basic CRP structure. Attempts to demonstrate an FlpA-based aerobic-anaerobic switch in the heterologous host E. coli were unsuccessful. However, studies with a series of FNR-dependent lac reporter fusions in strains of E. coli expressing flpA or flpB revealed that both homologues were able to activate expression of FNR-dependent promoters in vivo but only when positioned 61 base pairs upstream of the transcription start.

Biochemical and spectroscopic characterization of Escherichia coli aconitases (AcnA and AcnB)

Escherichia coli contains two major aconitases (Acns), AcnA and AcnB. They are distantly related monomeric Fe-S proteins that contain different arrangements of four structural domains. On the basis of the differential expression of the acnA and acnB genes, AcnA has been designated as an aerobic-stationary-phase enzyme that is specifically induced by iron and oxidative stress, whereas AcnB functions as the major citric-acid-cycle enzyme during exponential growth. The biochemical and kinetic properties of the purified enzymes have now shown that AcnA is more stable than AcnB, has a higher affinity for citrate, and operates optimally over a wider pH range, consistent with its role as a maintenance or survival enzyme during nutritional or oxidative stress. In contrast, the better performance at high substrate concentrations and greater instability of AcnB indicate that AcnB is specifically adapted to function as the main catabolic enzyme and, by inactivation, to rapidly modulate energy metabolism in response to oxidative or pH stress, either directly or indirectly by regulating post-transcriptional gene expression. EPR and magnetic-CD spectroscopy showed that the iron-sulphur clusters of the bacterial Acns (and their binding sites) strongly resemble those of the mammalian enzymes. The EPR and MCD spectra of the oxidized inactive form of AcnB confirmed the presence of a [3Fe-4S](1+) (S=1/2) cluster. Comparisons showed that the EPR spectrum of AcnB more closely resembled that of mammalian mitochondrial Acn (m-Acn), whereas the spectrum of AcnA more closely resembled that of the cytoplasmic enzyme (c-Acn). The MCD spectra revealed spectroscopic signatures similar to that of m-Acn. Reconstitution of the active [4Fe-4S](2+) forms followed by one-electron reduction gave rise to EPR spectra that are almost identical with those reported for the mammalian enzymes.