Transcription of tufA and other chloroplast-encoded genes is controlled by a circadian clock in Chlamydomonas.

Levels of mRNA for the chloroplast-encoded elongation factor Tu (tufA) showed a dramatic daily oscillation in the green alga Chlamydomonas reinhardtii, peaking once each day in the early light period. The oscillation of tufA mRNA levels continued in cells shifted to continuous light or continuous dark for at least 2-3 days. Run-off transcription analyses showed that the rate of tufA transcription also peaked early in the light period and, moreover, that this transcriptional oscillation continued in cells shifted to continuous conditions. The half-life of tufA mRNA was estimated at different times and found to vary considerably during a light-dark cycle but not in cells shifted to continuous light. Light-dark patterns of transcription of several other chloroplast-encoded genes were examined and also found to persist in cells shifted to continuous light or dark. These results indicate that a circadian clock controls the transcription of tufA and other chloroplast-encoded genes.

Genes that control a temperature-compensated ultradian clock in Caenorhabditis elegans.

Substantial progress has been made in understanding the genetic basis of temperature-compensated circadian clocks. Ultradian rhythms, with a period shorter than 24 h, are at least as widespread as circadian rhythms. We have initiated genetic analysis of defecation behavior, which is controlled by an ultradian clock in Caenorhabditis elegans. The defecation motor program is activated every 45 sec, and this rhythm is temperature compensated. We describe mutations in 12 genes that either shorten or lengthen the cycle period. We find that most of these mutations also disrupt temperature compensation, suggesting that this process is an integral part of the clock. These genes open the way for molecular genetic dissection of this ultradian clock.

The rat suprachiasmatic nucleus is a clock for all seasons.

Seasonal changes of daylength (photoperiod) affect the expression of hormonal and behavioral circadian rhythms in a variety of organisms. In mammals, such effects might reflect photoperiodic changes in the circadian pace-making system [located in the suprachiasmatic nucleus (SCN) of the hypothalamus] that governs these rhythms, but to date no functionally relevant, intrinsic property of the SCN has been shown to be photoperiod dependent. We have analyzed the temporal regulation of light-induced c-fos gene expression in the SCN of rats maintained in long or short photoperiods. Both in situ hybridization and immunohistochemical assays show that the endogenous circadian rhythm of light responsiveness in the SCN is altered by photoperiod, with the duration of the photosensitive subjective night under the short photoperiod 5-6 h longer than under the long photoperiod. Our results provide evidence that a functional property of the SCN is altered by photoperiod and suggest that the nucleus is involved in photoperiodic time measurement.

Direct measurement of hydrogen bonding in DNA nucleotide bases by atomic force microscopy.

We have used self-assembled purines and pyrimidines on planar gold surfaces and on gold-coated atomic force microscope (AFM) tips to directly probe intermolecular hydrogen bonds. Electron spectroscopy for chemical analysis (ESCA) and thermal programmed desorption (TPD) measurements of the molecular layers suggested monolayer coverage and a desorption energy of about 25 kcal/mol. Experiments were performed under water, with all four DNA bases immobilized on AFM tips and flat surfaces. Directional hydrogen-bonding interaction between the tip molecules and the surface molecules could be measured only when opposite base-pair coatings were used. The directional interactions were inhibited by excess nucleotide base in solution. Nondirectional van der Waals forces were present in all other cases. Forces as low as two interacting base pairs have been measured. With coated AFM tips, surface chemistry-sensitive recognition atomic force microscopy can be performed.

Quantum interference in atomic-sized point contacts

The conductance of atomic-sized metallic point contacts is shown to be strongly voltage dependent due to quantum interference with impurities even in samples with low impurity concentrations. Transmission through these small contacts depends not only on the local atomic structure at the contact but also on the distribution of impurities or defects within a coherence length of the contact. In contrast with other mesoscopic systems we show that transport through atomic contacts is coherent even at room temperature. The use of a scanning tunneling microscope (STM) makes it possible to fabricate one atom contacts of gold whose transmission can be controlled by manipulation of the contact allowing inelastic spectroscopy in such small contacts.

Absence of magnetically induced fractional quantization in atomic contacts

Using the mechanically controlled break junction technique at low temperatures and under cryogenic vacuum conditions we have studied atomic contacts of several magnetic (Fe, Co, and Ni) and nonmagnetic (Pt) metals, which recently were claimed to show fractional conductance quantization. In the case of pure metals we see no quantization of the conductance nor half quantization, even when high magnetic fields are applied. On the other hand, features in the conductance similar to (fractional) quantization are observed when the contact is exposed to gas molecules. Furthermore, the absence of fractional quantization when the contact is bridged by H2 indicates the current is never fully polarized for the metals studied here. Our results are in agreement with recent model calculations.

Analysis of the Kondo effect in ferromagnetic atomic-sized contacts

Atomic contacts made of ferromagnetic metals present zero-bias anomalies in the differential conductance due to the Kondo effect. These systems provide a unique opportunity to perform a statistical analysis of the Kondo parameters in nanostructures since a large number of contacts can be easily fabricated using break-junction techniques. The details of the atomic structure differ from one contact to another so a large number of different configurations can be statistically analyzed. Here we present such a statistical analysis of the Kondo effect in atomic contacts made from the ferromagnetic transition metals Ni, Co, and Fe. Our analysis shows clear differences between materials that can be understood by fundamental theoretical considerations. This combination of experiments and theory allows us to extract information about the origin and nature of the Kondo effect in these systems and to explore the influence of geometry and valence in the Kondo screening of atomic-sized nanostructures.

Evolution of conducting channels in metallic atomic contacts under elastic deformation

We investigate both experimentally and theoretically the evolution of conductance in metallic one-atom contacts under elastic deformation. While simple metals like Au exhibit almost constant conductance plateaus, Al and Pb show inclined plateaus with positive and negative slopes. It is shown how these behaviors can be understood in terms of the orbital structure of the atoms forming the contact. This analysis provides further insight into the issue of conductance quantization in metallic contacts revealing important aspects of their atomic and electronic structures.

Onset of energy dissipation in ballistic atomic wires

Electronic transport at finite voltages in free-standing gold atomic chains of up to seven atoms in length is studied at low temperatures using a scanning tunneling microscope. The conductance vs voltage curves show that transport in these single-mode ballistic atomic wires is nondissipative up to a finite voltage threshold of the order of several mV. The onset of dissipation and resistance within the wire corresponds to the excitation of the atomic vibrations by the electrons traversing the wire and is very sensitive to strain.

Observation of a parity oscillation in the conductance of atomic wires

Using a scanning tunnel microscope or mechanically controllable break junctions atomic contacts for Au, Pt, and Ir are pulled to form chains of atoms. We have recorded traces of conductance during the pulling process and averaged these for a large number of contacts. An oscillatory evolution of conductance is observed during the formation of the monoatomic chain suggesting a dependence on the numbers of atoms forming the chain being even or odd. This behavior is not only observed for the monovalent metal Au, as was predicted, but is also found for the other chain-forming metals, suggesting it to be a universal feature of atomic wires.

Mechanical annealing of metallic electrodes at the atomic scale

The process of creating an atomically defined and robust metallic tip is described and quantified using measurements of contact conductance between gold electrodes and numerical simulations. Our experiments show how the same conductance behavior can be obtained for hundreds of cycles of formation and rupture of the nanocontact by limiting the indentation depth between the two electrodes up to a conductance value of approximately 5G0 in the case of gold. This phenomenon is rationalized using molecular dynamics simulations together with density functional theory transport calculations which show how, after repeated indentations (mechanical annealing), the two metallic electrodes are shaped into tips of reproducible structure. These results provide a crucial insight into fundamental aspects relevant to nanotribology or scanning probe microscopies.

Formation of atomic-sized contacts controlled by electrochemical methods

Electrochemical methods have recently become an interesting tool for fabricating and characterizing nanostructures at room temperature. Simplicity, low cost and reversibility are some of the advantages of this technique that allows to work at the nanoscale without requiring sophisticated instrumentation. In our experimental setup, we measure the conductance across a nanocontact fabricated either by dissolving a macroscopic gold wire or by depositing gold in between two separated gold electrodes. We have achieved a high level of control on the electrochemical fabrication of atomic-sized contacts in gold. The use of electrochemistry as a reproducible technique to prepare nanocontacts will open several possibilities that are not feasible with other methodologies. It involves, also, the possibility of reproducing experiments that today are made by more expensive, complicated or irreversible methods. As example, we show here a comparison of the results when looking for shell effects in gold nanocontacts with those obtained by other techniques.

Cotunneling theory of atomic spin inelastic electron tunneling spectroscopy

We propose cotunneling as the microscopic mechanism that makes possible inelastic electron tunneling spectroscopy of magnetic atoms in surfaces for a wide range of systems, including single magnetic adatoms, molecules, and molecular stacks. We describe electronic transport between the scanning tip and the conducting surface through the magnetic system (MS) with a generalized Anderson model, without making use of effective spin models. Transport and spin dynamics are described with an effective cotunneling Hamiltonian in which the correlations in the magnetic system are calculated exactly and the coupling to the electrodes is included up to second order in the tip MS and MS substrate. In the adequate limit our approach is equivalent to the phenomenological Kondo exchange model that successfully describes the experiments. We apply our method to study in detail inelastic transport in two systems, stacks of cobalt phthalocyanines and a single Mn atom on Cu2N. Our method accounts for both the large contribution of the inelastic spin exchange events to the conductance and the observed conductance asymmetry.

Electronic structure and transport properties of atomic NiO spinvalves

Ab initio quantum transport calculations show that short NiO chains suspended in Ni nanocontacts present a very strong spin-polarization of the conductance.The generalized gradient approximation we use here predicts a similar polarization of the conductance as the one previously computed with non-local exchange, confirming the robustness of the result. Their use as nanoscopic spinvalves is proposed.

Understanding the structure of the first atomic contact in gold

We have studied experimentally jump-to-contact (JC) and jump-out-of-contact (JOC) phenomena in gold electrodes. JC can be observed at first contact when two metals approach each other, while JOC occurs in the last contact before breaking. When the indentation depth between the electrodes is limited to a certain value of conductance, a highly reproducible behaviour in the evolution of the conductance can be obtained for hundreds of cycles of formation and rupture. Molecular dynamics simulations of this process show how the two metallic electrodes are shaped into tips of a well-defined crystallographic structure formed through a mechanical annealing mechanism. We report a detailed analysis of the atomic configurations obtained before contact and rupture of these stable structures and obtained their conductance using first-principles quantum transport calculations. These results help us understand the values of conductance obtained experimentally in the JC and JOC phenomena and improve our understanding of atomic-sized contacts and the evolution of their structural characteristics.