Simple models suffice for the single dot quantum shuttle

A quantum shuttle is an archetypical nanoelectromechanical device, where the mechanical degree of freedom is quantized. Using a full-scale numerical solution of the generalized master equation describing the shuttle, we have recently shown [Novotn\'{y} {\it et al.}, Phys. Rev. Lett. {\bf 92}, 248302 (2004)] that for certain limits of the shuttle parameters one can distinguish three distinct charge transport mechanisms: (i) an incoherent tunneling regime, (ii) a shuttling regime, where the charge transport is synchronous with the mechanical motion, and (iii) a coexistence regime, where the device switches between the tunneling and shuttling regimes. While a study of the cross-over between these three regimes requires the full numerics, we show here that by identifying the appropriate time-scales it is possible to derive vastly simpler equations for each of the three regimes. The simplified equations allow a clear physical interpretation, are easily solved, and are in good agreement with the full numerics in their respective domains of validity.Comment: 23 pages, 14 figures, invited paper for the Focus issue of the New Journal of Physics on Nano-electromechanical system

Multiscale Modeling of a Nanoelectromechanical Shuttle

In this article, we report a theoretical analysis of a nanoelectromechanical shuttle based on a multiscale model that combines microscopic electronic structure data with macroscopic dynamics. The microscopic part utilizes a (static) density functional description to obtain the energy levels and orbitals of the shuttling particle together with the forces acting on the particle. The macroscopic part combines stochastic charge dynamics that incorporates the microscopically evaluated tunneling rates with a Newtonian dynamics. We have applied the multiscale model to describe the shuttling of a single copper atom between two gold-like jellium electrodes. We find that energy spectrum and particle surface interaction greatly influence shuttling dynamics; in the specific example that we studied the shuttling is found to involve only charge states Q=0 and Q=+e. The system is found to exhibit two quasi-stable shuttling modes, a fundamental one and an excited one with a larger amplitude of mechanical motion, with random transitions between them.Comment: 9 pages, 9 figure

Coulomb Blockade in a Coupled Nanomechanical Electron Shuttle

We demonstrate single electron shuttling through two coupled nanomechanical pendula. The pendula are realized as nanopillars etched out of the semiconductor substrate. Coulomb blockade is found at room temperature, allowing metrological applications. By controlling the mechanical shuttling frequency we are able to validate the different regimes of electron shuttling

Electromechanical instability in suspended carbon nanotubes

We have theoretically investigated electromechanical properties of freely suspended carbon nanotubes when a current is injected into the tubes using a scanning tunneling microscope. We show that a shuttle-like electromechanical instability can occur if the bias voltage exceeds a dissipation-dependent threshold value. An instability results in large amplitude vibrations of the carbon nanotube bending mode, which modify the current-voltage characteristics of the system

Low frequency current noise of the single-electron shuttle

Coupling between electronic and mechanical degrees of freedom in a single electron shuttle system can cause a mechanical instability leading to shuttle transport of electrons between external leads. We predict that the resulting low frequency current noise can be enhanced due to amplitude fluctuations of the shuttle oscillations. Moreover, at the onset of mechanical instability a pronounced peak in the low frequency noise is expected.Comment: 14 pages, 3 figures, 1 tabl

Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis

The diurnal cycle strongly influences many plant metabolic and physiological processes. Arabidopsis thaliana rosettes were harvested six times during 12-h-light/12-h-dark treatments to investigate changes in gene expression using ATH1 arrays. Diagnostic gene sets were identified from published or in-house expression profiles of the response to light, sugar, nitrogen, and water deficit in seedlings and 4 h of darkness or illumination at ambient or compensation point [CO2]. Many sugar-responsive genes showed large diurnal expression changes, whose timing matched that of the diurnal changes of sugars. A set of circadian-regulated genes also showed large diurnal changes in expression. Comparison of published results from a free-running cycle with the diurnal changes in Columbia-0 (Col-0) and the starchless phosphoglucomutase (pgm) mutant indicated that sugars modify the expression of up to half of the clock-regulated genes. Principle component analysis identified genes that make large contributions to diurnal changes and confirmed that sugar and circadian regulation are the major inputs in Col-0 but that sugars dominate the response in pgm. Most of the changes in pgm are triggered by low sugar levels during the night rather than high levels in the light, highlighting the importance of responses to low sugar in diurnal gene regulation. We identified a set of candidate regulatory genes that show robust responses to alterations in sugar levels and change markedly during the diurnal cycle

Impact of van der Waals forces on the classical shuttle instability

The effects of including the van der Waals interaction in the modelling of the single electron shuttle have been investigated numerically. It is demonstrated that the relative strength of the vdW-forces and the elastic restoring forces determine the characteristics of the shuttle instability. In the case of weak elastic forces and low voltages the grain is trapped close to one lead, and this trapping can be overcome by Coulomb forces by applying a bias voltage $V$ larger than a threshold voltage $V_{\rm u}$. This allows for grain motion leading to an increase in current by several orders of magnitude above the transition voltage $V_{\rm u}$. Associated with the process is also hysteresis in the I-V characteristics.Comment: minor revisions, updated references, Article published in Phys. Rev. B 69, 035309 (2004

Alignment between PIN1 Polarity and Microtubule Orientation in the Shoot Apical Meristem Reveals a Tight Coupling between Morphogenesis and Auxin Transport

Morphogenesis during multicellular development is regulated by intercellular signaling molecules as well as by the mechanical properties of individual cells. In particular, normal patterns of organogenesis in plants require coordination between growth direction and growth magnitude. How this is achieved remains unclear. Here we show that in Arabidopsis thaliana, auxin patterning and cellular growth are linked through a correlated pattern of auxin efflux carrier localization and cortical microtubule orientation. Our experiments reveal that both PIN1 localization and microtubule array orientation are likely to respond to a shared upstream regulator that appears to be biomechanical in nature. Lastly, through mathematical modeling we show that such a biophysical coupling could mediate the feedback loop between auxin and its transport that underlies plant phyllotaxis

A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula

<p>Abstract</p> <p>Background</p> <p><it>Medicago truncatula </it>is a model legume species that is currently the focus of an international genome sequencing effort. Although several different oligonucleotide and cDNA arrays have been produced for genome-wide transcript analysis of this species, intrinsic limitations in the sensitivity of hybridization-based technologies mean that transcripts of genes expressed at low-levels cannot be measured accurately with these tools. Amongst such genes are many encoding transcription factors (TFs), which are arguably the most important class of regulatory proteins. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is the most sensitive method currently available for transcript quantification, and one that can be scaled up to analyze transcripts of thousands of genes in parallel. Thus, qRT-PCR is an ideal method to tackle the problem of TF transcript quantification in Medicago and other plants.</p> <p>Results</p> <p>We established a bioinformatics pipeline to identify putative TF genes in <it>Medicago truncatula </it>and to design gene-specific oligonucleotide primers for qRT-PCR analysis of TF transcripts. We validated the efficacy and gene-specificity of over 1000 TF primer pairs and utilized these to identify sets of organ-enhanced TF genes that may play important roles in organ development or differentiation in this species. This community resource will be developed further as more genome sequence becomes available, with the ultimate goal of producing validated, gene-specific primers for all Medicago TF genes.</p> <p>Conclusion</p> <p>High-throughput qRT-PCR using a 384-well plate format enables rapid, flexible, and sensitive quantification of all predicted Medicago transcription factor mRNAs. This resource has been utilized recently by several groups in Europe, Australia, and the USA, and we expect that it will become the 'gold-standard' for TF transcript profiling in <it>Medicago truncatula</it>.</p