Temporal patterns of gene expression via nonmetric multidimensional scaling analysis

Motivation: Microarray experiments result in large scale data sets that require extensive mining and refining to extract useful information. We have been developing an efficient novel algorithm for nonmetric multidimensional scaling (nMDS) analysis for very large data sets as a maximally unsupervised data mining device. We wish to demonstrate its usefulness in the context of bioinformatics. In our motivation is also an aim to demonstrate that intrinsically nonlinear methods are generally advantageous in data mining. Results: The Pearson correlation distance measure is used to indicate the dissimilarity of the gene activities in transcriptional response of cell cycle-synchronized human fibroblasts to serum [Iyer et al., Science vol. 283, p83 (1999)]. These dissimilarity data have been analyzed with our nMDS algorithm to produce an almost circular arrangement of the genes. The temporal expression patterns of the genes rotate along this circular arrangement. If an appropriate preparation procedure may be applied to the original data set, linear methods such as the principal component analysis (PCA) could achieve reasonable results, but without data preprocessing linear methods such as PCA cannot achieve a useful picture. Furthermore, even with an appropriate data preprocessing, the outcomes of linear procedures are not as clearcut as those by nMDS without preprocessing.Comment: 11 pages, 6 figures + online only 2 color figures, submitted to Bioinformatic

Nanowire Acting as a Superconducting Quantum Interference Device

We present the results from an experimental study of the magneto-transport of superconducting wires of amorphous Indium-Oxide, having widths in the range 40 - 120 nm. We find that, below the superconducting transition temperature, the wires exhibit clear, reproducible, oscillations in their resistance as a function of magnetic field. The oscillations are reminiscent of those which underlie the operation of a superconducting quantum interference device.Comment: 4 pages, 4 figures, 1 tabl

Aperiodic tumbling of microrods advected in a microchannel flow

We report on an experimental investigation of the tumbling of microrods in the shear flow of a microchannel (40 x 2.5 x 0.4 mm). The rods are 20 to 30 microns long and their diameters are of the order of 1 micron. Images of the centre-of-mass motion and the orientational dynamics of the rods are recorded using a microscope equipped with a CCD camera. A motorised microscope stage is used to track individual rods as they move along the channel. Automated image analysis determines the position and orientation of a tracked rods in each video frame. We find different behaviours, depending on the particle shape, its initial position, and orientation. First, we observe periodic as well as aperiodic tumbling. Second, the data show that different tumbling trajectories exhibit different sensitivities to external perturbations. These observations can be explained by slight asymmetries of the rods. Third we observe that after some time, initially periodic trajectories lose their phase. We attribute this to drift of the centre of mass of the rod from one to another stream line of the channel flow.Comment: 14 pages, 8 figures, as accepted for publicatio

High-Yield of Memory Elements from Carbon Nanotube Field-Effect Transistors with Atomic Layer Deposited Gate Dielectric

Carbon nanotube field-effect transistors (CNT FETs) have been proposed as possible building blocks for future nano-electronics. But a challenge with CNT FETs is that they appear to randomly display varying amounts of hysteresis in their transfer characteristics. The hysteresis is often attributed to charge trapping in the dielectric layer between the nanotube and the gate. This study includes 94 CNT FET samples, providing an unprecedented basis for statistics on the hysteresis seen in five different CNT-gate configurations. We find that the memory effect can be controlled by carefully designing the gate dielectric in nm-thin layers. By using atomic layer depositions (ALD) of HfO$_{2}$ and TiO$_{2}$ in a triple-layer configuration, we achieve the first CNT FETs with consistent and narrowly distributed memory effects in their transfer characteristics.Comment: 6 pages, 3 figures; added one reference, text reformatted with smaller addition

Landau-Zener-Stuckelberg Interferometry of a Single Electron Charge Qubit

We perform Landau-Zener-Stuckelberg interferometry on a single electron GaAs charge qubit by repeatedly driving the system through an avoided crossing. We observe coherent destruction of tunneling, where periodic driving with specific amplitudes inhibits current flow. We probe the quantum dot occupation using a charge sensor, observing oscillations in the qubit population resulting from the microwave driving. At a frequency of 9 GHz we observe excitation processes driven by the absorption of up to 17 photons. Simulations of the qubit occupancy are in good agreement with the experimental data.Comment: Related papers at http://pettagroup.princeton.ed

Internally Electrodynamic Particle Model: Its Experimental Basis and Its Predictions

The internally electrodynamic (IED) particle model was derived based on overall experimental observations, with the IED process itself being built directly on three experimental facts, a) electric charges present with all material particles, b) an accelerated charge generates electromagnetic waves according to Maxwell's equations and Planck energy equation and c) source motion produces Doppler effect. A set of well-known basic particle equations and properties become predictable based on first principles solutions for the IED process; several key solutions achieved are outlined, including the de Broglie phase wave, de Broglie relations, Schr\"odinger equation, mass, Einstein mass-energy relation, Newton's law of gravity, single particle self interference, and electromagnetic radiation and absorption; these equations and properties have long been broadly experimentally validated or demonstrated. A specific solution also predicts the Doebner-Goldin equation which emerges to represent a form of long-sought quantum wave equation including gravity. A critical review of the key experiments is given which suggests that the IED process underlies the basic particle equations and properties not just sufficiently but also necessarily.Comment: Presentation at the 27th Int Colloq on Group Theo Meth in Phys, 200

Atomic Processes in Planetary Nebulae and H II Regions

Spectroscopic studies of Planetary Nebulae (PNe) and H {\sc ii} regions have driven much development in atomic physics. In the last few years the combination of a generation of powerful observatories, the development of ever more sophisticated spectral modeling codes, and large efforts on mass production of high quality atomic data have led to important progress in our understanding of the atomic spectra of such astronomical objects. In this paper I review such progress, including evaluations of atomic data by comparisons with nebular spectra, detection of spectral lines from most iron-peak elements and n-capture elements, observations of hyperfine emission lines and analysis of isotopic abundances, fluorescent processes, and new techniques for diagnosing physical conditions based on recombination spectra. The review is directed toward atomic physicists and spectroscopists trying to establish the current status of the atomic data and models and to know the main standing issues.Comment: 9 pages, 1 figur

Dynamical study on polaron formation in a metal/polymer/metal structure

By considering a metal/polymer/metal structure within a tight-binding one-dimensional model, we have investigated the polaron formation in the presence of an electric field. When a sufficient voltage bias is applied to one of the metal electrodes, an electron is injected into the polymer chain, then a self-trapped polaron is formed at a few hundreds of femtoseconds while it moves slowly under a weak electric field (not larger than $$ V/cm). At an electric field between $1.0\times 10^4$ V/cm and $$ V/cm, the polaron is still formed, since the injected electron is bounded between the interface barriers for quite a long time. It is shown that the electric field applied at the polymer chain reduces effectively the potential barrier in the metal/polymer interface

Observation of the Dynamical Casimir Effect in a Superconducting Circuit

One of the most surprising predictions of modern quantum theory is that the vacuum of space is not empty. In fact, quantum theory predicts that it teems with virtual particles flitting in and out of existence. While initially a curiosity, it was quickly realized that these vacuum fluctuations had measurable consequences, for instance producing the Lamb shift of atomic spectra and modifying the magnetic moment for the electron. This type of renormalization due to vacuum fluctuations is now central to our understanding of nature. However, these effects provide indirect evidence for the existence of vacuum fluctuations. From early on, it was discussed if it might instead be possible to more directly observe the virtual particles that compose the quantum vacuum. 40 years ago, Moore suggested that a mirror undergoing relativistic motion could convert virtual photons into directly observable real photons. This effect was later named the dynamical Casimir effect (DCE). Using a superconducting circuit, we have observed the DCE for the first time. The circuit consists of a coplanar transmission line with an electrical length that can be changed at a few percent of the speed of light. The length is changed by modulating the inductance of a superconducting quantum interference device (SQUID) at high frequencies (~11 GHz). In addition to observing the creation of real photons, we observe two-mode squeezing of the emitted radiation, which is a signature of the quantum character of the generation process.Comment: 12 pages, 3 figure