Tailoring the local interaction between graphene layers in graphite at the atomic scale and above using scanning tunneling microscopy.

With recent developments in carbon-based electronics, it is imperative to understand the interplay between the morphology and electronic structure in graphene and graphite. We demonstrate controlled and repeatable vertical displacement of the top graphene layer from the substrate mediated by the scanning tunneling microscopy (STM) tip-sample interaction, manifested at the atomic level as well as over superlattices spanning several tens of nanometers. Besides the full-displacement, we observed the first half-displacement of the surface graphene layer, confirming that a reduced coupling rather than a change in lateral layer stacking is responsible for the triangular/honeycomb atomic lattice transition phenomenon, clearing the controversy surrounding it. Furthermore, an atomic scale mechanical stress at a grain boundary in graphite, resulting in the localization of states near the Fermi energy, is revealed through voltage-dependent imaging. A method of producing graphene nanoribbons based on the manipulation capabilities of the STM is also implemented.

A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series.

Understanding the regulatory mechanisms that are responsible for an organism's response to environmental change is an important issue in molecular biology. A first and important step towards this goal is to detect genes whose expression levels are affected by altered external conditions. A range of methods to test for differential gene expression, both in static as well as in time-course experiments, have been proposed. While these tests answer the question whether a gene is differentially expressed, they do not explicitly address the question when a gene is differentially expressed, although this information may provide insights into the course and causal structure of regulatory programs. In this article, we propose a two-sample test for identifying intervals of differential gene expression in microarray time series. Our approach is based on Gaussian process regression, can deal with arbitrary numbers of replicates, and is robust with respect to outliers. We apply our algorithm to study the response of Arabidopsis thaliana genes to an infection by a fungal pathogen using a microarray time series dataset covering 30,336 gene probes at 24 observed time points. In classification experiments, our test compares favorably with existing methods and provides additional insights into time-dependent differential expression.

Bayesian two-sample tests

In this paper, we present two classes of Bayesian approaches to the two-sample problem. Our first class of methods extends the Bayesian t-test to include all parametric models in the exponential family and their conjugate priors. Our second class of methods uses Dirichlet process mixtures (DPM) of such conjugate-exponential distributions as flexible nonparametric priors over the unknown distributions.

Nanostructured carbon films from supersonic cluster beam deposition: Structure and morphology

Nanostructured carbon thin films have been grown by deposition of cluster beams produced by a supersonic expansion. Due to separation effects typical of supersonic beams, films with different nanostructures can be grown by the simple intercepting of different regions of the cluster beam with a substrate. Films show a low-density porous structure, which has been characterized by Raman and Brillouin spectroscopy. Film morphology suggests that growth processes are similar to those occurring in a ballistic deposition regime.

Effect of size, morphology and crystallinity of seed crystal on the nucleation and growth of single grain Y-Ba-Cu-O

The effect of size, morphology and crystallinity of seed crystals on the nucleation and growth of large grain Y-Ba-Cu-O (YBCO) bulk superconductors fabricated by top seeded melt growth (TSMG) has been investigated. Seeding bulk samples with small, square shaped seed crystals leads to point nucleation and growth of the superconducting YBa2Cu3O7-y (Y-123) phase that exhibits the usual square habitual growth symmetry. The use of triangular and circular shaped seed crystals, however, modifies significantly the growth habit geometry of the grain. The use of large area seeds both increases the rate of epitaxial nucleation of the Y-123 phase and produces relatively large crystals in the incongruent melt, which decreases significantly the processing times of large grain samples. The present study is relevant to decrease processing times of samples with both preferred or no growth sectors and for multiple seeding of large grain samples which contain clean grain boundaries. © 2005 Published by Elsevier Ltd.

On the relationship between hidden Markov Models and convex functional transforms for simulating scanning probe Microscopy

Models for simulating Scanning Probe Microscopy (SPM) may serve as a reference point for validating experimental data and practice. Generally, simulations use a microscopic model of the sample-probe interaction based on a first-principles approach, or a geometric model of macroscopic distortions due to the probe geometry. Examples of the latter include use of neural networks, the Legendre Transform, and dilation/erosion transforms from mathematical morphology. Dilation and the Legendre Transform fall within a general family of functional transforms, which distort a function by imposing a convex solution.In earlier work, the authors proposed a generalized approach to modeling SPM using a hidden Markov model, wherein both the sample-probe interaction and probe geometry may be taken into account. We present a discussion of the hidden Markov model and its relationship to these convex functional transforms for simulating and restoring SPM images.©2009 SPIE.