Comparative Enumeration Gene Expression

This paper is about differential gene expression measured by transcript counting methods such as SAGE or MPSS. It introduces two significance tests for detection of differential expressed tags: frequentist and Bayesian. Under the frequentist view, it is proposed a test that computes the critical level as a function of each tag total frequency. Under the Bayesian view the Full Bayesian Significance Test is used considering the logistic normal distribution. The two proposed significance levels, the frequentist and the Bayesian, are compared for a data set with four libraries. The linking function between them is a Beta distribution function with mean 0.39 and standard deviation 0.30

Positive Ricci curvature through Cheeger deformation

Let $(M,g)$ be a Riemannian manifold with an isometric $G$-action. If a principal orbit has finite fundamental group and $\mathrm{Ric}_{M^{reg}/G}\geq 1$, Searle--Wilhelm proved that $M$ admits a new metric $\tilde g$ of positive Ricci curvature. $\tilde g$ is obtained after a conformal change followed by a Cheeger deformation. The question remained on whether it is sufficient to consider only the Cheeger deformation to attain positive Ricci curvature on the new metric $\tilde g$. Here we approach this question by giving necessary and sufficient conditions on the $G$-action. In particular, we construct an infinite family of manifolds satisfying the hypothesis of Searle--Wilhelm that do not develop positive Ricci curvature after Cheeger deformation. Further exploring the theory, we give a alternative proofs for Lawson--Yau result on positive scalar curvature under non-abelian symmetry, among others.Comment: 26 pages. Exposition reviewed. Applications include

Scattering of Dirac and Majorana Fermions off Domain Walls

We investigate the interaction of fermions having both Dirac and left-handed and right-handed Majorana mass terms with vacuum domain walls. By solving the equations of motion in thin-wall approximation, we calculate the reflection and transmission coefficients for the scattering of fermions off walls.Comment: 6 pages, 1 figure, some typos corrected, one reference added, major revisions, title changed, version accepted for publication in Phys. Rev.

Long wavelength structural anomalies in jammed systems

The structural properties of static, jammed packings of monodisperse spheres in the vicinity of the jamming transition are investigated using large-scale computer simulations. At small wavenumber $k$, we argue that the anomalous behavior in the static structure factor, $S(k) \sim k$, is consequential of an excess of low-frequency, collective excitations seen in the vibrational spectrum. This anomalous feature becomes more pronounced closest to the jamming transition, such that $S(0) \to 0$ at the transition point. We introduce an appropriate dispersion relation that accounts for these phenomena that leads us to relate these structural features to characteristic length scales associated with the low-frequency vibrational modes of these systems. When the particles are frictional, this anomalous behavior is suppressed providing yet more evidence that jamming transitions of frictional spheres lie at lower packing fractions that that for frictionless spheres. These results suggest that the mechanical properties of jammed and glassy media may therefore be inferred from measurements of both the static and dynamical structure factors.Comment: 8 pages, 6 figure captions. Completely revised version to appear in Phys. Rev.

Vanishing conductivity of quantum solitons in polyacetylene

Quantum solitons or polarons are supposed to play a crucial role in the electric conductivity of polyacetylene, in the intermediate doping regime. We present an exact fully quantized calculation of the quantum soliton conductivity in polyacetylene and show that it vanishes exactly. This is obtained by applying a general method of soliton quantization, based on order-disorder duality, to a Z(2)-symmetric complex extension of the TLM dimerization effective field theory. We show that, in this theory, polyacetylene solitons are sine-Gordon solitons in the phase of the complex field.Comment: To appear in J. Phys. A: Math. Theor., 15 page

Modular Implementation of a Hybrid DSMC-NS Algorithm for Hypersonic Non-Equilibrium Flows

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/76683/1/AIAA-2007-613-871.pd

Hybrid Particle-Continuum Simulations of Hypersonic Flow Over a Hollow-Cylinder-Flare Geometry

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/77198/1/AIAA-36681-416.pd

Hybrid Particle-Continuum Simulations of Low Knudsen Number Hypersonic Flows

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/76429/1/AIAA-2007-3892-932.pd

Daytime turbulent exchange between the Amazon forest and the atmosphere

Detailed observations of turbulence just above and below the crown of the Amazon rain forest during the wet season are presented. The forest canopy is shown to remove high frequency turbulent fluctuations while passing lower frequencies. Filter characteristics of turbulent transfer into the Amazon rain forest canopy are quantified. Simple empirical relations that relate observed turbulent heat fluxes to horizontal wind variance are presented. Changes in the amount of turbulent coupling between the forest and the boundary layer associated with deep convective clouds are presented both as statistical averages and as a series of case studies. These convective processes during the rainy season are shown to alter the diurnal course of turbulent fluxes. In wake of giant coastal systems, no significant heat or moisture fluxes occur for up to a day after the event. Radar data is used to demonstrate that even small raining clouds are capable of evacuating the canopy of substances normally trapped by persistent static stability near the forest floor. Recovery from these events can take more than an hour, even during mid-day. In spite of the ubiquitous presence of clouds and frequent rain during this season, the average horizontal wind speed spectrum is well described by dry CBL similarity hypotheses originally found to apply in flat terrain