RepViz: A replicate-driven R tool for visualizing genomic regions

Objective: Visualization of sequencing data is an integral part of genomic data analysis. Although there are several tools to visualize sequencing data on genomic regions, they do not ofer user-friendly ways to view simultaneously diferent groups of replicates. To address this need, we developed a tool that allows efcient viewing of both intraand intergroup variation of sequencing counts on a genomic region, as well as their comparison to the output of user selected analysis methods, such as peak calling. Results: We present an R package RepViz for replicate-driven visualization of genomic regions. With ChIP-seq and ATAC-seq data we demonstrate its potential to aid visual inspection involved in the evaluation of normalization, outlier behavior, detected features from diferential peak calling analysis, and combined analysis of multiple data types. RepViz is readily available on Bioconductor (https://www.bioconductor.org/packages/devel/bioc/html/RepViz.html) and on Github (https://github.com/elolab/RepViz).</p

Tri-axial Octupole Deformations and Shell Structure

Manifestations of pronounced shell effects are discovered when adding nonaxial octupole deformations to a harmonic oscillator model. The degeneracies of the quantum spectra are in a good agreement with the corresponding main periodic orbits and winding number ratios which are found by classical analysis.Comment: 10 pages, Latex, 4 postscript figures, to appear in JETP Letter

From critters to cancers: bridging comparative and clinical research on oxygen sensing, HIF signaling, and adaptations towards hypoxia

The objective of this symposium at the First International Congress of Respiratory Biology (ICRB) was to enhance communication between comparative biologists and cancer researchers working on O2 sensing via the HIF pathway. Representatives from both camps came together on August 13-16, 2006, in Bonn, Germany, to discuss molecular adaptations that occur after cells have been challenged by a reduced (hypoxia) or completely absent (anoxia) supply of oxygen. This brief "critters-to-cancer” survey discusses current projects and new directions aimed at improving understanding of hypoxic signaling and developing therapeutic intervention

Close-Packing of Clusters: Application to Al_100

The lowest energy configurations of close-packed clusters up to N=110 atoms with stacking faults are studied using the Monte Carlo method with Metropolis algorithm. Two types of contact interactions, a pair-potential and a many-atom interaction, are used. Enhanced stability is shown for N=12, 26, 38, 50, 59, 61, 68, 75, 79, 86, 100 and 102, of which only the sizes 38, 75, 79, 86, and 102 are pure FCC clusters, the others having stacking faults. A connection between the model potential and density functional calculations is studied in the case of Al_100. The density functional calculations are consistent with the experimental fact that there exist epitaxially grown FCC clusters starting from relatively small cluster sizes. Calculations also show that several other close-packed motifs existwith comparable total energies.Comment: 9 pages, 7 figure

Ionic and electronic structure of sodium clusters up to N=59

We determined the ionic and electronic structure of sodium clusters with even electron numbers and 2 to 59 atoms in axially averaged and three-dimensional density functional calculations. A local, phenomenological pseudopotential that reproduces important bulk and atomic properties and facilitates structure calculations has been developed. Photoabsorption spectra have been calculated for $\mathrm{Na}_2$, $\mathrm{Na}_8$, and $\mathrm{Na}_9^+$ to $\mathrm{Na}_{59}^+$. The consistent inclusion of ionic structure considerably improves agreement with experiment. An icosahedral growth pattern is observed for $\mathrm{Na}_{19}^+$ to $\mathrm{Na}_{59}^+$. This finding is supported by photoabsorption data.Comment: To appear in Phys. Rev. B 62. Version with figures in better quality can be requested from the author

Sodium atoms and clusters on graphite: a density functional study

Sodium atoms and clusters (N<5) on graphite (0001) are studied using density functional theory, pseudopotentials and periodic boundary conditions. A single Na atom is observed to bind at a hollow site 2.45 A above the surface with an adsorption energy of 0.51 eV. The small diffusion barrier of 0.06 eV indicates a flat potential energy surface. Increased Na coverage results in a weak adsorbate-substrate interaction, which is evident in the larger separation from the surface in the cases of Na_3, Na_4, Na_5, and the (2x2) Na overlayer. The binding is weak for Na_2, which has a full valence electron shell. The presence of substrate modifies the structures of Na_3, Na_4, and Na_5 significantly, and both Na_4 and Na_5 are distorted from planarity. The calculated formation energies suggest that clustering of atoms is energetically favorable, and that the open shell clusters (e.g. Na_3 and Na_5) can be more abundant on graphite than in the gas phase. Analysis of the lateral charge density distributions of Na and Na_3 shows a charge transfer of about 0.5 electrons in both cases.Comment: 20 pages, 6 figure

An orbital-free molecular dynamics study of melting in K_20, K_55, K_92, K_142, Rb_55 and Cs_55 clusters

The melting-like transition in potasium clusters K_N, with N=20, 55, 92 and 142, is studied by using an orbital-free density-functional constant-energy molecular dynamics simulation method, and compared to previous theoretical results on the melting-like transition in sodium clusters of the same sizes. Melting in potasium and sodium clusters proceeds in a similar way: a surface melting stage develops upon heating before the homogeneous melting temperature is reached. Premelting effects are nevertheless more important and more easily established in potasium clusters, and the transition regions spread over temperature intervals which are wider than in the case of sodium. For all the sizes considered, the percentage melting temperature reduction when passing from Na to K clusters is substantially larger than in the bulk. Once those two materials have been compared for a number of different cluster sizes, we study the melting-like transition in Rb_55 and Cs_55 clusters and make a comparison with the melting behavior of Na_55 and K_55. As the atomic number increases, the height of the specific heat peaks decreases, their width increases, and the melting temperature decreases as in bulk melting, but in a more pronounced way.Comment: LaTeX file. 6 pages with 17 pictures. Final version with minor change

Thermodynamics of Na_8 and Na_{20} clusters studied with ab-initio electronic structure methods

We study the thermodynamics of Na_8 and Na_{20} clusters using multiple-histogram methods and an ab initio treatment of the valence electrons within density functional theory. We consider the influence of various electron kinetic-energy functionals and pseudopotentials on the canonical ionic specific heats. The results for all models we consider show qualitative similarities, but also significant temperature shifts from model to model of peaks and other features in the specific-heat curves. The use of phenomenological pseudopotentials shifts the melting peak substantially (~ 50--100 K) when compared to ab-initio results. It is argued that the choice of a good pseudopotential and use of better electronic kinetic-energy functionals has the potential for performing large time scale and large sized thermodynamical simulations on clusters.Comment: LaTeX file and EPS figures. 24 pages, 13 figures. Submitted to Phys. Rev.