Thermal expansion in small metal clusters and its impact on the electric polarizability

The thermal expansion coefficients of $\mathrm{Na}_{N}$ clusters with $8 \le N \le 40$ and $\mathrm{Al}_{7}$, $\mathrm{Al}_{13}^-$ and $\mathrm{Al}_{14}^-$ are obtained from {\it ab initio} Born-Oppenheimer LDA molecular dynamics. Thermal expansion of small metal clusters is considerably larger than that in the bulk and size-dependent. We demonstrate that the average static electric dipole polarizability of Na clusters depends linearly on the mean interatomic distance and only to a minor extent on the detailed ionic configuration when the overall shape of the electron density is enforced by electronic shell effects. The polarizability is thus a sensitive indicator for thermal expansion. We show that taking this effect into account brings theoretical and experimental polarizabilities into quantitative agreement.Comment: 4 pages, 2 figures, one table. Accepted for publication in Physical Review Letters. References 10 and 23 update

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

Dirichlet process mixture models for single-cell RNA-seq clustering

Clustering of cells based on gene expression is one of the major steps in single-cell RNA-sequencing (scRNA-seq) data analysis. One key challenge in cluster analysis is the unknown number of clusters and, for this issue, there is still no comprehensive solution. To enhance the process of defining meaningful cluster resolution, we compare Bayesian latent Dirichlet allocation (LDA) method to its non-parametric counterpart, hierarchical Dirichlet process (HDP) in the context of clustering scRNA-seq data. A potential main advantage of HDP is that it does not require the number of clusters as an input parameter from the user. While LDA has been used in single-cell data analysis, it has not been compared in detail with HDP. Here, we compare the cell clustering performance of LDA and HDP using four scRNA-seq datasets (immune cells, kidney, pancreas and decidua/placenta), with a specific focus on cluster numbers. Using both intrinsic (DB-index) and extrinsic (ARI) cluster quality measures, we show that the performance of LDA and HDP is dataset dependent. We describe a case where HDP produced a more appropriate clustering compared to the best performer from a series of LDA clusterings with different numbers of clusters. However, we also observed cases where the best performing LDA cluster numbers appropriately capture the main biological features while HDP tended to inflate the number of clusters. Overall, our study highlights the importance of carefully assessing the number of clusters when analyzing scRNA-seq data.</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

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

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

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

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

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.