Fock space relativistic coupled-Cluster calculations of Two-Valence Atoms

We have developed an all particle Fock-space relativistic coupled-cluster method for two-valence atomic systems. We then describe a scheme to employ the coupled-cluster wave function to calculate atomic properties. Based on these developments we calculate the excitation energies, magnetic hyperfine constants and electric dipole matrix elements of Sr, Ba and Yb. Further more, we calculate the electric quadrupole HFS constants and the electric dipole matrix elements of Sr$^+$, Ba$^+$ and Yb$^+$. For these we use the one-valence coupled-cluster wave functions obtained as an intermediate in the two-valence calculations. We also calculate the magnetic dipole hyperfine constants of Yb$^+$.Comment: 23 pages, 12 figures, 10 tables typos are corrected and some minor modifications in some of the section

Relativistic coupled-cluster calculations of 20^{20}Ne, 40^{40}Ar, 84^{84}Kr and 129^{129}Xe: correlation energies and dipole polarizabilities

We have carried out a detailed and systematic study of the correlation energies of inert gas atoms Ne, Ar, Kr and Xe using relativistic many-body perturbation theory and relativistic coupled-cluster theory. In the relativistic coupled-cluster calculations, we implement perturbative triples and include these in the correlation energy calculations. We then calculate the dipole polarizability of the ground states using perturbed coupled-cluster theory.Comment: 10 figures, 6 tables, submitted to PR

Theoretical determination of lifetimes of metastable states in Sc III and Y III

Lifetimes of the first two metastable states in Sc^{2+} and Y^{2+} are determined using the relativistic coupled-cluster theory. There is a considerable interest in studying the electron correlation effects in these ions as though their electronic configurations are similar to the neutral alkali atoms, their structures are very different from the latter. We have made a comparative study of the correlation trends between the above doubly ionized systems with their corresponding neutral and singly ionized iso-electronic systems. The lifetimes of the excited states of these ions are very important in the field of astrophysics, especially for the study of post-main sequence evolution of the cool giant stars.Comment: 13 pages, 1 figure and 5 table

Novel self-assembled morphologies from isotropic interactions

We present results from particle simulations with isotropic medium range interactions in two dimensions. At low temperature novel types of aggregated structures appear. We show that these structures can be explained by spontaneous symmetry breaking in analytic solutions to an adaptation of the spherical spin model. We predict the critical particle number where the symmetry breaking occurs and show that the resulting phase diagram agrees well with results from particle simulations.Comment: 4 pages, 4 figure

Investigations of Ra+^+ properties to test possibilities of new optical frequency standards

The present work tests the suitability of the narrow transitions $7s \ ^2S_{1/2} \to 6d ^2D_{3/2}$and$7s ^2S_{1/2} \to 6d ^2D_{5/2}$in Ra$^+$for optical frequency standard studies. Our calculations of the lifetimes of the metastable$6d$states using the relativistic coupled-cluster theory suggest that they are sufficiently long for Ra$^+$ to be considered as a potential candidate for an atomic clock. This is further corroborated by our studies of the hyperfine interactions, dipole and quadrupole polarizabilities and quadrupole moments of the appropriate states of this system.Comment: Latex files, 5 pages, 1 figur

Coarse-graining of cellular automata, emergence, and the predictability of complex systems

We study the predictability of emergent phenomena in complex systems. Using nearest neighbor, one-dimensional Cellular Automata (CA) as an example, we show how to construct local coarse-grained descriptions of CA in all classes of Wolfram's classification. The resulting coarse-grained CA that we construct are capable of emulating the large-scale behavior of the original systems without accounting for small-scale details. Several CA that can be coarse-grained by this construction are known to be universal Turing machines; they can emulate any CA or other computing devices and are therefore undecidable. We thus show that because in practice one only seeks coarse-grained information, complex physical systems can be predictable and even decidable at some level of description. The renormalization group flows that we construct induce a hierarchy of CA rules. This hierarchy agrees well with apparent rule complexity and is therefore a good candidate for a complexity measure and a classification method. Finally we argue that the large scale dynamics of CA can be very simple, at least when measured by the Kolmogorov complexity of the large scale update rule, and moreover exhibits a novel scaling law. We show that because of this large-scale simplicity, the probability of finding a coarse-grained description of CA approaches unity as one goes to increasingly coarser scales. We interpret this large scale simplicity as a pattern formation mechanism in which large scale patterns are forced upon the system by the simplicity of the rules that govern the large scale dynamics.Comment: 18 pages, 9 figure

Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement, and Pancrustacean Phylogeny

An ambitious, yet fundamental goal for comparative biology is to understand the evolutionary relationships for all of life. However, many important taxonomic groups have remained recalcitrant to inclusion into broader scale studies. Here, we focus on collection of 9 new 454 transcriptome data sets from Ostracoda, an ancient and diverse group with a dense fossil record, which is often undersampled in broader studies. We combine the new transcriptomes with a new morphological matrix (including fossils) and existing expressed sequence tag, mitochondrial genome, nuclear genome, and ribosomal DNA data. Our analyses lead to new insights into ostracod and pancrustacean phylogeny. We obtained support for three epic pancrustacean clades that likely originated in the Cambrian: Oligostraca (Ostracoda, Mystacocarida, Branchiura, and Pentastomida); Multicrustacea (Copepoda, Malacostraca, and Thecostraca); and a clade we refer to as Allotriocarida (Hexapoda, Remipedia, Cephalocarida, and Branchiopoda). Within the Oligostraca clade, our results support the unresolved question of ostracod monophyly. Within Multicrustacea, we find support for Thecostraca plus Copepoda, for which we suggest the name Hexanauplia. Within Allotriocarida, some analyses support the hypothesis that Remipedia is the sister taxon to Hexapoda, but others support Branchiopoda + Cephalocarida as the sister group of hexapods. In multiple different analyses, we see better support for equivocal nodes using slow-evolving genes or when excluding distant outgroups, highlighting the increased importance of conditional data combination in this age of abundant, often anonymous data. However, when we analyze the same set of species and ignore rate of gene evolution, we find higher support when including all data, more in line with a “total evidence” philosophy. By concatenating molecular and morphological data, we place pancrustacean fossils in the phylogeny, which can be used for studies of divergence times in Pancrustacea, Arthropoda, or Metazoa. Our results and new data will allow for attributes of Ostracoda, such as its amazing fossil record and diverse biology, to be leveraged in broader scale comparative studies. Further, we illustrate how adding extensive next-generation sequence data from understudied groups can yield important new phylo- genetic insights into long-standing questions, especially when carefully analyzed in combination with other data

Long-range forces between two excited mercury atoms and associative ionization

The long-range quadrupole-quadrupole ($\sim R^{-5}$) and leading dispersion ($\sim R^{-6}$) interactions between all pairs of excited Hg($6s6p$) $^3P_0$, $^3P_1$, $^3P_2$, and $^1P_1$ atoms are determined. The quadrupole moments are calculated using the {\it ab initio} relativistic configuration-interaction method coupled with many-body perturbation theory. The van der Waals coefficients are approximated using previously calculated static polarizabilities and expressions for the dispersion energy that are validated with similar systems. The long-range interactions are critical for associative ionization in thermal and cold collisions, and are found to be quite different for different pairs of interacting states. Based on this knowledge and the short-range parts of previously calculated potential curves, improved estimates of the chemi-ionization cross sections are obtained.Comment: accepted in Phys Rev

A quick RNA mini-prep for Neurospora mycelial cultures

Most RNA isolation techniques currently in use have been developed for the processing of large quantities of material. These typically involve multiple phenol extractions (Reinert et al. 1981 Mol. Cell Biol. 1:829-836) or guanadinium isothio-cyanate/cesium chloride gradients (Chirgwin et al. 1979 Biochem 18:5294-5299) and can be both expensive and time consuming. Often, however, needs arise where quantitatively smaller amounts of RNA are needed from many different samples, for example, during time series analyses or when screening transformants for expression of a transformed gene. Under such circumstances, existing techniques are overly time consuming and yield more RNA than is necessary. The availability of a rapid RNA mini-prep is thus desirable. Such a system has been developed for isolating plant RNA (Nagy et al. 1988 Plant Molecular Biology Manual, B4; ed. Gelvin and Schilperoort, Klewer Academic Publishing, pp. 1-29), and we have adapted this procedure for use with Neurospora and, potentially, other filamentous fungi. Below, we describe the use of this procedure with 50 ml mycelial cultures, although we have used in with equal success with 5 ml cultures without scaling down the amounts of any reagents

Arrays of Josephson junctions in an environment with vanishing impedance

The Hamiltonian operator for an unbiased array of Josephson junctions with gate voltages is constructed when only Cooper pair tunnelling and charging effects are taken into account. The supercurrent through the system and the pumped current induced by changing the gate voltages periodically are discussed with an emphasis on the inaccuracies in the Cooper pair pumping. Renormalisation of the Hamiltonian operator is used in order to reliably parametrise the effects due to inhomogeneity in the array and non-ideal gating sequences. The relatively simple model yields an explicit, testable prediction based on three experimentally motivated and determinable parameters.Comment: 13 pages, 9 figures, uses RevTeX and epsfig, Revised version, Better readability and some new result