Polarized quark distributions in nuclear matter

We compute the polarized quark distribution function of a bound nucleon. The Chiral Quark-Soliton model provides the quark and antiquark substructure of the nucleon embedded in nuclear matter. Nuclear effects cause significant modifications to the polarized distributions including an enhancement of the axial coupling constant.Comment: 5 Pages, 2 Postscript figures, Version to be published in Phys. Rev.

Chiral solitons in nuclei: Electromagnetic form factors

We calculate the electromagnetic form factors of a bound proton. The Chiral Quark-Soliton model provides the quark and antiquark substructure of the proton, which is embedded in nuclear matter. This procedure yields significant modifications of the form factors in the nuclear environment. The sea quarks are almost completely unaffected, and serve to mitigate the valence quark effect. In particular, the ratio of the isoscalar electric to the isovector magnetic form factor decreases by 20% at Q^2=1 GeV^2 at nuclear density, and we do not see a strong enhancement of the magnetic moment.Comment: 13 pages, 6 figures, Added references and a clearer connection to experimen

The Foundation of a Grand Unified Metaphysics

Philosophers from Leibniz to Parfit have tackled the problem of existence and the problem of arbitrarity. I divide the solutions to these two problems into three general categories: (1) infinite regress answers, (2) ex nihilo answers, and (3) self-caused cause answers. I show that the first two (infinite regress and ex nihilo) categories of answers either fail to answer the problem of existence or the problem of arbitrarity or fail to satisfy one or more reasonable assumptions about said problems. Believing it to be useful to a self-caused cause answer to the problem of existence and the problem of arbitrarily, I explicate Baruch de Spinoza’s metaphysics. Finally, I construct a self-caused cause answer to the problem of existence and the problem of arbitrarity using Spinozistic metaphysics

Exact nonadditive kinetic potentials for embedded density functional theory

We describe an embedded density functional theory (DFT) protocol in which the nonadditive kinetic energy component of the embedding potential is treated exactly. At each iteration of the Kohn–Sham equations for constrained electron density, the Zhao–Morrison–Parr constrained search method for constructing Kohn–Sham orbitals is combined with the King-Handy expression for the exact kinetic potential. We use this formally exact embedding protocol to calculate ionization energies for a series of three- and four-electron atomic systems, and the results are compared to embedded DFT calculations that utilize the Thomas–Fermi (TF) and the Thomas–Fermi–von Weisacker approximations to the kinetic energy functional. These calculations illustrate the expected breakdown due to the TF approximation for the nonadditive kinetic potential, with errors of 30%–80% in the calculated ionization energies; by contrast, the exact protocol is found to be accurate and stable. To significantly improve the convergence of the new protocol, we introduce a density-based switching function to map between the exact nonadditive kinetic potential and the TF approximation in the region of the nuclear cusp, and we demonstrate that this approximation has little effect on the accuracy of the calculated ionization energies. Finally, we describe possible extensions of the exact protocol to perform accurate embedded DFT calculations in large systems with strongly overlapping subsystem densities

Genomics clarifies taxonomic boundaries in a difficult species complex.

Efforts to taxonomically delineate species are often confounded with conflicting information and subjective interpretation. Advances in genomic methods have resulted in a new approach to taxonomic identification that stands to greatly reduce much of this conflict. This approach is ideal for species complexes, where divergence times are recent (evolutionarily) and lineages less well defined. The California Roach/Hitch fish species complex is an excellent example, experiencing a convoluted geologic history, diverse habitats, conflicting species designations and potential admixture between species. Here we use this fish complex to illustrate how genomics can be used to better clarify and assign taxonomic categories. We performed restriction-site associated DNA (RAD) sequencing on 255 Roach and Hitch samples collected throughout California to discover and genotype thousands of single nucleotide polymorphism (SNPs). Data were then used in hierarchical principal component, admixture, and FST analyses to provide results that consistently resolved a number of ambiguities and provided novel insights across a range of taxonomic levels. At the highest level, our results show that the CA Roach/Hitch complex should be considered five species split into two genera (4 + 1) as opposed to two species from distinct genera (1 +1). Subsequent levels revealed multiple subspecies and distinct population segments within identified species. At the lowest level, our results indicate Roach from a large coastal river are not native but instead introduced from a nearby river. Overall, this study provides a clear demonstration of the power of genomic methods for informing taxonomy and serves as a model for future studies wishing to decipher difficult species questions. By allowing for systematic identification across multiple scales, taxonomic structure can then be tied to historical and contemporary ecological, geographic or anthropogenic factors

Density functional theory embedding for correlated wavefunctions: Improved methods for open-shell systems and transition metal complexes

Density functional theory (DFT) embedding provides a formally exact framework for interfacing correlated wave-function theory (WFT) methods with lower-level descriptions of electronic structure. Here, we report techniques to improve the accuracy and stability of WFT-in-DFT embedding calculations. In particular, we develop spin-dependent embedding potentials in both restricted and unrestricted orbital formulations to enable WFT-in-DFT embedding for open-shell systems, and we develop an orbital-occupation-freezing technique to improve the convergence of optimized effective potential (OEP) calculations that arise in the evaluation of the embedding potential. The new techniques are demonstrated in applications to the van-der-Waals-bound ethylene-propylene dimer and to the hexaaquairon(II) transition-metal cation. Calculation of the dissociation curve for the ethylene-propylene dimer reveals that WFT-in-DFT embedding reproduces full CCSD(T) energies to within 0.1 kcal/mol at all distances, eliminating errors in the dispersion interactions due to conventional exchange-correlation (XC) functionals while simultaneously avoiding errors due to subsystem partitioning across covalent bonds. Application of WFT-in-DFT embedding to the calculation of the low-spin/high-spin splitting energy in the hexaaquairon(II) cation reveals that the majority of the dependence on the DFT XC functional can be eliminated by treating only the single transition-metal atom at the WFT level; furthermore, these calculations demonstrate the substantial effects of open-shell contributions to the embedding potential, and they suggest that restricted open-shell WFT-in-DFT embedding provides better accuracy than unrestricted open-shell WFT-in-DFT embedding due to the removal of spin contamination.Comment: 11 pages, 5 figures, 2 table

Assembly algorithms for next-generation sequencing data

AbstractThe emergence of next-generation sequencing platforms led to resurgence of research in whole-genome shotgun assembly algorithms and software. DNA sequencing data from the Roche 454, Illumina/Solexa, and ABI SOLiD platforms typically present shorter read lengths, higher coverage, and different error profiles compared with Sanger sequencing data. Since 2005, several assembly software packages have been created or revised specifically for de novo assembly of next-generation sequencing data. This review summarizes and compares the published descriptions of packages named SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths, and SOAPdenovo. More generally, it compares the two standard methods known as the de Bruijn graph approach and the overlap/layout/consensus approach to assembly