Hartree-Fock symmetry breaking around conical intersections

We study the behavior of Hartree-Fock (HF) solutions in the vicinity of conical intersections. These are here understood as regions of a molecular potential energy surface characterized by degenerate or nearly-degenerate eigenfunctions with identical quantum numbers (point group, spin, and electron number). Accidental degeneracies between states with different quantum numbers are known to induce symmetry breaking in HF. The most common closed-shell restricted HF instability is related to singlet-triplet spin degeneracies that lead to collinear unrestricted HF (UHF) solutions. Adding geometric frustration to the mix usually results in noncollinear generalized HF (GHF) solutions, identified by orbitals that are linear combinations of up and down spins. Near conical intersections, we observe the appearance of coplanar GHF solutions that break all symmetries, including complex conjugation and time-reversal, which do not carry good quantum numbers. We discuss several prototypical examples taken from the conical intersection literature. Additionally, we utilize a recently introduced a magnetization diagnostic to characterize these solutions, as well as a solution of a Jahn-Teller active geometry of H$_8^{+2}$.Comment: accepted to JCP December 2017, published online January 201

Enhanced propagation of motile bacteria on surfaces due to forward scattering

How motile bacteria move near a surface is a problem of fundamental biophysical interest and is key to the emergence of several phenomena of biological, ecological and medical relevance, including biofilm formation. Solid boundaries can strongly influence a cell's propulsion mechanism, thus leading many flagellated bacteria to describe long circular trajectories stably entrapped by the surface. Experimental studies on near-surface bacterial motility have, however, neglected the fact that real environments have typical microstructures varying on the scale of the cells' motion. Here, we show that micro-obstacles influence the propagation of peritrichously flagellated bacteria on a flat surface in a non-monotonic way. Instead of hindering it, an optimal, relatively low obstacle density can significantly enhance cells' propagation on surfaces due to individual forward-scattering events. This finding provides insight on the emerging dynamics of chiral active matter in complex environments and inspires possible routes to control microbial ecology in natural habitats

Parallel evolution of TCP and B-class genes in Commelinaceae flower bilateral symmetry

<p>Abstract</p> <p>Background</p> <p>Flower bilateral symmetry (zygomorphy) has evolved multiple times independently across angiosperms and is correlated with increased pollinator specialization and speciation rates. Functional and expression analyses in distantly related core eudicots and monocots implicate independent recruitment of class II TCP genes in the evolution of flower bilateral symmetry. Furthermore, available evidence suggests that monocot flower bilateral symmetry might also have evolved through changes in B-class homeotic MADS-box gene function.</p> <p>Methods</p> <p>In order to test the non-exclusive hypotheses that changes in TCP and B-class gene developmental function underlie flower symmetry evolution in the monocot family Commelinaceae, we compared expression patterns of <it>teosinte branched1 </it>(<it>TB1</it>)-like, <it>DEFICIENS </it>(<it>DEF</it>)-like, and <it>GLOBOSA </it>(<it>GLO</it>)-like genes in morphologically distinct bilaterally symmetrical flowers of <it>Commelina communis </it>and <it>Commelina dianthifolia</it>, and radially symmetrical flowers of <it>Tradescantia pallida</it>.</p> <p>Results</p> <p>Expression data demonstrate that <it>TB1</it>-like genes are asymmetrically expressed in tepals of bilaterally symmetrical <it>Commelina</it>, but not radially symmetrical <it>Tradescantia</it>, flowers. Furthermore, <it>DEF</it>-like genes are expressed in showy inner tepals, staminodes and stamens of all three species, but not in the distinct outer tepal-like ventral inner tepals of <it>C. communis</it>.</p> <p>Conclusions</p> <p>Together with other studies, these data suggest parallel recruitment of <it>TB1</it>-like genes in the independent evolution of flower bilateral symmetry at early stages of <it>Commelina </it>flower development, and the later stage homeotic transformation of <it>C. communis </it>inner tepals into outer tepals through the loss of <it>DEF</it>-like gene expression.</p

An expanded evolutionary role for flower symmetry genes

CYCLOIDEA (CYC)-like TCP genes are critical for flower developmental patterning. Exciting recent breakthroughs, including a study by Song et al. published in BMC Evolutionary Biology, demonstrate that CYC-like genes have also had an important role in the evolution of flower form. See research article http://www.biomedcentral.com/1471-2148/9/244 webcite

Insurance impacts survival for children, adolescents, and young adults with bone and soft tissue sarcomas.

BackgroundWhile racial/ethnic survival disparities have been described in pediatric oncology, the impact of income has not been extensively explored. We analyzed how public insurance influences 5-year overall survival (OS) in young patients with sarcomas.MethodsThe University of California San Francisco Cancer Registry was used to identify patients aged 0-39 diagnosed with bone or soft tissue sarcomas between 2000 and 2015. Low-income patients were defined as those with no insurance or Medicaid, a means-tested form of public insurance. Survival curves were computed using the Kaplan-Meier method and compared using log-rank tests and Cox models. Causal mediation was used to assess whether the association between public insurance and mortality is mediated by metastatic disease.ResultsOf 1106 patients, 39% patients were classified as low-income. Low-income patients were more likely to be racial/ethnic minorities and to present with metastatic disease (OR 1.96, 95% CI 1.35-2.86). Low-income patients had significantly worse OS (61% vs 71%). Age at diagnosis and extent of disease at diagnosis were also independent predictors of OS. When stratified by extent of disease, low-income patients consistently had significantly worse OS (localized: 78% vs 84%, regional: 64% vs 73%, metastatic: 23% vs 30%, respectively). Mediation analysis indicated that metastatic disease at diagnosis mediated 15% of the effect of public insurance on OS.ConclusionsLow-income patients with bone and soft tissue sarcomas had decreased OS regardless of disease stage at presentation. The mechanism by which insurance status impacts survival requires additional investigation, but may be through reduced access to care

A CYC–RAD–DIV–DRIF interaction likely pre-dates the origin of floral monosymmetry in Lamiales

Background An outstanding question in evolutionary biology is how genetic interactions defining novel traits evolve. They may evolve either by de novo assembly of previously non-interacting genes or by en bloc co-option of interactions from other functions. We tested these hypotheses in the context of a novel phenotype—Lamiales flower monosymmetry—defined by a developmental program that relies on regulatory interaction among CYCLOIDEA, RADIALIS, DIVARICATA, and DRIF gene products. In Antirrhinum majus (snapdragon), representing Lamiales, we tested whether components of this program likely function beyond their previously known role in petal and stamen development. In Solanum lycopersicum (tomato), representing Solanales which diverged from Lamiales before the origin of Lamiales floral monosymmetry, we additionally tested for regulatory interactions in this program. Results We found that RADIALIS, DIVARICATA, and DRIF are expressed in snapdragon ovaries and developing fruit, similar to their homologs during tomato fruit development. In addition, we found that a tomato CYCLOIDEA ortholog positively regulates a tomato RADIALIS ortholog. Conclusion Our results provide preliminary support to the hypothesis that the developmental program defining floral monosymmetry in Lamiales was co-opted en bloc from a function in carpel development. This expands our understanding of novel trait evolution facilitated by co-option of existing regulatory interactions

A Bose gas in a single-beam optical dipole trap

We study an ultracold Bose gas in an optical dipole trap consisting of one single focused laser beam. An analytical expression for the corresponding density of states beyond the usual harmonic approximation is obtained. We are thus able to discuss the existence of a critical temperature for Bose-Einstein condensation and find that the phase transition must be enabled by a cutoff near the threshold. Moreover, we study the dynamics of evaporative cooling and observe significant deviations from the findings for the well-established harmonic approximation. Furthermore, we investigate Bose-Einstein condensates in such a trap in Thomas-Fermi approximation and determine analytical expressions for chemical potential, internal energy and Thomas-Fermi radii beyond the usual harmonic approximation