TESTING THE ASSOCIATION OF PHENOTYPES WITH POLYPLOIDDY: AN EXAMPLE USING HERBACEOUS AND WOODY EUDICOTS
Rosana Zenil-Ferguson, Jose M. Ponciano, J. Gordon Burleigh. Testing the association of phenotypes with polyploiddy: An example using herbaceous and woody eudicots
Evolution Journal, 2017-03-29
Abstract: Although numerous studies have surveyed the frequency with which different plant characters are associated with polyploidy, few statistical tools are available to identify the factors that potentially facilitate polyploidy. We describe a new probabilistic model, BiChroM, designed to associate the frequency of polyploidy and chromosomal change with a binary phenotypic character in a phylogeny. BiChroM provides a robust statistical framework for testing differences in rates of polyploidy associated with phenotypic characters along a phylogeny while simultaneously allowing for evolutionary transitions between character states. We used BiChroM to test whether polyploidy is more frequent in woody or herbaceous plants, based on tree with 4711 eudicot species. Although polyploidy occurs in woody species, rates of chromosome doubling were over six times higher in herbaceous species. Rates of single chromosome increases or decreases were also far higher in herbaceous than woody species. Simulation experiments indicate that BiChroM performs well with little to no bias and relatively little variance at a wide range of tree depths when trees have at least 500 taxa. Thus, BiChroM provides a ﬁrst step toward a rigorous statistical framework for assessing the traits that facilitate polyploidy.
INCREASING THE APPLICABILITY OF DENSITY FUNCTIONAL THEORY. V. X-RAY ABSORPTION SPECTRA WITH IONIZATION POTENTIAL CORRECTED EXCHANGE AND CORRELATION POTENTIALS
Prakash Verma and Rodney J Bartlett. Increasing the applicability of density functional theory. V. X-ray absorption spectra with ionization potential corrected exchange and correlation potentials
J. Chem. Phys. 145, 034108 (2016), 2016-07-20
Abstract: Core excitation energies are computed with time-dependent density functional theory (TD-DFT) using the ionization energy corrected exchange and correlation potential QTP(0,0). QTP(0,0) provides C, N, and O K-edge spectra to about an electron volt. A mean absolute error (MAE) of 0.77 and a maximum error of 2.6 eV is observed for QTP(0,0) for many small molecules. TD-DFT based on QTP (0,0) is then used to describe the core-excitation spectra of the 22 amino acids. TD-DFT with conventional functionals greatly underestimates core excitation energies, largely due to the significant error in the Kohn-Sham occupied eigenvalues. To the contrary, the ionization energy corrected potential, QTP(0,0), provides excellent approximations (MAE of 0.53 eV) for core ionization energies as eigenvalues of the Kohn-Sham equations. As a consequence, core excitation energies are accurately described with QTP(0,0), as are the core ionization energies important in X-ray photoionization spectra or electron spectroscopy for chemical analysis.
IMPORTANCE OF FINITE-TEMPERATURE EXCHANGE CORRELATION FOR WARM DENSE MATTER CALCULATIONS
Valentin V. Karasiev,* L´azaro Calder´ın, and S. B. Trickey. Importance of finite-temperature exchange correlation for warm dense matter calculations
PHYSICAL REVIEW E 93, 063207 (2016), 2016-06-23
Abstract: The effects of an explicit temperature dependence in the exchange correlation (XC) free-energy functional upon calculated properties of matter in the warm dense regime are investigated. The comparison is between the Karasiev-Sjostrom-Dufty-Trickey (KSDT) finite-temperature local-density approximation (TLDA) XC functional [Karasiev et al., Phys. Rev. Lett. 112, 076403 (2014)] parametrized from restricted path-integral Monte Carlo data on the homogeneous electron gas (HEG) and the conventional Monte Carlo parametrization ground-state LDA XC [Perdew-Zunger (PZ)] functional evaluated with T -dependent densities. Both Kohn-Sham (KS) and orbital-free density-functional theories are used, depending upon computational resource demands.
Compared to the PZ functional, the KSDT functional generally lowers the dc electrical conductivity of low-density Al, yielding improved agreement with experiment. The greatest lowering is about 15% for T = 15kK. Correspondingly, the KS band structure of low-density fcc Al from the KSDT functional exhibits a clear increase in interband separation above the Fermi level compared to the PZ bands. In some density-temperature regimes, the deuterium equations of state obtained from the two XC functionals exhibit pressure differences as large as 4% and a 6% range of differences. However, the hydrogen principal Hugoniot is insensitive to the explicit XC T dependence because of cancellation between the energy and pressure-volume work difference terms in the Rankine-Hugoniot equation. Finally, the temperature at which the HEG becomes unstable is T 7200 K for the T -dependent XC, a result that the ground-state XC underestimates by about 1000 K.