**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.

DOI: 10.1111/evo.13226

]]>**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.

]]>**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.

]]>**Advances in Quantum Chemistry, vol. 71, pp. 221–245 (2015)**, 2015-06-17

Abstract: F.E. Harris has been a significant partner in our work on orbital-free density functional

approximations for use in ab initio molecular dynamics. Here we mention briefly the

essential progress in single-point functionals since our original paper (2006). Then

we focus on the advantages and limitations of generalized gradient approximation

(GGA) noninteracting kinetic energy (KE) functionals. We reconsider the constraints provided

by near-origin conditions in atomic-like systems and their relationship to regularized

versus physical external potentials. Then we seek the best empirical GGA for the

noninteracting KE for a modest-sized set of molecules with well-defined near-origin

behavior of their densities. The search is motivated by a desire for insight into GGA limitations

and for a target for constraint-based development.

Abstract: A new general computational procedure is presented to obtain photoconductivities starting from atomic structures, combining ab initio electronic energy band states with populations from density matrix theory, and implemented for a specific set of materials based on Si crystalline slabs and their nanostructured surfaces without and with adsorbed Ag clusters. The procedure accounts for charge mobility in semiconductors in photoexcited states, and specifically electron and hole photomobilities at Si(111) surfaces with and without adsorbed Ag clusters using ab initio energy bands and orbitals generated from a generalized gradient functional, however with excited energy levels modified to provide correct band gaps. Photoexcited state populations for each band and carrier type were generated using steady state solution of a reduced density matrix which includes dissipative medium effects. The present calculations provide photoexcited electronic populations, and photoinduced mobilities resulting from applied electric fields and obtained from the change of driven electron energies with their electronic momentum. Extensive results for Si slabs with 8 layers, without and with adsorbed Ag clusters, show that the metal adsorbates lead to substantial increases in the photomobility and photoconductivity of electrons and holes.DOI: 10.1063/1.4938560

]]>**Computer Physics Communications 192 (2015) 114–123**, 2015-03-09

Abstract: Smooth, highly accurate analytical representations of Fermi–Dirac (FD) integral combinations important

in free-energy density functional calculations are presented. Specific forms include those that occur in the

local density approximation (LDA), generalized gradient approximation (GGA), and fourth-order gradient

expansion of the non-interacting free energy as well as in the LDA and second-order gradient expansion

for exchange. By construction, all the representations and their derivatives of any order are continuous

on the full domains of their independent variables. The same type of technique provides an analytical

representation of the function inverse to the FD integral of order 1/2. It plays an important role in physical

problems related to the electron gas at finite temperature. From direct evaluation, the quality of these

improved representations is shown to be substantially superior to existing ones, many of which were

developed before the era of large-scale computation or early in the era.

**Journal of Climate**, 2014-09-15

Abstract: This study compared two types of approaches to downscale seasonal precipitation (P) and 2 meter air temperature (T2M) forecasts from the North American National Multi-Model Ensemble (NMME) over the states of Alabama, Georgia, and Florida in the southeastern United States (SEUS). Each NMME model forecast was evaluated. Two MME schemes were tested by assigning equal weight to all forecast members (SuperEns) or by assigning equal weights to each models’ ensemble mean (MeanEns). One type of downscaling approach used was a model output statistics (MOS) method, which was based on direct spatial disaggregation and bias correction of the NMME P and T2M forecasts using the quantile mapping technique (SDBC). The other type of approach used was a perfect prognosis (PP) approach using nonparametric locally weighted polynomial regression (LWPR) models, which used the NMME forecasts of Niño3.4 sea surface temperatures (SSTs) to predict local-scale P and T2M. Both SDBC and LWPR downscaled P showed skill in winter but no skill or limited skill in summer at all leads for all NMME models. The SDBC downscaled T2M were skillful only for the CFSv2 model even at far leads, whereas the LWPR downscaled T2M showed limited skill or no skill for all NMME models. In many cases, the LWPR method showed significantly higher skill than the SDBC. After bias correction, the SuperEns mostly showed higher skill than the MeanEns and most of the single models, but its skill did not outperform the best single model.

]]>**Organometallics dx.doi.org/10.1021/om5003792 |**, 2014-05-07

Abstract: We report the first successful synthesis of the

long-sought arene-solvated bridgehead silylium ion

[Si4Me3(CH2)6][CHB11Cl11] by hydride abstraction from the

tetrasilaadamantyl derivative HSi4Me3(CH2)6 with the trityl

salt [Ph3C][CHB11Cl11] in toluene, benzene, or bromobenzene

solution. The silylium···arene complex was characterized

by X-ray diffraction analysis and by NMR spectroscopy and

was studied computationally. NMR studies show that the

silylium species undergoes a dynamic solvate exchange in

BrPh/MePh mixed solvent.

**Journal of Chemical Theory and Computation.**, 2014-02-05

Abstract: By utilizing Graphics Processing Units, we show that constant pH molecular dynamics simulations (CpHMD) run in Generalized Born (GB) implicit solvent for long time scales can yield poor pKa predictions as a result of sampling unrealistic conformations. To address this shortcoming, we present a method for performing constant pH molecular dynamics simulations (CpHMD) in explicit solvent using a discrete protonation state model. The method involves standard molecular dynamics (MD) being propagated in explicit solvent followed by protonation state changes being attempted in GB implicit solvent at fixed intervals. Replica exchange along the pH-dimension (pH-REMD) helps to obtain acceptable titration behavior with the proposed method. We analyzed the effects of various parameters and settings on the titration behavior of CpHMD and pH-REMD in explicit solvent, including the size of the simulation unit cell and the length of the relaxation dynamics following protonation state changes. We tested the method with the amino acid model compounds, a small pentapeptide with two titratable sites, and hen egg white lysozyme (HEWL). The proposed method yields superior predicted pKa values for HEWL over hundreds of nanoseconds of simulation relative to corresponding predicted values from simulations run in implicit solvent.

DOI: 10.1021/ct401042b

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