A Method for Integrating Heterogeneous Datasets based on GO Term Similarity

This thesis presents a method for integrating heterogeneous gene/protein datasets at the functional level based on Gene Ontology term similarity. Often biologists want to integrate heterogeneous data sets obtain from different biological samples. A major challenge in this process is how to link the heterogeneous datasets. Currently, the most common approach is to link them through common reference database identifiers which tend to result in small number of matching identifiers. This is due to lack of standard accession schemes. Due to this problem, biologists may not recognize the underlying biological phenomena revealed by a combination of the data but by each data set individually. We discuss an approach for integrating heterogeneous datasets by computing the similarity among them based on the similarity of their GO annotations. Then we group the genes and/or proteins with similar annotations by applying a hierarchical clustering algorithm. The results demonstrate a more comprehensive understanding of the biological processes involved

The past, present and future of Scientific discourse.

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Tipping Point for Expansion of Layered Aluminosilicates in Weakly Polar Solvents: Supercritical CO2

Layered aluminosilicates play a dominant role in the mechanical and gas storage properties of the subsurface, are used in diverse industrial applications, and serve as model materials for understanding solvent-ion-support systems. Although expansion in the presence of H2O is well-known to be systematically correlated with the hydration free energy of the interlayer cation, particularly in environments dominated by nonpolar solvents (i.e., CO2), uptake into the interlayer is not well-understood. Using novel high-pressure capabilities, we investigated the interaction of dry supercritical CO2 with Na-, NH4-, and Cs-saturated montmorillonite, comparing results with predictions from molecular dynamics simulations. Despite the known trend in H2O and that cation solvation energies in CO2 suggest a stronger interaction with Na, both the NH4- and Cs-clays readily absorbed CO2 and expanded, while the Na-clay did not. The apparent inertness of the Na-clay was not due to kinetics, as experiments seeking a stable expanded state showed that none exists. Molecular dynamics simulations revealed a large endothermicity to CO2 intercalation in the Na-clay but little or no energy barrier for the NH4- and Cs-clays. Indeed, the combination of experiment and theory clearly demonstrate that CO2 intercalation of Na-montmorillonite clays is prohibited in the absence of H2O. Consequently, we have shown for the first time that in the presence of a low dielectric constant, gas swelling depends more on the strength of the interaction between the interlayer cation and aluminosilicate sheets and less on that with solvent. The finding suggests a distinct regime in layered aluminosilicate swelling behavior triggered by low solvent polarizability, with important implications in geomechanics, storage, and retention of volatile gases, and across industrial uses in gelling, decoloring, heterogeneous catalysis, and semipermeable reactive barriers

Emergence of comparable covalency in isostructural cerium(IV)- and uranium(IV)-carbon multiple bonds

We report comparable levels of covalency in cerium- and uranium-carbon multiple bonds in the isostructural carbene complexes [M(BIPMTMS)(ODipp)2] [M = Ce (1), U (2), Th (3); BIPMTMS = C(PPh2NSiMe3)2; Dipp = C6H3-2,6-Pri2] whereas for M = Th the M=C bond interaction is much more ionic. On the basis of single crystal X-ray diffraction, NMR, IR, EPR, and XANES spectroscopies, and SQUID magnetometry complexes 1-3 are confirmed formally as bona fide metal(IV) complexes. In order to avoid the deficiencies of orbital-based theoretical analysis approaches we probed the bonding of 1-3 via analysis of RASSCF- and CASSCF-derived densities that explicitly treats the orbital energy near-degeneracy and overlap contributions to covalency. For these complexes similar levels of covalency are found for cerium(IV) and uranium(IV), whereas thorium(IV) is found to be more ionic, and this trend is independently found in all computational methods employed. The computationally determined trends in covalency of Ce ~ U > Th are also reproduced in experimental exchange reactions of 1-3 with MCI4 salts where 1 and 2 do not exchange with ThCl4, but 3 does exchange with MCl4 (M = Ce, U) and 1 and 2 react with UCl4 and CeCl4, respectively, to establish equilibria. This study therefore provides complementary theoretical and experimental evidence that contrasts to the accepted description that generally lanthanide-ligand bonding in non-zero oxidation state complexes is overwhelmingly ionic but that of uranium is more covalent

Synthesis, Structures, and Optical Properties of Ruthenium(II) Complexes of the Tris(1-pyrazolyl)methane Ligand

Four new complex salts [Ru^(II)Cl(Tpm)(L^A)_2][PF_6]_n [Tpm = tris(1-pyrazolyl)methane; n = 1, L^A = pyridine (py) 1 or ethyl isonicotinate (EIN) 2; n = 3, L^A = N-methyl-4,4′-bipyridinium (MeQ^+) 3 or N-phenyl-4,4′-bipyridinium (PhQ^+) 4] have been prepared and characterized. Electronic absorption spectra show intense d → π^* metal-to-ligand charge-transfer (MLCT) absorption bands, while cyclic voltammetry reveals a reversible Ru^(III/II) wave, accompanied by quasireversible or irreversible L^A-based reductions for all except 1. Single crystal X-ray structures have been obtained for 1•Me_2CO, 2, and 3•Me_2CO. For 2–4, molecular first hyperpolarizabilities β have been measured in acetonitrile solutions via the hyper-Rayleigh scattering (HRS) technique at 800 nm. Stark (electroabsorption) spectroscopic studies on the MLCT bands in frozen butyronitrile allow the indirect estimation of static first hyperpolarizabilities β_0. The various physical data obtained for 3 and 4 are compared with those reported previously for related cis-{Ru^(II)(NH_3)_4}^(2+) species [Coe, B. J. et al. J. Am. Chem. Soc. 2005, 127, 4845]. TD-DFT calculations on the complexes in 1–4 confirm that their lowest energy absorption bands are primarily Ru^(II) → L^A MLCT in character, while Ru^(II) → Tpm MLCT transitions are predicted at higher energies. DFT agrees with the Stark, but not the HRS measurements, in showing that β_0 increases with the electron-accepting strength of L^A. The 2D nature of the chromophores is evidenced by dominant β_(xxy) tensor components

SOLVENT METHODS IN COUPLED-CLUSTER THEORY

This dissertation describes the implementation of the molecular electronic structure calculations with an implicit solvent model using coupled-cluster theory. The theory for and the implementation of the solvent reaction field method (SCRF) and the reference interaction site model (RISM) at the coupled-cluster singles and doubles (CCSD) are presented. In the SCRF model a solute molecule is placed in a spherical cavity, and the outer solvent is represented by a dielectric continuum, which is characterized by the dielectric constant of the solvent. The reaction field is introduced to the system by using the multipole moment expansion of the electronic structure of the solute molecule and the dielectric constant. The SCRF method has been used to calculate the conformational equilibrium and the rotational barriers of 1,2-dichloroethane in vacuum and in different solvents. The calculated results are compared with experimental values. In addition, the solvent effects on the energetics of the mechanism of nitration of benzene are reported using the implemented CCSD-SCRF model. The idea of RISM is to replace the reaction field in continuum models by a microscopic expression in terms of the site-site radial distribution functions between solute and solvent, which can be calculated from the RISM integral equations. The statistical solvent distribution around the solute is determined based on the electronic structure of the solute, while the electronic structure of solute is influenced by the surrounding solvent distribution. Therefore, the wave function and the RISM equations are solved self-consistently with CCSD. Pair correlation functions, partial atomic charges, and solvation free energies of water and N-methylacetamide are calculated in liquid water using proposed theory. Both the CC-SCRF and CC-RISM methods have been implemented in a developmental version of the Q-Chem 3.2 quantum chemistry package