database.bio: a web application for interpreting human variations.

UNLABELLED: Rapid advances of next-generation sequencing technology have led to the integration of genetic information with clinical care. Genetic basis of diseases and response to drugs provide new ways of disease diagnosis and safer drug usage. This integration reveals the urgent need for effective and accurate tools to analyze genetic variants. Due to the number and diversity of sources for annotation, automating variant analysis is a challenging task. Here, we present database.bio, a web application that combines variant annotation, prioritization and visualization so as to support insight into the individual genetic characteristics. It enhances annotation speed by preprocessing data on a supercomputer, and reduces database space via a unified database representation with compressed fields. AVAILABILITY AND IMPLEMENTATION: Freely available at https://database.bio.

Driving Force and Optical Signatures of Bipolaron Formation in Chemically Doped Conjugated Polymers.

Molecular dopants are often added to semiconducting polymers to improve electrical conductivity. However, the use of such dopants does not always produce mobile charge carriers. In this work, ultrafast spectroscopy is used to explore the nature of the carriers created following doping of conjugated push-pull polymers with both F4 TCNQ (2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane) and FeCl3 . It is shown that for one particular push-pull material, the charge carriers created by doping are entirely non-conductive bipolarons and not single polarons, and that transient absorption spectroscopy following excitation in the infrared can readily distinguish the two types of charge carriers. Based on density functional theory calculations and experiments on multiple push-pull conjugated polymers, it is argued that the size of the donor push units determines the relative stabilities of polarons and bipolarons, with larger donor units stabilizing the bipolarons by providing more area for two charges to co-reside.

Synthesis and characterization of functionalized silica-based nanohybrid materials for oxyanions adsorption.

This study investigates the structural evolution of a series of nanohybrid powders and coatings synthesized by direct co-condensation of amino-functionalized alkyltrialkoxysilanes and tetraalkoxysilanes with an aromatic carboxylic acid (trimesic acid, TMA) as a structure directing agent. Fourier transform infrared spectroscopy (FTIR) and (13)C CP-MAS NMR results have suggested the formation of secondary (-CO-NH-) amide linkages upon interaction of TMA with the amino functionalized silane thus creating a "scaffold" around which the silica network is formed and also assisting in more homogeneous distribution of nitrogen sites within the nanohybrid structure. Functionalized silica powders were investigated for their potential to remove toxic oxyanions from mildly acidic or basic solutions. The uptake of Mo(VI), Se(VI), and Cr(VI) oxyanions was investigated as a function of the nanohybrid composition, oxyanion concentration, and solution pH using laser diffraction particle sizing, gas adsorption, and various spectroscopic techniques. The adsorption data obtained for Mo and Se could be adequately described by Langmuir adsorption isotherms, while the Freundlich isotherm is employed to fit the adsorption data for Cr. An easily accessible processing window (of pH, aging time, etc.) has been identified allowing production of continuous and uniform thin nanohybrid coatings on silicon and glass substrates. These coatings were tested as chemical barriers against Mo leaching from specially prepared Mo-doped glass. Leaching studies were conducted over 200 days in water at 90 degrees C and the Mo leaching from coated and uncoated samples compared.

Binary Superlattices of Infrared Plasmonic and Excitonic Nanocrystals.

Self-assembled superlattices of nanocrystals offer exceptional control over the coupling between nanocrystals, similar to how solid-state crystals tailor the bonding between atoms. By assembling nanocrystals of different properties (e.g., plasmonic, excitonic, dielectric, or magnetic), we can form a wealth of binary superlattice metamaterials with new functionalities. Here, we introduce infrared plasmonic Cu2-xS nanocrystals to the limited library of materials that have been successfully incorporated into binary superlattices. We are the first to create a variety of binary superlattices with large excitonic (PbS) nanocrystals and small plasmonic (Cu2-xS) nanocrystals, both resonant in the infrared. Then, by controlling the surface chemistry of large Cu2-xS nanocrystals, we produced structurally analogous superlattices of large Cu2-xS and small PbS nanocrystals. Transmission electron microscopy (TEM) and grazing-incidence small-angle X-ray scattering (GISAXS) were used to characterize both types of superlattices. Furthermore, our unique surface modification of the large Cu2-xS nanocrystals also prevented them from chemically quenching the photoluminescence of the PbS nanocrystals, which occurred when the PbS nanocrystals were mixed with unmodified Cu2-xS nanocrystals. These synthetic achievements create a set of binary superlattices that can be used to understand how infrared plasmonic and excitonic nanocrystals couple in a variety of symmetries and stoichiometries.

Dopant-Induced Ordering of Amorphous Regions in Regiorandom P3HT.

Despite the fact that molecular doping of semiconducting polymers has emerged as a valuable strategy for improving the performance of organic electronic devices, the fundamental dopant-polymer interactions are not fully understood. Here we use 2-D grazing incidence wide-angle X-ray scattering (GIWAXS) to demonstrate that adding oxidizing small-molecule dopants, such as 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ) and FeCl3, into the amorphous conjugated polymer, regiorandom poly(3-hexylthiophene-2,5-diyl) (RRa-P3HT), improves polymer ordering and induces a change in domain orientation from isotropic to mostly edge-on. Doping thus causes RRa-P3HT to behave similarly to the more ordered regioregular P3HT. By comparing the optical, electrical, and structural properties of RRa-P3HT films doped with F4TNCQ and FeCl3 and those infiltrated with 7,7,8,8-tetracyanoquinodimethane (TCNQ), which occupies a similar volume as F4TCNQ but does not dope RRa-P3HT, we show that the increased ordering results not from the ability of the dopant to fill space but instead from the need to delocalize charge on the polymer in more than one dimension.

Poly(3-alkylthiophene)- block-poly(3-alkylselenophene)s: Conjugated Diblock Co-polymers with Atypical Self-Assembly Behavior.

Understanding self-assembly behavior and resulting morphologies in block co-polymer films is an essential aspect of chemistry and materials science. Although the self-assembly of amorphous coil-coil block co-polymers is relatively well understood, that of semicrystalline block co-polymers where each block has distinct crystallization properties remains unclear. Here, we report a detailed study to elucidate the rich self-assembly behavior of conjugated thiophene-selenophene (P3AT- b-P3AS) block co-polymers. Using a combination of microscopy and synchrotron-based X-ray techniques, we show that three different film morphologies, denoted as lamellae, co-crystallized fibers, and patchy fibers, arise from the self-assembly of these block co-polymers over a relatively narrow range of overall degrees of polymerization (30 < N < 90). Crystallization-driven phase separation occurs at a very low N (<35), and lamellar films are formed. Conversely, at medium N (50-60) and high N (>80), the thiophene and selenophene blocks co-crystallize into nanofibers, where medium N leads to much more mixing than high N. The overall tendency for phase separation in these systems follows rather different trends than phase separation in amorphous polymers in that we observe the greatest degree of phase separation at the lowest N. Finally, we demonstrate how each morphology influences transport properties in organic thin-film transistors comprised of these conjugated polymers.

Overcoming Film Quality Issues for Conjugated Polymers Doped with F4TCNQ by Solution Sequential Processing: Hall Effect, Structural, and Optical Measurements.

We demonstrate that solution-sequential processing (SqP) can yield heavily doped pristine-quality films when used to infiltrate the molecular dopant 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ) into pure poly(3-hexylthiophene) (P3HT) polymer layers. Profilometry measurements show that the SqP method produces doped films with essentially the same surface roughness as pristine films, and 2-D grazing-incidence wide-angle X-ray scattering (GIWAXS) confirms that SqP preserves both the size and orientation of the pristine polymer's crystallites. Unlike traditional blend-cast F4TCNQ/P3HT doped films, our sequentially processed layers have tunable and reproducible conductivities reaching as high as 5.5 S/cm even when measured over macroscopic (>1 cm) distances. The high conductivity and superb film quality allow for meaningful Hall effect measurements, which reveal p-type conduction and carrier concentrations tunable from 10(16) to 10(20) cm(-3) and hole mobilities ranging from ∼0.003 to 0.02 cm(2) V(-1) s(-1) at room temperature over the doping levels examined.

State of hydrophobic and hydrophilic ionic liquids in aqueous solutions: are the ions fully dissociated?

Molecular dynamics simulations were performed for aqueous solutions of five ionic liquids (ILs): 1-ethyl-3-methylimidazolium ([C2mim]) bis(trifluoromethanesulfonyl) imide ([NTf2]), 1-n-butyl-3-methylimidazolium ([C4mim]) [NTf2], 1-n-hexyl-3-methylimidazolium ([C6mim]) [NTf2], [C2mim] ethylsulfate ([C2H5SO4]), and [C2mim] chloride (Cl) to determine whether the ions of these ILs are associated at relatively high dilutions and whether the association is governed by hydrophobicity/hydrophilicity of the ILs. The adaptive biasing force technique was applied to calculate the potential of mean force (PMF) for each IL ion pair. For all of the ILs, the PMF is characterized by two distinct contact minima in which the ions have different relative conformations. The hydrophobic ILs bearing the anion [NTf2](-) exist predominantly in the associative state; the strength of the association of these ILs increases with increase in the alkyl chain length. The most hydrophilic IL [C2mim] Cl was determined to be almost fully dissociated at the concentration examined in the study. [C2mim] [C2H5SO4] showed hydration behavior that was intermediate between that exhibited by the ILs in which the anion is substituted with either Cl(-) or [NTf2](-) paired with [C2mim](+). Association constants for these ILs were also computed. Radial distribution functions calculated by constraining the ions at the contact minima showed that hydration of the anion plays the dominant role in determining the microscopic behavior of these ILs in aqueous solutions.

Mesoporous zirconium titanium oxides. Part 1: Porosity modulation and adsorption properties of xerogels.

A series of zirconium titanium oxide mesophases containing 33 atom % Zr have been prepared using carboxylic acids of different alkyl chain lengths (Cy ) from y=4-18 through organic-inorganic polymer phase segregation as the gel transition is approached. Thermal treatment of these transparent gels up to 450 degrees C eliminated the organic template, and domain coarsening occurred affording stable worm-hole mesoporous materials of homogeneous composition and pore diameters varying from about 3 to 4 nm in fine increments. With such materials, it was subsequently possible to precisely study the adsorption of vanadium oxo-anions and cations from aqueous solutions and, more particularly, probe the kinetics of intraparticle mass transport as a function of the associated pore dimension. The kinetics of mass transport through the pore systems was investigated using aqueous vanadyl (VO2+) and orthovanadate (VO3(OH)2-) probe species at concentrations ranging from 10 to 200 ppm (0.2 to 4 mmol/L) and pH values of 0 and 10.5, respectively. In the case of both of these vanadium species, the zirconium titanate mesophases displayed relatively slow kinetics, taking in excess of about 500 min to achieve maximum uptake. By using a pseudo-second-order rate law, it was possible to extract the instantaneous and overall rate of the adsorption processes and then relate these to the pore diameters. Both the instantaneous and overall rates of adsorption increased with increasing surface area and pore diameter over the studied pore size range. However, the equilibrium adsorption capacity increased linearly with pore diameter only for the higher concentrations and was independent of pore diameter for the lower concentration. These results have been interpreted using a model in which discrete adsorption occurs at low concentrations and is then followed by multilayer adsorption at higher concentration.