A modified silver staining protocol for visualization of proteins compatible with matrix-assisted laser desorption/ionization and electrospray ionization-mass spectrometry

The growing availability of genomic sequence information, together with improvements in analytical methodology, have enabled high throughput, high sensitivity protein identification. Silver staining remains the most sensitive method for visualization of proteins separated by two-dimensional gel electrophoresis (2-D PAGE). Several silver staining protocols have been developed which offer improved compatibility with subsequent mass spectrometric analysis. We describe a modified silver staining method that is available as a commercial kit (Silver Stain PlusOne; Amersham Pharmacia Biotech, Amersham, UK). The 2-D patterns abtained with this modified protocol are comparable to those from other silver staining methods. Omitting the sensitizing reagent allows higher loading without saturation, which facilitates protein identification and quantitation. We show that tryptic digests of proteins visualized by the modified stain afford excellent mass spectra by both matrix-assisted laser desorption/ionization and tandem electrospray ionization. We conclude that the modified silver staining protocol is highly compatible with subsequent mass spectrometric analysis.     

Cellular internalization and targeting of semiconductor quantum dots

Peptide-mediated internalization and organelle targeting of quantum dots.     

Small-angle x-ray scattering studies of crazed glassy polymers

A small-angle x-ray scattering (SAXS) study of the relaxed craze structure in polystyrene was performed using the Oak Ridge National Laboratory 10-m SAXS facility. Coupled with known results from transmission electron microscopy studies, the SAXS patterns can be interpreted as scattering from an open-cell foam with void spaces interspersed among the fibrils. Results have shown the scattering centers in crazed polystyrene can be modeled as cylinders the axes of symmetry of which are parallel to the tensile axes. Scattering centers are bimodal in their size distribution, with aspect ratios of 1.0 and 2.6. Crazes in lower-molecular-weight polystyrene have more and larger scattering centers than crazes in higher-molecular-weight polystyrene, while variations in strain rate and test temperature during craze formation have no effect on the relaxed craze morphology. A comparison of SAXS patterns from polystyrene and polycarbonate indicates that the morphologies of their respective crazes are significantly different.     

Shock‐tube spectroscopic water measurements and detailed kinetics modeling of 1‐pentene and 3‐methyl‐1‐butene

To understand the effects of the chemical structure of two C₅ alkene isomers on their combustion properties, and to highlight the major chemical reactions occurring during their high‐temperature oxidation, water time histories were measured behind reflected shock waves for the oxidation of 1‐pentene (C₅H₁₀‐1) and 3‐methyl‐1‐butene (3M1B) in 99.5% Ar. The experiments were carried out at three different equivalence ratios (φ = 0.5, 1.0, and 2.0) at pressures and temperatures ranging from 1.29 to 1.47 atm and 1 331 to 1 877 K, respectively. The H₂O quantification extends the database for 1‐pentene and provides new insights for 3M1B. These unique results were used to validate and to develop a new detailed kinetics model. Numerical predictions are presented, and the new model was able to capture the results with suitable accuracy, with 3M1B being notably more reactive than C₅H₁₀‐1. Sensitivity and rate‐of‐production analyses were performed to help explain the results. Under the present conditions, the reactivity is rapidly initiated by molecular dissociation of a fraction of the pentene isomers. The initiation phase then induces H‐atom abstraction by active radicals (H, OH, O, HO₂, and CH₃) to first produce alkenyl C₅H₉ radicals (or an alkyl radical and an alkenyl radical by breaking a C─C bond) and subsequent, smaller fragments. The difference in terms of reactivity between the isomers is essentially due to the fact that 3M1B has one particularly weak tertiary allylic C─H bond, which allows for fast H‐atom abstraction compared with 1‐pentene.     

Chemical kinetic modeling study of the effects of oxygenated hydrocarbons on soot emissions from diesel engines

A detailed chemical kinetic modeling approach is used to examine the phenomenon of suppression of sooting in diesel engines by the addition of oxygenated hydrocarbon species to the fuel. This suppression, which has been observed experimentally for a few years, is explained kinetically as a reduction in concentrations of soot precursors present in the hot products of a fuel-rich diesel ignition zone when oxygenates are included. The kinetic model is also used to show how different oxygenates, ester structures in particular, can have different soot-suppression efficiencies due to differences in the molecular structure of the oxygenated species.     

Fuel-specific influences on the composition of reaction intermediates in premixed flames of three C5H10O2 ester isomers

Measurements of the composition of reaction intermediates in low-pressure premixed flat flames of three simple esters, the methyl butanoate (MB), methyl isobutanoate (MIB), and ethyl propanoate (EP) isomers of C(5)H(10)O(2), enable further refinement and validation of a detailed chemical reaction mechanism originally developed in modeling studies of similar flames of methyl formate, methyl acetate, ethyl formate, and ethyl acetate. Photoionization mass spectrometry (PIMS), using monochromated synchrotron radiation, reveals significant differences in the compositions of key reaction intermediates between flames of the MB, MIB, and EP isomers studied under identical flame conditions. Detailed kinetic modeling describes how these differences are related to molecular structures of each of these isomers, leading to unique fuel destruction pathways. Despite the simple structures of these small esters, they contain structural functional groups expected to account for fuel-specific effects observed in the combustion of practical biodiesel fuels. The good agreement between experimental measurements and detailed reaction mechanisms applicable to these simple esters demonstrates that major features of each flame can be predicted with reasonable accuracy by building a hierarchical reaction mechanism based on three factors: (1) unimolecular decomposition of the fuel, especially by complex bond fission; (2) H-atom abstraction reactions followed by β-scission of the resulting radicals, leading to nearly all of the intermediate species observed in each flame; (3) the rates of H-atom abstraction reactions for each alkoxy or alkyl group (i.e., methoxy, ethoxy, methyl, ethyl, propyl) are effectively the same as in other ester fuels with the same structural groups.     

Raman fiber distributed feedback lasers

We demonstrate fiber distributed feedback (DFB) lasers using Raman gain in two germanosilicate fibers. Our DFB cavities were 124 mm uniform fiber Bragg gratings with a π phase shift offset from the grating center. Our pump was at 1480 nm and the DFB lasers operated on a single longitudinal mode near 1584 nm. In a commercial Raman gain fiber, the maximum output power, linewidth, and threshold were 150 mW, 7.5 MHz, and 39 W, respectively. In a commercial highly nonlinear fiber, these figures improved to 350 mW, 4 MHz, and 4.3 W, respectively. In both lasers, more than 75% of pump power was transmitted, allowing for the possibility of substantial amplification in subsequent Raman gain fiber.     

A detailed chemical kinetic reaction mechanism for oxidation of four small alkyl esters in laminar premixed flames

A detailed chemical kinetic reaction mechanism has been developed for a group of four small alkyl ester fuels, consisting of methyl formate, methyl acetate, ethyl formate, and ethyl acetate. This mechanism is validated by comparisons between computed results and recently measured intermediate species mole fractions in fuel-rich, low-pressure, premixed laminar flames. The model development employs a principle of similarity of functional groups in constraining the H atom abstraction and unimolecular decomposition reactions for each of these fuels. As a result, the reaction mechanism and formalism for mechanism development are suitable for extension to larger oxygenated hydrocarbon fuels, together with an improved kinetic understanding of the structure and chemical kinetics of alkyl ester fuels that can be extended to biodiesel fuels. Variations in concentrations of intermediate species levels in these flames are traced to differences in the molecular structure of the fuel molecules.     

Highly tunable birefringent microstructured optical fiber

We demonstrate a method for introducing and dynamically tuning birefringence in a microstructured optical fiber. Waveguide asymmetry in the fiber is obtained by selective filling of air holes with polymer, and tunability is achieved by temperature tuning of the polymer's index. The fiber is tapered such that the mode field expands into the cladding and efficiently overlaps the polymer that has been infused into the air holes, ensuring enhanced tunability and low splice loss. Experimental results are compared with numerical simulations made with the beam propagation method and confirm birefringence tuning that corresponds to a phase change of 6pi for a 1-cm length of fiber.