Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

High Temperature Single Pulse Shock Tube Studies of Combustion Relevant Chemistry

An increasing demand for energy, as well as a need to decrease harmful emissions, necessitates better utilization of hydrocarbon fuels derived from biological and fossil sources. The single pulse shock tube experiment has been used extensively to gather validation data for the combustion of real and surrogate fuels, probe individual reactions, and aid the development of chemical kinetic models. A new lower pressure, single pulse shock tube has been constructed at the University of Illinois at Chicago. Its operation has been demonstrated in the 1-10 bar range, 650-1500 K, and ~1.7 ms reaction time. This thesis covers the work on three distinct, but broadly related studies. New pyrolysis experiments were conducted with n-heptane and oxidation experiments of mixtures of n-heptane-ethylene-methane and n-heptane-isooctane, examining how the reactivity may be influenced by the interactive chemistry of fuels and their pyrolytic and oxidative decomposition products. Several chemical kinetic models from literature were used in simulating the experimental results and were found to be inadequate for use in interpreting the results. In the second study, the recombination and disproportionation of allyl radicals has been studied in the lower pressure, single pulse shock tube. 1,5-hexadiene and allyl iodide were used as precursors. Simulation of the results using derived rate expressions from a complementary diaphragmless shock tube/laser schlieren densitometry study provided excellent agreement with precursor consumption and formation of all major stable intermediates. The final study focused on the chemical kinetic effects of the double bond position in unsaturated biodiesel molecules and long alkenes. High pressure, single pulse shock tube experiments were conducted with four decene isomers, two methyl nonenoate isomers, and two octene isomers. Increased reactivity was observed with decenes and octenes when the double bond was moved toward the center. Significantly different yields in most of the intermediate species measured were observed. The results for the methyl nonenoate isomers showed a difference in the relative yields of some stable intermediates but no increase in reactivity. Chemical kinetic models, developed with the aid of the Reaction Mechanism Generator and an updated database of relevant reaction rate rules, were used to interpret the results. Uncertainty analysis in the predicted results, using a simple Monte Carlo method, showed significant variation in the final results

Chemical Kinetic Influences of Alkyl Chain Structure on the High Pressure and Temperature Oxidation of a Representative Unsaturated Biodiesel: Methyl Nonenoate

The high pressure and temperature oxidation of methyl <i>trans</i>-2-nonenoate, methyl <i>trans</i>-3-nonenoate, 1-octene, and <i>trans</i>-2-octene are investigated experimentally to probe the influence of the double bond position on the chemical kinetics of long esters and alkenes. Single pulse shock tube experiments are performed in the ranges <i>p</i> = 3.8–6.2 MPa and <i>T</i> = 850–1500 K, with an average reaction time of 2 ms. Gas chromatographic measurements indicate increased reactivity for <i>trans</i>-2-octene compared to 1-octene, whereas both methyl nonenoate isomers have reactivities similar to that of 1-octene. A difference in the yield of stable intermediates is observed for the octenes when compared to the methyl nonenoates. Chemical kinetic models are developed with the aid of the Reaction Mechanism Generator to interpret the experimental results. The models are created using two different base chemistry submodels to investigate the influence of the foundational chemistry (i.e., C0–C4), whereas Monte Carlo simulations are performed to examine the quality of agreement with the experimental results. Significant uncertainties are found in the chemistry of unsaturated esters with the double bonds located close to the ester groups. This work highlights the importance of the foundational chemistry in predictive chemical kinetics of biodiesel combustion at engine relevant conditions

Single Pulse Shock Tube Study of Allyl Radical Recombination

The recombination and disproportionation of allyl radicals has been studied in a single pulse shock tube with gas chromatographic measurements at 1–10 bar, 650–1300 K, and 1.4–2 ms reaction times. 1,5-Hexadiene and allyl iodide were used as precursors. Simulation of the results using derived rate expressions from a complementary diaphragmless shock tube/laser schlieren densitometry study provided excellent agreement with precursor consumption and formation of all major stable intermediates. No significant pressure dependence was observed at the present conditions. It was found that under the conditions of these experiments, reactions of allyl radicals in the cooling wave had to be accounted for to accurately simulate the experimental results, and this unusual situation is discussed. In the allyl iodide experiments, higher amounts of allene, propene, and benzene were found at lower temperatures than expected. Possible mechanisms are discussed and suggest that iodine containing species are responsible for the low temperature formation of allene, propene, and benzene

Low temperature autoignition of 5-membered ring naphthenes: Effects of substitution

The development and design of future internal combustion engines requires fundamental understanding and the capability to model the autoignition and pollutant formation behavior of petroleum-based and other fuels. Naphthenes are an important constituent of gasoline, and they can comprise larger portions of unconventionally-derived gasoline. There is a lack of data and validated models for 5-membered ring naphthenes. In this work, the autoignition characteristics of cyclopentane, and two of its substituted analogues, methylcyclopentane, and ethylcyclopentane are investigated using a twin-piston rapid compression machine. Each fuel is studied at engine-representative conditions: 20, 50 bar and 700–980 K, with mixtures containing stoichiometric fuel/oxygen ratios at various extents of dilution with inert gases. Negative temperature coefficient (NTC) behavior is observed for cyclopentane, though first-stage ignition and associated low temperature heat release behavior are only evident at temperatures below that for the transition to NTC. Pressure is found to have a larger impact on the reactivity than oxygen dilution, with both effects amplified in the NTC region. The cyclopentane experiments in this study are challenged by the sensitivity of this molecule to non-uniform, or mild ignition phenomena within the NTC region. The addition of saturated sidechains in methyl- and ethylcyclopentane significantly increases the reactivity of the molecules, especially at low temperature and NTC conditions. At the highest temperatures though, there is little difference between the three naphthenes. Typical two-stage ignition behavior is observed across a wide range of temperatures for these alkyl cyclopentanes with no mild ignition observed within the NTC region. A recently developed model for cyclopentane is extended to include reactions for methylcyclopentane, and this is used to simulate the new experiments. The simulation results indicate that low temperature reactivity of cyclopentane is dominated by HO2 elimination of the RO2 species producing cyclopentene, and this inhibits autoignition since it is a very stable molecule. When a methyl group is substituted on the ring, additional RO2 isomerization pathways are available, and these substantially increase the fuel reactivity. HO2 elimination is also important with methylcyclopentane, and this leads to significant production of cyclic olefins which can further react to produce diolefins. These findings are consistent with observations that have been made in other experimental apparatuses

Auto-ignition study of FACE gasoline and its surrogates at advanced IC engine conditions

Robust surrogate formulation for gasoline fuels is challenging, especially in mimicking auto-ignition behavior observed under advanced combustion strategies including boosted spark-ignition and advanced compression ignition. This work experimentally quantifies the auto-ignition behavior of bi- and multi-component surrogates formulated to represent a mid-octane (Anti-Knock Index 91.5), full boiling-range, research grade gasoline (Fuels for Advanced Combustion Engines, FACE-F). A twin-piston rapid compression machine is used to achieve temperature and pressure conditions representative of in-cylinder engine operation. Changes in low- and intermediate-temperature behavior, including first-stage and main ignition times, are quantified for the surrogates and compared to the gasoline. This study identifies significant discrepancies in the first-stage ignition behavior, the influence of pressure for the bi- to ternary blends, and highlights that better agreement is achieved with multi-component surrogates, particularly at lower temperature regimes. A recently-updated detailed kinetic model for gasoline surrogates is also used to simulate the measurements. Sensitivity analysis is employed to interpret the kinetic pathways responsible for reactivity trends in each gasoline surrogate