ALBERT

Description: The mechanisms that cause jet-flame blowout, particularly in the presence of air coflow, are not completely understood. This work examines the role of fuel velocity and air coflow in the blowout phenomenon by examining the transient behavior of the reaction zone at blowout. The results of video imaging of a lifted methane-air diffusion flame at near blowout conditions are presented. Two types of experiments are described. In the first investigation, a flame is established and stabilized at a known, predetermined downstream location with a constant coflow velocity, and then the fuel velocity is subsequently increased to cause blowout. In the other, an ignition source is used to maintain flame burning near blowout and the subsequent transient behavior to blowout upon removal of the ignition source is characterized. Data from both types of experiments are collected at various coflow and jet velocities. Images are used to ascertain the changes in the leading edge of the reaction zone prior to flame extinction that help to develop a physically-based model to describe jet-flame blowout. The data report that a consistent predictor of blowout is the prior disappearance of the axially oriented flame branch. This is witnessed despite a turbulent flames' inherent variable behavior. Interpretations are also made in the light of analytical mixture fraction expressions from the literature that support the notion that flame blowout occurs when the leading edge reaches the vicinity of the lean-limit contour, which coincides approximately with the conditions for loss of the axially oriented flame structure.

Description: ABSTRACT Formation of extensive phreatic caves in eogenetic karst aquifers is widely believed to require mixing of fresh and saltwater. Extensive phreatic caves also occur, however, in eogenetic karst aquifers where fresh and saltwater do not mix, for example in the upper Floridan aquifer. These caves are thought to have formed in their modern settings by dissolution from sinking streams or by convergence of groundwater flow paths on springs. Alternatively, these caves have been hypothesized to have formed at lower water tables during sea level low-stands. These hypotheses have not previously been tested against one another. Analyzing morphological data and water chemistry from caves in the Suwannee River Basin in north-central Florida and water chemistry from wells in the central Florida carbonate platform indicates that phreatic caves within the Suwannee River Basin most likely formed at lower water tables during lower sea levels. Consideration of the hydrological and geochemical constraints posed by the upper Floridan aquifer leads to the conclusion that cave formation was most likely driven by dissolution of vadose CO 2 gas into the groundwater. Sea level rise and a wetter climate during the mid-Holocene lifted the water table above the elevation of the caves and placed the caves 10s of meters below the modern water table. When rising water tables reached the land surface, surface streams formed. Incision of surface streams breached the pre-existing caves to form modern springs, which provide access to the phreatic caves. Phreatic caves in the Suwannee River Basin are thus relict and have no causal relationship with modern surficial drainage systems. Neither mixing dissolution nor sinking streams are necessary to form laterally extensive phreatic caves in eogenetic karst aquifers. Dissolution at water tables, potentially driven by vadose CO 2 gas, offers an underappreciated mechanism to form cavernous porosity in eogenetic carbonate rocks. Copyright © 2012 John Wiley & Sons, Ltd.

Description: Motivation: Dynamic simulation of genome-scale molecular interaction networks will enable the mechanistic prediction of genotype–phenotype relationships. Despite advances in quantitative biology, full parameterization of whole-cell models is not yet possible. Simulation methods capable of using available qualitative data are required to develop dynamic whole-cell models through an iterative process of modelling and experimental validation. Results: We formulate quasi-steady state Petri nets (QSSPN), a novel method integrating Petri nets and constraint-based analysis to predict the feasibility of qualitative dynamic behaviours in qualitative models of gene regulation, signalling and whole-cell metabolism. We present the first dynamic simulations including regulatory mechanisms and a genome-scale metabolic network in human cell, using bile acid homeostasis in human hepatocytes as a case study. QSSPN simulations reproduce experimentally determined qualitative dynamic behaviours and permit mechanistic analysis of genotype–phenotype relationships. Availability and implementation: The model and simulation software implemented in C++ are available in supplementary material and at http://sysbio3.fhms.surrey.ac.uk/qsspn/ . Contact: a.kierzek@surrey.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Genome-wide expression analysis can result in large numbers of clusters of co-expressed genes. Although there are tools for ab initio discovery of transcription factor-binding sites, most do not provide a quick and easy way to study large numbers of clusters. To address this, we introduce a web tool called MEME-LaB. The tool wraps MEME (an ab initio motif finder), providing an interface for users to input multiple gene clusters, retrieve promoter sequences, run motif finding and then easily browse and condense the results, facilitating better interpretation of the results from large-scale datasets. Availability: MEME-LaB is freely accessible at: http://wsbc.warwick.ac.uk/wsbcToolsWebpage/ . Contact: p.e.brown@warwick.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Analytical Chemistry DOI: 10.1021/ac402105s

Description: Research that combines all available studies of biological responses to regional and global climate change shows that 81–83% of all observations were consistent with the expected impacts of climate change. These findings were replicated across taxa and oceanic basins. Nature Climate Change 3 919 doi: 10.1038/nclimate1958

Description: Author(s): Christopher J. Moore and Jonathan R. Gair Posterior distributions on parameters computed from experimental data using Bayesian techniques are only as accurate as the models used to construct them. In many applications, these models are incomplete, which both reduces the prospects of detection and leads to a systematic error in the parameter... [Phys. Rev. Lett. 113, 251101] Published Mon Dec 15, 2014

Description: Author(s): Anubhav Jain, Geoffroy Hautier, Shyue Ping Ong, Charles J. Moore, Christopher C. Fischer, Kristin A. Persson, and Gerbrand Ceder Standard approximations to the density functional theory exchange-correlation functional have been extraordinary successful, but calculating formation enthalpies of reactions involving compounds with both localized and delocalized electronic states remains challenging. In this work we examine the sh... [Phys. Rev. B 84, 045115] Published Tue Jul 12, 2011

Description: Geologic carbon capture and storage (CCS) is an option for reducing CO 2 emissions, but leakage to the surface is a risk factor. Natural CO 2 reservoirs that erupt from abandoned oil and gas holes leak to the surface as spectacular cold geysers in the Colorado Plateau, United States. A better understanding of the mechanisms of CO 2 -driven cold-water geysers will provide valuable insight about the potential modes of leakage from engineered CCS sites. A notable example of a CO 2 -driven cold-water geyser is Crystal Geyser in central Utah. We investigated the fluid mechanics of this regularly erupting geyser by instrumenting its conduit with sensors and measuring pressure and temperature every 20 sec over a period of 17 days. Analyses of these measurements suggest that the timescale of a single-eruption cycle is composed of four successive eruption types with two recharge periods ranging from 30 to 40 h. Current eruption patterns exhibit a bimodal distribution, but these patterns evolved during past 80 years. The field observation suggests that the geyser's eruptions are regular and predictable and reflect pressure and temperature changes resulting from Joule–Thomson cooling and endothermic CO 2 exsolution. The eruption interval between multiple small-scale eruptions is a direct indicator of the subsequent large-scale eruption.

Description: ABSTRACT In variably confined carbonate platforms, impermeable confining units collect rainfall over large areas and deliver runoff to rivers or conduits in unconfined portions of platforms. Runoff can increase river stage or conduit heads in unconfined portions of platforms faster than local infiltration of rainfall can increase groundwater heads, causing hydraulic gradients between rivers, conduits and the aquifer to reverse. Gradient reversals cause flood waters to flow from rivers and conduits into the aquifer where they can dissolve limestone. Previous work on impacts of gradient reversals on dissolution has primarily emphasized individual caves and little research has been conducted at basin scales. To address this gap in knowledge, we used legacy data to assess how a gradient of aquifer confinement across the Suwannee River Basin, north-central Florida affected locations, magnitudes and processes of dissolution during 2005-2007, a period with extreme ranges of discharge. During intense rain events, runoff from the confining unit increased river stage above groundwater heads in unconfined portions of the platform, hydraulically damming inputs of groundwater along a 200 km reach of river. Hydraulic damming allowed allogenic runoff with SI CAL  〈 -4 to fill the entire river channel and flow into the aquifer via reversing springs. Storage of runoff in the aquifer decreased peak river discharges downstream and contributed to dissolution within the aquifer. Temporary storage of allogenic runoff in karst aquifers represents hyporheic exchange at a scale that is larger than found in streams flowing over non-karst aquifers because conduits in karst aquifers extend the area available for exchange beyond river beds deep into aquifers. Post depositional porosity in variably confined carbonate platforms should thus be enhanced along rivers that originate on confining units. This distribution should be considered in models of porosity distribution used to manage water and hydrocarbon resources in carbonate rocks. Copyright © 2013 John Wiley & Sons, Ltd.