Computational mechanics research and support for aerodynamics and hydraulics at TFHRC. Quarterly report January through March 2011. Year 1 Quarter 2 progress report.

This project was established with a new interagency agreement between the Department of Energy and the Department of Transportation to provide collaborative research, development, and benchmarking of advanced three-dimensional computational mechanics analysis methods to the aerodynamics and hydraulics laboratories at the Turner-Fairbank Highway Research Center for a period of five years, beginning in October 2010. The analysis methods employ well-benchmarked and supported commercial computational mechanics software. Computational mechanics encompasses the areas of Computational Fluid Dynamics (CFD), Computational Wind Engineering (CWE), Computational Structural Mechanics (CSM), and Computational Multiphysics Mechanics (CMM) applied in Fluid-Structure Interaction (FSI) problems. The major areas of focus of the project are wind and water loads on bridges - superstructure, deck, cables, and substructure (including soil), primarily during storms and flood events - and the risks that these loads pose to structural failure. For flood events at bridges, another major focus of the work is assessment of the risk to bridges caused by scour of stream and riverbed material away from the foundations of a bridge. Other areas of current research include modeling of flow through culverts to assess them for fish passage, modeling of the salt spray transport into bridge girders to address suitability of using weathering steel in bridges, vehicle stability under high wind loading, and the use of electromagnetic shock absorbers to improve vehicle stability under high wind conditions. This quarterly report documents technical progress on the project tasks for the period of January through March 2011

Phosphonic Acid-Functionalized Diblock Copolymer Nano-Objects via Polymerization-Induced Self-Assembly: Synthesis, Characterization, and Occlusion into Calcite Crystals

Dialkylphosphonate-functionalized and phosphonic acid-functionalized macromolecular chain transfer agents (macro-CTAs) were utilized for the reversible addition–fragmentation chain transfer (RAFT) dispersion polymerization of benzyl methacrylate (BzMA) at 20% w/w solids in methanol at 64 °C. Spherical, worm-like and vesicular nano-objects could all be generated through systematic variation of the mean degree of polymerization of the core-forming PBzMA block when using relatively short macro-CTAs. Construction of detailed phase diagrams is essential for the reproducible targeting of pure copolymer morphologies, where these were characterized using transmission electron microscopy (TEM) and dynamic light scattering (DLS). For nano-objects prepared using the phosphonic acid-based macro-CTA, transfer from methanol dispersion to water leads to the development of anionic surface charge as a result of ionization of the stabilizer chains, but this does not adversely affect the copolymer morphology. Given the well-known strong affinity of phosphonic acid for calcium ions, selected nano-objects were evaluated for their in-situ occlusion within growing CaCO3 crystals. Scanning electron microscopy (SEM) studies provide convincing evidence for the occlusion of both worm-like and vesicular phosphonic acid-based nano-objects and hence the production of a series of interesting new organic-inorganic nanocomposites

Generation IV nuclear energy system initiative. Large GFR core subassemblydesign for the Gas-Cooled Fast Reactor.

Gas-cooled fast reactor (GFR) designs are being developed to meet Gen IV goals of sustainability, economics, safety and reliability, and proliferation resistance and physical protection as part of an International Generation IV Nuclear Energy System Research Initiative effort. Different organizations are involved in the development of a variety of GFR design concepts. The current analysis has focused on the evaluation of low-pressure drop, pin-core designs with favorable passive cooling properties. Initial evaluation of the passive cooling safety case for the GFR during depressurized decay heat removal accidents with concurrent loss of electric power have resulted in requirements for a reduction of core power density to the 100 w/cc level and a low core pressure drop of 0.5 bars. Additional design constraints and the implementation of their constraints are evaluated in this study to enhance and passive cooling properties of the reactor. Passive cooling is made easier by a flat radial distribution of the decay heat. One goal of this study was to evaluate the radial power distribution and determine to what extent it can be flattened, since the decay heat is nearly proportional to the fission power at shutdown. In line with this investigation of the radial power profile, an assessment was also made of the control rod configuration. The layout provided a large number of control rod locations with a fixed area provided for control rods. The number of control rods was consistent with other fast reactor designs. The adequacy of the available control rod locations was evaluated. Future studies will be needed to optimize the control rod designs and evaluate the shutdown system. The case for low pressure drop core can be improved by the minimization of pressure drop sources such as the number of required fuel spacers in the subassembly design and by the details of the fuel pin design. The fuel pin design is determined by a number of neutronic, thermal-hydraulic (gas dynamics) and fuel performance considerations. For the purposes of this study, the starting point is the fuel pin design established by the CEA-ANL/US I-NERI collaboration project for the selected 2400 MWt large rector option. Structural mechanics factors are now included in the design assessment. In particular, thermal bowing establishes a bound on the minimum of fuel pin spacers required in each fuel subassembly to prevent the local flow channel restrictions and pin-to-pin mechanical interaction. There are also fabrication limitations on the maximum length of SiC fuel pin cladding which can be manufactured. This geometric limitation effects the minimum ceramic clad thickness which can be produced. This ties into the fuel pin heat transfer and temperature thresholds. All these additional design factors were included in the current iteration on the subassembly design to produce a lower core pressure drop. A more detailed definition of the fuel pin/subassembly design is proposed here to meet these limitations. This subassembly design was then evaluated under low pressure natural convection conditions to assess its acceptability for the decay heat removal accidents. A number of integrated decay heat removal (DHR) loop plus core calculations were performed to scope the thermal-hydraulic response of the subassembly design to the accidents of interest. It is evident that there is a large sensitivity to the guard containment back pressure for these designs. The implication of this conclusion and possible design modifications to reduce this sensitivity will be explored under the auspices of the International GENIV GFR collaborative R&D plan. Chapter 2 describes the core reference design for the 2,400 MWt GFR being evaluated. The methodology, modeling, and codes used in the analysis of the fuel pin structural behavior are described in Chapter 3. Chapter 4 provides the result of the thermal-hydraulic study of the assembly design for the accidents of interest. An evaluation of the performance and control rod reactivity control is also presented in Chapter 2

In search of the origins and enduring impact of agile software development

The Agile Manifesto is a philosophical touchpoint for all agile software development (ASD) methods. We examine the manifesto and some of its associated agile methods in an effort to identify the major impacts of ASD. We have encountered some difficulty in delineating agile and non-agile software processes, which is partially the result of terminological confusion. It is clear from the volume of published research that ASD has made a significant contribution, and we have identified two lasting and important impacts. Firstly, the reduction in iteration durations and secondly, the push for reduced levels of documentation (especially in relation to software requirements). Other aspects of the Agile Manifesto may not have exerted a significant impact; for example, the use of tooling to automate processes has become central to continuous software engineering (CSE) and may not be wholly congruent with the manifesto. Furthermore, many organisations may still rely on business contracts despite calls in the manifesto for greater levels of informal customer collaboration

Copper(II) Complexes with Tetradentate Piperazine-Based Ligands: DNA Cleavage and Cytotoxicity

Five-coordinate Cu(II) complexes, [Cu(Ln)X]ClO4/PF6, where Ln = piperazine ligands bearing two pyridyl arms and X = ClO4− for Ln = L1 (1-ClO4), L2 (2-ClO4), L3 (3-ClO4), and L6 (6-ClO4) as well as [Cu(Ln)Cl]PF6 for Ln = L1 (1-Cl), L4 (4-Cl), and L5 (5-Cl) have been synthesized and characterized by spectroscopic techniques. The molecular structures of the last two complexes were determined by X-ray crystallography. In aqueous acetonitrile solutions, molar conductivity measurements and UV-VIS spectrophotometric titrations of the complexes revealed the hydrolysis of the complexes to [Cu(Ln)(H2O)]2+ species. The biological activity of the Cu(II) complexes with respect to DNA cleavage and cytotoxicity was investigated. At micromolar concentration within 2 h and pH 7.4, DNA cleavage rate decreased in the order: 1-Cl ≈ 1-ClO4 > 3-ClO4 ≥ 2-ClO4 with cleavage enhancements of up to 23 million. Complexes 4-Cl, 5-Cl, and 6-ClO4 were inactive. In order to elucidate the cleavage mechanism, the cleavage of bis(4-nitrophenyl)phosphate (BNPP) and reactive oxygen species (ROS) quenching studies were conducted. The mechanistic pathway of DNA cleavage depends on the ligand’s skeleton: while an oxidative pathway was preferable for 1-Cl/1-ClO4, DNA cleavage by 2-ClO4 and 3-ClO4 predominantly proceeds via a hydrolytic mechanism. Complexes 1-ClO4, 3-ClO4, and 5-Cl were found to be cytotoxic against A2780 cells (IC50 30–40 µM). In fibroblasts, the IC50 value was much higher for 3-ClO4 with no toxic effect

The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics

Hybrid quadrupole time-of-flight (QTOF) mass spectrometry is one of the two major principles used in proteomics. Although based on simple fundamentals, it has over the last decades greatly evolved in terms of achievable resolution, mass accuracy, and dynamic range. The Bruker impact platform of QTOF instruments takes advantage of these developments and here we develop and evaluate the impact II for shotgun proteomics applications. Adaption of our heated liquid chromatography system achieved very narrow peptide elution peaks. The impact II is equipped with a new collision cell with both axial and radial ion ejection, more than doubling ion extraction at high tandem MS frequencies. The new reflectron and detector improve resolving power compared with the previous model up to 80%, i.e. to 40,000 at m/z 1222. We analyzed the ion current from the inlet capillary and found very high transmission (>80%) up to the collision cell. Simulation and measurement indicated 60% transfer into the flight tube. We adapted MaxQuant for QTOF data, improving absolute average mass deviations to better than 1.45 ppm. More than 4800 proteins can be identified in a single run of HeLa digest in a 90 min gradient. The workflow achieved high technical reproducibility (R2 > 0.99) and accurate fold change determination in spike-in experiments in complex mixtures. Using label-free quantification we rapidly quantified haploid against diploid yeast and characterized overall proteome differences in mouse cell lines originating from different tissues. Finally, after high pH reversed-phase fractionation we identified 9515 proteins in a triplicate measurement of HeLa peptide mixture and 11,257 proteins in single measurements of cerebellum-the highest proteome coverage reported with a QTOF instrument so far

Droplet Microfluidics XRD Identifies Effective Nucleating Agents for Calcium Carbonate

The ability to control crystallization reactions is required in a vast range of processes including the production of functional inorganic materials and pharmaceuticals and the prevention of scale. However, it is currently limited by a lack of understanding of the mechanisms underlying crystal nucleation and growth. To address this challenge, it is necessary to carry out crystallization reactions in well‐defined environments, and ideally to perform in situ measurements. Here, a versatile microfluidic synchrotron‐based technique is presented to meet these demands. Droplet microfluidic‐coupled X‐ray diffraction (DMC‐XRD) enables the collection of time‐resolved, serial diffraction patterns from a stream of flowing droplets containing growing crystals. The droplets offer reproducible reaction environments, and radiation damage is effectively eliminated by the short residence time of each droplet in the beam. DMC‐XRD is then used to identify effective particulate nucleating agents for calcium carbonate and to study their influence on the crystallization pathway. Bioactive glasses and a model material for mineral dust are shown to significantly lower the induction time, highlighting the importance of both surface chemistry and topography on the nucleating efficiency of a surface. This technology is also extremely versatile, and could be used to study dynamic reactions with a wide range of synchrotron‐based techniques

The effect of nitrogen on the synthesis of porous carbons by iron-catalyzed graphitization †

This paper reports a systematic study into the effect of nitrogen on iron-catalyzed graphitization of biomass. Chitin, chitosan, N-acetylglucosamine, gelatin and glycine were selected to represent nitrogen-rich saccharides and amino-acid/polypeptide biomass precursors. The materials were pyrolyzed with an iron catalyst to produce carbons with a wide range of chemical and structural features such as mesoporosity and nitrogen-doping. Many authors have reported the synthesis of nitrogen-doped carbons by pyrolysis and these have diverse applications. However, this is the first systematic study of how nitrogen affects pyrolysis of biomass and importantly the catalytic graphitization step. Our data demonstrates that nitrogen inhibits graphitization but that some nitrogen survives the catalytic graphitization process to become incorporated into various chemical environments in the carbon product