Consistent thermodynamic derivative estimates for tabular equations of state

Numerical simulations of compressible fluid flows require an equation of state (EOS) to relate the thermodynamic variables of density, internal energy, temperature, and pressure. A valid EOS must satisfy the thermodynamic conditions of consistency (derivation from a free energy) and stability (positive sound speed squared). When phase transitions are significant, the EOS is complicated and can only be specified in a table. For tabular EOS's such as SESAME from Los Alamos National Laboratory, the consistency and stability conditions take the form of a differential equation relating the derivatives of pressure and energy as functions of temperature and density, along with positivity constraints. Typical software interfaces to such tables based on polynomial or rational interpolants compute derivatives of pressure and energy and may enforce the stability conditions, but do not enforce the consistency condition and its derivatives. We describe a new type of table interface based on a constrained local least squares regression technique. It is applied to several SESAME EOS's showing how the consistency condition can be satisfied to round-off while computing first and second derivatives with demonstrated second-order convergence. An improvement of 14 orders of magnitude over conventional derivatives is demonstrated, although the new method is apparently two orders of magnitude slower, due to the fact that every evaluation requires solving an 11-dimensional nonlinear system.Comment: 29 pages, 9 figures, 16 references, submitted to Phys Rev

Integrated Radiation Transport and Nuclear Fuel Performance for Assembly-Level Simulations

The Advanced Multi-Physics (AMP) Nuclear Fuel Performance code (AMPFuel) is focused on predicting the temperature and strain within a nuclear fuel assembly to evaluate the performance and safety of existing and advanced nuclear fuel bundles within existing and advanced nuclear reactors. AMPFuel was extended to include an integrated nuclear fuel assembly capability for (one-way) coupled radiation transport and nuclear fuel assembly thermo-mechanics. This capability is the initial step toward incorporating an improved predictive nuclear fuel assembly modeling capability to accurately account for source-terms and boundary conditions of traditional (single-pin) nuclear fuel performance simulation, such as the neutron flux distribution, coolant conditions, and assembly mechanical stresses. A novel scheme is introduced for transferring the power distribution from the Scale/Denovo (Denovo) radiation transport code (structured, Cartesian mesh with smeared materials within each cell) to AMPFuel (unstructured, hexagonal mesh with a single material within each cell), allowing the use of a relatively coarse spatial mesh (10 million elements) for the radiation transport and a fine spatial mesh (3.3 billion elements) for thermo-mechanics with very little loss of accuracy. In addition, a new nuclear fuel-specific preconditioner was developed to account for the high aspect ratio of each fuel pin (12 feet axially, but 1 4 inches in diameter) with many individual fuel regions (pellets). With this novel capability, AMPFuel was used to model an entire 17 17 pressurized water reactor fuel assembly with many of the features resolved in three dimensions (for thermo-mechanics and/or neutronics), including the fuel, gap, and cladding of each of the 264 fuel pins; the 25 guide tubes; the top and bottom structural regions; and the upper and lower (neutron) reflector regions. The final, full assembly calculation was executed on Jaguar using 40,000 cores in under 10 hours to model over 162 billion degrees of freedom for 10 loading steps. The single radiation transport calculation required about 50% of the time required to solve the thermo-mechanics with a single loading step, which demonstrates that it is feasible to incorporate, in a single code, a high-fidelity radiation transport capability with a high-fidelity nuclear fuel thermo-mechanics capability and anticipate acceptable computational requirements. The results of the full assembly simulation clearly show the axial, radial, and azimuthal variation of the neutron flux, power, temperature, and deformation of the assembly, highlighting behavior that is neglected in traditional axisymmetric fuel performance codes that do not account for assembly features, such as guide tubes and control rods

Kelvin-Helmholtz instabilities with Godunov SPH

Numerical simulations for the non-linear development of Kelvin-Helmholtz instability in two different density layers have been performed with the particle-based method (Godunov SPH) developed by Inutsuka (2002). The Godunov SPH can describe the Kelvin-Helmholtz instability even with a high density contrast, while the standard SPH shows the absence of the instability across a density gradient (Agertz et al. 2007). The interaction of a dense blob with a hot ambient medium has been performed also. The Godunov SPH describes the formation and evolution of the fingers due to the combinations of Rayleigh-Taylor, Richtmyer-Meshkov, and Kelvin-Helmholtz instabilities. The blob test result coincides well with the results of the grid-based codes. An inaccurate handling of a density gradient in the standard SPH has been pointed out as the direct reason of the absence of the instabilities. An unphysical force happens at the density gradient even in a pressure equilibrium, and repulses particles from the initial density discontinuity. Therefore, the initial perturbation damps, and a gap forms at the discontinuity. The unphysical force has been studied in terms of the consistency of a numerical scheme. Contrary to the standard SPH, the momentum equation of the Godunov SPH doesnt use the particle approximation, and has been derived from the kernel convolution or a new Lagrangian function. The new Lagrangian function used in the Godunov SPH is more analogous to the real Lagrangian function for continuum. The momentum equation of the Godunov SPH has much better linear consistency, so the unphysical force is greatly reduced compared to the standard SPH in a high density contrast.Comment: 11 pages, 7 figures, Accepted for publication in MNRA

Isoprene fluxes measured by enclosure, relaxed eddy accumulation, surface layer gradient, mixed layer gradient, and mixed layer mass balance techniques

Isoprene fluxes were estimated using eight different measurement techniques at a forested site near Oak Ridge, Tennessee, during July and August 1992. Fluxes from individual leaves and entire branches were estimated with four enclosure systems, including one system that controls leaf temperature and light. Variations in isoprene emission with changes in light, temperature, and canopy depth were investigated with leaf enclosure measurements. Representative emission rates for the dominant vegetation in the region were determined with branch enclosure measurements. Species from six tree genera had negligible isoprene emissions, while significant emissions were observed for Quercus, Liquidambar, and Nyssa species. Abovecanopy isoprene fluxes were estimated with surface layer gradients and relaxed eddy accumulation measurements from a 44-m tower. Midday net emission fluxes from the canopy were typically 3 to 5 mg C m-2 h-1, although net isoprene deposition fluxes of-0.2 to -2 mg C m-2 h-1 were occasionally observed in early morning and late afternoon. Above-canopy CO2 fluxes estimated by eddy correlation using either an open path sensor or a closed path sensor agreed within ±5%. Relaxed eddy accumulation estimates of CO2 fluxes were within 15% of the eddy correlation estimates. Daytime isoprene mixing ratios in the mixed layer were investigated with a tethered balloon sampling system and ranged from 0.2 to 5 ppbv, averaging 0.8 ppbv. The isoprene mixing ratios in the mixed layer above the forested landscape were used to estimate isoprene fluxes of 2 to 8 mg C m-2 h-1 with mixed layer gradient and mixed layer mass balance techniques. Total foliar density and dominant tree species composition for an approximately 8100 km2 region were estimated using high-resolution (30 m) satellite data with classifications supervised by ground measurements. A biogenic isoprene emission model used to compare flux measurements, ranging from leaf scale (10 cm2) to landscape scale (102 km2), indicated agreement to within ±25%, the uncertainty associated with these measurement techniques. Existing biogenic emission models use isoprene emission rate capacities that range from 14.7 to 70 μg C g-1 h-1 (leaf temperature of 30°C and photosynthetically active radiation of 1000 μmol m-2 s-1) for oak foliage. An isoprene emission rate capacity of 100 μg C g-1 h-1 for oaks in this region is more realistic and is recommended, based on these measurements

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

Integrated Radiation Transport and Nuclear Fuel Performance for Assembly-Level Simulations

The Advanced Multi-Physics (AMP) Nuclear Fuel Performance code (AMPFuel) is focused on predicting the temperature and strain within a nuclear fuel assembly to evaluate the performance and safety of existing and advanced nuclear fuel bundles within existing and advanced nuclear reactors. AMPFuel was extended to include an integrated nuclear fuel assembly capability for (one-way) coupled radiation transport and nuclear fuel assembly thermo-mechanics. This capability is the initial step toward incorporating an improved predictive nuclear fuel assembly modeling capability to accurately account for source-terms and boundary conditions of traditional (single-pin) nuclear fuel performance simulation, such as the neutron flux distribution, coolant conditions, and assembly mechanical stresses. A novel scheme is introduced for transferring the power distribution from the Scale/Denovo (Denovo) radiation transport code (structured, Cartesian mesh with smeared materials within each cell) to AMPFuel (unstructured, hexagonal mesh with a single material within each cell), allowing the use of a relatively coarse spatial mesh (10 million elements) for the radiation transport and a fine spatial mesh (3.3 billion elements) for thermo-mechanics with very little loss of accuracy. In addition, a new nuclear fuel-specific preconditioner was developed to account for the high aspect ratio of each fuel pin (12 feet axially, but 1 4 inches in diameter) with many individual fuel regions (pellets). With this novel capability, AMPFuel was used to model an entire 17 17 pressurized water reactor fuel assembly with many of the features resolved in three dimensions (for thermo-mechanics and/or neutronics), including the fuel, gap, and cladding of each of the 264 fuel pins; the 25 guide tubes; the top and bottom structural regions; and the upper and lower (neutron) reflector regions. The final, full assembly calculation was executed on Jaguar using 40,000 cores in under 10 hours to model over 162 billion degrees of freedom for 10 loading steps. The single radiation transport calculation required about 50% of the time required to solve the thermo-mechanics with a single loading step, which demonstrates that it is feasible to incorporate, in a single code, a high-fidelity radiation transport capability with a high-fidelity nuclear fuel thermo-mechanics capability and anticipate acceptable computational requirements. The results of the full assembly simulation clearly show the axial, radial, and azimuthal variation of the neutron flux, power, temperature, and deformation of the assembly, highlighting behavior that is neglected in traditional axisymmetric fuel performance codes that do not account for assembly features, such as guide tubes and control rods

Sequence Diversity of the Factor H Binding Protein Vaccine Candidate in Epidemiologically Relevant Strains of Serogroup B Neisseria meningitidis

International audienceBackground. Recombinant forms of Neisseria meningitidis human factor H binding protein (fHBP) are undergoing clinical trials in candidate vaccines against invasive meningococcal serogroup B disease. We report an extensive survey and phylogenetic analysis of the diversity of fhbp genes and predicted protein sequences in invasive clinical isolates obtained in the period 2000-2006. Methods. Nucleotide sequences of fhbp genes were obtained from 1837 invasive N. meningitidis serogroup B (MnB) strains from the United States, Europe, New Zealand, and South Africa. Multilocus sequence typing (MLST) analysis was performed on a subset of the strains. Results. Every strain contained the fhbp gene. All sequences fell into 1 of 2 subfamilies (A or B), with 60%-75% amino acid identity between subfamilies and at least 83% identity within each subfamily. One fHBP sequence may have arisen via inter-subfamily recombination. Subfamily B sequences were found in 70% of the isolates, and subfamily A sequences were found in 30%. Multiple fHBP variants were detected in each of the common MLST clonal complexes. All major MLST complexes include strains in both subfamily A and subfamily B. Conclusions. The diversity of strains observed underscores the importance of studying the distribution of the vaccine antigen itself rather than relying on common epidemiological surrogates such as MLST