Large-scale grid-enabled lattice Boltzmann simulations of complex fluid flow in porous media and under shear

Well-designed lattice Boltzmann codes exploit the essentially embarrassingly parallel features of the algorithm and so can be run with considerable efficiency on modern supercomputers. Such scalable codes permit us to simulate the behaviour of increasingly large quantities of complex condensed matter systems. In the present paper, we present some preliminary results on the large-scale three-dimensional lattice Boltzmann simulation of binary immiscible fluid flows through a porous medium, derived from digitized X-ray micro-tomographic data of Bentheimer sandstone, and from the study of the same fluids under shear. Simulations on such scales can benefit considerably from the use of computational steering, and we describe our implementation of steering within the lattice Boltzmann code, called LB3D, making use of the RealityGrid steering library. Our large-scale simulations benefit from the new concept of capability computing, designed to prioritize the execution of big jobs on major supercomputing resources. The advent of persistent computational grids promises to provide an optimal environment in which to deploy these mesoscale simulation methods, which can exploit the distributed nature of computer, visualization and storage resources to reach scientific results rapidly; we discuss our work on the grid-enablement of lattice Boltzmann methods in this context.     

Self-reported injuries among seafarers. Questionnaire validity and results from an international study

International surveys of occupational injuries among seafarers have so far been missing. It was the aim to test the method of self-report of injuries and length of time at risk during the latest duty period and second to study the injury incidence rate among seafarers by use of the method. A pilot study was conducted (n = 1068) in Finland, Denmark, the Philippines, Croatia and Spain using self-completed questionnaires with questions about the person, the ship, the duration of latest duty period and injuries. The duration of the self-reporting duty period was in the Danish part compared with information from the crew register of the Maritime Authority. For seafarers from merchant ships in the Danish sub-study there was acceptable correspondence between the information from the seafarers and the Maritime Authority, but not when referring to ferries and non-specified types of ship. Unadjusted and adjusted injury incidence rates-ratios (IRRs) based on number of injuries per number of work hours were calculated. Adjusted IRRs for ordinary seamen/officers: IRR = 2.43 (95% CI: 1.25-4.72); for age < 35/35+ years: IRR = 1.97 (1.02-3.81); length of tour: 117 days or longer compared with < 117 days: IRR = 0.46 (95% CI: 0.22-0.95); 57-70 working hours per week compared with < 57 h: IRR = 1.26 (0.48-3.29), 71+h compared with < 57 h: IRR = 2.12 (0.84-5.36). Non-significant IRRs >1.00 were found for ships under 10,000 GT compared with larger ships and for own flagged ships compared with ships under flag of convenience. In conclusion, more than 70 h of work per week was related to a higher rate of injuries for seafarers on merchant ships, but the result was not statistically significant. Self-report of the duration of the latest tour of duty is useful for seafarers from merchant ships with short-term employments, but not for ferries and other, non-specified types of ship with other or permanent employment.     

Aerosol lidar intercomparison in the framework of the EARLINET project. 3. Raman lidar algorithm for aerosol extinction, backscatter, and lidar ratio

An intercomparison of the algorithms used to retrieve aerosol extinction and backscatter starting from Raman lidar signals has been performed by 11 groups of lidar scientists involved in the European Aerosol Research Lidar Network (EARLINET). This intercomparison is part of an extended quality assurance program performed on aerosol lidars in the EARLINET. Lidar instruments and aerosol backscatter algorithms were tested separately. The Raman lidar algorithms were tested by use of synthetic lidar data, simulated at 355, 532, 386, and 607 nm, with realistic experimental and atmospheric conditions taken into account. The intercomparison demonstrates that the data-handling procedures used by all the lidar groups provide satisfactory results. Extinction profiles show mean deviations from the correct solution within 10% in the planetary boundary layer (PBL), and backscatter profiles, retrieved by use of algorithms based on the combined Raman elastic-backscatter lidar technique, show mean deviations from solutions within 20% up to 2 km. The intercomparison was also carried out for the lidar ratio and produced profiles that show a mean deviation from the solution within 20% in the PBL. The mean value of this parameter was also calculated within a lofted aerosol layer at higher altitudes that is representative of typical layers related to special events such as Saharan dust outbreaks, forest fires, and volcanic eruptions. Here deviations were within 15%.     

Aerosol lidar intercomparison in the framework of the EARLINET project. 1. Instruments

In the framework of the European Aerosol Research Lidar Network to Establish an Aerosol Climatology (EARLINET), 19 aerosol lidar systems from 11 European countries were compared. Aerosol extinction or backscatter coefficient profiles were measured by at least two systems for each comparison. Aerosol extinction coefficients were derived from Raman lidar measurements in the UV (351 or 355 nm), and aerosol backscatter profiles were calculated from pure elastic backscatter measurements at 351 or 355, 532, or 1064 nm. The results were compared for height ranges with high and low aerosol content. Some systems were additionally compared with sunphotometers and starphotometers. Predefined maximum deviations were used for quality control of the results. Lidar systems with results outside those limits could not meet the quality assurance criterion. The algorithms for deriving aerosol backscatter profiles from elastic lidar measurements were tested separately, and the results are described in Part 2 of this series of papers [Appl. Opt. 43, 977-989 (2004)]. In the end, all systems were quality assured, although some had to be modified to improve their performance. Typical deviations between aerosol backscatter profiles were 10% in the planetary boundary layer and 0.1 x 10(-6) m(-1) sr(-1) in the free troposphere.     

Hierarchical supply chain planning using artificial neural networks to anticipate base-level outcomes

Most Advanced Planning Systems decompose the task of production planning according to the planning horizon in two levels, mid-term and short-term planning. The mid-term planning level sets the targets for the short-term level. In response, the short-term planning level gives feedback to the mid-term level. Moreover, due to detailed knowledge, the short-term planning level should provide relevant input to the mid-term planning run. To compute accurate targets for the short-term planning level the mid-term planning should anticipate its major behaviour. In this article we present an artificial neural network based anticipation of a short-term planning level for a single-stage, multi-product flow line production environment.     

Slicing, Chopping, and Path Conditions with Barriers

One of the critiques on program slicing is that slices presented to the user are hard to understand. This is mainly related to the problem that slicing dumps the results onto the user without any explanation. This work will present an approach that can be used to filter slices. This approach basically introduces barriers which are not allowed to be passed during slice computation. An earlier filtering approach is chopping which is also extended to obey such a barrier. The barrier variants of slicing and chopping provide filtering possibilities for smaller slices and better comprehensibility. The concept of barriers is then applied to path conditions, which provide necessary conditions under which an influence between the source and target criterion exists. Barriers make those conditions more precise.     

The complexity of checking consistency of pedigree information and related problems

Consistency checking is a fundamental computational problem in genetics. Given a pedigree and information on the genotypes (of some) of the individuals in it, the aim of consistency checking is to determine whether these data are consistent with the classic Mendelian laws of inheritance. This problem arose originally from the geneticists‘ need to filter their input data from erroneous information, and is well motivated from both a biological and a sociological viewpoint. This paper shows that consistency checking is NP-complete, even with focus on a single gene and in the presence of three alleles. Several other results on the computational complexity of problems from genetics that are related to consistency checking are also offered. In particular, it is shown that checking the consistency of pedigrees over two alleles, and of pedigrees without loops, can be done in polynomial time.     

Selecting informative data for developing peptide-MHC binding predictors using a query by committee approach

Strategies for selecting informative data points for training prediction algorithms are important, particularly when data points are difficult and costly to obtain. A Query by Committee (QBC) training strategy for selecting new data points uses the disagreement between a committee of different algorithms to suggest new data points, which most rationally complement existing data, that is, they are the most informative data points. In order to evaluate this QBC approach on a real-world problem, we compared strategies for selecting new data points. We trained neural network algorithms to obtain methods to predict the binding affinity of peptides binding to the MHC class I molecule, HLA-A2. We show that the QBC strategy leads to a higher performance than a baseline strategy where new data points are selected at random from a pool of available data. Most peptides bind HLA-A2 with a low affinity, and as expected using a strategy of selecting peptides that are predicted to have high binding affinities also lead to more accurate predictors than the base line strategy. The QBC value is shown to correlate with the measured binding affinity. This demonstrates that the different predictors can easily learn if a peptide will fail to bind, but often conflict in predicting if a peptide binds. Using a carefully constructed computational setup, we demonstrate that selecting peptides with a high QBC performs better than low QBC peptides independently from binding affinity. When predictors are trained on a very limited set of data they cannot be expected to disagree in a meaningful way and we find a data limit below which the QBC strategy fails. Finally, it should be noted that data selection strategies similar to those used here might be of use in other settings in which generation of more data is a costly process.     

Structural Superplasticity at High Strain Rates of Super Duplex Stainless Steel Fe‐25Cr‐7Ni‐3Mo‐0.3N

The fine‐grained super duplex stainless steel Fe‐25Cr‐7Ni‐3Mo‐0.3N consisting of two phases (δ‐ferrite/austenite) exhibits structural super‐plasticity at higher strain rates of ? ≈ 10^?2s^?1 in the temperature range between 975 and 1100°C. The equiaxed microstructure with an average grain size of was produced by thermomechanical processing. Maximum strain‐rate‐sensitivity exponents of m ≈ 0.5 and elongations to failure of more than 500% were achieved. From thermal activation analysis an activation energy for superplastic flow of Q = 310 ± 20 kJ/mole was derived. The superplastic behaviour at higher strain rates is quantitatively described by a deformation model where grain or interphase boundary sliding is accommodated by sequential steps of dislocation glide and climb. The high strain‐rate‐sensitivity exponent and the observed dislocation density indicate that dislocation climb in the slightly solid solution strengthened austenite is the rate controlling step for superplastic flow. The deformation mechanism reveals that the investigated super duplex stainless steel exhibits superplastic behaviour that is typical for class II solid solution alloys.     

Chip-based analysis of protein-protein interactions by fluorescence detection and on-chip immunoprecipitation combined with microLC-MS/MS analysis

A new chip-based method to identify protein-protein interactions was developed using the guanine nucleotide exchange factor GRF2 and two interacting proteins, Ras and calmodulin, as model proteins. A generic immobilization strategy for FLAG-tagged bait proteins on a protein-repellent streptavidin chip surface was implemented by presentation of an oriented anti-FLAG antibody. A flow cell device, integrating different chip surfaces, was developed, and the interaction of immobilized GRF2 with the two analytes was verified by fluorescence assays. On-chip tryptic digest assays were then performed on the capture surface and analyzed by microLC-MS/MS. The interaction of GRF2 with calmodulin and Ras was demonstrated, and the lower limit of detection was determined. We also implemented an on-chip immunoprecipitation assay to identify GRF2-binding partners from complex protein mixtures. Cells overexpressing FLAG-GRF2 were lysed and then incubated with the anti-FLAG chip. In addition to detecting GRF2, we also identified calmodulin, demonstrating that this technique can successfully identify endogenous levels of proteins, bound to recombinant bait proteins. This chip-based method has the advantage that no subsequent gel separations of protein complexes prior to LC-MS analysis are required and is therefore amenable to miniaturized high-throughput determination of protein-protein interactions.