WeNMR: Structural Biology on the Grid

The WeNMR (http://www.wenmr.eu) project is a European Union funded international effort to streamline and automate analysis of Nuclear Magnetic Resonance (NMR) and Small Angle X-Ray scattering (SAXS) imaging data for atomic and near-atomic resolution molecular structures. Conventional calculation of structure requires the use of various software packages, considerable user expertise and ample computational resources. To facilitate the use of NMR spectroscopy and SAXS in life sciences the WeNMR consortium has established standard computational workflows and services through easy-to-use web interfaces, while still retaining sufficient flexibility to handle more specific requests. Thus far, a number of programs often used in structural biology have been made available through application portals. The implementation of these services, in particular the distribution of calculations to a Grid computing infrastructure, involves a novel mechanism for submission and handling of jobs that is independent of the type of job being run. With over 450 registered users (September 2012), WeNMR is currently the largest Virtual Organization (VO) in life sciences. With its large and worldwide user community, WeNMR has become the first Virtual Research Community officially recognized by the European Grid Infrastructure (EGI).     

Simulation of electron spin resonance spectroscopy in diverse environments: An integrated approach

We discuss in this work a new software tool, named E-SpiReS (Electron Spin Resonance Simulations), aimed at the interpretation of dynamical properties of molecules in fluids from electron spin resonance (ESR) measurements. The code implements an integrated computational approach (ICA) for the calculation of relevant molecular properties that are needed in order to obtain spectral lines. The protocol encompasses information from atomistic level (quantum mechanical) to coarse grained level (hydrodynamical), and evaluates ESR spectra for rigid or flexible single or multi-labeled paramagnetic molecules in isotropic and ordered phases, based on a numerical solution of a stochastic Liouville equation.E-SpiReS automatically interfaces all the computational methodologies scheduled in the ICA in a way completely transparent for the user, who controls the whole calculation flow via a graphical interface.Parallelized algorithms are employed in order to allow running on calculation clusters, and a web applet Java has been developed with which it is possible to work from any operating system, avoiding the problems of recompilation.E-SpiReS has been used in the study of a number of different systems and two relevant cases are reported to underline the promising applicability of the ICA to complex systems and the importance of similar software tools in handling a laborious protocol.

Program summary

Program title: E-SpiReSCatalogue identifier: AEEM_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEM_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GPL v2.0No. of lines in distributed program, including test data, etc.: 311 761No. of bytes in distributed program, including test data, etc.: 10 039 531Distribution format: tar.gzProgramming language: C (core programs) and Java (graphical interface)Computer: PC and MacintoshOperating system: Unix and WindowsHas the code been vectorized or parallelized?: YesRAM: 2 048 000 000Classification: 7.2External routines: Babel-1.1, CLAPACK, BLAS, CBLAS, SPARSEBLAS, CQUADPACK, LEVMARNature of problem:Ab initio simulation of cw-ESR spectra of radicals in solutionSolution method: E-SpiReS uses an hydrodynamic approach to calculate the diffusion tensor of the molecule, DFT methodologies to evaluate magnetic tensors and linear algebra techniques to solve numerically the stochastic Liouville equation to obtain an ESR spectrum.Running time: Variable depending on the task. It takes seconds for small molecules in the fast motional regime to hours for big molecules in viscous and/or ordered media.     

Annealing Behavior of a Nanostructured Fe1.5Mo Alloy

In-situ synchrotron radiation X-ray powder diffraction is shown to be complementary to thermal analysis for the study of the annealing of a ball-milled nanocrystalline Fe 1.5 wt pct Mo powder. The evolution of domain size distribution and defects is quantified via whole powder pattern modeling (WPPM) of the diffraction data. A possible annealing mechanism is proposed for the powder.     

Influence of oxide layer morphology on hydrogen concentration in tin and niobium containing zirconium alloys after high temperature steam oxidation

The influence of the oxide layer morphology on the hydrogen uptake during steam oxidation of (Zr,Sn) and Zr-Nb nuclear fuel rod cladding alloys was investigated in isothermal separate-effect tests and large-scale fuel rod bundle simulation experiments. From both it can be concluded that the concentration of hydrogen in the remaining metal strongly depends on the existence of tangential cracks in the oxide layers formed by the tetragonal - monoclinic phase transition in the oxide, known as breakaway effect. In these cracks hydrogen is strongly enriched. It results in very local high hydrogen partial pressure at the oxide/metal interface and in an increase of the hydrogen concentration in the metal at local regions where such cracks in the oxide layer exist. Due to this effect the hydrogen uptake of the remaining zirconium alloy does not depend monotonically on temperature. Differences between (Zr,Sn) and Zr-Nb alloys are caused by differences in the hydrogen production due to different oxidation kinetics and in the crack forming phase transformation in the oxides as well as in the mechanical stability of the oxides.     

Bandgap opening in oxygen plasma-treated graphene

We report a change in the semimetallic nature of single-layer graphene after exposure to oxygen plasma. The resulting transition from semimetallic to semiconducting behavior appears to depend on the duration of the exposure to the plasma treatment. The observation is confirmed by electrical, photoluminescence and Raman spectroscopy measurements. We explain the opening of a bandgap in graphene in terms of functionalization of its pristine lattice with oxygen atoms. Ab initio calculations show more details about the interaction between carbon and oxygen atoms and the consequences on the optoelectronic properties, that is, on the extent of the bandgap opening upon increased functionalisation density.     

Microstructure and Tensile Properties of Nanostructured and Ultrafine Grained FeMoB Alloys Produced by Spark Plasma Sintering of Mechanically Alloyed Powders

Boron alloyed Fe-1.5%Mo alloys (B from 0.42 to 1.66%) were produced starting from a prealloyed ferrous powder and an elemental boron powder, by mechanical alloying and spark plasma sintering. Near full density samples were obtained (density >99%) with a nano- and ultrafine grained structure, consisting in a ferritic matrix with a fine dispersion of Fe and Mo borides. High boron content and a low sintering temperature are favorable to minimize grain growth on sintering. On increasing the boron content from 0.42% up to 1.66%, yield strength increases and ductility decreases; this effect is enhanced by the sintering temperature because of the structural coarsening. Both ultrafine grained and nanostructured materials have a dimpled ductile fracture. On increasing the crystallite size, a mixed dimpled-cleavage fracture is observed.     

A Framework for the Evaluation of Trainee Performance in Cyber Range Exercises

This paper proposes a novel approach for the evaluation of the performance achieved by trainees involved in cyber security exercises implemented in modern cyber ranges. Our main contributions include: the definition of a distributed monitoring architecture for gathering relevant information about trainees activities; an algorithm for modeling the trainee activities using directed graphs; novel scoring algorithms, based on graph operations, that evaluate different aspects (speed, precision) of a trainee during an exercise. With respect to previous work, our proposal allows to measure exactly how fast a user is progressing towards an objective and where he does wrong. We highlight that this is currently not possible in the most popular cyber ranges.

     

P450scc mutant nanostructuring for optimal assembly

Molecular modeling and protein engineering were synergically employed to improve the fabrication of cytochrome P450scc mutant nanostructures for biodevice assembly. The optimization of protein three-dimensional structure by molecular modeling was performed using two models: in vacuum and simulating the presence of a polar solvent. Calculations were performed on a model to predict a P450scc mutant which could improve the process of molecules' immobilization onto solid supports. Engineerized cytochrome P450scc thin films were prepared and characterized by various biophysical techniques such as /spl pi/-A isotherms, surface potential measurements, Brewster angle microscopy, UV-vis spectroscopy, circular dichroism, nanogravimetry, and electrochemical analysis. This paper takes into consideration biomolecules modified by protein engineering that represent a new and powerful approach for obtaining synthetic simpler artificial structures with new or improved properties (i.e., specificity, stability, sensitivity, etc.) useful for biosensors development.     

Fatigue assessment using an integrated threshold curve method - applications

This paper deals with the analysis and prediction of a high-cycle fatigue behaviour in notched and damaged specimens, as well as butt-welded joints by using a threshold curve for fatigue crack propagation that includes the short crack regime (a function of crack length, a). The approach regards the effective driving force applied to the crack as the difference between the total applied driving force defined by the applied stress distribution corresponding to a given geometrical and loading configuration, ΔK(a), and the threshold for crack propagation, ΔK_th(a). Chapetti’s model is used to estimate the threshold for crack propagation by using the plain fatigue limit, Δσ_eR, the threshold for long cracks, ΔK_thR, and the microstructural characteristic dimension (e.g. grain size). Applications, predictions and results, in good agreement with experimental results from the literature, demonstrate the ability of the method to carry out quantitative analyses of the high cycle fatigue propagation behavior (near threshold) of short cracks in different geometrical, mechanical and microstructural configurations.     

Dislocation Configurations in Nanocrystalline FeMo Sintered Components

Net-shape compaction of a nanocrystalline ball-milled commercial Fe-1.5 wt pct Mo powder was done via spark plasma sintering (SPS) and capacitor discharge sintering (CDS). A detailed microstructure analysis, performed by X-ray diffraction–whole powder pattern modeling (XRD-WPPM), shows that CDS, owing to the faster sintering conditions, retains a much finer and more uniform microstructure with dislocations uniformly distributed inside the nanocrystalline grains. Conversely, SPS causes dislocations to pile up and extensive grain growth to occur, especially when high sintering temperatures are employed.