OGSA first impressions: a case study re-engineering a scientific applicationwith the open grid services architecture

We present a case study of our experience re-engineeringa scientific application using the Open Grid Services Architecture(OGSA), a new specification for developing Gridapplications using web service technologies such as WSDLand SOAP. During the last decade, UCL?s Chemistry departmenthas developed a computational approach for predictingthe crystal structures of small molecules. However,each search involves running large iterations of computationallyexpensive calculations and currently takes a fewmonths to perform. Making use of early implementationsof the OGSA specification we have wrapped the Fortranbinaries into OGSI-compliant service interfaces to exposethe existing scientific application as a set of loosely coupledweb services. We show how the OGSA implementationfacilitates the distribution of such applications across alarge network, radically improving performance of the systemthrough parallel CPU capacity, coordinated resourcemanagement and automation of the computational process.We discuss the difficulties that we encountered turning Fortranexecutables into OGSA services and delivering a robust,scalable system. One unusual aspect of our approachis the way we transfer input and output data for the Fortrancodes. Instead of employing a file transfer service wetransform the XML encoded data in the SOAP message tonative file format, where possible using XSLT stylesheets.We also discuss a computational workflow service that enablesusers to distribute and manage parts of the computationalprocess across different clusters and administrativedomains. We examine how our experience re-engineeringthe polymorph prediction application led to this approachand to what extent our efforts have succeeded

An Approach of Domain Polymorph Component Design

International audienceHeterogeneous modelling and design tools allow the design of software systems using several computation models. The designed system is built by assembling components that obey a computation model. The internal behavior of a component is specified either in some programming language or by assembling sub-components that obey a possibly different computation model. When the same behavior is used in several computation models, it must be implemented in as many components as there are models, or, if the design platform supports it, it may be implemented as a generic component. Model-specific components require the recoding of the same core behavior several times, and generic components may not take model- specific features into account. In this paper, we introduce the notion of domain-polymorph component. Such a component is able to adapt a core behavior to the semantics of several computation models. The core behavior is implemented only once and is automatically adapted to the semantics of different computation models. Domain-polymorph components can be chosen by a system designer and integrated in a computation model: they will benefit from an appropriate execution environment and their semantics will be adapted to the host model. The designer will have the choice for several parameters of the adaptation. Contrary to generic components, such components adapt their behavior to the host model instead of letting the host model interpret their generic behavior. We also present an implementation of the concept of domain-polymorph component in the Ptolemy~II framework

Polymorphic phase boundary in piezoelectric oxides

The design of phase boundaries has now become a consolidated strategy to improve the functional properties of piezoelectric oxides because of the unique properties that may be obtained in their vicinity. In particular, polymorphic phase boundaries (PPBs) have attracted significant interest in recent years because they represent a significant breakthrough in terms of enhanced piezoelectric activity of lead-free piezoelectric oxides. PPBs are temperature-driven phase transitions where both intrinsic and extrinsic contributions maximize, thereby enhancing the macroscopic properties of piezoelectric materials. This tutorial discusses potassium–sodium–niobate-based systems as model materials to reveal some of the most relevant advances in the design of PPBs through compositional modifications. We focus on how PPBs can be modulated by engineered doping and also discuss the direct relation between PPBs and the enhancement of piezoelectric activity. Finally, we briefly describe the main experimental techniques for detecting PPBs.Postprint (author's final draft

Insights into the Structure of Dot@Rod and Dot@Octapod CdSe@CdS Heterostructures

CdSe@CdS dot@rods with diameter around 6 nm and length of either 20, 27, or 30 nm and dot@octapods with pod diameters of ?15 nm and lengths of ?50 nm were investigated by X-ray absorption spectroscopy. These heterostructures are prepared by seed-mediated routes, where the structure, composition, and morphology of the CdSe nanocrystals used as a seed play key roles in directing the growth of the second semiconducting domain. The local structural environment of all the elements in the CdSe@CdS heterostructures was investigated at the Cd, S, and Se K-edges by taking advantage of the selectivity of X-ray absorption spectroscopy, and was compared to pure reference compounds. We found that the structural features of dot@rods are independent of the size of the rods. These structures can be described as made of a CdSe dot and a CdS rod, both in the wurtzite phase with a high crystallinity of both the core and the rod. This result supports the effectiveness of high temperature colloidal synthesis in promoting the formation of core@shell nanocrystals with very low defectivity. On the other hand, data on the CdSe@CdS with octapod morphology suggest the occurrence of a core composed of a CdSe cubic sphalerite phase with eight pods made of CdS wurtzite phase. Our findings are compared to current models proposed for the design of functional heterostructures with controlled nanoarchitecture

Magnetic properties of epsilon iron(III) oxide nanorod arrays functionalized with gold and copper(II) oxide

A sequential chemical vapor deposition (CVD) - radio frequency (RF)-sputtering approach was adopted to fabricate supported nanocomposites based on the scarcely investigated \u3b5-iron(III) oxide polymorph. In particular, \u3b5-Fe2O3 nanorod arrays were obtained by CVD, and their subsequent functionalization with Au and CuO nanoparticles (NPs) was carried out by RF-sputtering under mild operational conditions. Apart from a multi-technique characterization of material structure, morphology and chemical composition, particular efforts were dedicated to the investigation of their magnetic properties. The pertaining experimental data, discussed in relation to the system chemico-physical characteristics, are directly dependent on the actual chemical composition, as well as on the spatial distribution of Au and CuO nanoparticles. The approach adopted herein can be further implemented to control and tailor different morphologies and phase compositions of iron oxide-based nanomaterials, meeting thus the open requests of a variety of technological utilizations

Cellular Models of Aggregation-Dependent Template-Directed Proteolysis to Characterize Tau Aggregation Inhibitors for Treatment of Alzheimer's Disease

Copyright © 2015, The American Society for Biochemistry and Molecular Biology. Acknowledgements-We thank Drs Timo Rager and Rolf Hilfiker (Solvias, Switzerland) for polymorph analyses.Peer reviewedPublisher PD

SR-FTiR microscopy and FTIR imaging in the earth sciences

During the last decades, several books have been devoted to the application of spectroscopic methods in mineralogy. Several short courses and meetings have addressed particular aspects of spectroscopy, such as the analysis of hydrous components in minerals and Earth materials. In these books, complete treatment of the infrared theory and practical aspects of instrumentation and methods, along with an exhaustive list of references, can be found. The present chapter is intended to cover those aspects of infrared spectroscopy that have been developed in the past decade and are not included in earlier reviews such as Volume 18 of Reviews in Mineralogy. These new topics involve primarily: (1) the use of synchrotron radiation (SR), which, although not a routine method, is now rather extensively applied in infrared studies, in particular those requiring ultimate spatial and time resolution and the analysis of extremely small samples (a few tens of micrometers); (2) the development of imaging techniques also for foreseen time resolved studies of geo-mineralogical processes and environmental studies.Comment: 36 pages, 24 figures - Reviews in Mineralogy & Geochemistry - Vol. 78 (2013) in pres

Evaluation of the Energetic Factors in Crystalline Pharmaceuticals Using Solid-state Density Functional Theory and Low-frequency Vibrational Spectroscopy

Due to the importance of maintaining stable and effective pharmaceutical solid doses, it is critical to study the variety of solid forms that active pharmaceutical ingredients can adopt including polymorphs, hydrates, and cocrystals. In this work, low-frequency vibrational spectroscopies and rigorous quantum mechanical simulations are combined to provide a new technique for characterizing and investigating pharmaceutically relevant polymorphs, hydrates, and cocrystals as well as a series of model cocrystals. Low-frequency spectra in the sub-200 cm-1 range provide not only unique and characteristic spectra for all of the systems explored here but, along with X-ray structural parameters, they offer a way to benchmark computational models and ensure that the models are fully capturing essential components such as the packing arrangement and the intermolecular forces present. Accurate quantum mechanical simulations allow us to determine the exact motions associated with specific low-frequency vibrational modes and this work demonstrates that large pharmaceuticals, including ones with multiple species like cocrystals, can be successfully modeled with solid-state density functional theory. Solid-state density functional theory also delivers a way to investigate how the conformations of molecules differ between polymorphs and how manipulation of the hydrogen bonding network of a solid may affect the overall stability. By studying the intermolecular forces present in the different forms, insights into stability can be made to aid future pharmaceutical crystal engineering endeavors