A software framework based on a conceptual unified model for evolutionary multiobjective optimization: ParadisEO-MOEO

This paper presents a general-purpose software framework dedicated to the design and the implementation of evolutionary multiobjective optimization techniques: ParadisEO-MOEO. A concise overview of evolutionary algorithms for multiobjective optimization is given. A substantial number of methods has been proposed so far, and an attempt of conceptually unifying existing approaches is presented here. Based on a fine-grained decomposition and following the main issues of fitness assignment, diversity preservation and elitism, a conceptual model is proposed and is validated by regarding a number of state-of-the-art algorithms as simple variants of the same structure. This model is then incorporated into the ParadisEO-MOEO software framework. This framework has proven its validity and high flexibility by enabling the resolution of many academic, real-world and hard multiobjective optimization problems.     

Growth and structural characterization of YMnO3 thin films grown by pulsed liquid injection MOCVD on Si and SrTiO3 substrates

Optimum parameters for the growing of YMnO₃ films by pulsed liquid injection metalorganic chemical vapor deposition have been studied. Si substrates were used for the optimization of the deposition process. X-ray diffraction (XRD) and transmission electron microscopy (TEM) results show that polycrystalline single phase YMnO₃ films can be obtained for an optimal ratio of Y and Mn on the injected solution and either amorphous, metastable orthorhombic, and/or hexagonal YMnO₃ phases can be obtained depending on the deposition temperature and precursors ratio. In a second stage, YMnO₃ films were grown on SrTiO₃ substrates. Pure epitaxial orthorhombic YMnO₃ phase was confirmed by XRD. The films microstructure, characterized by scanning electron microscopy and TEM, shows a columnar growth. Each columnar grain grows epitaxially with three possible orientations.     

Synthesis and attachment of silver nanowires on atomic force microscopy cantilevers for tip‐enhanced Raman spectroscopy

Surface‐enhanced Raman spectroscopy is based on the absorption of light by nanometer‐sized metal particles, resulting in large enhancement of the Raman signal. By replacing the metal particles by a metallic nanotip, the enhancement can be localized. The resulting tip‐enhanced Raman spectroscopy is capable of measuring Raman spectra with high spatial resolution, effectively overcoming the diffraction limit. A successful tip‐enhanced Raman spectroscopy experiment depends heavily on the ability to fabricate tips of a definite metal with the appropriate shape and size, which is still a challenging process. We have prepared silver nanowires with a diameter of 200–300 nm by templated electrochemical deposition and attached them onto atomic force microscope cantilevers by focused electron beam induced deposition. We found that they produce a reproducible enhancement of the Raman signal intensity. Other metals and smaller nanostructures might also be produced, suggesting an interesting development potential for these novel nanoprobes. Copyright © 2011 John Wiley & Sons, Ltd.     

Global existence result for thermoviscoelastic problems with hysteresis

We consider viscoelastic solids undergoing thermal expansion and exhibiting hysteresis effects due to plasticity or phase transformations. Within the framework of generalized standard solids, the problem is described in a three-dimensional setting by the momentum equilibrium equation, the flow rule describing the dependence of the stress on the strain history, and the heat transfer equation. Under appropriate regularity assumptions on the data, a local existence result for this thermodynamically consistent system is established, by combining existence results for ordinary differential equations in Banach spaces with a fixed-point argument. Then global estimates are obtained by using both the classical energy estimate and more specific techniques for the heat equation introduced by Boccardo and Gallouët. Finally a global existence result is derived.     

Synergies between operations research and data mining: The emerging use of multi-objective approaches

Operations research and data mining already have a long-established common history. Indeed, with the growing size of databases and the amount of data available, data mining has become crucial in modern science and industry. Data mining problems raise interesting challenges for several research domains, and in particular for operations research, as very large search spaces of solutions need to be explored. Hence, many operations research methods have been proposed to deal with such challenging problems. But the relationships between these two domains are not limited to these natural applications of operations research approaches. The counterpart is also important to consider, since data mining approaches have also been applied to improve operations research techniques. The aim of this article is to highlight the interplay between these two research disciplines. A particular emphasis will be placed on the emerging theme of applying multi-objective approaches in this context.     

Synthesis of polylactide/clay nanocomposites by in situ intercalative polymerization in supercritical carbon dioxide

Polylactide (PLA)/clay nanocomposites have been prepared by in situ ring-opening polymerization in supercritical carbon dioxide. Depending on the type of organoclay used, polylactide chains can be grafted onto the clay surface, leading to an exfoliated morphology. Nanocomposites with high clay contents (30-50 wt.%), called masterbatches, have also been successfully prepared and were recovered as fine powders thanks to the unique properties of the supercritical fluid. Dilution of these masterbatches into commercial l-polylactide by melt blending has led to essentially exfoliated nanocomposites containing 3 wt.% of clay. The mechanical properties of these materials have been assessed by flexion and impact tests. Significant improvements of stiffness and toughness have been observed for the PLA/clay nanocomposites compared to the pure matrix, together with improved impact resistance.     

Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site

Eg5, a mitotic kinesin exclusively involved in the formation and function of the mitotic spindle has attracted interest as an anticancer drug target. Eg5 is co-crystallized with several inhibitors bound to its allosteric binding pocket. Each of these occupies a pocket formed by loop 5/helix α2 (L5/α2). Recently designed inhibitors additionally occupy a hydrophobic pocket of this site. The goal of the present study was to explore this hydrophobic pocket with our MED-SuMo fragment-based protocol, and thus discover novel chemical structures that might bind as inhibitors. The MED-SuMo software is able to compare and superimpose similar interaction surfaces upon the whole protein data bank (PDB). In a fragment-based protocol, MED-SuMo retrieves MED-Portions that encode protein-fragment binding sites and are derived from cross-mining protein-ligand structures with libraries of small molecules. Furthermore we have excluded intra-family MED-Portions derived from Eg5 ligands that occupy the hydrophobic pocket and predicted new potential ligands by hybridization that would fill simultaneously both pockets. Some of the latter having original scaffolds and substituents in the hydrophobic pocket are identified in libraries of synthetically accessible molecules by the MED-Search software. Ksenia Oguievetskaia and Laetitia Martin-Chanas contributed equally to this work.     

KRAS Binders Hidden in Nature

Natural products have proven to be a rich source of molecular architectures for drugs. Here, an integrated approach to natural product screening is proposed, which uncovered eight new natural product scaffolds for KRAS—the most frequently mutated oncogenic driver in human cancers, which has remained thus far undrugged. The approach combines aspects of virtual screening, fragment-based screening, structure-activity relationships (SAR) by NMR, and structure-based drug discovery to overcome the limitations in traditional natural product approaches. By using our approach, a new “snugness of fit” scoring function and the first crystal-soaking system of the active form of KRAS^G12D, the protein–ligand X-ray structures of a tricyclic indolopyrrole fungal alkaloid and an indoloisoquinolinone have been successfully elucidated. The natural product KRAS hits discovered provide fruitful ground for the optimization of highly potent natural-product-based inhibitors of the active form of oncogenic RAS. This integrated approach for screening natural products also holds promise for other “undruggable” targets.     

Unambiguous NMR Structural Determination of (+)-Catechin—Laccase Dimeric Reaction Products as Potential Markers of Grape and Wine Oxidation

(+)-Catechin—laccase oxidation dimeric standards were hemi-synthesized using laccase from Trametes versicolor in a water-ethanol solution at pH 3.6. Eight fractions corresponding to eight potential oxidation dimeric products were detected. The fractions profiles were compared with profiles obtained with two other oxidoreductases: polyphenoloxidase extracted from grapes and laccase from Botrytis cinerea. The profiles were very similar, although some minor differences suggested possible dissimilarities in the reactivity of these enzymes. Five fractions were then isolated and analyzed by 1D and 2D NMR spectroscopy. The addition of traces of cadmium nitrate in the samples solubilized in acetone-d₆ led to fully resolved NMR signals of phenolic protons, allowing the unambiguous structural determination of six reaction products, one of the fractions containing two enantiomers. These products can further be used as oxidation markers to investigate their presence and evolution in wine during winemaking and wine ageing.     

The pattern of methylcyclopentane and n-hexane reactions on Rh/Al2O3 in catalytic runs of various length

Methylcyclopentane and n-hexane were reacted on a Rh/alumina catalyst in a closed-loop reactor. The product composition was analyzed at different moments of the run. In spite of a slow self-deactivation, the distribution of primary products and the depth of hydrogenolysis showed hardly any dependence on the sampling time in the conversion range of 1.5% and 50%. This is discussed in terms of accumulation of hydrocarbonaceous residues and the low readsorption probability of primary products on rhodium surface.