New fitting scheme to obtain effective potential from Car-Parrinello molecular dynamics simulations: Application to silica

A fitting scheme is proposed to obtain effective potentials from Car-Parrinello molecular dynamics (CPMD) simulations. It is used to parameterize a new pair potential for silica. MD simulations with this new potential are done to determine structural and dynamic properties and to compare these properties to those obtained from CPMD and a MD simulation using the so-called BKS potential. The new potential reproduces accurately the liquid structure generated by the CPMD trajectories, the experimental activation energies for the self-diffusion constants and the experimental density of amorphous silica. Also lattice parameters and elastic constants of alpha-quartz are well-reproduced, showing the transferability of the new potential.Comment: 6 pages, 5 figure

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies

Background: Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is the smallest free-living photosynthetic eukaryote known to date, a coccoid green alga that was first isolated in 1995 in a lagoon by the Mediterranean sea. Its simple features, ease of culture and the sequencing of its 13 Mb haploid nuclear genome have promoted this microalga as a new model organism for cell biology. Here, we investigated the quality of genome assemblies of Illumina GAIIx 75 bp paired-end reads from Ostreococcus tauri, thereby also improving the existing assembly and showing the genome to be stably maintained in culture. Results: The 3 assemblers used, ABySS, CLCBio and Velvet, produced 95% complete genomes in 1402 to 2080 scaffolds with a very low rate of misassembly. Reciprocally, these assemblies improved the original genome assembly by filling in 930 gaps. Combined with additional analysis of raw reads and PCR sequencing effort, 1194 gaps have been solved in total adding up to 460 kb of sequence. Mapping of RNAseq Illumina data on this updated genome led to a twofold reduction in the proportion of multi-exon protein coding genes, representing 19% of the total 7699 protein coding genes. The comparison of the DNA extracted in 2001 and 2009 revealed the fixation of 8 single nucleotide substitutions and 2 deletions during the approximately 6000 generations in the lab. The deletions either knocked out or truncated two predicted transmembrane proteins, including a glutamate-receptor like gene. Conclusion: High coverage (>80 fold) paired-end Illumina sequencing enables a high quality 95% complete genome assembly of a compact ~13 Mb haploid eukaryote. This genome sequence has remained stable for 6000 generations of lab culture

Manufacturing human machine interface design using plant models

International audienc

Introduction

Élément fondamental de notre univers, phénomène physique, marqueur du temps et des saisons, critère esthétique… la « lumière » a été déclarée thématique de l’année 2015 par les Nations-Unies. Se saisissant de cette occasion, les doctorants de l’IRHiS – laboratoire de recherche regroupant historiens et historiens de l’art – ont entrepris d’organiser une journée d’études sur cette thématique qui constitue rarement un champ de recherches propre aux sciences humaines. Ces deux journées, organisé..

A methodology to design and check a plant model

International audienceApplications on manufacturing systems (diagnosis, control, supervision, ...) often require a plant model. Obtaining the plant model is a difficult task because of systems complexity and deepth knowledge of physical materials. A necessary condition that must be verified by the plant model is its capability to respond to all the requests of the specification model. This paper ends by two complementary approaches a mathematical property is proposed to check formally and this capability and a methodology to design the plant model is proposed in order to guarantee the model capability according to the most permissive control model

Influence of Moisture and Temperature on Mechanical Properties of the Concrete

International audienceThe scenario of a severe accident in the containment building of a nuclear plant results in an increase in pressure, temperature and relative humidity that can reach respectively 5 bars, 140 C and the water vapour saturation. Accurate knowledge of the thermal and mechanical behaviour of materials and more specifically of concrete is required to carry out more precise numerical simulations, in order to be able improve the precision of regulatory calculations. Our study aims to investigate the mechanical behaviour of concrete under homogeneous conditions of moisture and temperature. An experimental apparatus was designed in order to assess the evolutions of the fracture energy, the modulus of elasticity and the traction resistance of concrete. Different temperature levels up to a maximum of 140 C and at different values of the controlled moisture content were investigated. The equipment was used to perform DCT (Disk-shape Compact Tension) tests at 30, 90, 110 and 140 C. Five levels of degree of liquid water saturation ( Sw) were investigated for each temperature level between 36 and 100 %

GeneCloud Reveals Semantic Enrichment in Lists of Gene Descriptions

International audienceRevealing the over-represented functions in a particular gene list is a particular important post-genomic challenge. Genome-wide investigations generate gene lists from which meaningful information has to be extracted. This information is key to orient in planta investigations and to define the biological significance of genome-wide reprogramming. Here we describe the development and use of the GeneCloud algorithm, which retrieves the over-represented semantic terms in the description of a gene list

Evolution of Mechanical Properties of Concrete with Temperature and Humidity at High Temperatures

International audienceThe mechanical behavior of concrete in tension is studied at different values of water saturation for temperatures ranging from 110 °C to 160 °C. In order to prevent the concrete from drying, the experiments are performed at the vapor saturation pressure in a specific vessel. Inverse analysis based on numerical simulation is used to compute the values of fracture energy, tension strength and elasticity modulus. The experimental results show that the fracture energy is increasing with saturation and temperature, while the tension strength and the modulus of elasticity are decreasing for a saturation ranging from 35% to 65% and then increasing for higher values of saturation, while they decrease slightly with temperature