Validation Test Cases for Multi-Physic Problems: Application to Magneto-Hydrodynamic Numerical Simulations

In the present paper, some elementary test cases in laminar flow with magnetic forcing terms are analyzed (Hartmann flow, Couette flow, Rayleigh flow); equations of the coupled problem are exposed and analytical solutions are derived in each case, highlighting the relevant non-dimensional number which drives the physics of the problem. Several analytical calculations are then proposed and discussed, in particular in the context of MHD propulsion by a nozzle.Comment: 10

Visualisation de la répartition d'intensité des rayons X dans un cristal déformé

National audienceNous nous proposons de présenter le résultat d'études théoriques sur la propagation des rayons X dans un cristal contenant une dislocation

Wafer-scale integration of piezoelectric actuation capabilities in nanoelectromechanical systems resonators

In this work, we demonstrate the integration of piezoelectric actuation means on arrays of nanocantilevers at the wafer scale. We use lead titanate zirconate (PZT) as piezoelectric material mainly because of its excellent actuation properties even when geometrically constrained at extreme scal

Wafer-scale integration of piezoelectric actuation capabilities in nanoelectromechanical systems resonators

In this work, we demonstrate the integration of piezoelectric actuation means on arrays of nanocantilevers at the wafer scale. We use lead titanate zirconate (PZT) as piezoelectric material mainly because of its excellent actuation properties even when geometrically constrained at extreme scal

Images Of Serial Sectioning In Electron Microscopy : 3D Visualisation Of Objects Of Biological Interest

International audienceIn the case of serial sections observed by the means of an electron microscope, it is possible to rebuild an image of an object, using the local intelligence of an image workstation without the need of a powerful computer. We will explain the basic principles of a program that we have written and explain its further developments

Enzyme sequestration as a tuning point in controlling response dynamics of signalling networks

Signalling networks result from combinatorial interactions among many enzymes and scaffolding proteins. These complex systems generate response dynamics that are often essential for correct decision-making in cells. Uncovering biochemical design principles that underpin such response dynamics is a prerequisite to understand evolved signalling networks and to design synthetic ones. Here, we use in silico evolution to explore the possible biochemical design space for signalling networks displaying ultrasensitive and adaptive response dynamics. By running evolutionary simulations mimicking different biochemical scenarios, we find that enzyme sequestration emerges as a key mechanism for enabling such dynamics. Inspired by these findings, and to test the role of sequestration, we design a generic, minimalist model of a signalling cycle, featuring two enzymes and a single scaffolding protein. We show that this simple system is capable of displaying both ultrasensitive and adaptive response dynamics. Furthermore, we find that tuning the concentration or kinetics of the sequestering protein can shift system dynamics between these two response types. These empirical results suggest that enzyme sequestration through scaffolding proteins is exploited by evolution to generate diverse response dynamics in signalling networks and could provide an engineering point in synthetic biology applications

In silico evolution of signaling networks using rule-based models: bistable response dynamics

One of the ultimate goals in biology is to understand the design principles of biological systems. Such principles, if they exist, can help us better understand complex, natural biological systems and guide the engineering of de novo ones. Towards deciphering design principles, in silico evolution of biological systems with proper abstraction is a promising approach. Here, we demonstrate the application of in silico evolution combined with rule-based modelling for exploring design principles of cellular signaling networks. This application is based on a computational platform, called BioJazz, which allows in silico evolution of signaling networks with unbounded complexity. We provide a detailed introduction to BioJazz architecture and implementation and describe how it can be used to evolve and/or design signaling networks with defined dynamics. For the latter, we evolve signaling networks with switch-like response dynamics and demonstrate how BioJazz can result in new biological insights on network structures that can endow bistable response dynamics. This example also demonstrated both the power of BioJazz in evolving and designing signaling networks and its limitations at the current stage of development.Comment: 24 pages, 7 figure

Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica

Salmonella enterica subspecies enterica is traditionally subdivided into serovars by serological and nutritional characteristics. We used Multilocus Sequence Typing (MLST) to assign 4,257 isolates from 554 serovars to 1092 sequence types (STs). The majority of the isolates and many STs were grouped into 138 genetically closely related clusters called eBurstGroups (eBGs). Many eBGs correspond to a serovar, for example most Typhimurium are in eBG1 and most Enteritidis are in eBG4, but many eBGs contained more than one serovar. Furthermore, most serovars were polyphyletic and are distributed across multiple unrelated eBGs. Thus, serovar designations confounded genetically unrelated isolates and failed to recognize natural evolutionary groupings. An inability of serotyping to correctly group isolates was most apparent for Paratyphi B and its variant Java. Most Paratyphi B were included within a sub-cluster of STs belonging to eBG5, which also encompasses a separate sub-cluster of Java STs. However, diphasic Java variants were also found in two other eBGs and monophasic Java variants were in four other eBGs or STs, one of which is in subspecies salamae and a second of which includes isolates assigned to Enteritidis, Dublin and monophasic Paratyphi B. Similarly, Choleraesuis was found in eBG6 and is closely related to Paratyphi C, which is in eBG20. However, Choleraesuis var. Decatur consists of isolates from seven other, unrelated eBGs or STs. The serological assignment of these Decatur isolates to Choleraesuis likely reflects lateral gene transfer of flagellar genes between unrelated bacteria plus purifying selection. By confounding multiple evolutionary groups, serotyping can be misleading about the disease potential of S. enterica. Unlike serotyping, MLST recognizes evolutionary groupings and we recommend that Salmonella classification by serotyping should be replaced by MLST or its equivalents