Hydromechanical modeling of pulse tests that measure both fluid pressure and fracture-normal displacement of the Coaraze Laboratory site, France

21International audienceIn situ fracture mechanical deformation and fluid flow interactions are investigated through a series of hydraulic pulse injection tests, using specialized borehole equipment that can simultaneously measure fluid pressure and fracture displacements. The tests were conducted in two horizontal boreholes spaced one meter apart vertically and intersecting a near-vertical highly permeable fault located within a shallow fractured carbonate rock. The field data were evaluated by conducting a series of coupled hydromechanical numerical analyses, using both distinct-element and finite-element modeling techniques and both two- and three-dimensional model representations that can incorporate various complexities in fracture network geometry. One unique feature of these pulse injection experiments is that the entire test cycle, both the initial pressure increase and subsequent pressure fall-off, is carefully monitored and used for the evaluation of the in situ hydromechanical behavior. Field test data are evaluated by plotting fracture normal displacement as a function of fluid pressure, measured at the same borehole. The resulting normal displacement-versus-pressure curves show a characteristic loop, in which the paths for loading (pressure increase) and unloading (pressure decrease) are different. By matching this characteristic loop behavior, the fracture normal stiffness and an equivalent stiffness (Young's modulus) of the surrounding rock mass can be back-calculated. Evaluation of the field tests by coupled numerical hydromechanical modeling shows that initial fracture hydraulic aperture and normal stiffness vary by a factor of 2 to 3 for the two monitoring points within the same fracture plane. Moreover, the analyses show that hydraulic aperture and the normal stiffness of the pulse-tested fracture, the stiffness of surrounding rock matrix, and the properties and geometry of the surrounding fracture network significantly affect coupled hydromechanical responses during the pulse injection test. More specifically, the pressure-increase path of the normal displacement-versus-pressure curve is highly dependent on the hydromechanical parameters of the tested fracture and the stiffness of the matrix near the injection point, whereas the pressure-decrease path is highly influenced by mechanical processes within a larger portion of the surrounding fractured rock

Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator

BACKGROUND: Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces) in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported. RESULTS: We present a set of syntactic components and algebraic operators capable of representing analytical workflows in bioinformatics. Iteration, recursion, the use of conditional statements, and management of suspend/resume tasks have traditionally been implemented on an ad hoc basis and hard-coded; by having these operators properly defined it is possible to use and parameterize them as generic re-usable components. To illustrate how these operations can be orchestrated, we present GPIPE, a prototype graphic pipeline generator for PISE that allows the definition of a pipeline, parameterization of its component methods, and storage of metadata in XML formats. This implementation goes beyond the macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results) can be reproduced or shared among users. Availability: (interactive), (download). CONCLUSION: From our meta-analysis we have identified syntactic structures and algebraic operators common to many workflows in bioinformatics. The workflow components and algebraic operators can be assimilated into re-usable software components. GPIPE, a prototype implementation of this framework, provides a GUI builder to facilitate the generation of workflows and integration of heterogeneous analytical tools

Bioinformatic workflows : G-PIPE as an implementation

We present G-PIPE, a graphic pipeline generator for PISE that allows the definition of pipelines, parameterization of its component methods, and storage of metadata in XML formats. Our implementation goes beyond macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results) can be reproduced or shared among users. We also discuss the role of ontologies as as guidance systems in order to provide users with the possibility to define abstract work-flows, and execute them. A relevant baseline ontology is presented. Availability: http://if-web.imb.uq.edu.a

Tackling functional redundancy of Arabidopsis fatty acid elongase complexes

Very-long-chain fatty acids (VLCFA) are precursors for various lipids playing important physiological and structural roles in plants. Throughout plant tissues, VLCFA are present in multiple lipid classes essential for membrane homeostasis, and also stored in triacylglycerols. VLCFA and their derivatives are also highly abundant in lipid barriers, such as cuticular waxes in aerial epidermal cells and suberin monomers in roots. VLCFA are produced by the fatty acid elongase (FAE), which is an integral endoplasmic reticulum membrane multi-enzymatic complex consisting of four core enzymes. The 3-ketoacyl-CoA synthase (KCS) catalyzes the first reaction of the elongation and determines the chain-length substrate specificity of each elongation cycle, whereas the other three enzymes have broad substrate specificities and are shared by all FAE complexes. Consistent with the co-existence of multiple FAE complexes, performing sequential and/or parallel reactions to produce the broad chain-length-range of VLCFA found in plants, twenty-one KCS genes have been identified in the genome of Arabidopsis thaliana. Using CRISPR-Cas9 technology, we established an expression platform to reconstitute the different Arabidopsis FAE complexes in yeast. The VLCFA produced in these yeast strains were analyzed in detail to characterize the substrate specificity of all KCS candidates. Additionally, Arabidopsis candidate proteins were transiently expressed in Nicotiana benthamiana leaves to explore their activity and localization in planta. This work sheds light on the genetic and biochemical redundancy of fatty acid elongation in plants

Nanoscopic interactions of colloidal particles can suppress millimetre drop splashing

The splashing of liquid drops onto a solid surface is important for a wide range of applications, including combustion and spray coating. As the drop hits the solid surface, the liquid is ejected into a thin horizontal sheet expanding radially over the substrate. Above a critical impact velocity, the liquid sheet is forced to separate from the solid surface by the ambient air, and breaks up into smaller droplets. Despite many applications involving complex fluids, their effects on splashing remain mostly unexplored. Here we show that the splashing of a nanoparticle dispersion can be suppressed at higher impact velocities by the interactions of the nanoparticles with the solid surface. Although the dispersion drop first shows the classical transition from deposition to splashing when increasing the impact velocity, no splashing is observed above a second higher critical impact velocity. This result goes against the commonly accepted understanding of splashing, that a higher impact velocity should lead to even more pronounced splashing. Our findings open new possibilities to deposit large amount of complex liquids at high speeds

Hydromechanical modeling of pulse tests that measure fluid pressure and fracture normal displacement at the coaraze laboratory site

Abstract In situ fracture mechanical deformation and fluid flow interactions are investigated through a series of hydraulic pulse injection tests, using specialized borehole equipment that can simultaneously measure fluid pressure and fracture displacements. The tests were conducted in two horizontal boreholes spaced one meter apart vertically and intersecting a near-vertical highly permeable fault located within a shallow fractured carbonate rock. The field data were evaluated by conducting a series of coupled hydromechanical numerical analyses, using both distinct-element and finite-element modeling techniques and both two-and three-dimensional model representations that can incorporate various complexities in fracture network geometry. One unique feature of these pulse injection experiments is that the entire test cycle, both the initial pressure increase and subsequent pressure fall-off, is carefully monitored and used for the evaluation of the in situ hydromechanical behavior. Field test data are evaluated by plotting fracture normal displacement as a function of fluid pressure, measured at the same borehole. The resulting normal displacement-versus-pressure curves show a characteristic loop, in which the paths for loading (pressure increase) and unloading (pressure decrease) are different. By matching this characteristic loop behavior, the fracture normal stiffness and an equivalent stiffness (Young's modulus) of the surrounding rock mass can be back-calculated. Evaluation of the field tests by coupled numerical hydromechanical modeling shows that initial fracture hydraulic aperture and normal stiffness vary by a factor of 2 to 3 for the two 2 monitoring points within the same fracture plane. Moreover, the analyses show that hydraulic aperture and the normal stiffness of the pulse-tested fracture, the stiffness of surrounding rock matrix, and the properties and geometry of the surrounding fracture network significantly affect coupled hydromechanical responses during the pulse injection test. More specifically, the pressure-increase path of the normal displacement-versus-pressure curve is highly dependent on the hydromechanical parameters of the tested fracture and the stiffness of the matrix near the injection point, whereas the pressure-decrease path is highly influenced by mechanical processes within a larger portion of the surrounding fractured rock