Mineral precipitation-induced porosity reduction and its effect on transport parameters in diffusion-controlled porous media

Background: In geochemically perturbed systems where porewater and mineral assemblages are unequilibrated the processes of mineral precipitation and dissolution may change important transport properties such as porosity and pore diffusion coefficients. These reactions might alter the sealing capabilities of the rock by complete pore-scale precipitation (cementation) of the system or by opening new migration pathways through mineral dissolution. In actual 1D continuum reactive transport codes the coupling of transport and porosity is generally accomplished through the empirical Archie\u27s law. There is very little reported data on systems with changing porosity under well controlled conditions to constrain model input parameters. In this study celestite (SrSO4) was precipitated in the pore space of a compacted sand column under diffusion controlled conditions and the effect on the fluid migration properties was investigated by means of three complementary experimental approaches: (1) tritiated water (HTO) tracer through diffusion, (2) computed micro-tomography (μ-CT) imaging and (3) post-mortem analysis of the precipitate (selective dissolution, SEM/EDX). Results: The through-diffusion experiments reached steady state after 15days, at which point celestite precipitation ceased and the non-reactive HTO flux became constant. The pore space in the precipitation zone remained fully connected using a 6μm μ-CT spatial resolution with 25% porosity reduction in the approx. 0.35mm thick dense precipitation zone. The porosity and transport parameters prior to pore-scale precipitation were in good agreement with a porosity of 0.42±0.09 (HTO) and 0.40±0.03 (μ-CT), as was the mass of SrSO4 precipitate estimated by μ-CT at 25±5mg and selective dissolution 21.7±0.4mg, respectively. However, using this data as input parameters the 1D single continuum reactive transport model was not able to accurately reproduce both the celestite precipitation front and the remaining connected porosity. The model assumed there was a direct linkage of porosity to the effective diffusivity using only one cementation value over the whole porosity range of the system investigated. Conclusions: The 1D single continuous model either underestimated the remaining connected porosity in the precipitation zone, or overestimated the amount of precipitate. These findings support the need to implement a modified, extended Archie\u27s law to the reactive transport model and show that pore-scale precipitation transforms a system (following Archie\u27s simple power law with only micropores present) towards a system similar to clays with micro- and nanoporosity. © 2015 Chagneau et al

A densification mechanism to model the mechanical effect of methane hydrates in sandy sediments

Recent pore‐scale observations and geomechanical investigations suggest the lack of true cohesion in methane hydrate‐bearing sediments (MHBSs) and propose that their mechanical behavior is governed by kinematic constrictions at pore‐scale. This paper presents a constitutive model for MHBS, which does not rely on physical bonding between hydrate crystals and sediment grains but on the densification effect that pore invasion with hydrate has on the sediment mechanical properties. The Hydrate‐CASM extends the critical state model Clay and Sand Model (CASM) by implementing the subloading surface model and introducing the densification mechanism. The model suggests that the decrease of the sediment available void volume during hydrate formation stiffens its structure and has a similar mechanical effect as the increase of sediment density. In particular, the model attributes stress‐strain changes observed in MHBS to the variations in sediment available void volume with hydrate saturation and its consequent effect on isotropic yield stress and swelling line slope. The model performance is examined against published experimental data from drained triaxial tests performed at different confining stress and with distinct hydrate saturation and morphology. Overall, the simulations capture the influence of hydrate saturation in both the magnitude and trend of the stiffness, shear strength, and volumetric response of synthetic MHBS. The results are validated against those obtained from previous mechanical models for MHBS that examine the same experimental data. The Hydrate‐CASM performs similarly to previous models, but its formulation only requires one hydrate‐related empirical parameter to express changes in the sediment elastic stiffness with hydrate saturation

In vivo Bioluminescence Imaging of Ca(2+) Signalling in the Brain of Drosophila

Many different cells' signalling pathways are universally regulated by Ca(2+) concentration [Ca(2+)] rises that have highly variable amplitudes and kinetic properties. Optical imaging can provide the means to characterise both the temporal and spatial aspects of Ca(2+) signals involved in neurophysiological functions. New methods for in vivo imaging of Ca(2+) signalling in the brain of Drosophila are required for probing the different dynamic aspects of this system. In studies here, whole brain Ca(2+) imaging was performed on transgenic flies with targeted expression of the bioluminescent Ca(2+) reporter GFP-aequorin (GA) in different neural structures. A photon counting based technique was used to undertake continuous recordings of cytosolic [Ca(2+)] over hours. Time integrals for reconstructing images and analysis of the data were selected offline according to the signal intensity. This approach allowed a unique Ca(2+) response associated with cholinergic transmission to be identified by whole brain imaging of specific neural structures. Notably, [Ca(2+)] transients in the Mushroom Bodies (MBs) following nicotine stimulation were accompanied by a delayed secondary [Ca(2+)] rise (up to 15 min. later) in the MB lobes. The delayed response was sensitive to thapsigargin, suggesting a role for intra-cellular Ca(2+) stores. Moreover, it was reduced in dunce mutant flies, which are impaired in learning and memory. Bioluminescence imaging is therefore useful for studying Ca(2+) signalling pathways and for functional mapping of neurophysiological processes in the fly brain

Defense Against Cannibalism: The SdpI Family of Bacterial Immunity/Signal Transduction Proteins

The SdpI family consists of putative bacterial toxin immunity and signal transduction proteins. One member of the family in Bacillus subtilis, SdpI, provides immunity to cells from cannibalism in times of nutrient limitation. SdpI family members are transmembrane proteins with 3, 4, 5, 6, 7, 8, or 12 putative transmembrane α-helical segments (TMSs). These varied topologies appear to be genuine rather than artifacts due to sequencing or annotation errors. The basic and most frequently occurring element of the SdpI family has 6 TMSs. Homologues of all topological types were aligned to determine the homologous TMSs and loop regions, and the positive-inside rule was used to determine sidedness. The two most conserved motifs were identified between TMSs 1 and 2 and TMSs 4 and 5 of the 6 TMS proteins. These showed significant sequence similarity, leading us to suggest that the primordial precursor of these proteins was a 3 TMS–encoding genetic element that underwent intragenic duplication. Various deletional and fusional events, as well as intragenic duplications and inversions, may have yielded SdpI homologues with topologies of varying numbers and positions of TMSs. We propose a specific evolutionary pathway that could have given rise to these distantly related bacterial immunity proteins. We further show that genes encoding SdpI homologues often appear in operons with genes for homologues of SdpR, SdpI’s autorepressor. Our analyses allow us to propose structure–function relationships that may be applicable to most family members

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