Carbonate rocks are of global importance as they contain about 50% of the world’s remaining hydrocarbon reserves and are also a major host to the world’s groundwater resources. Therefore, understanding and modelling the fluid flow processes in carbonates are of great importance. A critical problem is that, unlike homogenous media (such as sandstones), carbonates often show features, including porosity, that span across a wide spatial range, from sub-micron porosity to fractures of meters length-scale. In this study X-ray computed micro-tomography (μCT) has been utilised as a tool to monitor two phase (oil-brine) flow in porous carbonate (dolomite) plugs at ambient temperature and pressures smaller than 690 kPa. A simple, low-cost and highly X-ray transparent core-holder was utilised for which the design is introduced. Capillary end effects were recognised and avoided in data analysis. Displacement processes that occur in the dolomite under water-wet, oil-wet, and partially mixed-wet states were investigated. The experiments consisted of a series of drainage and imbibition processes occurring under capillary and viscous dominated flow regimes. Pore-scale mechanisms of piston-like displacement and snap-off (or at least clear results of them), that were previously observed in sandstones and 2D micro-models, were observed in the dolomite under study. In addition, a new pore-scale mechanism was identified which occurred at high capillary numbers, referred to as droplet-fragmentation. This new pore-scale mechanism may provide an explanation to the capillary-desaturation process for heterogeneous media. In the experiments performed on the oil-wet plug formation of a stable water in oil emulsion was observed which appears to be the first 3D observation of in situ emulsion formation made using μCT. Direct visualisation of the oil-brine-rock configurations and measurement of the contact angles are presented. A comparison was made for the contact angle distributions measured for the water-wet and oil-wet conditions. Observation of fluid displacement processes as well as oil-brine-rock contact angle distributions demonstrate that pore-scale imaging provides a promising tool for wettability characterisation on both pore and core scales. Such detailed wettability data can also be used in pore-scale flow models. For the dolomite under study multiple-scale pore network models were constructed by integrating single-scale networks extracted from μCT images acquired at different length-scales. Mercury injection capillary pressure laboratory measurements were used to evaluate the capillary pressure (vs. saturation) curves calculated using single, two-scale, and three-scale network models of this dolomite. The integrated networks displayed an improved match to the laboratory measurements in comparison with the single-scale network model. The three-scale network provided the closest simulated curve, this result confirms that a more representative model displays closer properties. While simulated capillary pressure curves are close (converging) for the integrated networks the calculated relative permeability curves show variability for different multiple-scale networks. The present work demonstrates that the pore-scale fluid displacement processes occurring in heterogeneous porous media are more complex than those occurring in homogeneous media. In addition, successful fluid flow simulations require construction of multiple-scale models as well as consideration of the pore-scale processes (such as droplet-fragmentation) that are specific to such complex pore systems.

In CO2 storage sites, seal has a vital role in inhibiting migration of the supercritical CO2 to other geological strata. The major difficulties in studying seals include two aspects: lack of available samples (especially for saline aquifers), and the difficulty to study over geological time and spatial scales. The analysis of natural analogue has been chosen to overcome these difficulties. Hydrocarbon fields are used to investigate the pore throat radii, which is the major factor for capillary sealing of caprocks, using newly established statistics model. Natural CO2 springs at Green River, Utah are used to study how the long-term CO2 charge triggers chemical reactions and migration in shales. One of the major sealing mechanism of caprocks is capillary sealing. Pore throat radius, as the main factor to decide the capillary sealing, has been investigated in this study. As an alternative to the traditional method of mercury injection porosimetry, a statistical model for effective pore throat radii determination has been established. The cumulative percentage and the probability distribution of the effective pore throat radii of the shale caprocks in the UK North Sea oil fields are obtained, which would be used as a reference for the saline aquifers in CO2 storage siting in the future work. Monte Carlo simulation is utilised to get the distribution of the effective pore throat radii. The cumulative distribution from this study has been compared with the distribution by Yang and Aplin (1998). The distribution by the statistical model enables to narrow down the range of effective pore throat radii to 37nm~1700nm, and help to make a better prediction on the pore throat radii. The correlation between the controlling factors of faulting, burial depth, caprock thickness and the pore throat radii have been examined. Good correlation between the depth less than 3000m and the effective pore throat radii indicates clay diagenesis should be the major factor for shallowly buried caprocks. Faulting and caprock thickness present no significant correlation with the effective pore throat radii. Crystal Geyser is used as an ideal natural analogue to study the Mancos Shale alteration. The interacted fluid that deposited travertine is important for the study. Hence, carbonate veins and reduction zones that associated with the activity of the main fault are used as records of the geochemistry of the paleo-fluid, the features of which are compared to the present spring water. The result shows the paleo-fluid was much more saline than the present fluid, with greater flow-rate. The decreased flow-rate might be owing to the self-healing of the fault during the time. Mancos shales outcropped in the hanging wall of the Little Grand Wash fault were sampled to investigate on the alterations triggered by the CO2-charged fluid from the fault and fractures. The result shows the alteration radius of the Mancos has limited within the distance of 20m away from the fault. CO2-rich fluid could interact with deformed shale (both dissolution and precipitation might happen), but no evidence shows the intact Mancos has been altered. The calcite cements in Mancos derived from CO2 sequestration could reach up to 27% (%weight of the whole rock) at 15m away from the fault. The conclusion facilitates the carbon storage siting criteria by Chadwick et al., (2009), who proposed the cautionary thickness of the caprock to be 20m.

Legionella pneumophila, o agente etiológico da doença dos Legionários, é conhecida por desencadear a formação de poro em membranas de macrófagos derivados de medula óssea (BMMs) por mecanismos dependentes do sistema de secreção do tipo IV conhecido como Dot/Icm. Neste trabalho, foram utillizados vários mutantes de L. pneumophila em combinação com camundongos nocautes para investigar os fatores bacterianos e do hospedeiro envolvidos na formação de poro em BMMs. Observamos que apesar da atividade do Dot/Icm, a formação de poro não ocorre em BMMs deficientes para caspase-1 e Nlrc4. A formação de poro foi temporalmente associada com a secreção de IL-1b e precedeu a lise celular e a piroptose. A formação de poro foi dependente do Dot/Icm, mas independente de várias proteínas efetoras, da multiplicação bacteriana e da síntese de novo de proteínas. A flagelina, a qual é conhecida em ativar o inflamassoma de Nlrc4, foi necessária para a formação de poro; a bactéria mutante flaA falhou em induzir a permeabilização celular. Consequentemente, a transfecção da flagelina purificada foi suficiente para desencadear a formação de poro independente da infecção. Utilizando 11 diferentes espécies de Legionella, nós observamos alta formação de poro em resposta à L. micdadei, L. bozemanii, L. gratiana, L. jordanis e L. rubrilucens, e essa resposta estava correlacionada com a expressão de flagelina por essas espécies. Além disso, verificamos que as proteínas Asc e Caspase-11 apresentam fenótipo intermediário na formação de poro, sugerindo que outras vias podem estar envolvidas no processo. Observamos também que a formação de poro desencadeada por L. pneumophila difere daquela induzida pelo ATP. Em conjunto, nossos resultados sugerem que a formação de poro não é uma resposta específica de L. pneumophila nem o resultado de dano da membrana induzido pelo Dot/Icm. Ao invés disso, a formação de poro é uma resposta do hospedeiro altamente coordenada, dependente dos componentes do inflamassoma Nlrc4 e caspase-1 e é desencadeada em resposta a bactérias que expressam o sistema de secreção do tipo IV e flagelina. / Legionella pneumophila, the etiological agent of Legionnaires disease, is known to trigger pore formation in bone marrow-derived macrophages (BMMs) by mechanisms dependent on the type IVB secretion system known as Dot/Icm. Here, we used several mutants of L. pneumophila in combination with knockout mice to assess the host and bacterial factors involved in pore formation in BMMs. We found that regardless of Dot/Icm activity, pore formation does not occur in BMMs deficient in caspase-1 and Nlrc4/Ipaf. Pore formation was temporally associated with IL-1b secretion and preceded host cell lysis and pyroptosis. Pore-forming ability was dependent on bacterial Dot/Icm but independent of several effector proteins, multiplication and de novo protein synthesis. Flagellin, which is known to trigger the Nlrc4 inflammasome, was required for pore formation as flaA mutant bacteria failed to induce cell permeabilization. Accordingly, transfection of purified flagellin was sufficient to trigger pore formation independent of infection. By using 11 different Legionella species, we found robust pore formation in response to L. micdadei, L. bozemanii, L. gratiana, L. jordanis and L. rubrilucens, and this trait correlated with flagellin expression by these species. Furthermore, we found that Asc and Caspase-11 showed an intermediate phenotype in pore formation, suggesting that other pathways may be involved in this process. We also observed that the pore formation triggered by L. pneumophila differs from the pore induced by ATP. Together, the results suggest that pore formation is neither L. pneumophilaspecific nor the result of membrane damage induced by Dot/Icm activity; instead, it is a highly coordinated host cell response dependent on host Nlrc4 and caspase-1 and on bacterial flagellin and type IV secretion system.

Particle-particle interactions are of paramount importance in every multi-body system as they determine the collective behaviour and coupling strength. Many well-known interactions like electro-static, van der Waals or screened Coulomb, decay exponentially or with negative powers of the particle spacing r. Similarly, hydrodynamic interactions between particles undergoing Brownian motion decay as 1/r in bulk, and are assumed to decay in small channels. Such interactions are ubiquitous in biological and technological systems. Here I confine multiple particles undergoing Brownian motion in narrow, microfluidic channels and study their coupling through hydrodynamic interactions. Our experiments show that the hydrodynamic particle-particle interactions are distance-independent in these channels. We also show that these interactions affect actively propelled particles via electrophoresis or gravity, resulting in non-linear transport phenomena. These findings are of fundamental importance for understanding transport of dense mixtures of particles or molecules through finite length, water-filled channels or pore networks.

Traditionally-constructed wells are commonly used to measure hydraulic head in all saturated systems, even in fine-grained sediments. Previous studies (Hvorslev 1951, Penman 1961) have shown that time lag in response to head changes between traditional wells and the surrounding fine-grained sediments can be a significant source of error. Time lag is caused by the time required for water to flow into or out of the well to reflect the appropriate change in head. A low-volume piezometer was constructed to measure changes in hydraulic head without requiring a change in fluid volume within the piezometer by directly measuring pore pressure in the surrounding sediments. The low-volume piezometer used a commercially-available pressure transducer that is hydraulically connected to the surrounding sediment by a porous-ceramic cylinder. The device is attached to a drive point that allows for quick insertion without creating excessive over-pressure so that equilibrium is achieved rapidly. The low-volume piezometer was inserted near traditionally-constructed wells in 3-4 m thick, saturated clay in west-central Florida. The low-volume piezometer was field tested to compare measured pore pressures with observed levels in traditionally-constructed wells. The comparison highlights any head difference between the two methods, and determines if there is a time lag between the two measurement methods and its magnitude. The low-volume piezometer was installed next to a traditionally-constructed well and heads in both wells were monitored for three months. Results show that the low-volume piezometer can take up to a month to reach equilibrium. Using Hvorslev's equations, traditionally-constructed wells have time lag of roughly 6 orders of magnitude greater than the low-volume piezometer. If this is correct, it could take up to 83,000 years for a traditionally-constructed well to reach equilibrium. However, when a trend analysis is performed on the hydrographs from the low-volume piezometer and the two traditional wells, the correlation coefficients are 0.95 and 0.96. The very strong correlation suggests that the low-volume piezometer and the traditional wells both respond similarly to changes in head. More field data need to be collected, but it appears that contrary to theory, time lag in traditionally-constructed wells may be negligible.

<p>The carbon metabolism in costal sediments is of major importance for the global carbon cycle. Costal sediments are also subjected to physical forcing generating water fluxes above and through the sediments, but how the physical affect the carbon metabolism is currently poorly known. In this study, the effect of advective pore water flow on degradation of organic matter in permeable sandy sediment was investigated in a laboratory study during wintertime. Sediments were collected from both brackish water (Askö) and from a fresh water stream (Getå Stream). In two chamber experiments, with and without advective pore water flow, the degradation of organic matter was measured through carbon dioxide analysis from water and headspace. In Askö sediments mineralization rates ranged from 3.019 - 5.115 mmol C m-2 d-1 and 3.139 mmol C m-2 d-1 with and without advective pore water flow, respectively. Those results correspond with results from earlier studies of carbon mineralization rates in sediment in the North Sea and the Baltic Sea. There were no significant differences between the two groups in the Askö sediment. In Getå Stream sediments mineralization rates ranged between 4.059 mmol C m-2 d-1 and 6.806 mmol C m-2 d-1 with and without advective flow, respectively. The mineralization rates for Getå Stream correspond with earlier studies of carbon mineralization rates in a stream in New Hampshire.</p>

Pannexins are vertebrate proteins with limited sequence homology to the invertebrate gap junction proteins, the innexins. However, in contrast to innexins and the vertebrate connexins, pannexins do not form gap junction channels. Instead they appear to solely function as unpaired membrane channels allowing the flux of molecules, including ATP, across the plasma membrane. We provided additional evidence for their ATP release function by demonstrating that the connexin mimetic peptides, which were thought to inhibit ATP release through connexin channels, do not inhibit their host connexin channels but instead inhibit pannexin1 channels by a mechanism of steric block. Therefore, the inhibitory effects of mimetic peptides on ATP release may represent supporting evidence for a role of pannexin1 in ATP release. We also analyzed the pore structure of pannexin1 channels with the Substituted Cysteine Accessibility Method. The thiol reagents MBB and MTSET reacted with several positions in the external portion of the first transmembrane segment and the first extracellular loop. In addition, MTSET reactivity was found in the internal portion of TM3. These data suggest that portions of TM1, E1 and TM3 line the pore of pannexin1 channels. Thus, the pore structure of pannexin1 is similar to that of connexin channels.

Proteins of the nuclear envelope play important roles in a variety of cellular processes e.g. transport of proteins between the nucleus and cytoplasm, co-ordination of nuclear and cytoplasmic events, anchoring of chromatin to the nuclear periphery and regulation of transcription. Defects in proteins of the nuclear envelope and the nuclear pore complexes have been related to a number of human diseases. To understand the cellular functions in which nuclear envelope proteins participate it is crucial to map the functions of these proteins. The present study was done in order to characterize the role of three different proteins in functions related to the nuclear envelope in the yeast Saccharomyces cerevisiae. The arginine methyltransferase Rmt2 was demonstrated to associate with proteins of the nuclear pore complexes and to influence nuclear export. In addition, Rmt2 was found to interact with the Lsm4 protein involved in RNA degradation, splicing and ribosome biosynthesis. These results provide support for a role of Rmt2 at the nuclear periphery and potentially in nuclear transport and RNA processing. The integral membrane protein Cwh43 was localized to the inner nuclear membrane and was also found at the nucleolus. A nuclear function for Cwh43 was demonstrated by its ability to bind DNA in vitro. A link to nucleolar functions was demonstrated by genetic analysis. Furthermore, Cwh43 is interacting with signalling pathways perhaps acting as a sensor for signals transmitted from the cytoplasm to the nucleus. The Myr1 protein was found to be membrane-associated and to interact with proteins involved in vesicular traffic. Overexpression of Myr1 affects nuclear morphology and nuclear pore distribution suggesting a function in membrane dynamics. In conclusion, the presented results aid in a deeper understanding of functions related to the nuclear envelope in revealing a novel link between arginine methylation and the nuclear periphery, identifying a novel inner nuclear membrane protein and a new membrane-associated protein.

A P56S mutation in the VAPB MSP domain is linked to adult-onset amyotrophic lateral sclerosis 8. The objective of this study is to characterize the functional role of VAPB in transport of NE and NPC proteins from the ER to the NE. Over-expression of VAPB-P56S blocked the transport of nucleoporins (Nups) and NE proteins, resulting in their sequestration in dilated cytoplasmic membranes. Simultaneous overexpression of the FFAT motif (two phenylalanines in an acidic track) antagonizes mutant VAPB effects and restores transport to the NE. VAPB function is required for transport to the NE because knockdown of endogenous VAPB recapitulates this phenotype. Moreover, the compartment in which Nups and NE proteins are sequestered and retained was identified as ER-Golgi intermediate compartment (ERGIC). Moreover, a defect in the transport of NE and NPC proteins attenuates nucleocytoplasmic shuttling of the glucocorticoid receptor (GR). Further, VAPB-P56S which is only soluble in SDS was solubilized in the Triton-X-100 fraction similar to VAPB-WT upon co-transfection with the FFAT motif suggesting that FFAT interacts with the insoluble VAPB-P56S protein changing its biophysical properties.

The pore diameter of a catalyst support controls the diffusion of reactant molecules to the catalytic active sites; thus, affecting the rates and conversions of the hydrotreating reactions. Desirable textural properties of SBA-15 makes it a potential alternative to the conventionally used γ-Al2O3 support due to the fact that its pore size can be manipulated via controlling the synthesis parameters, while maintaining relatively high surface area. Larger pore diameter SBA-15 supports may facilitate the diffusion of bulky molecules as that of the asphaltenes present in the heavy petroleum fractions, making it a potential catalyst support for hydrotreating operations. Considering the very sour nature of Canadas bitumen with high sulfur contents in the range of 2-6 wt %, the appreciably high sulfur contents particularly present in Athabasca derived heavy gas oils (about 4 wt % sulfur), the rising demand for cleaner fuels, and also the increasing stringency on environmental standards, the need for novel and improved hydrotreating catalysts cannot be overemphasized. By varying the molar ratio of hexane to ammonium fluoride, the pore channels of SBA-15 could be varied. Controlling the pore diameter of these supports via micelle swelling facilitated the production of larger pore diameter SBA-15-supported catalysts. In this project, four mesoporous silica SBA-15 catalyst supports with pore diameters in the range of 5-20 nm were synthesized in the preliminary phase using hexane as the micelle swelling agent and subsequently utilized for the loading of 2 wt.% Fe and 15 wt.% W catalyst metals, respectively. The hexagonal mesoscopic structure of these materials were characterized using powder small-angle X-ray scattering (SAXS), N2 adsorption-desorption isotherms, TEM and SEM images. Powder XRD analysis evidenced inhomogeneous metal dispersion on the largest pore diameter catalyst. An optimum pore diameter of 10 nm was found for Cat-B and subsequently used to obtain the optimum Fe and W loadings required to achieve the best hydrodesulfurization (HDS) and hydrodenitrogenation (HDN) activities. The optimum catalyst was found to be Cat-H with metal loadings of 3 wt.% Fe and 30 wt.% W. At these loadings and temperatures of 375°C, 388°C, and 400°C, HDS activities of 53.4%, 64.1%, and 73.3% with corresponding HDN activities of 21.9%, 26.2%, and 38.3%, respectively, were recorded. Catalytic performance evaluations conducted on equal mass loading using a reference commercial γ-Al2O3-supported FeW catalyst offered HDS activities of 69.3%, 80.4%, and 89.1%, with corresponding HDN activities of 16.4%, 32.4%, and 49.3% at the same temperatures studied. However, no significant changes in HDS and HDN activities were observed for similar evaluations on volume percent metals loading basis. Kinetic studies performed with the optimum FeW/SBA-15 catalyst suggested activation energies of 147.2 and 150.6 kJ/mol for HDS and HDN, respectively, by the Langmuir-Hinshelwoods model. Similar results were predicted by the Power Law and Multi-parameter models for HDS (129.6 and 126.7 kJ/mol, respectively), which does not conclusively make the latter model clearly stand out as the best. Data fitting by the Power Law suggested reaction orders of 2 and 1.5 for HDS and HDN, which seem to be consistent for the hydrotreatment of heavy gas oil. Finally, a long-term deactivation study spanning a period of 60 days time-on-stream showed the optimum catalyst to be stable under hydrotreating experiments conducted in a downward flow micro-trickle bed reactor at temperature, pressure, liquid hourly space velocity (LHSV), and gas/oil ratio of 375400˚C, 8.8 MPa, 1h-1, and 600 mL/mL (at STP), respectively.