I conducted an amplitude vs. offset (AVO) analysis on newly acquired 3D seismic reflection data to detect elevated pore fluid content and pore fluid pressure along the Costa Rica convergent margin to address dewatering processes of subduction zone sediments. These data provide the highest quality 3D seismic data acquired to date along a convergent margin for detailed analysis of geophysical properties along the plate boundary fault interface. In 2011, a 55 km by 11 km 3D seismic reflection survey was completed using the R/V Marcus G. Langseth offshore western Costa Rica at the convergent margin of the Cocos and Caribbean plates. We applied pre-stack Kirchhoff time migration to a subset of these data across the frontal prism where amplitude versus offset (AVO) attributes were extracted along the decollement. When pore fluid pressure, l , exceeds 0.7, the pressure at which Poisson’s ratio begins to approach that of water, the AVO response of a fluid-filled, clay-rich decollement requires a high Poisson’s ratio and an excessively low seismic P-wave and S-wave velocity. Acute wedge taper, undercompacted subducted hemipelagic and pelagic sediments, and a smooth decollement in the northwest half of the survey correspond with decollement AVO response of relatively high values of Poisson’s ratio. These findings suggest increased pore fluid content and vertical containment of near-lithostatic pore fluid pressures within the decollement. In contrast, increased wedge taper angles, thin hemipelagic and pelagic sediments, and a rugose decollement beneath the southeastern frontal prism produce an AVO response interpreted as due to lower pore fluid contents and pressures. We propose that large-offset subducting basement normal faults in this area, as close as 20 m from the decollement, induce vertical fractures within the decollement that allow for fluid expulsion into the frontal prism and lower fluid pressure. Lateral variability of overpressure within the decollement shear zone of subduction margins is important in understanding the evolution of frontal prism strain accumulation and seismogenic rupture. / text

A pore-scale understanding of fluid flow underpins the constitutive laws of continuum-scale porous media flow. Porous media flow laws are founded on simplified pore structure such as the classical capillary tube model or the pore-network model, both of which do not include diverging-converging pore geometry in the direction of flow. Therefore, modifications in the fluid flow field due to different pore geometries are not well understood. Thus this may translate to uncertainties on how flow in porous media is predicted in practical applications such as geological sequestration of carbon dioxide, petroleum recovery, and contaminant’s fate in aquifers. To fill this gap, we have investigated the role of a spectrum of diverging-converging pore geometries likely formed due to different grain shapes which may be due to a variety of processes such as weathering, sediment transport, and diagenesis. Our findings describe the physical mechanisms for the failure of Darcy’s Law and the characteristics of Forchheimer Law at increasing Reynolds Number flows. Through fundamental fluid physics, we determined the forces which are most responsible for the continuum-scale porous media hydraulic conductivity (K) or permeability. We show that the pore geometry and the eddies associated therein significantly modify the flow field and the boundary stresses. This has important implications on mineral precipitation-dissolution and microbial growth. We present a new non-dimensional geometric factor β, a metric for diverging-converging pore geometry, which can be used to predict K. This model for K based on β generalizes the original and now widely-used Kozeny (1927) model which was based on straight capillary tubes. Further, in order to better quantify the feasibility of geological CO2 sequestration, we have conducted laboratory fluid flow experiments at reservoir conditions to investigate the controls of media wettability and grain shapes on pore-scale capillary trapping. We present experimental evidence for the snap-off or formation of trapped CO2 ganglion. The total trapping potential is found to be 15% of porosity for a water-wet media. We show that at the pore-scale media wettability and viscous-fingering play a critical role in transport and trapping of CO2. Our investigations clearly show that that in single-phase flow pore geometry significantly modifies pore-scale stresses and impacts continuum-scale flow laws. In two-phase flows, while the media wettability plays a vital role, the mobility ratio of CO2 - brine system significantly controls the CO2 capillary trapping potential- a result which should be taken into consideration while managing CO2 sequestration projects. / text

Local displacement efficiency in miscible floods is significantly affected by mixing taking place in the medium. Laboratory experiments usually measure flow-averaged ("cup mixed") effluent concentration histories. The core-scale averaged mixing, termed as dispersion, is used to quantify mixing in flow through porous media. The dispersion coefficient has the contributions of convective spreading and diffusion lumped together. Despite decades of research there remain questions about the nature and origin of dispersion. The main objective of this research is to understand the basic physics of solute transport and mixing at the pore scale and to use this information to explain core-scale mixing behavior (dispersion). We use two different approaches to study the interaction between convective spreading and diffusion for a range of flow conditions and the influence of their interaction on dispersion. In the first approach, we perform a direct numerical simulation of pore scale solute transport (by solving the Navier Stokes and convection diffusion equations) in a surrogate pore space. The second approach tracks movement of solute particles through a network model that is physically representative of real granular material. The first approach is useful in direct visualization of mixing in pore space whereas the second approach helps quantify the effect of pore scale process on core scale mixing (dispersion). Mixing in porous media results from interaction between convective spreading and molecular diffusion. The converging-diverging flow around sand grains causes the solute front to stretch, split and rejoin. In this process the area of contact between regions of high and low solute concentrations increases by an order of magnitude. Diffusion tends to reduce local variations in solute concentration inside the pore body. If the fluid velocity is small, diffusion is able to homogenize the solute concentration inside each pore. On the other hand, in the limit of very large fluid velocity (or no diffusion) local mixing because of diffusion tends to zero and dispersion is entirely caused by convective spreading. Flow reversal provides insights about mixing mechanisms in flow through porous media. For purely convective transport, upon flow reversal solute particles retrace their path to the inlet. Convective spreading cancels and echo dispersion is zero. Diffusion, even though small in magnitude, causes local mixing and makes dispersion in porous media irreversible. Echo dispersion in porous media is far greater than diffusion and as large as forward (transmission) dispersion. In the second approach, we study dispersion in porous media by tracking movement of a swarm of solute particles through a physically representative network model. We developed deterministic rules to trace paths of solute particles through the network. These rules yield flow streamlines through the network comparable to those obtained from a full solution of Stokes' equation. In the absence of diffusion the paths of all solute particles are completely determined and reversible. We track the movement of solute particles on these paths to investigate dispersion caused by purely convective spreading at the pore scale. Then we superimpose diffusion and study its influence on dispersion. In this way we obtain for the first time an unequivocal assessment of the roles of convective spreading and diffusion in hydrodynamic dispersion through porous media. Alternative particle tracking algorithms that use a probabilistic choice of an out-flowing throat at a pore fail to quantify convective spreading accurately. For Fickian behavior of dispersion it is essential that all solute particles encounter a wide range of independent (and identically distributed) velocities. If plug flow occurs in the pore throats a solute particle can encounter a wide range of independent velocities because of velocity differences in pore throats and randomness of pore structure. Plug flow leads to a purely convective spreading that is asymptotically Fickian. Diffusion superimposed on plug flow acts independently of convective spreading causing dispersion to be simply the sum of convective spreading and diffusion. In plug flow hydrodynamic dispersion varies linearly with the pore-scale Peclet number. For a more realistic parabolic velocity profile in pore throats particles near the solid surface of the medium do not have independent velocities. Now purely convective spreading is non-Fickian. When diffusion is non-zero, solute particles can move away from the low velocity region near the solid surface into the main flow stream and subsequently dispersion again becomes asymptotically Fickian. Now dispersion is the result of an interaction between convection and diffusion and it results in a weak nonlinear dependence of dispersion on Peclet number. The dispersion coefficients predicted by particle tracking through the network are in excellent agreement with the literature experimental data. We conclude that the essential phenomena giving rise to hydrodynamic dispersion observed in porous media are (i) stream splitting of the solute front at every pore, thus causing independence of particle velocities purely by convection, (ii) a velocity gradient within throats and (iii) diffusion. Taylor's dispersion in a capillary tube accounts for only the second and third of these phenomena, yielding a quadratic dependence of dispersion on Peclet number. Plug flow in the bonds of a physically representative network accounts for the only the first and third phenomena, resulting in a linear dependence of dispersion upon Peclet number. / text

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Lentiviruses can infect non-dividing cells, and various cellular nuclear transport proteins provide crucial functions for lentiviral nuclear entry and integration. Genome-wide small interfering RNA screens previously identified nuclear pore complex component nucleoporin 153 (NUP153) as being important for infection by human immunodeficiency virus type 1 (HIV-1). We found that HIV-1 infection of NUP153 depleted cells resulted in normal levels of reverse transcription, a moderate reduction of 2-long terminal repeat circles, and a relatively large reduction in integrated proviruses, consistent with a role for NUP153 during nuclear entry of the HIV-1 pre-integration complex. We ascertained the capsid (CA) to be the major viral determinant for NUP153 dependence during infection, and accordingly observed a direct interaction between the CA N-terminal domain and the phenylalanine-glycine (FG)-repeat enriched NUP153 C-terminal domain (NUP153C). NUP153C fused to the effector domains of the rhesus Trim5alpha restriction factor (Trim-NUP153C) potently restricted HIV-1, providing an intracellular readout for the NUP153C-CA interaction during retroviral infection. Primate lentiviruses and equine infectious anemia virus (EIAV) bound NUP153C under these conditions, results that correlated with direct binding between purified recombinant proteins in vitro. These binding phenotypes moreover correlated with the requirement for endogenous NUP153 function during infection. Mutagenesis experiments identified NUP153C and CA residues important for binding, and different FG motifs within NUP153C mediated binding to HIV-1 versus EIAV CA proteins. HIV-1 CA binding mapped to residues that line a common alpha helix 3/4 hydrophobic pocket that also mediates binding to the small molecule PF-3450074 (PF74) inhibitor and cleavage and polyadenylation specific factor 6 (CPSF6) protein, with Asn57 (Asp58 in EIAV) playing a particularly important role. PF74 and CPSF6 each competed with NUP153C for binding to HIV-1 CA, and significantly higher concentrations of PF74 were needed to inhibit HIV-1 infection in the face of Trim-NUP153C expression or NUP153 knockdown. Correlation between CA mutant viral cell cycle and NUP153 dependencies moreover indicated that the NUP153C-CA interaction underlies the ability of HIV-1 to infect non-dividing cells. We propose that HIV-1 CA binds NUP153 FG motifs to affect viral nuclear import, serving as a novel example of viral hijacking of a fundamental cellular process.

There are many complications associated with abnormally high fluid pressures in overpressured formations. Pore pressure can directly influence all parts of operations including drilling, geological studies, completion, and production. Accurate predictions of pore pressure and fracture pressure are vital aspects to the production and completion of safe, time efficient, and cost efficient projects. Knowledge of pressure distribution in the formation can greatly reduce complexities associated with drilling and completing a well. A three-method pore pressure and fracture pressure study was performed on two prospect deepwater wells located in the Gulf of Mexico. More than thirty offset wells in the greater region were initially analyzed for similarities with the two prospect wells. In the final analysis, only six wells were used to create pore pressure and fracture pressure models due to inconsistencies in similarities or lack of usable data in many of the offset wells. Pore pressure and fracture pressure models were constructed for the offset wells, and then applied and calibrated for the two prospect wells using drilling data such as mud weights, MDTs (Modular Dynamic Testing), and LOTs (Leak-off Test). Three types of pore pressure and fracture pressure models were used in the study: Eaton’s deep resistivity method; Eaton’s acoustic sonic method; and Bower’s interval seismic velocity method. Pore pressure and fracture pressure prediction was complicated by abnormal pressure in the formation due to undercompaction and seals. Both prospects were located in a deep subsalt environment. Low permeability and traps prevents fluid from escaping as rapidly as pore space compacts thus creating overpressure. Drilling through salt in deep water is expensive and risky. Elevated pore pressure and reduced fracture pressure underneath salt seals can create very tight mud weight windows and cause many drilling problems, as seen in the results of the offset wells’ pore pressure and fracture pressure models. Results indicate very small pore pressure and fracture pressure windows, or mud weight windows, because of overpressures in the formation caused by such a deep subsalt environment. Many casing points were needed in the final casing design of prospect wells to accommodate the smaller mud weight windows. Pore pressure has the most significant increase immediately below the salt, while the mud weight window remained constant or decreased with depth. The average mud weight window ranged between 1 to 2 pounds per gallon below the salt. / text

No description available.

No description available.

Modeling of airflow resistance in grain bulk requires knowledge of the tortuosity and velocity of the air flow through the grain bulk. In this study, experiments were carried out to determine these characteristics of airflow paths by analyzing digital images of smoke-visualized airflow paths inside a grain bulk obtained with a high speed camera. Colored smoke with approximately the same density as air was introduced into the test box for the visualization of the airflow through the grain bulk. Soybeans with a moisture content of 8.82% on wet basis were used in this study. The high quality videos obtained by recoding the fast movement of the smoke through the grain bulk was first separated into frames using a commercial software, VirtualDub (CRIM, Montreal, Québec, Canada), and the 512× 384 pixel RGB image files (frames) extracted from the recorded videos and read into ImageJ an image processing Java-based software developed by the United State National institute of Health, to track the movement of the smoke in the images, frame by frame to determine lengths, tortuosities of the different flow paths, as well as their velocities.

Natural gas hydrates occur on most continental margins in organic-rich sediments at water depths >450 m (in polar regions >150 m). Gas hydrate distribution and abundance, however, varies significantly from margin to margin and with tectonic environment. The National Gas Hydrate Program (NGHP) Expedition 01 cored 10 sites in the Krishna-Godawari (K-G) basin, located on the southeastern passive margin of India. The drilling at the K-G basin was comprehensive, providing an ideal location to address questions regarding processes that lead to variations in gas hydrate concentration and distribution in marine sediments. Pore fluids recovered from both pressurized and non-pressurized cores were analyzed for salinity, Cl-, SO4 2-, alkalinity, Ca2+, Mg2+, Sr2+, Ba2+, Na+, and Li+ concentrations, as well as 􀀂13C-DIC, 􀀂18O, and 87/86Sr isotope ratios. This comprehensive suite of pore fluid concentration and isotopic profiles places important constraints on the fluid/gas sources, transport pathways, and CH4 fluxes, and their impact on gas hydrate concentration and distribution. Based on the Cl- and 􀀂18􀀁 depth profiles, catwalk infrared images, pressure core CH4 concentrations, and direct gas hydrate sampling, we show that the occurrence and concentration of gas hydrate varies considerably between sites. Gas hydrate was detected at all 10 sites, and occurs between 50 mbsf and the base of the gas hydrate stability zone (BGHSZ). In all but three sites cored, gas hydrate is mainly disseminated within the pore space with typical pore space occupancies being 􀀁2%. Massive occurrences of gas hydrate are controlled by high-angle fractures in clay/silt sediments at three sites, and locally by lithology (sand/silt) at the more “diffuse” sites with a maximum pore space occupancy of ~67%. Though a majority of the sites cored contained sand/silt horizons, little gas hydrate was observed in most of these intervals. At two sites in the K-G basin, we observe higher than seawater Cl- concentrations between the sulfate-methane transition (SMT) and ~80 mbsf, suggesting active gas hydrate formation at rates faster than Cl- diffusion and pore fluid advection. The fluids sampled within this depth range are chemically distinct from the fluids sampled below, and likely have been advected from a different source depth. These geochemical results provide the framework for a regional gas hydrate reservoir model that links the geology, geochemistry, and subsurface hydrology of the basin, with implications for the lateral heterogeneity of gas hydrate occurrence in continental margins.