James Connolly - Academia.edu (original) (raw)

Papers by James Connolly

npj Biofilms and Microbiomes, 2015

Background/Objectives: Biofilms and specifically urea-hydrolysing biofilms are of interest to the... more Background/Objectives: Biofilms and specifically urea-hydrolysing biofilms are of interest to the medical community (for example, urinary tract infections), scientists and engineers (for example, microbially induced carbonate precipitation). To appropriately model these systems, biofilm-specific reaction rates are required. A simple method for determining biofilm-specific reaction rates is described and applied to a urea-hydrolysing biofilm. Methods: Biofilms were grown in small silicon tubes and influent and effluent urea concentrations were determined. Immediately after sampling, the tubes were thin sectioned to estimate the biofilm thickness profile along the length of the tube. Urea concentration and biofilm thickness data were used to construct an inverse model for the estimation of the urea hydrolysis rate. Results/Conclusions: It was found that urea hydrolysis in Escherichia coli MJK2 biofilms is well approximated by first-order kinetics between urea concentrations of 0.003 a...

Journal of Microbiological Methods, 2013

Contributions to Mineralogy and Petrology, 1989

To date numerical studies in geosciences have concentrated on single-scale modeling, such as mode... more To date numerical studies in geosciences have concentrated on single-scale modeling, such as modeling of global scale processes in the mantle or local scale modeling of shear zones. Recent advances in shared- memory supercomputer technology enables 2D thermo-mechanical modeling with up to 10 billion randomly distributed markers, providing unprecedented resolution and facilitating the modeling of complex geometries . This approach provides an opportunity to study the influence of global scale processes on small scale structures. For our case studies we have chosen an intra-oceanic subduction setting to study the evolution of thermal-chemical plumes. They originate from subducted slabs as a consequence of Raleigh-Taylor instability and are a potentially important mechanism for transporting slab and mantle wedge material to volcanic arcs. The size of our model is 400x200 km with an effective resolution (240001x120001 pixels) of the lithological field on the order of 1m (one pixel corresponds to 1.63x1.63m). With this method we have studied chaotic streamline mixing of the lithological components of a plume. We observed plume materials mixing chaotically resulting in attenuation and duplication of the original layering on scales of 1-1000m. The resulting patters are comparable to those observed in the ~30km2 Horoman ultramafic complex from Japan, which is characterized by well-developed layered structure.

ABSTRACT Recent advances in petrology and experimental measurements of ultrasonic waves on rock s... more ABSTRACT Recent advances in petrology and experimental measurements of ultrasonic waves on rock samples provided new insight in the interpretation of seismic properties and earthquake hypocenter distribution within and outside the Alpine region. The near Alpine northern foreland is characterized by a lower crust with relatively low P-wave velocities around 6.2 km/s and a seismic activity down to Moho depths. This is at first a contradiction, since normally low velocities in the lower crust are correlated with high temperatures, while deep crustal earthquakes suggest a brittle regime at lower crustal levels associated with relatively low temperatures. To address this incompatibility we have chosen to measure seismic velocities of metapelites under pressure-temperature conditions of the middle to lower crust. We selected metapelites because they are among the most common rock types of continental crust and possibly constitute a significant part of lower crust. Metapelites are rich in quartz and hydrous minerals (e.g. biotite, muscovite, chlorite). They are thus good candidates to investigate dehydration reactions and phase transitions of the middle to lower crust. Here we report on results of petrophysical experiments with metapelitic rocks, in terms of seismic velocity variations with increasing temperatures (up to 750 °C) and pressures(up to 400MPa). Near a temperature of 580°C (at 400 MPa), using the Perplex_X software, we predicted a dehydration reaction that produced water. This should reduce Vp (if water cannot escape) or increase slightly the Vp (if water can escape). After the experiments peacking at 750°C we observed a small amount of water indicating that a dehydration reaction has occurred. At a temperature of 675°C (at 400 MPa) the alfa-beta quartz transition caused an abrupt increase in Vp (up to 12%, in a rock with 14% anisotropy). Application of our results to the Alpine region (presumably at higher pressure conditions) suggests that the observed low velocities and deep earthquakes in the lower crust can be promoted by dehydration reaction or by partial melt in deep seated metapelites.

Agu Fall Meeting Abstracts, Dec 1, 2006

We have obtained information on the Martian mantle composition, thermal profile, core size, compo... more We have obtained information on the Martian mantle composition, thermal profile, core size, composition and state, from an inversion of geophysical data pertinent to its interior. The data include the most recent determinations of Martian radius, mean moment of inertia, mean density, second degree tidal Love number and tidal dissipation factor. We have modeled the composition of the silicate portion of Mars using the model system CaO-FeO-MgO-Al2O3-SiO2. Combining self-consistent thermodynamic methods with a stochastic-based inversion algorithm allows us to invert directly for composition and temperature, which transform to parameters crucial to our understanding of Mars, such as mineralogy, bulk mantle and core physical properties. Our results generally suggest an iron-enriched, but more Earth-like mantle composition than has been inferred from the SNC meteorites. Most probable core mantle boundary temperatures are around 2100 °C, implying a liquid core ~1540-1620 km in radius, with a density of ~7.6 g/cm3, most consistent with a metallic composition containing ~12 wt%S.

Agu Fall Meeting Abstracts, Dec 1, 2007

Deep mantle dynamics and the resulting thermo-chemical-phase structures are here studied using th... more Deep mantle dynamics and the resulting thermo-chemical-phase structures are here studied using thermo- chemical mantle convection simulations in a 3D spherical shell that incorporate composition-dependent phase diagrams calculated by free energy minimization. This improves on our previous studies, which used simple depth-dependent thermodynamic properties and calculated seismic anomalies based on linearized derivatives around a pyrolitic mean composition. Realistic mineral assemblages of mantle rocks have several high pressure and temperature phases, which vary substantially as composition changes from MORB-like to harzburgitic. Linearized treatments probably do not adequately capture the variation of physical properties with composition and temperature. In order to get closer to a realistic mineralogy, we here calculate composition- dependent mineral assemblages and their physical properties using the code PERPLEX, which minimizes free energy for a given combination of oxides as a function of temperature and pressure, and use the resulting properties in a 3-D spherical numerical model of thermo-chemical mantle convection, with three-dimensionally- varying physical properties [Nakagawa et al., 2007 in Goldschmidt conference]. Preliminary results are that while thermo-chemical structures are not greatly different from in the previous treatment, the spectral profiles of seismic anomalies seem to match seismic tomographic models more closely. Here we extend these results to focus on seismic signatures of the deep mantle including the post-perovskite phase transition. There is still uncertainty in the thermodynamic properties of the post-perovskite phase; hence the phase relationship of post-perovskite and its composition-dependence is treated as 'adjustable' within mineral physics uncertainties. The thermal- chemical-phase structures in our latest numerical simulation models are compared to the latest seismologically- observed structures.

One of the most striking surface features on Mars is the crustal dichotomy. The crustal dichotomy... more One of the most striking surface features on Mars is the crustal dichotomy. The crustal dichotomy, a large difference in elevation and crustal thickness between the southern highlands and the northern lowlands, is the oldest geological feature on Mars. It was formed more than 4.1 Ga ago [Solomon et al., 2005; Nimmo and Tanaka, 2005; Frey, 2006] owing to either

Calphad Comput Coup Phase Dia, 1987

Phys Earth Planet Interiors, 2000

Geochimica Et Cosmochimica Acta Supplement, Jun 1, 2009

Tectonophysics, Oct 1, 1990

Because of the plastic behavior of rocks at high temperature and confining pressure, the porosity... more Because of the plastic behavior of rocks at high temperature and confining pressure, the porosity, φ, of lower crustal rocks is a variable dependent on the amount of free fluid present. On the basis of hydrologic theory it is predicted that the permeability, k, of such rocks can be expressed by a relationship of the form k ≈ ωφn, where ω and n are material specific constants. The exponent n is likely to vary between 3 and 6, whereas ω, which is ultimately related to grain size and shape, probably varies over several orders of magnitude. Consequently, substantial contrasts between the φ- k relationships of lower crustal rocks are to be expected. The case in which thin crustal layers, "aquitards", are characterized by relatively low values of ω or n, with respect to the crust in general, is of particular interest. Such layers would acquire high porosities in the presence of miniscule steady state crustal fluid fluxes and are a possible explanation for anomalous seismic "brightspots" and high electrical conductivities in the lower crust. Modelling of collision belt metamorphism suggests that even long after the cessation of active metamorphism and isostatic reequilibration, relict metamorphic fluid fluxes could generate aquitard porosities, between 0.1 and 0.4%, adequate to explain such geophysical anomalies.

Egu General Assembly Conference Abstracts, May 1, 2010

Organic maturation during contact metamorphism is well known, although most studies are concernin... more Organic maturation during contact metamorphism is well known, although most studies are concerning the localized effects of one intrusion only. Large scale fluid generation can occur when a sedimentary basin is intruded by multiple igneous sills during formation of Large Igneous Provinces, like the Karoo Basin, South Africa (~183 Ma). In this study we aim at quantifying the generation of organic and inorganic devolatilization reactions in such basins. Geochemical data from boreholes intruded by multiple sills are used to constrain our model. Both depth and thickness of the intrusions are important parameters in determining the hydrocarbon yield. Modeling also illustrates an essential dependence on the background temperature of the sediments. The organic-rich formations are commonly located at the base of a sedimentary basin, which coincides with the intrusion level of the thickest sills (>100 meters) and the warmest parts of the basin. Hence, conditions are favorable for large-scale contact metamorphism of the sedimentary rocks. Our model is applied to borehole data from the organic-rich Ecca Formation in the Karoo Basin to get realistic estimates of the fluid generation in the shales. We show how the thermal influence of multiple levels of sill intrusion results in much larger fluid generation than what can be attributed to separate, single intrusions. A shale formation squeezed between two thick sills is exposed to extensive contact metamorphism. Geological evidence suggests that the root system of breccia pipes originates in such a heavily metamorphosed formation, implying a pressure-buildup in association with the devolatilization reactions. Basin scale extrapolation of our modeling shows that several thousand gigatons of carbon gases were generated during the contact metamorphic event. The generated fluids were effectively released to the atmosphere through the deep-rooted pipes. Such large scale release of greenhouse gases to the atmosphere has the ultimate consequence of perturbing the global carbon cycle with catastrophic outcome for life on Earth.

We propose that a mechanical flow channeling instability, which arises because of rock weakening ... more We propose that a mechanical flow channeling instability, which arises because of rock weakening at high fluid overpressure, facilitates segregation and transport of fluids and melts. To characterize the weakening effect the ratio of the matrix viscosity during decompaction to that for compaction is treated as a free parameter R. Two-dimensional numerical simulations with this rheology reveal that solitary, vertically elongated, porosity waves with spacing on the compaction length scale initiate from minuscule porosity perturbations, a geometry that increases fluid fluxes by a factor of 1/R. The waves grow by draining fluid from the background porosity, but leave a wake of elevated porosity that localizes subsequent flow. Wave amplitudes grow linearly with time. Such waves may provoke the elastic response necessary to nucleate, and localize the melt necessary to sustain, more effective transport mechanisms. The numerical results can be understood in the context of an analytical solution of the compaction equations that is completely general with respect to the constitutive relations used to define the matrix rheology and permeability. This solution combines the porosity dependence of the rheology and permeability in a single hydromechanical potential, which can be used to construct phase diagrams depicting the conditions for smooth pervasive flow, wave propagated fluid or melt extraction and matrix disaggregation (veins or dike formation).

We analyze the mechanical and rheological behavior of a two-phase system consisting of rigid grai... more We analyze the mechanical and rheological behavior of a two-phase system consisting of rigid grains and an interconnecting viscous fluid. For this purpose we use 2D direct numerical finite element simulations on the spatial scale of individual grains. We derived expressions for the effective viscosity for both Newtonian and non-Newtonian rheologies. Simulations using instantaneous deformation demonstrate that the effective rheology of the assemblage is non-Newtonian only if the fluid has a non-Newtonian rheology. At low fluid fractions the strain rates within the fluid are locally up to three orders of magnitude higher than the overall applied background strain rate. This may explain experimentally observed Newtonian to non-Newtonian rheological transitions. Laboratory experimental studies indicate that melt-grain systems behave non-linearly for moderate to high strain rates. However, the relative importance of shear heating, non-linear rheology, elasticity, plasticity and finite strain of the assemblage remains to be examined and may influence the effective rheology in a counter-intuitive manner. We have developed a 0D visco-elastic inversion model, which allows us to extract the effective rheological parameters from both numerical and laboratory experiments. We test the model against a series of 2D finite strain grain-scale numerical simulations. The rheology of each phase is controlled independently. Rheologies can be either linear or non-linear visco-elastic and the viscosity can be either temperature and composition dependent or independent. The simulations also account for shear heating. The 0D model reproduces well the rheological parameters (viscosity, temperature, elastic shear modulus) for the synthetic models. From this success we conclude that the model can be used to extract rheological information from laboratory data. Simulations with realistic grain shapes and linear visco-elastic rheology show no evidence that grain rearrangement causes a change to non-linear aggregate rheology. Thermal effects for strain rates <10-3 s-1 are too small to induce significant shear heating. However, realistic grain shapes do cause higher local stresses compared to regular grain shapes, e.g. spherical grains. Higher stresses enhance plastic failure, which aids in turn to locally reduce the viscosity. Such a process may additionally induce non-linear behaviour of the melt-grain system. The new findings can be applied to laboratory experiments on the effective rheology of partially molten rocks and have implications for volcanic eruptions and batholith emplacement.

Geochmica Et Cosmochimica Acta, Jun 1, 2009

As a plate subducts, fluid release from the subducting slab lowers the melting point of the surro... more As a plate subducts, fluid release from the subducting slab lowers the melting point of the surrounding mantle, which results in the configuration of more dense and viscous dry mantle overlying a thin layer of hydrated mantle with lowered density and viscosity. These processes trigger Rayleigh-Taylor (RT) type instabilities in a low-viscosity wedge with complex three-dimensional (3-D) geometries. RT-type cold plumes atop the slab were previously studied in 2-D. Here we use 3-D petrological-thermomechanical numerical simulations to investigate the dynamics of 3-D hydrous thermal-chemical plumes in the mantle wedge. The simulations were carried out with the I3ELVIS code which is based on a multigrid approach combined with marker-in-cell methods and conservative finite difference schemes. Our numerical simulations show that three types of upwelling plumes occur above the slab-mantle interface: (1) finger-like plumes forming roll/sheet-like structures parallel to the trench; (2) ridge-like structures perpendicular to the trench; and (3) flattened, wave-like instabilities propagating upward along the upper surface of the slab and forming zigzag patterns parallel to the trench. Plume-related melt productivity correlates well with volcanic activity clustering in natural intraoceanic arcs, such as in northeast Japan. Why do the above different plume patterns form atop the slab? Variation in partially molten rock viscosity notably affects plume patterns and lateral dimensions: wave-like plumes are most pronounced at higher (10^19 Pa s) viscosity, which also favors the development of larger plumes compared to models with lower (10^18 Pa s) viscosity. The "effective" density contrast between solid and molten rocks, which is closely related to melt extraction processes, is the key factor in determining plume patterns. A large to moderate density contrast of >200 kg/m3 (i.e. low to moderate degree of melt extraction) promotes the development of three distinct patterns of the cold plumes (finger-like, ridge-like and wave-like). In contrast, a low density contrast of 0-50 kg/m3 (i.e. high to complete melt extraction) suppresses pronounced plumes and is associated with low-amplitude (50-100 km wide and 10-15 km high) cold domal structures developing atop the slab due to the chemical buoyancy of subducted hydrated non-molten rocks (oceanic crust, sediments, serpentinites). Overall melt production intensity is notably different for cases with low (larger melt production) and high (lower melt production) degrees of melt extraction. All models are characterized by both spatially and temporally variable melt production, which may explain clustering and periodicity of volcanic activity observed in magmatic arcs. A simplified model (consisting of dry cold mantle and asthenosphere overlying the hydrated mantle) for the complex situation atop the slab is setup to systematically investigate the influence of different parameters on the development of plumes atop the slab, such as the thickness of the hydrated mantle, the viscosity contrast between the hydrated mantle and surrounding mantle and the dip angle of the slab.