Martin O. Saar

Using pyrosequencing to shed light on deep mine microbial ecology

BackgroundContrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence data was a costly and time-consuming process in defining an environment. Here we have used pyrosequencing, a rapid and relatively inexpensive sequencing technology, to generate environmental genome sequences from two sites in the Soudan Mine, Minnesota, USA. These sites were adjacent to each other, but differed significantly in chemistry and hydrogeology.ResultsComparisons of the microbes and the subsystems identified in the two samples highlighted important differences in metabolic potential in each environment. The microbes were performing distinct biochemistry on the available substrates, and subsystems such as carbon utilization, iron acquisition mechanisms, nitrogen assimilation, and respiratory pathways separated the two communities. Although the correlation between much of the microbial metabolism occurring and the geochemical conditions from which the samples were isolated could be explained, the reason for the presence of many pathways in these environments remains to be determined. Despite being physically close, these two communities were markedly different from each other. In addition, the communities were also completely different from other microbial communities sequenced to date.ConclusionWe anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages. Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.

Permeability‐porosity relationship in vesicular basalts

The permeability k and porosity of vesicular basalts are measured. The relationship between k and re- flects the formation and emplacement of the basalts and can be related to the crystal and vesicle microstructure obtained by image analysis. Standard theoretical models relating k and that work well for granular materials are unsuccessful for vesicular rocks due to the fundamental dierence in pore structure. Specically, k in vesicular rocks is governed by apertures between bubbles. The dierence between calcu- lated and measured k reflects the small size of these aper- tures with aperture radii typically O(10) times smaller than the mean bubble radii.

Numerical models of the onset of yield strength in crystal–melt suspensions

The formation of a continuous crystal network in magmas and lavas can provide finite yield strength, dy, and can thus cause a change from Newtonian to Bingham rheology. The rheology of crystal^melt suspensions affects geological processes, such as ascent of magma through volcanic conduits, flow of lava across the Earth’s surface, melt extraction from crystal mushes under compression, convection in magmatic bodies, and shear wave propagation through partial melting zones. Here, three-dimensional numerical models are used to investigate the onset of ‘static’ yield strength in a zero-shear environment. Crystals are positioned randomly in space and can be approximated as convex polyhedra of any shape, size and orientation. We determine the critical crystal volume fraction, Pc, at which a crystal network first forms. The value of Pc is a function of object shape and orientation distribution, and decreases with increasing randomness in object orientation and increasing shape anisotropy. For example, while parallel-aligned convex objects yield Pc = 0.29, randomly oriented cubes exhibit a maximum Pc of 0.22. Approximations of plagioclase crystals as randomly oriented elongated and flattened prisms (tablets) with aspect ratios between 1:4:16 and 1:1:2 yield 0.086Pc 6 0.20, respectively. The dependence of Pc on particle orientation implies that the flow regime and resulting particle ordering may affect the onset of yield strength. Pc in zero-shear environments is a lower bound for Pc. Finally the average total excluded volume is used, within its limitation of being a ‘quasi-invariant’, to develop a scaling relation between dy and P for suspensions of different particle shapes. fl 2001 Elsevier Science B.V. All rights reserved.

Seismicity induced by seasonal groundwater recharge at Mt. Hood, Oregon

Groundwater recharge at Mt. Hood, Oregon, is dominated by spring snow melt which provides a natural largeamplitude and narrow-width pore-fluid pressure signal. Time delays between this seasonal groundwater recharge and seismicity triggered by groundwater recharge can thus be used to estimate large-scale hydraulic diffusivities and the state of stress in the crust. We approximate seasonal variations in groundwater recharge with discharge in runoffdominated streams at high elevations. We interpolate the time series ofnumber ofearthquakes, N, seismic moment, Mo, and stream discharge, Q, and determine cross-correlation coefficients at equivalent frequency bands between Q and both N and Mo. We find statistically significant correlation coefficients at a mean time lag of about 151 days. This time lag and a mean earthquake depth of about 4.5 km are used in the solution to the pressure diffusion equation, under periodic (1 year) boundary conditions, to estimate a hydraulic diffusivity of UW10 31 m 2 /s, a hydraulic conductivity ofabout KhW10 37 m/s, and a permeability ofabout kW10 315 m 2 . Periodic boundary conditions also allow us to determine a critical pore-fluid pressure fraction, PP/P0W0.1, ofthe applied near-surf ace pore-fluid pressure perturbation, P0W0.1 MPa, that has to be reached at the mean earthquake depth to cause hydroseismicity. The low magnitude of PPW0.01 MPa is consistent with other studies that propose 0.019 PP9 0.1 MPa and suggests that the state of stress in the crust near Mt. Hood could be near critical for failure. Therefore, we conclude that, while earthquakes occur throughout the year at Mt. Hood, elevated seismicity levels along pre-existing faults south of Mt. Hood during summer months are hydrologically induced by a reduction in effective stress.

Accelerating Lattice Boltzmann Fluid Flow Simulations Using Graphics Processors

Lattice Boltzmann Methods (LBM) are used for the computational simulation of Newtonian fluid dynamics. LBM-based simulations are readily parallelizable; they have been implemented on general-purpose processors, field-programmable gate arrays (FPGAs), and graphics processing units (GPUs). Of the three methods, the GPU implementations achieved the highest simulation performance per chip. With memory bandwidth of up to 141 GB/s and a theoretical maximum floating point performance of over 600 GFLOPS, CUDA-ready GPUs from NVIDIA provide an attractive platform for a wide range of scientific simulations, including LBM. This paper improves upon prior single-precision GPU LBM results for the D3Q19 model by increasing GPU multiprocessor occupancy, resulting in an increase in maximum performance by 20%, and by introducing a space-efficient storage method which reduces GPU RAM requirements by 50% at a slight detriment to performance. Both GPU implementations are over 28 times faster than a single-precision quad-core CPU version utilizing OpenMP.

A new partial-bounceback lattice-Boltzmann method for fluid flow through heterogeneous media

Partial-bounceback lattice-Boltzmann methods employ a probabilistic meso-scale model that varies individual lattice node properties to reflect a materials local permeability. These types of models have great potential in a range of geofluid, and other science and engineering, simulations of complex fluid flow. However, there are several different possible approaches for formulating partial-bounceback algorithms. This paper introduces a new partial-bounceback algorithm and compares it to two pre-existing partial-bounceback models. Unlike the two other partial-bounceback methods, the new approach conserves mass in heterogeneous media and shows improvements in simulating buoyancy-driven flow as well as diffusive processes. Further, the new model is better-suited for parallel processing implementations, resulting in faster simulations. Finally, we derive an analytical expression for calculating the permeability in all three models; a critical component for accurately matching simulation parameters to physical permeabilities.

Accelerating geoscience and engineering system simulations on graphics hardware

Many complex natural systems studied in the geosciences are characterized by simple local-scale interactions that result in complex emergent behavior. Simulations of these systems, often implemented in parallel using standard central processing unit (CPU) clusters, may be better suited to parallel processing environments with large numbers of simple processors. Such an environment is found in graphics processing units (GPUs) on graphics cards. This paper discusses GPU implementations of three example applications from computational fluid dynamics, seismic wave propagation, and rock magnetism. These candidate applications involve important numerical modeling techniques, widely employed in physical system simulations, that are themselves examples of distinct computing classes identified as fundamental to scientific and engineering computing. The presented numerical methods (and respective computing classes they belong to) are: (1) a lattice-Boltzmann code for geofluid dynamics (structured grid class); (2) a spectral-finite-element code for seismic wave propagation simulations (sparse linear algebra class); and (3) a least-squares minimization code for interpreting magnetic force microscopy data (dense linear algebra class). Significant performance increases (between 10x and 30x in most cases) are seen in all three applications, demonstrating the power of GPU implementations for these types of simulations and, more generally, their associated computing classes.

Experimental observation of permeability changes in dolomite at CO2 sequestration conditions.

Injection of cool CO2 into geothermally warm carbonate reservoirs for storage or geothermal energy production may lower near-well temperature and lead to mass transfer along flow paths leading away from the well. To investigate this process, a dolomite core was subjected to a 650 h, high pressure, CO2 saturated, flow-through experiment. Permeability increased from 10(-15.9) to 10(-15.2) m(2) over the initial 216 h at 21 °C, decreased to 10(-16.2) m(2) over 289 h at 50 °C, largely due to thermally driven CO2 exsolution, and reached a final value of 10(-16.4) m(2) after 145 h at 100 °C due to continued exsolution and the onset of dolomite precipitation. Theoretical calculations show that CO2 exsolution results in a maximum pore space CO2 saturation of 0.5, and steady state relative permeabilities of CO2 and water on the order of 0.0065 and 0.1, respectively. Post-experiment imagery reveals matrix dissolution at low temperatures, and subsequent filling-in of flow passages at elevated temperature. Geochemical calculations indicate that reservoir fluids subjected to a thermal gradient may exsolve and precipitate up to 200 cm(3) CO2 and 1.5 cm(3) dolomite per kg of water, respectively, resulting in substantial porosity and permeability redistribution.

Nanoscale constraints on porosity generation and fluid flow during serpentinization

Field samples of olivine-rich rocks are nearly always serpentinized—commonly to completion—but, paradoxically, their intrinsic porosity and permeability are diminishingly low. Serpentinization reactions occur through a coupled process of fluid infiltration, volumetric expansion, and reaction-driven fracturing. Pores and reactive surface area generated during this process are the primary pathways for fluid infiltration into and reaction with serpentinizing rocks, but the size and distribution of these pores and surface area have not yet been described. Here, we utilize neutron scattering techniques to present the first measurements of the evolution of pore size and specific surface area distribution in partially serpentinized rocks. Samples were obtained from the ca. 2 Ma Atlantis Massif oceanic core complex located off-axis of the Mid-Atlantic Ridge and an olivine-rich outcrop of the ca. 1.1 Ga Duluth Complex of the North American Mid-Continent Rift. Our measurements and analyses demonstrate that serpentine and accessory phases form with their own, inherent porosity, which accommodates the bulk of diffusive fluid flow during serpentinization and thereby permits continued serpentinization after voluminous serpentine minerals fill reaction-generated porosity.

Short note: DBCreate: A SUPCRT92-based program for producing EQ3/6, TOUGHREACT, and GWB thermodynamic databases at user-defined T and P

SUPCRT92 is a widely used software package for calculating the standard thermodynamic properties of minerals, gases, aqueous species, and reactions. However, it is labor-intensive and error-prone to use it directly to produce databases for geochemical modeling programs such as EQ3/6, the Geochemists Workbench, and TOUGHREACT. DBCreate is a SUPCRT92-based software program written in FORTRAN90/95 and was developed in order to produce the required databases for these programs in a rapid and convenient way. This paper describes the overall structure of the program and provides detailed usage instructions.