This book provides a comprehensive overview of reaction processes in the Earth's crust and on its surface, both in the laboratory and in the field. A clear exposition of the underlying equations and calculation techniques is balanced by a large number of fully worked examples. The book uses The Geochemist's Workbench® modeling software, developed by the author and already installed at over 1000 universities and research facilities worldwide. Since publication of the first edition, the field of reaction modeling has continued to grow and find increasingly broad application. In particular, the description of microbial activity, surface chemistry, and redox chemistry within reaction models has become broader and more rigorous. These areas are covered in detail in this new edition, which was originally published in 2007. This text is written for graduate students and academic researchers in the fields of geochemistry, environmental engineering, contaminant hydrology, geomicrobiology, and numerical modeling.

A new numerical method allows calculation of compaction‐driven groundwater flow and associated heat transfer in evolving sedimentary basins. The model is formulated in Lagrangian coordinates and considers two‐dimensional flow in heterogeneous, anisotropic, and accreting domains. Both the continuity of the deforming medium and aquathermal pressuring are explicitly taken into account. A calculation of compaction‐driven flow during evolution of an idealized intracratonic sedimentary basin including a basal aquifer predicts slow groundwater movement over long time periods. Fluids in shallow sediments tend to move upward toward the sedimentation surface, and deeper fluids move laterally. The hydraulic potential gradient with depth reverses itself near the basal aquifer, and fluids in this area have a tendency to migrate obliquely into stratigraphically lower sediments. Only small excess pressures develop, suggesting that intracratonic basins are not subject to overpressuring during their evolutions. Owing to the small fluid velocities, heat transfer is conduction‐dominated, and the geothermal gradient is not disturbed. Variational studies show that excess hydraulic potentials, but not fluid velocities, depend on assumptions of permeability and that both excess potentials and velocities scale with sedimentation rate. Aquathermal pressuring is found to account for <1% of the excess potentials developed during compaction. These results cast doubt on roles of compaction‐driven flow within intracratonic basins in processes of secondary petroleum migration, osmotic concentration of sedimentary brines, and formation of Mississippi Valley‐type ore deposits. Results might also be combined with chemical models to investigate the relationship of compaction flow to cementation in sediments.

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A new way of thinking about groundwater age is changing the field of groundwater age dating. Following a rigorous definition of age, a groundwater sample is seen not as water that recharged the flow regime at a point in the past, but as a mixture of waters that have resided in the subsurface for varying lengths of time. This recognition resolves longstanding inconsistencies encountered in age dating and suggests new ways to carry out age dating studies. Tomorrow's studies will likely employ sets of marker isotopes and molecules spanning a broad spectrum of age and incorporate a wide range of chemical and physical data collected from differing stratigraphic levels. The observations will be inverted using reactive transport modeling, allowing flow to be characterized not in one direction along a single aquifer, but in two or three dimensions over an entire flow regime.

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The rate of microbial respiration can be described by a rate law that gives the respiration rate as the product of a rate constant, biomass concentration, and three terms: one describing the kinetics of the electron-donating reaction, one for the kinetics of the electron-accepting reaction, and a thermodynamic term accounting for the energy available in the microbe's environment. The rate law, derived on the basis of chemiosmotic theory and nonlinear thermodynamics, is unique in that it accounts for both forward and reverse fluxes through the electron transport chain. Our analysis demonstrates how a microbe's respiration rate depends on the thermodynamic driving force, i.e., the net difference between the energy available from the environment and energy conserved as ATP. The rate laws commonly applied in microbiology, such as the Monod equation, are specific simplifications of the general law presented. The new rate law is significant because it affords the possibility of extrapolating in a rigorous manner from laboratory experiment to a broad range of natural conditions, including microbial growth where only limited energy is available. The rate law also provides a new explanation of threshold phenomena, which may reflect a thermodynamic equilibrium where the energy released by electron transfer balances that conserved by ADP phosphorylation.Understanding the rate at which microbes respire in biological and geochemical systems is central to developing quantitative descriptions of a broad range of problems in microbiology, from the propagation of disease to the attenuation of contaminants in drinking-water supplies. Microbiologists have in recent years expended considerable effort in investigating microbial respiration rates under specific conditions (22,33,36,41).In virtually all cases, the results of such studies have been cast in terms of a semi-empirical rate law such as the Monod equation (15). Application of such rate laws is limited in two senses. First, because of their semi-empirical nature, they are best suited to interpolating the results of a set of experiments within the range of chemical conditions tested (7). Second, none of the laws accounts for the thermodynamic effects of the energy available in the cell's environment. As such, there is no basis for applying a rate law derived for a laboratory experiment, where the available energy is typically maintained at a high level to provide for microbial growth at acceptable rates, to natural conditions, where much less energy may be available. As a result, the rate laws invariably predict positive activities even where there is no energy available to drive the cell's metabolism forward.In a recent paper (13), we performed, on the basis of the chemiosmotic model of cellular respiration (19) and nonlinear nonequilibrium thermodynamics (6), a rigorous analysis of the problem of respiration in eukaryotic cells by mitochondria. In our analysis, we accounted for a simultaneous forward and backward flux of electrons through the respiratory chain. The resultin...

Inverse hydrologic analysis of compaction-driven groundwater flow provides insights to the distribution and origin of geopressured zones in subsiding sedimentary basins, such as those found in the U.S. Gulf Coast. Occurrences of Gulf Coast-type geopressures are most frequently attributed to "disequilibrium compaction" caused by slow rates of fluid escape from compacting sediments, "aquathermal pressuring" from thermal expansion of pore fluids, or the subsurface dehydration of smectite. This paper presents an inverse solution to the Lagrangian equation of compaction flow that includes effects of aquathermal pressuring and dehydration reactions. The solution gives the permeability profile required to maintain a lithostatic pressure gradient in a subsiding basin. Comparison of the closed-form solution with measured permeabilities shows that geopressured zones are likely to form in shaly basins subsiding more than about 1 mm/yr but unlikely to develop in shale-poor basins or basins subsiding less than 0.1 mm/yr. This result correctly predicts geopressures in the Gulf Coast but suggests that many important sedimentary basins were not significantly overpressured during compaction. Solutions that consider only thermal expansion of pore fluids give required permeabilities about 1.3-1.8 orders of magnitude (factor of 20-60) less than those considering only sediment compaction, indicating that aquathermal pressuring is much less important than disequilibrium compaction in causing geopressures. Solutions accounting for the effects of dehydration reactions show that release of structural water during smectite dehydration can be a significant and perhaps necessary factor in geopressuring. Hydrologic effects of a possible increase in the volume of structural water during dehydration are less significant. The most important contribution of smectite dehydration to development of geopressured zones, however, may be the accompanying reduction of host rock permeability. several kilometers thick. Conditions at greater depths are poorly known I-Hanor and Bailey, 1983]. Many authors divide geopressured columns in the Gulf Coast into three sections (Figure 1). Fluid pressures in the lithostatic section approach but do not reach the lithostatic limit [Dickinson, 1953]. The lithostatic and overlying hydrostatic sections are separated by a transition interval. Sediment porosity increases across the transition interval and then decreases in the lithostatic section with increasing depth [Weaver and Beck, 1971]. The most actively discussed causes of geopressures in GulfCoast-type settings (review by Graf 1-1982]) are rapid accumulation of fine-grained sediments, "aquathermal pressuring" from thermal expansion of pore fluids, and dehydration reactions of clay minerals. Dickinson [1953] interpreted Gulf Coast geopressures to result from the inability of fine-grained sediments to expel pore fluids rapidly enough to accommodate normal gravitational compaction. In this case, sediments cannot compact to their normal or "equilibrium" porosity and ...

Natural arsenic contamination of groundwater, increasingly recognized as a threat to human health worldwide, is characterized by arsenic concentrations that vary sharply over short distances. Variation in arsenic levels in the Mahomet aquifer system, a regional glacial aquifer in central Illinois, appears to arise from variable rates of bacterial sulfate reduction in the subsurface, not differences in arsenic supply. Where sulfate-reducing bacteria are active, the sulfide produced reacts to precipitate arsenic, or coprecipitate it with iron, leaving little in solution. In the absence of sulfate reduction, methanogenesis is the dominant type of microbial metabolism, and arsenic accumulates to high levels.