Geochemical modeling

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Geochemical modeling or theoretical geochemistry is the practice of using chemical thermodynamics, chemical kinetics, or both, to analyze the chemical reactions that affect geologic systems, commonly with the aid of a computer. It is used in high-temperature geochemistry to simulate reactions occurring deep in the Earth's interior, in magma, for instance, or to model low-temperature reactions in aqueous solutions near the Earth's surface, the subject of this article.

Contents

Applications to aqueous systems

Geochemical modeling is used in a variety of fields, including environmental protection and remediation, [1] the petroleum industry, and economic geology. [2] Models can be constructed, for example, to understand the composition of natural waters; the mobility and breakdown of contaminants in flowing groundwater or surface water; the ion speciation of plant nutrients in soil and of regulated metals in stored solid wastes; the formation and dissolution of rocks and minerals in geologic formations in response to injection of industrial wastes, steam, or carbon dioxide; the dissolution of carbon dioxide in seawater and its effect on ocean acidification; and the generation of acidic waters and leaching of metals from mine wastes.

Development of geochemical modeling

Garrels and Thompson (1962) first applied chemical modeling to geochemistry in 25 °C and one atmosphere total pressure. Their calculation, computed by hand, is now known as an equilibrium model, which predicts species distributions, mineral saturation states, and gas fugacities from measurements of bulk solution composition. By removing small aliquots of solvent water from an equilibrated spring water and repeatedly recalculating the species distribution, Garrels and Mackenzie (1967) simulated the reactions that occur as spring water evaporated. [3] This coupling of mass transfer with an equilibrium model, known as a reaction path model, enabled geochemists to simulate reaction processes.

Helgeson (1968) introduced the first computer program to solve equilibrium and reaction path models, [4] which he and coworkers used to model geological processes like weathering, sediment diagenesis, evaporation, hydrothermal alteration, and ore deposition. [5] Later developments in geochemical modeling included reformulating the governing equations, first as ordinary differential equations, then later as algebraic equations. Additionally, chemical components came to be represented in models by aqueous species, minerals, and gases, rather than by the elements and electrons which make up the species, simplifying the governing equations and their numerical solution. [2]

Recent improvements in the power of personal computers and modeling software have made geochemical models more accessible and more flexible in their implementation. [6] Geochemists are now able to construct on their laptops complex reaction path or reactive transport models which previously would have required a supercomputer. [7]

Setting up a geochemical model

An aqueous system is uniquely defined by its chemical composition, temperature, and pressure. [8] Creating geochemical models of such systems begins by choosing the basis, the set of aqueous species, minerals, and gases which are used to write chemical reactions and express composition. The number of basis entries required equals the number of components in the system, which is fixed by the phase rule of thermodynamics. Typically, the basis is composed of water, each mineral in equilibrium with the system, each gas at known fugacity, and important aqueous species. Once the basis is defined, a modeler can solve for the equilibrium state, which is described by mass action and mass balance equations for each component. [2]

In finding the equilibrium state, a geochemical modeler solves for the distribution of mass of all species, minerals, and gases which can be formed from the basis. This includes the activity, activity coefficient, and concentration of aqueous species, the saturation state of minerals, and the fugacity of gases. Minerals with a saturation index (log Q/K) equal to zero are said to be in equilibrium with the fluid. Those with positive saturation indices are termed supersaturated, indicating they are favored to precipitate from solution. A mineral is undersaturated if its saturation index is negative, indicating that it is favored to dissolve. [8]

Geochemical modelers commonly create reaction path models to understand how systems respond to changes in composition, temperature, or pressure. By configuring the manner in which mass and heat transfer are specified (i.e., open or closed systems), models can be used to represent a variety of geochemical processes. Reaction paths can assume chemical equilibrium, or they can incorporate kinetic rate laws to calculate the timing of reactions. In order to predict the distribution in space and time of the chemical reactions that occur along a flowpath, geochemical models are increasingly being coupled with hydrologic models of mass and heat transport to form reactive transport models. [2] Specialized geochemical modeling programs that are designed as cross-linkable re-entrant software objects enable construction of reactive transport models of any flow configuration. [9]

Types of reactions

Geochemical models are capable of simulating many different types of reactions. Included among them are:

Simple phase diagrams or plots are commonly used to illustrate such geochemical reactions. Eh-pH (Pourbaix) diagrams, for example, are a special type of activity diagram which represent acid-base and redox chemistry graphically.

Uncertainties in geochemical modelling

Various sources can contribute to a range of simulation results. The range of the simulation results is defined as model uncertainty. One of the most important sources not possible to quantify is the conceptual model, which is developed and defined by the modeller. Further sources are the parameterization of the model regarding the hydraulic (only when simulating transport) and mineralogical properties. [10] The parameters used for the geochemical simulations can also contribute to model uncertainty. These are the applied thermodynamic database and the parameters for the kinetic minerals dissolution. [11] Differences in the thermodynamic data (i.e. equilibrium constants, parameters for temperature correction, activity equations and coefficients) can result in large uncertainties. Furthermore, the large spans of experimentally derived rate constants for minerals dissolution rate laws can cause large variations in simulation results. Despite this is well-known, uncertainties are not frequently considered when conducting geochemical modelling. [12]

Reducing uncertainties can be achieved by comparison of simulation results with experimental data, although experimental data does not exist at every temperature-pressure condition and for every chemical system. [12] Although such a comparison or calibration can not be conducted consequently the geochemical codes and thermodynamic databases are state-of-the-art and the most useful tools for predicting geochemical processes.

Software programs in common use

The USGS website provides free access to many of the software listed above. [35]

See also

Further reading

Related Research Articles

In physics, statistical mechanics is a mathematical framework that applies statistical methods and probability theory to large assemblies of microscopic entities. It does not assume or postulate any natural laws, but explains the macroscopic behavior of nature from the behavior of such ensembles.

Geochemistry is the science that uses the tools and principles of chemistry to explain the mechanisms behind major geological systems such as the Earth's crust and its oceans. The realm of geochemistry extends beyond the Earth, encompassing the entire Solar System, and has made important contributions to the understanding of a number of processes including mantle convection, the formation of planets and the origins of granite and basalt. It is an integrated field of chemistry and geology.

<span class="mw-page-title-main">Solvation</span> Association of molecules of a solvent with molecules or ions of a solute

Solvation describes the interaction of a solvent with dissolved molecules. Both ionized and uncharged molecules interact strongly with a solvent, and the strength and nature of this interaction influence many properties of the solute, including solubility, reactivity, and color, as well as influencing the properties of the solvent such as its viscosity and density. In the process of solvation, ions are surrounded by a concentric shell of solvent. Solvation is the process of reorganizing solvent and solute molecules into solvation complexes. Solvation involves bond formation, hydrogen bonding, and van der Waals forces. Solvation of a solute by water is called hydration.

<span class="mw-page-title-main">Solubility</span> Capacity of a substance to dissolve in a solvent in a homogeneous way

In chemistry, solubility is the ability of a substance, the solute, to form a solution with another substance, the solvent. Insolubility is the opposite property, the inability of the solute to form such a solution.

Solubility equilibrium is a type of dynamic equilibrium that exists when a chemical compound in the solid state is in chemical equilibrium with a solution of that compound. The solid may dissolve unchanged, with dissociation, or with chemical reaction with another constituent of the solution, such as acid or alkali. Each solubility equilibrium is characterized by a temperature-dependent solubility product which functions like an equilibrium constant. Solubility equilibria are important in pharmaceutical, environmental and many other scenarios.

Extractive metallurgy is a branch of metallurgical engineering wherein process and methods of extraction of metals from their natural mineral deposits are studied. The field is a materials science, covering all aspects of the types of ore, washing, concentration, separation, chemical processes and extraction of pure metal and their alloying to suit various applications, sometimes for direct use as a finished product, but more often in a form that requires further working to achieve the given properties to suit the applications.

In chemical thermodynamics, the fugacity of a real gas is an effective partial pressure which replaces the mechanical partial pressure in an accurate computation of the chemical equilibrium constant. It is equal to the pressure of an ideal gas which has the same temperature and molar Gibbs free energy as the real gas.

Robert Minard Garrels was an American geochemist. Garrels applied experimental physical chemistry data and techniques to geology and geochemistry problems. The book Solutions, Minerals, and Equilibria co-authored in 1965 by Garrels and Charles L. Christ revolutionized aqueous geochemistry.

Chemical WorkBench is a proprietary simulation software tool aimed at the reactor scale kinetic modeling of homogeneous gas-phase and heterogeneous processes and kinetic mechanism development. It can be effectively used for the modeling, optimization, and design of a wide range of industrially and environmentally important chemistry-loaded processes. Chemical WorkBench is a modeling environment based on advanced scientific approaches, complementary databases, and accurate solution methods. Chemical WorkBench is developed and distributed by Kintech Lab.

<span class="mw-page-title-main">DWSIM</span> Chemical process simulation software

DWSIM is an open-source CAPE-OPEN compliant chemical process simulator for Windows, Linux and macOS. DWSIM is built on top of the Microsoft .NET and Mono Platforms and features a Graphical User Interface (GUI), advanced thermodynamics calculations, reactions support and petroleum characterization / hypothetical component generation tools.

The Geochemist's Workbench (GWB) is an integrated set of interactive software tools for solving a range of problems in aqueous chemistry. The graphical user interface simplifies the use of the geochemical code.

Reactive transport modeling in porous media refers to the creation of computer models integrating chemical reaction with transport of fluids through the Earth's crust. Such models predict the distribution in space and time of the chemical reactions that occur along a flowpath. Reactive transport modeling in general can refer to many other processes, including reactive flow of chemicals through tanks, reactors, or membranes; particles and species in the atmosphere; gases exiting a smokestack; and migrating magma.

Aqion is a hydrochemistry software tool. It bridges the gap between scientific software and the calculation/handling of "simple" water-related tasks in daily routine practice. The software aqion is free for private users, education and companies.

<span class="mw-page-title-main">Fred T. Mackenzie</span> American sedimentary biogeochemist

Frederick T. Mackenzie is an American sedimentary and global biogeochemist. Mackenzie applies experimental and field data coupled to a sound theoretical framework to the solution of geological, geochemical, and oceanographic problems at various time and space scales.

Reverse weathering generally refers to the formation of a clay neoformation that utilizes cations and alkalinity in a process unrelated to the weathering of silicates. More specifically reverse weathering refers to the formation of authigenic clay minerals from the reaction of 1) biogenic silica with aqueous cations or cation bearing oxides or 2) cation poor precursor clays with dissolved cations or cation bearing oxides.

<span class="mw-page-title-main">Dimitri Sverjensky</span> Geochemistry professor

Dimitri Alexander Sverjensky is a professor in Earth and Planetary Sciences at Johns Hopkins University where his research is focused on geochemistry.

Joint Expert Speciation System (JESS) is a package of computer software and data developed collaboratively at Murdoch University and elsewhere by researchers interested in the chemical thermodynamics of water solutions with important applications in industry, biochemistry, medicine and the environment. Using information from the chemical literature, stored in databases for numerous chemical properties, JESS achieves coherence between frequently conflicting sources by automatic methods.

<span class="mw-page-title-main">Patricia Dove</span> American geochemist and crystal growth researcher

Patricia Martin Dove is an American geochemist. She is a University Distinguished Professor and the C.P. Miles Professor of Science at Virginia Tech with appointments in the Department of Geosciences and Department of Chemistry. Her research focuses on the kinetics and thermodynamics of mineral reactions with aqueous solutions in biogeochemical systems. Much of her work is on crystal nucleation and growth during biomineralization and biomaterial synthesis. She was elected a member of the National Academy of Sciences (NAS) in 2012 and currently serves as chair of Class I, Physical and Mathematical Sciences.

A Lippmann diagram is a graphical plot showing the solidus/solutus equilibrium states for a given binary solid solution in equilibrium with an aqueous solution containing the two substituting ions: Ba2+
 and Sr2+
. It was proposed in the 1970s by F. Lippmann to determine excess Gibbs functions. This diagram summarizes the thermodynamic basis of solid-solution aqueous-solution systems (SS-AS) equilibria and helps to predict the nucleation kinetics for solid solutions crystallizing from an aqueous solution.

<span class="mw-page-title-main">Groundwater contamination by pharmaceuticals</span>

Groundwater contamination by pharmaceuticals, which belong to the category of contaminants of emerging concern (CEC) or emerging organic pollutants (EOP), has been receiving increasing attention in the fields of environmental engineering, hydrology and hydrogeochemistry since the last decades of the twentieth century.

References

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  2. 1 2 3 4 Bethke, C.M., 2008, Geochemical and Biogeochemical Reaction Modeling. Cambridge University Press, 547 pp.
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  4. ↑ Helgeson, H.C., 1968, Evaluation of irreversible reactions in geochemical processes involving minerals and aqueous solutions, I. Thermodynamic relations. Geochemica et Cosmochimica Acta32, 853-877
  5. ↑ Helgeson, H.C., R.M. Garrels and F.T. Mackenzie, 1969, Evaluation of irreversible reactions in geochemical processes involving minerals and aqueous solutions, II. Applications. Geochemica et Cosmochimica Acta33, 455-481
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  12. 1 2 Haase, Christoph; Ebert, Markus; Dethlefsen, Frank (2016-04-01). "Uncertainties of geochemical codes and thermodynamic databases for predicting the impact of carbon dioxide on geologic formations". Applied Geochemistry. 67: 81–92. doi:10.1016/j.apgeochem.2016.01.008.
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