Development and application of a numerical model of kinetic and equilibrium microbiological and geochemical reactions (BIOKEMOD)

Karen M. Salvage, Gour Tsyh Yeh

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48 Scopus citations


This paper presents the conceptual and mathematical development of the numerical model titled BIOKEMOD, and verification simulations performed using the model. BIOKEMOD is a general computer model for simulation of geochemical and microbiological reactions in batch aqueous solutions. BIOKEMOD may be coupled with hydrologic transport codes for simulation of chemically and biologically reactive transport. The chemical systems simulated may include any mixture of kinetic and equilibrium reactions. The pH, pe, and ionic strength may be specified or simulated. Chemical processes included are aqueous complexation, adsorption, ion-exchange and precipitation/dissolution. Microbiological reactions address growth of biomass and degradation of chemicals by microbial metabolism of substrates, nutrients, and electron acceptors. Inhibition or facilitation of growth due to the presence of specific chemicals and a lag period for microbial acclimation to new substrates may be simulated if significant in the system of interest. Chemical reactions controlled by equilibrium are solved using the law of mass action relating the thermodynamic equilibrium constant to the activities of the products and reactants. Kinetic chemical reactions are solved using reaction rate equations based on collision theory. Microbiologically mediated reactions for substrate removal and biomass growth are assumed to follow Monod kinetics modified for the potentially limiting effects of substrate, nutrient, and electron acceptor availability. BIOKEMOD solves the ordinary differential and algebraic equations of mixed geochemical and biogeochemical reactions using the Newton-Raphson method with full matrix pivoting. Simulations may be either steady state or transient. Input to the program includes the stoichiometry and parameters describing the relevant chemical and microbiological reactions, initial conditions, and sources/sinks for each chemical species. Output includes the chemical and biomass concentrations at desired times. BIOKEMOD has been coupled with a hydrologic transport code, HYDROGEOCHEM, to allow the simulation of coupled advective-dispersive transport and biogeochemical transformation of pollutants in groundwater. Three verification exercises are compared with analytical solutions to demonstrate the correctness of the code. Two validation simulations of batch laboratory systems are compared with the laboratory data to demonstrate the code's ability to replicate behavior observed in real systems, and two validation exercises simulating reactive transport are presented to demonstrate the code's performance in simulating mixed equilibrium and kinetic biogeochemical reactions coupled with hydrologic transport.

Original languageEnglish
Pages (from-to)27-52
Number of pages26
JournalJournal of Hydrology
Issue number1-4
StatePublished - Aug 1998


  • Biochemistry
  • Geochemistry
  • Groundwater
  • Numerical models
  • Reactive transport


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