Accepted credit cards: VISA, MasterCard, American Express, and Discover 



Overview
BIO1D is a onedimensional modeling code which simulates biodegradation
and sorption in contaminant transport. Our objective was
to provide an interactive, userfriendly software package to serve
as an educational tool for understanding the relative importance
of various physicochemical and biochemical processes.
Applications
BIO1D may be applied to solute transport problems involving a reactive substrate. The reactions may include aerobic and
anaerobic degradation and/or adsorption described by linear, Freundlich, or Langmuir isotherm. Figure 1 shows the simulation
at a waste site in Conroe, Texas, and is based on an earlier study by Borden, et al. (1984).
Figure 1. Simulation of aerobic biodegradation at Conroe site, Texas
The code may be used in conceptualization mode for many applications to help determine the importance of transport processes.
The applications can involve a number of reactive substrates such as organic solvents and petroleum products. In addition,
because anaerobic degradation is considered, nonorganic solutes, such as radionuclides with decay can be simulated. The
code will be especially useful for analyzing laboratory data from column experiments.
Model Features
 Advective and dispersive transport of a hydrocarbon and an electron acceptor (e.g., oxygen)
 Aerobic biodegradation using modified Monod function
 Anaerobic biodegradation using MichaelisMenten kinetics
 Firstorder degradation for both substances
 Linear, Freundlich, and Langmuir adsorption isotherms for both substances
 Dirichlet, Neumann, and Cauchy boundary conditions modified to include firstorder degradation
 Cumulative mass balance report
Limitations
 Transport is onedimensional.
 The flow field is uniform (constant velocity).
 Material properties of both substances are uniform throughout the medium.
 Only one reactive substrate is considered per simulation.
 Microbial density is assumed constant.
Governing Equations
A summary of the equations solved in BIO1D is presented below.
where
S 
substrate concentration in the pore fluid (ML3); 
O 
oxygen concentration in the pore fluid (ML3); 
D 
longitudinal hydrodynamic dispersion coefficient (L2T1); 
x 
distance (L); 
V 
interstitial velocity (LT1), assumed uniform; 
B(S,O) 
biodegradation term (ML3T1), expressed as a function of the dependent variables S and O; 
F 
ratio of oxygen to substrate consumed; 
A(S) 
substrate adsorption term; 
A(O) 
oxygen adsorption term; and 
t 
time (T). 
Aerobic Biodegradation (Monod Function)
where
B(S,O) 
aerobic biodegradation term, a function of substrate and oxygen concentration (ML3T1); 
M 
microbial mass (ML3) assumed constant; 
K 
maximum substrate utilization rate per unit mass of micro organisms (T1); 
ks 
substrate halfsaturation constant (ML3); 
kO 
oxygen halfsaturation constant (ML3); 
Smin 
minimum substrate concentration that limits growth and decay (ML3); and 
Omin 
minimum oxygen concentration that limits growth and decay (ML3). 
Anaerobic Biodegradation (MichaelisMenten Kinetics)
where the terms, Mn, kn, and kSn are counterparts of M, k and kS under anaerobic conditions. As a special case, Mn, kn,
and kSn may be set equal to M, k, and kS, respectively.
FirstOrder Decay
where uS is a firstorder degradation coefficient (T1).
Linear Adsorption Isotherm
where
rb 
bulk mass density of the porous medium (ML3); 
phi 
effective porosity; and 
Kd 
distribution coefficient (L3M1). 
Freundlich Adsorption Isotherm
where
Kf 
rate constant; and 
n 
Freundlich isotherm exponent. 
Langmuir Adsorption Isotherm
where
b 
constant; and 
K 
maximum sorption capacity of solid. 
Uncoupled Simulation Option
When the biodegradation option is not used, the equations (1) and (2) are uncoupled and may be solved simultaneously. Two
sets of input values are used for all parameters except those defining the grid and time steps. This permits a wide range
of possible comparison studies. Some are listed below.
 Different velocities. This is an indirect way of comparing the effect of two hydraulic conductivity values. Figure 2
illustrates a field application of BIO1D where the predicted breakthrough curves are bracketed with two estimates of clay
permeability. Similarly, hydraulic gradients may also be used for comparison.
Figure 2. Varying clay permeability
 Different dispersion coefficients
 Different adsorption rates. BIO1D is an excellent tool for comparing two isotherms, or varying coefficients of
the same isotherm. Figure 3 illustrates a study on varying Freundlich isotherm exponent.
 Different firstorder rates. As a special case, one of the decay rates may be set to zero.
 Different boundary conditions. Three types of boundary conditions with builtin first order degradations are
available. In field situations, boundary conditions are not always clearly understood. Thus the importance of assumptions
made at the boundary may be studied.
Figure 3. Uncoupled simulation option; Varying Freundlich isotherm constant
Interactive Preprocessor
A preprocessor has been built into BIO1D which enables the user to prepare input data interactively. The preparation includes
features such as inputting new data and storing them in a disk file, or reading data from a file and editing them. The preprocessor
has builtin error recovery procedures to forgive most input errors made by a user during interaction.
For the firstorder decay and linear, Freundlich, or Langmuir adsorption isotherms, definitions found in the literature
are not always uniform. The preprocessor provides the user with alternative definitions, and the user may select the one
that is most familiar. Figure 4 illustrates the definitions available for linear isotherm. The user may define the isotherm
in terms of linear isotherm coefficient, distribution coefficient and bulk density, or retardation factor. Many such useful
features may be found throughout the interaction.
Figure 4. BIO1D data preparation: Alternative definitions.
RunTime Options
Taking advantage of the singleuser microcomputer environment, many simulation options are provided at runtime. A runtime
monitor as illustrated in Figure 5 is displayed and updated constantly as the simulation progresses. The user may run the
simulation for a certain time period, monitoring its behavior, and then choose a different set of runtime options for the
rest of the simulation. The options include printing concentrations, cumulative mass balance information, and selecting
plotting intervals. Advanced debugging options such as iteration information, nodal mass balance tables, displacement matrices,
and matrix solver monitors are also available at runtime. These options can be useful when the processes simulated are
highly nonlinear, or if the results of the simulation show unusual behavior.
Figure 5. BIO1D runtime monitor.
The advanced debugging options may also be used by students learning numerical methods. Every step of the nonlinear iterative
solution scheme used in BIO1D may be monitored by the user. The Peclet and Courant stability numbers are displayed automatically
during data preparation, and a stop watch (Figure 5) is activated to measure the CPU time during the simulation. These features
are useful in understanding the effects of varying the input parameters such as, grid spacing, time step size, and convergence
criteria which are associated with the numerical solution.
Graphical Results
Concentration vs. distance at a certain time, or concentration vs. time (or pore volume) at any node may be plotted. Concentration
may be plotted in linear or log scale. Figures 1, 2 and 3 illustrate these options. Plots may be previewed on the screen
and sent to any of the plotters listed under hardware {link}. For comparative studies, hard copy plots from uncoupled simulation
runs (eg., Figures 2 and 3) can be readily used in reports.
Verification Tests
The features available in BIO1D have been tested in a systematic manner. A variety of problems have been selected to test
major options in biodegradation, adsorption, and boundary conditions. The data files for the above problems have also been
carefully prepared to test many of the minor options (grid spacing, plotting, etc.) available in BIO1D. Table 1 shows the
features tested by the problem sets A through F.
Table 1. BIO1D features tested
FEATURES 
PROBLEM SETS 
Advection / Dispersion 
A 
B 
C 
D 
E 
F 
Degradation 
 aerobic
 anaerobic
 firstorder 

B




F
F
F 
Uncoupled simulation 



D 


Adsorption 
 linear
 Freundlich
 Langmuir 

B

C

D

E


Bounday condn. 
 Dirichlet
 Neumann
 Cauchy 
A

B*

C*

D*

E*

F

Solution 
 tridiagonal
 pentadiagonal 
A

B

C

D 
E

F 
Grid 
 uniform
 variable 
A

B

C

D

E

F

Plots 
 C vs. X
 C vs. T
 C vs PV 
A

B

C 
D 
E 
F

Features that are not yet tested may also be identified from this table. A description of each test along with a complete
list of corresponding input and output files of the BIO1D simulations are presented in the BIO1D documentation.
Documentation
The documentation for BIO1D is comprehensive. It is divided into two major parts. The first part covers the theoretical
aspects of BIO1D which include: derivation of the mathematical model; development of the numerical solution; and verification
tests. The second part serves as the User’s Manual for the code. The sections included are: stepbystep installation instructions;
three guided tours to familiarize the user with the data preparation, simulation, and plotting of the results; detailed
input data instructions; interpretation of output; and error conditions and handling.
Hardware
BIO1D runs any PC compatible computer. As it is a DOS program, special configuration files are supplied for running
BIO1D with Windows 2000 or XP. A generic HP LaserJet printer is supported for plotting results.
Availability
BIO1D is available from CertainTech, Inc. Please contact us at sales@certaintech.com.

