Numerical Modeling of

Biodegradation
Analytical and Numerical Methods
By
Philip B. Bedient
 Modeling Biodegradation
• Three main methods for modeling biodegradation

 Monod kinetics

 First-order decay

 Instantaneous reaction

• Methods can be used where appropriate for

aerobic, anaerobic, hydrocarbon, or chlorinated
• Region 1:
Lag phase
Microbial Growth
 microbes are adjusting to
the new substrate (food
source)

• Region 2
Exponential growth phase,
 microbes have acclimated
to the conditions

• Region 3 log [X]

Stationary phase, 1 2 3 4
 limiting substrate or
electron acceptor limits the
growth rate

• Region 4
Decay phase,
 substrate supply has been
exhausted
Time
 Monod Kinetics
• The rate of biodegradation or biotransformation is
generally the focus of environmental studies
• Microbial growth and substrate consumption rates
have often been described using ‘Monod kinetics’
dC max CM t
 
dt KC  C
• C is the substrate concentration [mg/L]
• Mt is the biomass concentration [mg/ L]
• µmax is the maximum substrate utilization rate [sec-1]
• KC is the half-saturation coefficient [mg/L]
 Monod Kinetics dC
  max Mt
• First-order region, dt
C << KC the equation can
be approximated by Zero-order
region
exponential decay
–dC
(C = C0e–kt) dt
First-
order
region
• Center region, Monod
kinetics must be used

• Zero-order region,
C >> KC, the equation C
can be approximated by dC kCMt
linear decay
 
dt KC
(C = C0 – kt)
 Modeling Monod Kinetics
• Reduction of concentration expressed as:

 C 
C  Mt max  t
 K c  C 
• Mt = total microbial concentration
• µmax = maximum contaminant utilization rate per mass
of microorganisms
• KC = contaminant half-saturation constant
• ∆t = model time step size
• C = concentration of contaminant
 Bioplume II Equation - Monod
• Including the previous equation for reaction
results in this advection-dispersion-reaction
equation:

C  C
2
C  C 
 Dx 2  v  Mt  max  
t x x Kc  C 
 Multi-Species Monod Kinetics
• For multiple species, one must track the species
together, and the rate is dependent on the
concentrations of both species
 C  O 
C  Mt max   t

Kc  C  Ko  O 
 C  O 
O  Mt max F   t
 Kc  CKo  O 
 Multi-Species
• Adding these equations to the advection-
dispersion equation results in one equation for
each component (including microbes)

C 1   C  O 
  (DC  vC)  Mt max 
Rc Kc  C  
=
t Rc Ko  O 
O  C  O 
=   (DO  vO)  Mt  max F  K  O 
t  c
K  C  o 
M s 1  C  O  k cY (OC)
=   (DMs - vMs )  M smax Y      bM s
t Rm Kc  C  Ko  O  Rm

• BIOPLUME III doesn’t model microbes

 Modeling First-Order Decay
• Cn+1 = Cn e–k∆t
• Generally assumes nothing about limiting
substrates or electron acceptors
• Degradation rate is proportional to the
concentration
• Generally used as a fitting parameter,
encompassing a number of uncertain parameters

• BIOPLUME III can limit first-order decay to the

available electron acceptors (this option has bugs)
 Modeling
Instantaneous Biodegradation
• Excess Hydrocarbon: Hn > On/F

• On+1 = 0 Hn+1 = Hn - On/F

• Excess Oxygen: Hn < On/F

• On+1 = On - HnF Hn+1 = 0

• All available substrate is biodegraded, limited only by the

availability of terminal electron acceptors
• First used in BIOPLUME II - 1987
 Sequential Electron Acceptor
Models
• Newer models, such as BIOPLUME III, RT3D,
and SEAM3D allow a sequential process - 1998
• After O2 is depleted, begin using NO3–
• Continue down the list in this order

O2 ––> NO3– ––> Fe3+ ––> SO42– ––> CO2

 Superposition of Components
• Electron donor and acceptor are each modeled
separately (advection/dispersion/sorption)

• The reaction step is performed on the resulting

plumes

• Each cell is treated independently

• Technique is called Operator Splitting

 Principle of Superposition
Initial Hydrocarbon
Concentration Reduced Hydrocarbon
Concentration

+ =
Background D.O.

Oxygen Reduced Oxygen

Depletion Concentration
Oxygen Utilization of Substrates
• Benzene: C6H6 + 7.5O2 ––> 6CO2 + 3H2O
• Stoichiometric ratio (F) of oxygen to benzene

7.5 molO 2 32 mgO 2 1 molC 6 H6

F
1 molC 6 H 6 1 molO 2 (12  6 1 6) mgC 6 H 6

F  3.07 mgO 2 mgC 6 H 6

• Each mg/L of benzene consumes 3.07 mg/L of O2

 Biodegradation in BIOPLUME II
A A' H
Without Oxygen

With
Zone of Treatment Oxygen
Zone of Reduced
Hydrocarbon Concentrations A A'

B Background D.O. B' D.O.

Background D.O.

Depleted
Oxygen
Zone of Reduced B B'
Zone of Oxygen
Depletion Oxygen Concentration
Initial Contaminant Plume

Concentration
1.00e + 3 x Injection Well
xx x 8.89e + 2 o Production Well
7.78e + 2
6.67e + 2
2.22e + 2
oo o 1.11e + 2
0.00e + 0

Values represent upper limits

for corresponding color.
 Model Parameters
Grid Size 20 x 20 cells
Cell Size 50 ft x 50 ft
Transmissivity 0.002 ft2/sec
Thickness 10 ft
Hydraulic Gradient .001 ft/ft
Longitudinal Dispersivity 10 ft
Transverse Dispersivity 3 ft
Effective Porosity 0.3
 Biodegrading Plume
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 11 1 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 6 123 6 0 0 0 0 0 0 0 0 0 0 0 0
0 0 1 38 1000 38 1 0 0 0 0 0 0 0 0 0 0 0
0 0 4 71 831 71 4 0 0 0 0 1 1 1 1 1 0 0
0 0 7 97 710 97 7 0 0 0 0 2 3 4 3 2 0 0
0 1 9 104 600 104 9 1 0 0 0 3 7 12 8 3 1 0
0 0 9 90 449 90 9 0 0 0 0 4 11 20 13 5 0 0
0 0 5 54 285 54 5 0 0 0 0 2 8 11 8 2 0 0
0 0 2 19 109 19 2 0 0 0 0 0 2 4 2 0 0 0
0 0 0 4 24 4 0 0 0 0 0 0 0 1 0 0 0 0
0 0 0 1 4 1 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Original Plume Concentration Plume after two years

Extraction Only - No Added O2
 Plume Concentrations
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 2 6 2 0 0 0 0 0 0 0 0 0 0 0 0
0 0 3 7 15 8 3 0 0 0 0 1 2 9 3 1 0 0
0 0 2 6 10 7 1 0 0 0 0 1 5 8 5 1 0 0
0 0 0 1 3 1 0 0 0 0 0 0 1 3 1 0 0 0
0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Plume after two years Plume after two years

O2 Injected at 20 mg/L O2 Injected at 40 mg/L
 Biodegradation Models
• Bioscreen -GSI
• Biochlor - GSI
• BIOPLUME II and III - Bedient & Rifai
• RT3D - Clement
• MT3D MS
• SEAM 3D
 Biodegradation Models
Name Dimension Description Author
X 1 aerobic, microcolony, Monod Molz, et al. (1986)
BIOPLUME 1 aerobic, Monod Borden, et al. (1986)
X 1 analytical f ir st-order Domenico (1987)
BIOID 1 aerobic and anaerobic, Monod Srinivasan and Mercer (1988)
X 1 cometabolic, Monod Semprini and McCarty (1991)
aerobic, anaerobic, nutrient
X 1 Widdowson, et al. (1988)
limitations, microcolony, Monod
aerobic, cometabolic, multiple
X 1 Celia, et al. (1989)
substrates, f ermentative, Monod
BIOSCREEN 1 analytical f ir st-order, instantaneous Newell, et al. (1996)
BIOCHLOR 1 analytical Aziz, et al. (1999)
BIOPLUME II 2 aerobic, instantaneous Rifai, et al. (1988)
X 2 Monod MacQuarrie, et al. (1990)
X 2 denitrification Kinzelbach, et al. (1991)
X 2 Monod, biofilm Odencrantz, et al. (1990)
BIOPLUME III 2 aerobic and anaerobic Rifai, et al. (1997)
RT3D 3 aerobic and anaerobic Clement (1998)
 Dehalogenation of PCE

• PCE (perchloroethylene Cl
C C
Cl
PCE
or tetrachloroethylene) Cl Cl

Cl H
• TCE (trichloroethylene) C C TCE
Cl Cl

• DCE (cis-, trans-, H H Cl H Cl H

and Cl
C C
Cl H
C C
Cl Cl
C C
H
DCE's

1,1-dichloroethylene
H H

• VC (vinyl chloride)
C C VC
Cl H
 Dehalogenation
• Dehalogenation refers to the process of stripping
halogens (generally Chlorine) from an organic
molecule
• Dehalogenation is generally an anaerobic process,
and is often referred to as reductive dechlorination
R–Cl + 2e– + H+ ––> R–H + Cl–
• Can occur via dehalorespiration or cometabolism
• Some rare cases show cometabolic dechlorination
in an aerobic environment
 Chlorinated Hydrocarbons
• Multiple pathways
• Electron donor – similar to hydrocarbons
• Electron acceptor – depends on human-added electron
donor
• Cometabolic
• Mechanisms hard to define
• First-order decay often used due to uncertainties in
mechanism
 Modeling Dechlorination
• Few models specifically designed to simulate
dechlorination
• Some general models can accommodate
dechlorination
• Dechlorination is generally modeled as a first-
order biodegradation process
• Often, the first dechlorination step results in a
second compound that must also be dechlorinated
 Sequential Dechlorination
• Models the series of dechlorination steps between
a parent compound and a non-hazardous product
• Each compound will have a unique decay constant
• For example, the reductive dechlorination of PCE
requires at least four constants
• PCE –k1–> TCE
• TCE –k2–> DCE
• DCE –k3–> VC
• VC –k4–> Ethene