Advances in Water Resources 32 (2009) 1336–1351

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Advances in Water Resources

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Upscaling of the advection–diffusion–reaction equation with Monod reaction

F. Heße a, F.A. Radu a,b,*, M. Thullner c, S. Attinger a,b
a
Department of Computational Hydrosystems, UFZ-Helmholtz Center for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany
b
Institute of Geoscience, University of Jena, Wöllnitzerstr. 7, D-07749 Jena, Germany
c
Department of Environmental Microbiology, UFZ-Helmholtz Center for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany

a r t i c l e i n f o a b s t r a c t

Article history: The need for reliable models for the reactive transport of contaminants in the subsurface is well recog-
Received 11 September 2008 nized. The predictive power of these models is determined by the accurate description of bioavailability
Received in revised form 27 May 2009 of contaminants to microorganisms in porous media. Among many other factors influencing bioavailabil-
Accepted 28 May 2009
ity, diffusive mass transfer processes may limit the substrate availability at the pore scale and hence
Available online 6 June 2009
reduce the effective degradation rate considerably. In this study we used a combination of analytical
and numerical methods to upscale surface catalyzed Monod-type reaction rates within a single pore,
Keywords:
to obtain effective rate expression at a larger scale. Results show that in the upscaled description Monod
Upscaling
Pore-scale processes
kinetics lead to a concentration dependent transition between a reaction and diffusion-limited regime.
Monod reaction Strictly, the effective rate repression does not follow Monod-type kinetics. However, we can present
Effective parameters appropriate effective parameters relations, which provide an acceptable approximation of degradation
Bioavailability dynamics using an effective Monod-type reaction rate.
Ó 2009 Elsevier Ltd. All rights reserved.

1. Introduction tions are – among many other aspects – challenged by finding an

Anthropogenic groundwater contamination is a severe problem
in many industrialized countries. Ex situ remediation means, such
as pump-and-treat systems, are often neither technically nor finan-
cially feasible due to the size of the contaminated sites. For many
organic carbon compounds in situ bioremediation, either passive
or enhanced, has shown to be a cost-effective alternative. En-
hanced bioremediation uses the ability of subsurface microorgan-
isms to degrade organic contaminants [55].
The biodegradation of groundwater contaminants has been
extensively investigated, both in the field and in the laboratory.
However, due to the complex interplay of microbial, chemical
and physical processes occurring in groundwater, a direct quantifi-
cation of in situ biodegradation is often hard to achieve. In order to
judge the effectiveness of biodegradation on contaminated sites
the experimental characterization is often combined with numer-
ical simulations using reactive transport models (e.g.
[36,4,10,40]). Yet, their predictive power is restricted by the accu-
racy of the implemented process descriptions.
The extrapolation of laboratory results on microbial degrada-
tion processes to in situ biodegradation processes in the field and
the incorporation of these processes in reactive transport simula-
* Corresponding author. Address: Department of Computational Hydrosystems,
UFZ-Helmholtz Center for Environmental Research, Permoserstr. 15, D-04318
Leipzig, Germany.
E-mail address: florin.radu@ufz.de (F.A. Radu).
adequate description of the bioavailability of the substrate
[20,51]. Factors controlling the bioavailability include the phys-
ico-chemical structure of the substrate [8,22], physical occlusion
by small pores [32,58,27] or mineral coatings [45], and macro-
scopic mixing processes [12,50]. Most importantly, the bioavail-
ability of a dissolved contaminant in porous media is highly
affected by mass transfer processes at the pore or sub-pore scale.
The activity of microorganisms is controlled by substrate concen-
trations in their immediate vicinity [19,47,23]. In porous media
microorganisms primarily reside on the surface of the solid matrix
(Fig. 1, right part). Microscopic transport processes within each
pore must provide the supply of the contaminant from the bulk
pore water to the location of the microbial cells. This transport lim-
its bioavailability, besides any of the other processes mentioned
above, which might impose an additional restriction to bioavaila-
bilty. As a consequence, the bioavailable concentration, to which
microorganisms are exposed to, may differ considerably from the
average concentration measured at the macroscale [43,33].
To understand the limitations of macroscopic degradation rates
by such pore-scale mass fluxes, research has focused on simple
representations of the pore space [3,28,30]. Looking at the pore
scale it can be shown that the effective reaction rate can be signif-
icantly reduced when pore-scale diffusion becomes a limiting fac-
tor for bioavailability [3,9,16,25,34]. However, the reaction rate in
most of these studies was assumed to follow first-order kinetics
with respect to the concentration of the degraded species. In case
of microbially catalyzed reaction first-order kinetics valid for low

0309-1708/$ - see front matter Ó 2009 Elsevier Ltd. All rights reserved.
doi:10.1016/j.advwatres.2009.05.009
 F. Heße et al. / Advances in Water Resources 32 (2009) 1336–1351 1337

Nomenclature

Latin Cf boundary of X with the fluid

A amplitude of W Cif inlet of Xp
c concentration of the solute Cof outlet of Xp
c0 concentration at Cif Cs boundary of X with the solid
cbio bioavailable concentration U2 Thiele modulus
cref reference concentration W transversal part of solution c
C macroscale concentration k eigenvalue of W
D microscale diffusion coefficient sij coupling constant between mode i and j
Km half-saturation constant X whole domain
Lref reference length scale Xp pore domain
L microscale differential operator
n unit vector normal to Cs Miscellaneous
Pe Péclet number hi averaged quantity
qmax maximum conversion rate e deviation quantity
R general reaction rate ^ scaled quantity
v microscale fluid velocity eff upscaled parameter
V pore-scale average velocity eqv constant approximation for eff
i ith mode
Greek
g scaling coefficient

concentrations only [6]. In reality, the biodegradation of organic
contaminants often follows Monod-type kinetics [35]. Recently,
Wood et al. [56] have performed investigations assuming a
Monod-type reaction rate within a single pore. They derived
upscaling rules in the cases of either very low or very high sub-
strate concentration. However, by comparing their upscaled equa-
tion with numerical simulations in a complex array of pores they
got a mismatch for concentrations in the range of the Monod-
half-saturation constant.
In this work we use a channel geometry comparable to [25,3]
but consider a Monod-type reaction rate for the reactive surface
of the pore. We chose this simple geometry in order to be able to
make use of analytical tools in the upscaling process. With our ap-
proach we aim to verify: (i) whether the upscaled reaction rate
laws can be sufficiently described by Monod-type kinetics, and
whether the problems reported by Wood et al. can be resolved
and if yes: (ii) how the parameters of such macroscopic Monod
kinetics can be linked to microscopic reaction rate parameters that
are valid at the local scale. The results obtained in this study for
pore-scale systems may provide the base for interpreting results
from laboratory column experiments. With further upscaling steps
and additionally taking into account large scale heterogeneities,
our results can be applied for describing biodegradation efficiency
at the field scale.
In the following sections of this paper we will first introduce the
conceptual approach used in this study including the underlying
equations, the geometric representation of the pore system, and
the applied numerical schemes and upscaling concepts (Section
2). This is followed by the description of the analytical tools used
to obtain explicit solutions for the microscale problems and effec-
tive equations for the macroscale continuum (Section 3). Analytical
and numerical results are presented and discussed in Section 4 and
final conclusions for the scaling behavior of bioavailabilty con-
trolled Monod-type reactions are given in Section 5.
2. Conceptual model
This section describes the conceptual approach used in this
study. This includes the governing equations describing transport
and degradation of a reactive species as well as the pore geometry
these equations are applied to. Furthermore, the applied upscaling
concepts and numerical schemes are introduced.
2.1. Mathematical description
In the following we will derive the mathematical model for
reactive transport at the pore scale. Starting with a general descrip-
tion we will introduce appropriate scaling units and apply a few
simplifications before stating the definite mathematical
description.
The scale of interest is that of a single pore (Fig. 2). All flow and
transport processes are taking place in the fluid phase X, only. For a
single pore, the boundaries of the fluid phase domain can be sepa-
rated into a fluid–solid interface Cs and a fluid–fluid interface Cf .

Continuum-Scale Pore-Scale Subpore-Scale

Fig. 1. Schematic of the complexity of the subsurface and the variety the different scales involved.
1338 F. Heße et al. / Advances in Water Resources 32 (2009) 1336–1351

Using the definitions given by Eqs. (2)–(4) we write Eqs. (1a)

and (1b)
s @ L2 @2 @2
s o ~ ^c ¼ y;ref
^c þ Per  v 2
^c þ ^c in Xp ; ð5aÞ
f
i
p f @^t Lx;ref @ ^x2 ^2
@y
U2 ^c
r^c  n ¼  on Cs : ð5bÞ
bm
1 þ ^c= K

Fig. 2. Schematic of the computational domain. Eqs. (1c) and (1d) exhibit no significant changes using non-dimen-
sional variables. In the remainder of this publication, we will use
the same symbols for dimensional as well as for non-dimensional
The latter can be further separated into the inlet boundary Cif and variables. The occurrence of the Péclet number and the Thiele mod-
the outlet boundary Cof , each of them described by different bound- ulus in the equations will be the indicator whether dimensional or
ary conditions. In a single pore, the fate of a single species with non-dimensional variables are considered.
concentration c is described by (a) the advective diffusive transport Before stating the definite system of equations we will apply
in the fluid phase, (b) microbial degradation following Monod-type three simplifications justified by the scope of the study. First, we
kinetics at the fluid–solid interface, (c) a constant concentration will drop the time derivative, since we are mainly interested in
along the inlet boundary, and (d) a zero-concentration gradient the steady state solution. Second, we restrict our analysis to travel
at the outlet boundary paths of the contaminant with L2y;ref  L2x;ref . This is corresponding
@ to a flow path of the contaminant being effectively longer along
c þ Vr  v
~ c ¼ DDc in Xp ; ð1aÞ than perpendicular to the flow field. Rephrasing this constraint
@t
q c as L2y;ref =L2x;ref  1 shows that we can neglect the longitudinal diffu-
Drc  n ¼  max on Cs ; ð1bÞ sion in Eq. (5a). The assumption is for example supported by the
Km þ c
findings of Liedl et al. [31] who showed that the longitudinal dis-
c ¼ c0 on Cif ; ð1cÞ
persivity has practically no impact on the steady state plume
rc  n ¼ 0 on Cof : ð1dÞ length. The last simplification regards the velocity field, which
Here, the water flux v is given as v ¼ V v ~ , with V being the pore- has only a component in the direction along the flow path. With
scale average velocity and v ~ the rescaled velocity, D is the molecular these simplifications and using the inlet boundary concentration
diffusivity, n is the outer unit normal, qmax is the maximum conver- as a reference (cref ¼ c0 ) the pore system is described by
sion rate and K m is the half-saturation constant. The implementa- @ @2
tion of the reaction rate in Eq. (1b) assumes the microorganisms Pef ðyÞ c ¼ 2c in Xp ; ð6aÞ
@x @y
to be localized at the solid liquid interface in a thin biofilm being
constant in space and time. c ¼ 1 on Cif ; ð6bÞ
Eqs. (1a)–(1c) were transferred into a non-dimensional form U2 c
using reference lengths Lx;ref and Ly;ref as well as a reference concen-
rc  n ¼  on Cs : ð6cÞ
1 þ c=K m
tration cref (values for Lx;ref ; Ly; ref and cref are addressed in Section
2.2). This allows for the definition of the following dimensionless Eqs. 6a, 6b and 6c were used to perform all analysis presented in the
variables following sections. The coefficient function f ðyÞ in Eq. (6a) is a
placeholder for an arbitrary velocity profile. Note that for first-order
x y c b m ¼ K m ; and ^t ¼ Dt : reaction rates or c  K m Eq. (6c) reads rc  n ¼ U2 c.
^x ¼ ^¼
; y ; ^c ¼ ; K ð2Þ
Lx;ref Ly;ref cref cref L2y;ref
2.2. Geometrical description
Furthermore, two-dimensionless quantities are used: the Péclet
number and the Thiele modulus. The Péclet number The pore system to which we apply Eqs. 6a, 6b and 6c is repre-
VL2y;ref sented by a channel extending in x- and y-direction (Fig. 3). A sin-
Pe ¼ ð3Þ gle pore with such a geometry will lead to a porous medium
DLx;ref
consisting of a compound of capillary tubes [15]. Compared to
indicates whether the advective or the diffusive transport is domi- other two-dimensional arrays of single pores (e.g. [28,30,17]) this
nant at the scale of interest. High Péclet numbers mean advection represents a simplification of the pore geometry which is necessary
dominates diffusion and vice versa. At the pore scale of groundwa- to obtain analytical solutions in closed form expressions. Such a
ter systems, typical values of Ly;ref < 1 mm and V < 1 m=d result in single pore system, although simple, has been proven to give
values of Pe  10 or below. This is in contrast to the continuum appropriate indications on the relation between pore geometry,
scale were Péclet numbers can be considerably higher. The Thiele diffusion and reaction in general ([26,38]) and the geometry used
modulus [49]
qmax Ly;ref
U2 ¼ ð4Þ y
DK m
compares the dynamics of the reactive consumption and the diffu-
Reaction L y,ref
sive flux. This dimensionless quantity is related to the Damköhler
numbers Da [14], commonly used in chemical engineering to relate & x
the kinetics of reactions to mass transfer processes [18]. The Thiele Contaminant p

modulus can be used to describe the bioavailabilty of a substrate

(e.g. [37,11]). In pore-scale systems U2 as well as K m can vary over
several orders of magnitude. In our work we will focus on values
comprising the transition from the reaction-limited to the diffu- Fig. 3. Schematic sketch of the semi-infinite channel used to describe processes in a
sion-limited as well as from a first-order to a zeroth-order regime. single pore.
 F. Heße et al. / Advances in Water Resources 32 (2009) 1336–1351
here has previously been used by other authors to describe reactive
processes in porous media (e.g. [25,34,53]). Results obtained for
single pores can be transferred to more realistic porous media rep-
resentations using the ratio of the reactive surface and the free vol-
ume as a shape factor [56].
The reference length Ly;ref is chosen to be half the width of the
pore resulting in a pore space Xp given by the dimensionless coordi-
nate ranges of 0 < x < 1 and 1 < y < 1. The reference length Lx;ref
is the characteristic length for which the concentration should be
determined. As described in Eq. (6b), the fixed concentration con-
sidered at the inlet boundary is used as reference concentration cref .
The pore space, the boundaries and thus all obtained solutions
of Eqs. 6a, 6b and 6c are symmetric with respect to the x-axis
(Fig. 3). For this reason the domain was split along the y-axis. All
analytical and numerical solutions were calculated for 0 < y < 1,
considering rc  n ¼ 0 as boundary condition at y ¼ 0.
2.3. Scenarios considered for calculations
In Eq. (6a) the form of the coefficient function regarding the
velocity profile was not further specified. For the given pore geom-
etry a parabolic profile is the most realistic velocity distribution
[48,1]. The focus of this study is on the scaling behavior of
Monod-type reaction kinetics. However, in order to verify the re-
sults of our approach with those presented and discussed in the lit-
erature for first-order reaction rates and uniform velocity profiles
[25], we here consider the same in form of scenario I. Next to the
most simple (scenario I) and the most realistic scenario (scenario
IV), two further scenarios (II and III) of intermediate complexity
were considered (Fig. 4). In scenarios II and III the remaining com-
binations of reaction kinetics and velocity profile were addressed
to investigate the influence of each individual feature on the ob-
tained results.
2.4. Upscaling of the pore-scale processes
The focus of this study is to use upscaling methods to obtain an
effective one-dimensional representation of the system described
by Eq. (6). Generally the purpose of upscaling is to find an effective
description of the process of interest on a coarse level by starting
with a well defined representation of the process on a fine level.
The most common methods for upscaling in subsurface hydrology
[44,57] are homogenization [2,39] and volume averaging [54].
To arrive at an effective representation we have to average the
process over the y-axis (Fig. 3). The scheme of the upscaling pro-
cess used in this study is outlined in Fig. 5.
Starting point of the analysis is the system of two-dimensional
partial differential equations as given by Eqs. 6a, 6b and 6c. The
most ‘straight forward’ analysis is first solving these equations
I II
f irst − order reaction
uni f orm velocity f ield
III
Monod − type reaction
uni f orm velocity f ield
Fig. 4. Schematic of the different scenarios (I–IV) investigated in this study.
1339
either numerically or analytically (left side of Fig. 5). The resulting
two-dimensional concentration distribution is then averaged over
the width of the pore (i.e. the y-axis; Fig. 3) providing a one-dimen-
sional concentration profile along the length of the pore. The de-
rived concentration profiles were used as references for an
alternative approach where the steps of analytical solution and
averaging are permuted (right side of Fig. 5). In the latter approach,
first the averaging over the y-axis results in a new one-dimensional
effective differential operator Leff with a reduced complexity but
new effective parameters (see Section 3). The evaluation of these
parameters is the main part of the analytical upscaling process.
After that, the upscaled parameters are used to calculate an effec-
tive solution (one-dimensional concentration profile along the
length of the pore). A comparison between the solutions is a good
measure for the accuracy of the effective parameters (Fig. 5).
2.5. Numerical scheme
To support the analytically derived results numerical solutions
for Eqs. 6a, 6b and 6c were calculated (see Fig. 5). These numerical
simulations were performed using the software platform UG
(‘Unstructured Grids’, [5]). Steady state results were obtained by
simulating a transient problem with arbitrary initial conditions un-
til steady state was reached. The time derivative is discretized by
the one-step implicit Euler method. In order to ensure the local
mass conservation, the mixed finite element method is applied
for the spatial discretization. More precisely, the lowest order finite
elements of Raviart–Thomas type are used for the approximation
of the fluxes and piecewise constants for the concentrations. The
resulting algebraic system of equations is hybridized by adding La-
grange multipliers on the edges according to Radu et al. [41,42].
Then the nonlinear problem is linearized by a damped Newton
method and the resulting linear systems are solved by a multigrid
algorithm.
3. Upscaling and analytical methods
In this section we present (i) analytical solutions for the coupled
transport degradation problem in two-dimensions and the subse-
quent averaging over the y-axes, as well as (ii) one-dimensional
effective equations obtained by the upscaling theory. Both ap-
proaches are first applied for first-order reaction rates and after-
wards modified to solve the case of a Monod-type reaction rate.
3.1. First-order reaction rate
Assuming a first-order reaction rate, Eq. (6c) can be written as
rc  n ¼ U2 cbio ð7Þ
f irst − order reaction
parabolic velocity f ield
IV
Monod − type reaction
parabolic velocity f ield
1340 F. Heße et al. / Advances in Water Resources 32 (2009) 1336–1351

Fig. 5. Schematic of the upscaling process.

introducing cbio as cðx; yÞjy¼1 or the concentration available to the For a comprehensive derivation of this solution and the calculation
surface bound microorganisms. To solve the resulting system of of the coefficients Ai and ki see Appendix A.2. The y-averaged solu-
equations we assume the concentration to be given as an infinite se- tion can be written as
quence of modes
X
N k2
i
2
4 sin ðki Þ
X
1 CðxÞ ¼ e Pe x : ð12Þ
cðx; yÞ ¼ C i ðxÞWi ðyÞ: ð8Þ i¼1
ki ðsinð2ki Þ þ 2ki Þ
i¼1
From Eq. (11) it can be concluded, that only the first few modes are
This ansatz separates every mode into a longitudinal and a transver- required to obtain a good approximation of CðxÞ. Since the elements
sal component (relative to the flow direction), under the assump- of fki giP1 are monotonously increasing (see Fig. 18) the respective
tion that the velocity field is constant along the longitudinal modes exhibit a steeper exponential decay. Furthermore, the coeffi-
direction. Thus both sides of Eq. (8) are not coupled by the coeffi- cients Ai in Eq. (11) are decreasing with increasing i (see Eq. (36)).
cient function f ðyÞ from Eq. (6a). A comprehensive discussion on Consequently, the contribution of higher modes to CðxÞ is
the solution of Eq. (8) can be found in the Appendix A.1. As a result insignificant.
we get the following expression
3.1.1.2. Effective equation. Details on the direct upscaling of the sys-
@
T C ¼ KC ð9Þ tem given by Eqs. 6a, 6b and 6c can be found in the Appendix A.2.
@x As a result of this procedure we get the following differential
which can be rearranged to equation:

@ @ U2
C ¼ T1 KC ¼ CC: ð10Þ CðxÞ ¼  eff CðxÞ ð13Þ
@x @x Pe
The entries of the unknown vector C are the longitudinal modes C i which exhibits a first-order dependency on the y-averaged concen-
of the concentration c. The entries of the system matrix C depend on tration. The new effective coefficient U2eff will be discussed in Sec-
the velocity field f ðyÞ. In this form Eq. (10) represents a system of tion 4.1 in more detail.
linear ordinary differential equations. In the following subsections
we will solve this system for the cases of a uniform and a parabolic 3.1.2. Parabolic velocity field
velocity field. For a parabolic velocity field the coefficient function in Eq. (6a)
is now given by f ðyÞ ¼ 1:5ð1  y2 Þ. The details of the determination
3.1.1. Uniform velocity field of the analytical solution as well as the effective equation are given
For a uniform velocity field the coefficient function in Eq. (6a) is in Appendix A.3.
given by f ðyÞ ¼ 1.
3.1.2.1. Analytical solution. For this velocity field the different
3.1.1.1. Analytical solution. For this velocity field the system matrix modes of the unknown vector C are now coupled and have to be
C is diagonal so the single longitudinal modes are decoupled diagonalized before they can be solved in analogy to Eq. (11). Con-
sequently we get
sinðki Þ k2i x
C i ðxÞ ¼ Ai e Pe : ð11Þ wi ðxÞ ¼ wi ð0Þedii x ; ð14Þ
ki
 F. Heße et al. / Advances in Water Resources 32 (2009) 1336–1351 1341

where dii are the entries of the diagonalized Matrix C from Eq. (10) convergence of the iteration scheme, we see it numerically. More-
and the vector of the initial conditions is wð0Þ ¼ G1 Cð0Þ. The re- over, for all investigated parameter settings we see a good agree-
quired solution is then found by re-transforming the solution of ment between the semi-analytical solution and the numerically
Eq. (14). calculated solution (see Section 4).

3.1.2.2. Effective equation. For a parabolic velocity field we get an 3.2.1.2. Effective equation. The direct upscaling described above for
ordinary, second order differential equation for the first mode of first-order reaction rates is now applied using Eq. (6b) instead of
the concentration (6a). This leads to

@ @2 @ U2 cbio
v eff C 1 ðxÞ ¼ Deff 2 C 1 ðxÞ þ Reff C 1 ðxÞ ð15Þ Pe C¼ : ð21Þ
@x @x @x 1 þ cbio =K m
In comparison to Eq. (13) new transport parameters v eff and Deff are Furthermore, we introduce a new coefficient function
introduced. Since all quantities in Eq. (15) are non-dimensionalized
C
these effective parameters represent the ratio between the micro- K m;eff ¼ Km: ð22Þ
scale and the physically effective values. The transport parameters cbio
can be determined by solving Eq. (46) With this new effective half-saturation constant and the effective
Thiele modulus U2eff , given in analogy to Eq. (52), we obtain
k21
v eff ¼ s11 þ s22 ; ð16aÞ
k22 @ U2eff C
Pe C¼ : ð23Þ
Pe @x 1 þ C=K m;eff
Deff ¼ ðs21 s12  s11 s22 Þ and ð16bÞ
k22 Both effective coefficient functions U2eff and K m;eff are scaled by the
k21 same scaling factor
Reff ¼  : ð16cÞ
Pe cbio
g¼ ; ð24Þ
Here sij are the entries of the matrix T from Eq. (9). Note that the C
representation of the effective parameters is arbitrary. The present which is the ratio of the bioavailable concentration cbio and the y-
form has been chosen such that Reff is a good approximation of the averaged or upscaled concentration C. Using Eq. (24), we can re-
reaction rate in the former scenario (see Eq. (47)). write Eq. (23) to obtain an analytical expression of the governing
differential equation for the upscaled concentration C
3.2. Monod-type reaction rate
@ U2 C
Pe C¼ : ð25Þ
For Monod-type reaction rates given by Eq. (6c) the coefficients @x 1=g þ C=K m
ki ðxÞ are now x-dependent so Eq. (10) must be modified
If the coefficients U2eff and K m;eff are constant and if Cð0Þ ¼ 1 is used
@ as boundary condition, the analytical solution of Eq. (23) is given by
C ¼ CðxÞC: ð17Þ
@x 0 U2
1
1PeK eff x
Further details on the calculations are again given in the Appendix Be m;eff
C
C ¼ K m;eff LambertW @ A: ð26Þ
A.4. The solution of Eq. (17) depends on the velocity field f ðyÞ and is K m;eff
in the following discussed in analogy to Section 3.1.
The function LambertWðzÞ is the solution of z ¼ wew (see [13])
3.2.1. Uniform velocity field which has already been used in the context of microbial reaction
3.2.1.1. Analytical solution. As mentioned above in the case of a uni- kinetics (e.g. [46,21]). Comparing Eq. (26) to the analytical or
form velocity field all modes in Eq. (10) are decoupled. Therefore, numerical solutions of the two-dimensional problem allows to ob-
each single mode C i ðxÞ is given by the differential equation tain direct estimates for the effective parameters Ueff and K m;eff .
@
C i ðxÞ ¼ cii C i ðxÞ: ð18Þ 3.2.2. Parabolic velocity field
@x
3.2.2.1. Analytical solution. Because of the x-dependency of the
Here cii are the respective entries of CðxÞ from Eq. (17). Due to the x- coefficients ki ðxÞ, Eq. (19) has to be modified in analogy to Eq. (11):
dependency of the coefficient function we have to modify Eq. (11)
to C0 ¼ CðxÞC ¼ GðxÞDðxÞG1 ðxÞC
Rx G1 ðxÞC0 ¼ DðxÞG1 ðxÞC
sinðki ð0ÞÞ  cii ðx0 Þ dx0
C i ðxÞ ¼ Ai ð0Þ e 0 : ð19Þ
ki ð0Þ w0 ¼ DðxÞw:
This leads to the y-averaged solution for the concentration By decoupling the system we have arrived at a form comparable to
Rx Eq. (17). The analytical solution in analogy to Eq. (19) is now
X
N  c ðx0 Þ dx0 Rx
4 sinðki ð0ÞÞ sinðki ðxÞÞe 0 ii  dii ðx0 Þdx0
CðxÞ ¼ pffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi pffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi : wi ðxÞ ¼ wi ð0Þe 0 : ð27Þ
i¼1 ki ð0Þki ðxÞ sinð2ki ð0ÞÞ þ 2ki ð0Þ sinð2ki ðxÞÞ þ 2ki ðxÞ
The required solution is found by re-transforming the solution of
ð20Þ
Eq. (27).
Because of the nonlinear Monod term in Eq. (6c) the coefficients ki
depend on the solution c. Therefore, Eq. (19) has to be solved itera- 3.2.2.2. Effective equation. As in the case of a first-order reaction
tively. Using the solution for first-order reaction rates as an initial rate with a parabolic velocity field, no closed solution for the direct
guess c0 , we solve the system to get the new approximation c1 upscaling exists. However, by applying a similar scheme as used
and iterate the proceedings. The fixed point cI of the iterative loop for first-order reaction rates we can derive an effective equation
is then the required solution. Although, we have not proven the for the first longitudinal mode C 1 ðxÞ
1342 F. Heße et al. / Advances in Water Resources 32 (2009) 1336–1351
@ @2
v eff ðxÞ C 1 ðxÞ ¼ Deff ðxÞ 2 C 1 ðxÞ þ Reff ðxÞC 1 ðxÞ:
@x @x
All coefficients of the effective Eq. (28) are now x-dependent func-
tions. Their evaluation has therefore, become cumbersome for prac-
tical applications compared to the case of a first-order reaction rate.
Nonetheless, these coefficient functions are useful for theoretical
considerations
c11 c12 @ 1
v eff ¼ 1 þ  ;
c22 c22 @x c12
1 analytical
Deff ¼  and
c22
c12 c21 c12 @ c11
Reff ¼ ðc11   Þ:
c22 c22 @x c12
Here the coefficients cij are the entries of the system matrix C of Eq.
(17). The increase in complexity is attributed to the new mixing
terms for the effective velocity v eff and the effective reaction term
Reff . Though the effective dispersion Deff contains no additional
terms all coefficient functions are x-dependent (see also Eq. (23)).
3.3. Synopsis of analytical methods
In Table 1 a summary of the analytical solutions and effective
equations derived from Eqs. 6a, 6b and 6c for the different pore
velocity profiles and reaction rates is given. For first-order reaction
rates our results are comparable to those found in the literature
[25,3]. In the case of the parabolic velocity field the effective equa-
tion only provides results for the first mode. The introduced error
by neglecting higher modes is confined to small values of x.
4. Results and discussion
In this section we first present and discuss the analytical and
numerical results obtained by applying the different approaches
outlined in Fig. 5 for different combinations of velocity fields and
reaction kinetics (see Fig. 4). Calculated values of the effective
parameters used in the one-dimensional upscaled equation, and
the dependency of these parameters on local parameters are eval-
uated. Finally, the applicability of an effective Monod-type reaction
rate is discussed.
4.1. First-order reaction rate with uniform velocity field
The case of a first-order reaction rate with a uniform velocity
field is well studied in the literature [25]. We briefly review and
compare those results vis-à-vis our numerical findings. Calculated
concentration profiles exhibit an exponential decrease along the x-
direction and a cosine-like profile along the y-direction (see Fig. 6
for an arbitrary example). The strong gradient in the y-direction
shows that the transversal diffusion is not fully able to transport
the contaminant from the bulk of the domain to the reactive
boundary at y ¼ 1. The y-averaged profile of the numerical and
the analytical solution match very well in all investigated scenar-
ios, which indicates the soundness of the used numerical scheme.
Calculated values for U2eff , using Eq. (13), show a hyperbolic
behavior with respect to U2 (Fig. 7). Consequently, we can identify
Table 1
Summary of cases and corresponding equations.
First-order reaction rate Monod-type reaction rate
Analytical Effective Analytical
Uniform vel. profile (12) (13) (20)
Parabolic vel. profile (14) (15) (27)
ð28Þ
1
ð29aÞ
numerical
0.8
ð29bÞ
0.6
C
ð29cÞ
0.4
0.2
0
0 1 2 3 4 5
x
Fig. 6. Examples for first-order reaction rate with uniform velocity field. The local
parameters are U2 ¼ 10 and Pe ¼ 2. Top: simulated two-dimensional results.
Bottom: comparison of one-dimensional analytical and numerical solutions.
three different regimes. The first one is termed reaction-limited and
is valid for low U2 values. Here U2eff shows a nearly linear depen-
dency and the scaling unit g is accordingly close to 1. This indicates
a strong coupling between the local and global behavior. Thus, the
reaction in this regime is sufficiently slow for the transversal diffu-
sion to provide the reactive boundary with enough substrate. The
bioavailable concentration cbio is therefore nearly the same as the
y-averaged concentration C. As a result the upscaled reaction rate
is mostly governed by the small scale reaction henceforth the
name. The second regime is called diffusion-limited and is valid
for high values of U2 . Here U2eff asymptotically approaches p2 =4,
corresponding to a linear decrease of g (Fig. 7). In this regime the
reaction is too fast for the transversal diffusion to transport suffi-
cient amounts of substrate to the reactive boundary. As a result,
strong concentration gradients occur along the width of the pore
and the bioavailable concentration is much smaller than the y-
averaged concentration, i.e. cbio  C. The third regime is the transi-
tion zone between the two other regimes and is characterized by
reaction as well as diffusion. Both are limiting processes and con-
trol the upscaled behavior. These findings agree with results from
the literature [25,56], which in case of [56] also shows that, by
applying appropriate scaling steps, the results from a simple geom-
etry can be extended to more realistic scenarios.
4.2. First-order reaction rate with parabolic velocity field
All other boundary conditions assuming the same as in Section
4.1, we discuss the case of a first-order reaction rate with a para-
bolic velocity field. As noted in Section 2, this case has been dis-
cussed in the literature [3], but for different conditions as
considered here. Nevertheless, our results are similar to those pre-
viously reported. Calculated concentration profiles for a parabolic
velocity field (Fig. 8) show only minor differences to profiles ob-
tained for a uniform velocity field. For small values of x, i.e. close
to the inlet, y-averaged concentrations are slightly smaller in the
case of a parabolic velocity field. For increasing x however, higher
concentrations are observed for the parabolic velocity field.
Effective
The differences between the two velocity fields can be attrib-
uted to the occurrence of the effective dispersion coefficient Deff
(23)
(28)
and the effective velocity v eff (see Eq. (15)), which result in a faster
transport of substrate along the length of the pore. The relation
 F. Heße et al. / Advances in Water Resources 32 (2009) 1336–1351 1343

0
10

0
10 −1
10

Φ2eff

η
−2
10

−1 −3
10 0 2
10 0 2
10 10 10 10
2 2
Φ Φ
(a) Development of Φeff
2 .
(b) Development of η.

Fig. 7. Dependency of U2eff and g on U2 in case of a first-order reaction rate with a uniform velocity field. Together with the linear and constant asymptotes representing the
reaction-limited (reached for low values of U2 ) and the diffusion-limited regime (reached for high values of U2 ). The value of U2eff has been evaluated using Eq. (52).

between the effective velocity v eff and U2 depends on the regime abolic velocity fields, yield almost identical results. The effective
governing the overall consumption of the substrate (see Fig. 9a). velocity increases with increasing U2 and eventually saturates for
In the reaction-limited regime the effective velocity is close to 1 high U2 -values in the diffusion-limited regime. In the latter regime
(i.e. equal to the average flow velocity) and both, uniform and par- strong transversal concentration gradients exist and highest con-
centrations correlate with highest flow velocities. As a result the
bulk of the substrate mass is transported faster downstream. The
effective dispersion coefficient Deff remains small compared to
the molecular diffusion coefficient (i.e. Deff < 1) and shows a re-
verse dependency on U2 than observed for v eff (see Fig. 9b). The
steep gradient at the immediate vicinity of pore inlet (Fig. 8) is
caused by the uniform constant concentration distribution used
as boundary condition along the entire inlet. This results in high
substrate concentrations at the reactive pore wall, leading to reac-
tion rates that are not limited by any transversal mass transfer at
1 uniform velocity field the vicinity of the inlet.
parabolic velocity field
0.8 numerical
parabolic velocity field 4.3. Monod-type reaction rate with uniform velocity field
analitical
0.6
For the combination of a Monod-type reaction rate and uniform
C

velocity field analytical and numerical results agree well (Fig. 10)
0.4
which confirms the semi-analytical scheme used for the analysis.
The two-dimensional concentration distribution obtained for the
0.2
Monod-type reaction rate (Fig. 10 top) is qualitatively similar to
the one presented above for a first-order reaction rate (Fig. 6
0
0 1 2 3 4 5 top). The one-dimensional concentration profile, however, shows
x a clear contrast between the two cases (Fig. 10 bottom). At high
y-averaged concentrations C, the concentration decrease is much
Fig. 8. Examples of a first-order reaction rate with a parabolic velocity field. The
local parameters are U2 ¼ 10 and Pe ¼ 2. Top: simulated two-dimensional results. weaker for the Monod-type reaction rate because at these concen-
Bottom: comparison of one-dimensional analytical and numerical solution with trations the upscaled reaction rate approximately follows zeroth-
results for a uniform velocity field. order kinetics. The slope of the concentration profile is therefore

1.5 0.19

0.18
1.4
0.17
1.3 0.16
Deff
eff
v

1.2 0.15

0.14
1.1
0.13

1 −2 0 2
0.12 −2 0 2
10 10 10 10 10 10
2 2
Φ Φ
(a) Development of veff . (b) Development of Deff .

Fig. 9. Dependency on the effective parameters v eff and Deff from U2 for the case of a first-order reaction rate with a uniform velocity field. The values were evaluated by
solving Eqs. (16a) and (16b).
1344 F. Heße et al. / Advances in Water Resources 32 (2009) 1336–1351

ary conditions), the behavior of g is more complex for a Monod-

type reaction rate. The parameter now depends on the y-averaged
concentration C (Fig. 11a) approaching a constant value only for
sufficiently small concentrations (C  K m ; Fig. 11b–d). Besides
the sensitivity of g towards K m , results also vary with U2 . Lower
values of U2 extend the concentration range where g depends on C.
This characteristic allows to distinguish between three different
regimes: an effective zeroth-order, an effective first-order and a
1 transition regime. For an effective zeroth-order regime with
First−order reaction rate
K m  C, g is nearly constant and close to 1. This regime is character-
Monod type reaction rate
0.8 ized by a combination of high concentration values and low values
numerical
Monod type reaction rate of U2 (Fig. 11d in the upper left part). For K m  C we have a transi-
0.6 analytical tion regime were g, and therefore the correlation between the local
C

and the global parameters, shows a strong dependency on C. In the

0.4 third regime, characterized by low concentrations and/or high U2; g
is well approximated by constant values representing an effective
0.2 first-order regime, i.e. K m > C. A comparison of Fig. 11a–d shows
that the behavior of g for high values of U2 is very similar for all
0 K m . Therefore, the results for first-order reaction rates can be
0 1 2 3 4 5
x applied to Monod-type reactions rates with high values of U2 .

Fig. 10. Examples for the Monod-type reaction rate with uniform velocity field. The
local parameters are U2 ¼ 10; Pe ¼ 2 and K m ¼ 0:1. Top: simulated two-dimen-
sional solution. Bottom: comparison of analytical and numerical one-dimensional
solutions with results from a first-order reaction rate.
nearly linear in contrast to the exponential decrease observed for a
first-order reaction rate. Only when C drops to small values (i.e.
C 6 K m ), the upscaled reaction rate approaches a first-order kinet-
ics. This qualitative analysis shows, that in the upscaled equations
the characteristics of a Monod-type reaction rate is preserved.
As in case of a first-order reaction rate the scaling parameter g
describes the coupling between local and global parameters (Eq.
(25)). Compared to the former case, where g does not depend on
C (the slight variations for C  1 are attributed to the inlet bound-
4.4. Monod-type reaction rate with parabolic velocity field
This case is the most complex of the scenarios investigated and
the obtained results (Fig. 12) represent a combination of the effects
discussed in Sections 4.3 and 4.2.
As for a first-order reaction rate, a reaction-limited and a
diffusion-limited regime can be distinguished. The behavior of
the upscaled equation in the reaction-limited case (see Fig. 13a)
can qualitatively be understood as a superposition of the cases de-
scribed in Sections 4.2 and 4.3. Compared to the uniform velocity
field, the concentration decreases relatively sharp in the vicinity
of the inlet but exhibits weaker gradients further downstream of
the pore. These effects have already been discussed in Section

0 0
10 10

5 5

10 10
−1 −1
10 20 10 20

50 50
η

100 100

−2 200 −2 200
10 10
500 500

1000 1000

−3 −3
10 −1 −2 −3
10 −1 −2 −3
10 10 10 10 10 10
C C
(a) Development of η forthefirst-orderreactionrate. (b) Development of η for Km = 1.

0 0
10 10
5
5 10
10 20

20 50
−1 −1
10 10
50 100
η

100
200
−2 200 −2
10 10
500
500

1000 1000

−3 −3
10 −1 −2 −3
10 −1 −2 −3
10 10 10 10 10 10
C C
(c) Development of η for Km = 0.1. (d) Development of η for Km = 0.01.

Fig. 11. Development of g for different U2 and K m for the case of a Monod-type reaction rate with uniform velocity field. The respective value of U2 are tagged along the
curves. The results were evaluated by using Eq. (24).
 F. Heße et al. / Advances in Water Resources 32 (2009) 1336–1351 1345

that g is not constant but a function of concentration (Fig. 11a–d),

we attempt to find a simple constant approximation of g which we
call geqv . To estimate geqv we fitted Eq. (25) to the exact one-dimen-
sional concentration profiles derived from the two-dimensional
solutions.
The results of the fitting procedure reveal that geqv depends on
U2 and K m (Fig. 14). For higher K m results for the Monod-type reac-
tion rate are comparable to those obtained for a first-order reaction
1 rate. Both reaction kinetics show a similar decrease of geqv with
numerical increasing U2 . This indicates a transient shift in the regime from
0.8 analytical reaction-limited (geqv  1) to diffusion-limited (geqv  1). In turn,
for lower K m results for Monod-type reaction rates differ, with
0.6 the reaction-limited regime apparently prevailing longer with
C

increasing U2 . This leads to higher values for geqv compared to

0.4
0.2
0 centration profiles obtained using geqv is given by the differences
0 1 2 3 4 5
x between fitted and exact solutions (Fig. 15). In general, a good
Fig. 12. Examples for the Monod-type reaction rate with a parabolic velocity field.
The local parameters are U2 ¼ 10; K m ¼ 0:1, and Pe ¼ 2. Top: simulated two-
dimensional solution. Bottom: comparison of analytical and numerical one-
dimensional solutions.
4.2. Furthermore, for the Monod-type reaction rate, a zeroth-order
behavior is observed for high concentrations and a first-order
behavior for low concentrations (see Section 4.3). In contrast, for
the diffusion-limited regime the upscaled concentration profiles
show a similar dependency on the velocity field. The results for
the first-order and Monod-type reaction rate are almost identical
(see Fig. 13b). This again emphasizes that the relation between dif-
fusion and reaction rate determines the upscaled behavior.
those obtained for first-order reaction rates. At sufficiently high
U2 results for Monod-type and first-order reaction rates again con-
verge asymptotically to values of geqv  p2 =ð4U2 Þ supporting the
statements made in Section 4.2. The accuracy of the estimated con-
accuracy (errors 6 1%) is only found in the extreme cases of either
low or high values of U2 . The much higher errors found in the tran-
sition regime (errors > 10%) correspond to the values of U2 where
g exhibits the strongest dependency on C (Fig. 11). Furthermore, it
was noticed that errors increase with decreasing K m (results not
shown).
To improve the quality of the estimates obtained by fitting
effective Monod-type reaction rates to the exact solutions we
introduced an additional degree of freedom and fitted Eq. (26).
Considering now both parameters, U2 and K m , to be independent
of each other. The improvement resulted in two new equivalent
parameters, U2eqv and K m;eqv . This procedure gives us significantly
smaller errors in the transition zone between reaction- and diffu-

4.5. Equivalent Monod-type parameters

0
10
Results presented in Section 4.3 show that the coupling between
the local and global coefficients is concentration dependent in the
case of a Monod-type reaction rate (Fig. 11). However, a qualitative −1
10
analysis of the results in Sections 4.3 and 4.4 demonstrates a
Monod-like behavior of the reaction rate in the upscaled equations,
η eqv

First−order reaction rate

too. This suggests that approximations for concentration indepen- −2 Km = 1
dent parameters for the upscaled rate expression can be found. In 10
Km = 0.1
the following we investigate these equivalent parameters for the
K = 0.01
m
case of (i) a uniform and (ii) a parabolic velocity field.
−3
10 0 2
10 10
4.5.1. Uniform velocity field Φ2

In case of a Monod-type reaction rate and a uniform velocity

field Eq. (25) shows the importance of the ratio g for the behavior Fig. 14. Dependency of the approximated equivalent scaling parameter geqv on U2
of the upscaled reaction rate. Although a rigorous analysis revealed in case of a Monod-type reaction rate with uniform velocity field.

1 First−order reaction rate 1 First−order reaction rate

Uniform velocity field
Uniform velocity field
First−order reaction rate
0.8 First−order reaction rate
0.8 Parabolic velocity field
Parabolic velocity field
Monod reaction rate
Monod reaction rate
Uniform velocity field
0.6 0.6 Uniform velocity field
Monod reaction rate
C

Monod reaction rate

Parabolic velocity field
Parabolic velocity field
0.4 0.4

0.2 0.2

0 0
0 1 2 3 4 5 0 1 2 3 4 5
x x
(a) Reaction-limited regime Φ 2 = 10. (b) Diffusion-limited regime Φ 2 = 100.

Fig. 13. Examples for a Monod-type reaction rate with a parabolic velocity field. The local parameters are K m ¼ 0:1 and Pe ¼ 2.
1346 F. Heße et al. / Advances in Water Resources 32 (2009) 1336–1351

12 coefficients. The effective transport and reaction expressions result

in four unknown parameters in this case. However, to avoid over-
10
parametrization we consider the transport parameters determined
Monod 2 for a first-order reaction rate to be applicable for Monod-type reac-
8
Monod 1
tions, and fit only U2eqv and K m;eqv , the two parameters of the reac-
Δ C [%]

6 tion term.
4
2 Fig. 7). In contrast, for K m < 1 significant differences can be ob-
0 0 1 2 3 4
10 10 10 10 10
Φ2
Fig. 15. Concentration error DC by applying geqv (dashed line) compared to fitting
with two independent parameters (dotted line) in case of a Monod-type reaction
rate with uniform velocity field, K m ¼ 0:1.
sion-limited regimes (Fig. 15), e.g. for K m ¼ 0:1 errors remain be-
low 1–2 %. In all investigated cases, i.e. 0:01 6 K m 6 100, the error
of the improved fitting procedure was always less than 3 %, which
is in the lower range of the experimental accuracy for concentra-
tion measurements indicating the applicability of the approach.
4.5.1.1. Parabolic velocity field. As explained in Section 4.4 the scal-
ing behavior in this case can qualitatively be seen as a superposi-
tion of the cases described in Sections 4.3 and 4.2. The
calculation of the coefficient functions in Eq. (28) shows the
appearance of complex mixing terms prohibiting the derivation
of the parameter for the effective equation. Thus, numerical solu-
tions were used as a reference to obtain constant rate parameters
applying again a fitting procedure using Eq. (28) but with constant
For K m P 1 the behavior of U2eqv with respect to U2 is similar to
the results of a first-order reaction rate (Figs. 16 and 17, see also
served. In the latter case, the linear dependency between U2eqv
and U2 proceeds till larger values. This shows that the reaction-
limited regime is extended towards higher values of U2 , which cor-
responds to the behavior of geqv (Fig. 14). Nevertheless for high val-
ues of U2 ; U2eqv converges towards p2 =4 regardless of the value of
K m . The dependency of K m;eqv on U2 supports these statements
(Fig. 16b). In the reaction-limited regime, i.e. for low values of
U2 , the local and the global half-saturation constants are approxi-
mately identical, i.e. K m  K m; eqv . Again, with increasing U2 the lo-
cal and global behavior diverge with higher values of K m showing
earlier divergence. Eventually, for high values of U2 all global half-
saturation constants K m;eqv increase to high values (100 or above).
For such values the global behavior is always well approximated by
a first-order reaction rate regardless of the value of K m at the local
level.
The concentration independent parameters and their depen-
dency on local reaction rate parameters determined by this proce-
dure could be used for larger scale simulations, e.g. in the form of
look-up tables, in pore network models of porous media
([51,7,29]). Such simulations would allow investigations of further
effects, caused for example by the tortuosity and pore connectivity
of the medium.

2
6 10
first−order
5 K =1
m 1
K = 0.1 10
4 m
Km = 0.01
Km,eqv
Φ2eqv

0
3 10

2 Km = 1
−1
10
K = 0.1
1 m
K = 0.01
−2 m
0 0 1 2 3 10 0 2 4
10 10 10 10 10 10 10
2
Φ Φ
2

(a) Φ2eqv . (b) K m eqv .

Fig. 16. Dependency of the approximated equivalent parameters U2eqv and K m;eqv on U2 for several K m in case of a Monod-type reaction rate with a parabolic velocity field.

1 1
10 diffusion 10
limited first−order
behavior
0 0
10 10
m
Km

transition
K

−1 −1
transition
10 reaction 10
limited
zeroth−order
−2
behavior
−2
10 0 2 10 0 2
10 10 10 10
2 2
Φ Φ
(a) Dominating local process (diffusion- or reaction- (b) Behavior of the upscaled equations (zeroth- or
limited). first-order).

Fig. 17. General survey of the upscaling behavior in case of a Monod-type reaction rate. Borders of the zones with different regimes are drawn for demonstration purposes
using arbitrary threshold values.
 F. Heße et al. / Advances in Water Resources 32 (2009) 1336–1351
4.6. Synopsis
In case of a Monod-type reaction rate and a uniform velocity
field the assumption of a single constant scaling parameter, link-
ing local and global reaction parameters, leads to significant er-
rors for the transition between reaction-limited and diffusion-
limited regimes. Specifically, the upscaled rate expression does
not follow a Monod-type reaction rate. This can explain the
problems reported in studies, assuming a single scaling parame-
ter for the reaction rate expression [56]. However, the errors ob-
tained by assuming a Monod-type reaction rate can be clearly
reduced by using two independent scaling relations for U2 and
K m . This results in two new, equivalent parameters U2eqv and
K m;eqv . Though we lack a rigorous analytical derivation of an
effective rate expression for a parabolic velocity field, the analy-
sis of the numerical results support the extension of the above
statements to parabolic flow fields as well. Consequently, our re-
sults can be applied to Monod-type reactions with a parabolic
velocity field, that enable us to formulate general upscaling
rules.
In the case of a first-order reaction rate the global behavior of
the y-averaged solution can be separated into a reaction-limited
and a diffusion-limited regime (Fig. 7) whereby the transition be-
tween them is controlled by U2 . In addition, for a Monod-type reac-
tion rate we also have to distinguish between a first-order and a
zeroth-order regime, the transition of which is now controlled by
U2 and K m . Furthermore, K m also has an impact on the transition
between reaction-limited and diffusion-limited regimes (Fig. 16).
As a result the ratio between K m and the concentration C has a
strong influence on the scaling behavior of Monod-type reaction
rates making it far more complex as for first-order reaction rates.
Such concentration dependent transitions between reaction- and
diffusion-limited systems have been reported before ([52,24]). This
further supports that scaling rules obtained for first-order reaction
rates can not easily be expanded to Monod-type reaction rates.
Only for C  K m , or in the marginal cases of either high or low
U2 , the different reaction rates scale similarly.
5. Summary and conclusion
We have presented an new upscaling approach from a two-
dimensional system with transport and surface catalyzed degrada-
tion of a single reactive species in a simple pore geometry to an
effective one-dimensional reactive transport equation. For the
analysis we neglected the longitudinal diffusion and motivated
the decision in mathematical and physical terms. The validity of
the developed model was tested with results from analytical and
numerical solutions to verify the soundness of the upscaling pro-
cess and to evaluate the effective parameters of the upscaled
equation.
The main focus was the scaling behavior of Monod-type reac-
tion rates. Two cases have been considered regarding the velocity
profile within the pore: a simple uniform and a more realistic par-
abolic velocity distribution. For both distributions, the results for
Monod-type reaction rates have been compared with results ob-
tained for first-order reaction rates.
The first two investigated scenarios of the analysis were simple
cases of reactive transport with a first-order reaction at the reac-
tive boundary of the medium (scenario I and II in Fig. 4). Solutions
for the upscaled system are already known [3,25] and served as a
verification of the conceptual approach applied in this study and
the resulting effective reaction rates. Results show that the macro-
scopic reaction rate can be strongly reduced when diffusion is the
limiting factor and that effective transport parameters must be
considered for a parabolic velocity field.
1347
For Monod-type reactions (scenarios III and IV in Fig. 4) the
upscaling results showed a concentration dependent coupling be-
tween local and global scales with highest sensitivities for local
concentrations in the same order of magnitude as the Monod-
half-saturation constant (i.e. K m  cbio ). For scenario III where K m
was either much higher or much smaller than the bioavailable con-
centration cbio , the upscaled reaction rate could be well approxi-
mated by a first-order or zeroth-order reaction rate, respectively.
Coupling of local and global behaviors using a single parameter
demonstrated that scaling parameters either required concentra-
tion dependent scaling or resulted in significant errors when
remaining constant. The use of this parameter is therefore either
cumbersome or inaccurate. However, by using two independent,
constant scaling parameters the global behavior could be repro-
duced reasonably well. Such independent scaling parameters could
be derived for both types of velocity fields by fitting the effective
one-dimensional profiles to explicit solutions of the two-dimen-
sional problem. For scenario IV our study revealed that the upscal-
ing in case of a parabolic velocity field is analytically as well as
numerically cumbersome, thus limiting the applicability of the
analytical upscaling approach. However, by using the effective
transport parameters obtained for the first-order reaction and re-
determining the upscaled reaction rate parameters through fitting
the numerical results, we could achieve acceptable results. These
upscaled parameters, determined by fitting, now represent a good
tradeoff between accuracy and applicability.
Results of this work provide an effective upscaled reaction rate
considering mass transfer limitations taking place at the scale of a
single pore. The use of a simplified representation of a pore al-
lowed an analytical treatment and understanding of the physical
processes involved. By considering Monod-type reactions at the
pore scale, the obtained effective equations comprise the restric-
tions of substrate bioavailability caused by pore-scale diffusion.
For such processes the obtained scaling behavior depends on the
substrate concentration. This result is caused by the concentration
dependent transition between reaction-limited and diffusion-lim-
ited regimes and is not observed for first-order reactions. The ap-
proach presented in this study allows the determination of
concentration independent scaling parameters, which provide glo-
bal concentration estimates of an acceptable accuracy. The ob-
tained relations between local and global reaction rate
parameters can be transferred to larger scale models, e.g. by using
them in pore network simulations. Future steps should include the
experimental validation of these theoretical results.
Acknowledgements
We would like to use the opportunity to acknowledge the con-
tribution of Arne Nägel, Jan Friesen, Christoph Schneider, Anke Hil-
debrandt, Rohini Kumar and one anonymous reviewer for the
technical support, several proofreadings and important sugges-
tions on this work.
Appendix A. Development of the upscaled solution
In this appendix we will provide the details for the upscaling of
the pore-scale processes. This comprises (i) the analytical solution
as well as (ii) the effective differential equation. Eqs. (6a)–(6c)
describing these processes can be found in the body of the paper
and will not be listed again.
A.1. Separation of the variables
The scheme used to arrive at an analytical solution in case of a
first-order reaction rate can be found in [3]. It has been modified to
1348 F. Heße et al. / Advances in Water Resources 32 (2009) 1336–1351

sffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi
account for the mathematical and geometrical description used in ki
this study. Wi ðyÞ ¼ 2 cosðki yÞ: ð37Þ
sinð2ki Þ þ 2ki

A.1.1. Transversal direction

Let fki giP1 be the set of eigenvalues and fWi giP1 the respective A.1.2. Longitudinal direction
set of orthonormal eigenfunctions of the following self-adjoint In order to solve for the longitudinal part of every mode we in-
eigenvalue problem sert Eq. (8) into Eq. (6a)
@2 X
1
@ X1
@2
Wi ðyÞ ¼ k2i Wi ðyÞ; ð30aÞ Pef ðyÞ Wi ðyÞ C i ðxÞ ¼ C i ðxÞ 2 Wi ðyÞ: ð38Þ
@y2 @x @y
i¼1 i¼1
@
Wi jy¼0 ¼ 0; ð30bÞ Multiplying this equation by Wj and integrating over y yields
@y
1 Z
X 1
@ @
Wi jy¼1 ¼ U2 Wi jy¼1 : ð30cÞ Pe f ðyÞWi ðyÞWj ðyÞ dy C i ðxÞ
@y i¼1 0 @x
X Z
The boundary condition given by Eq. (30b) reflects the symmetry of 1 1
@2
the medium and Eq. (30c) is the reaction term in case of a first-order ¼ C i ðxÞ Wi ðyÞWj ðyÞ dy: ð39Þ
i¼1 0 @y2
reaction rate. The solution of Eq. (30a) is known to consist of the
trigonometric functions sine and cosine. Therefore we can write By defining
Z 1
Wi ðyÞ ¼ Ai cosðki yÞ þ Bi sinðki yÞ: ð31Þ
f ðyÞWi Wj dy ¼ sij ð40Þ
Here ki is the frequency and Ai and Bi are the respective amplitudes. 0

These coefficients have to match the boundary conditions. First we and inserting Eq. (30a), because of the ortho-normality of the Wi ’s
use the boundary condition given by Eq. (30b) (35) we get
@
Wi jy¼0 ¼ 0 ¼ Bi cosð0Þ  Ai sinð0Þ ð32Þ
X
1
@ k2j
@y sij C i ðxÞ ¼  C j ðxÞ: ð41Þ
i¼1
@x Pe
from which is clear that Bi ¼ 0. The boundary condition given by Eq.
To get a good approximation of the complete solution a finite num-
(30c) yields
ber of modes will certainly be sufficient. By considering only N
@ modes of the series we can rewrite Eq. (41) in a matrix notation
Wi jy¼1 ¼ U2 Ai cosðki Þ ¼ Ai ki sinðki Þ: ð33Þ
@y
@
Rearranging this expression we get T C ¼ KC ð42Þ
@x
2
ki tanðki Þ ¼ U : ð34Þ with
The behavior of the left hand side of Eq. (34) is that of a strictly 0 1
s11    s1N
monotonously increasing curve from 1 to þ1 within each inter- B . .. .. C
    T¼B C
val 2i p; 2i þ 1 p with ði ¼ 1; 3; 5; . . .Þ. The solutions ki are then @ .. . . A; ð43Þ
determined by evaluate this expression within each of this intervals sN1    sNN
(Fig. 18). 0 1
k2
For the calculation of the amplitudes Ai we refer to the ortho-  Pe1 0
B C
normality of the eigenfunctions, i.e. B .. C
K¼B C ð44Þ
@ . A
Z 1 k2
Wi Wj dy ¼ di;j : ð35Þ 0  PeN
0
and
When we use this condition and insert Eq. (31), we get 1 0
Z 12 sffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi C1
1
ki B . C
Ai ¼ 2
cos ðki yÞ dy ¼2 : ð36Þ C¼B C
@ .. A ð45Þ
0 sinð2ki Þ þ 2ki
CN
Now we can formulate the explicit solution for every transversal
mode of Eq. (8) by introducing the values for Ai and Bi into Eq. (31) for the unknown vector C, whose entries are the longitudinal modes
of the solution c. Eq. (42) can be rearranged into

@
C ¼ T1 KC ¼ CC ð46Þ
@x
In this form we have a simple system of homogeneous linear differ-
ential equations of order one with constant coefficients.

A.2. Analysis of the case of a first-order reaction rate with a uniform

velocity field

Fig. 18. Solution of the eigenvalue problem described by Eq. (34) displayed as the
interfaces of the k tanðkÞ function (continuous line) and a constant reaction rate
(dashed line, arbitrarily set to U2 ¼ 50 in this example).
In this part of the appendix we will give the details for the case
of a first-order reaction rate with a uniform velocity field. This
comprises the analytical solution as well as the effective equation
(see Fig. 5).
 F. Heße et al. / Advances in Water Resources 32 (2009) 1336–1351 1349

A.2.1. Analytical solution A.3. Analysis of the case of a first-order reaction rate with a parabolic
In case of a uniform velocity field the matrix T is the identity velocity field
matrix according to Eq. (40). Therefore C is diagonal and Eq. (10)
are decoupled. The governing ordinary differential equation for A.3.1. Analytical solution
every mode then reads The matrix T is no longer a diagonal matrix in case of a parabolic
velocity field. As a result the entries of C in Eq. (10) are now cou-
@ k2 pled and must be solved in a closed form. Nevertheless, the matrix
C i ðxÞ ¼  i C i ðxÞ ð47Þ T is still symmetric, so sij ¼ sji (Fig. 19).
@x Pe
To find the solution of Eq. (10) we diagonalize the system ma-
The solution of this equation is given by trix C. To that end we have to find a representation of the form
C ¼ GDG1 . Here D is a diagonal matrix and G is the orthogonal ma-
k2
i trix of the eigenvectors of C. Applying this transformation we can
C i ðxÞ ¼ C i ð0Þe Pe x : ð48Þ rewrite Eq. (10) into

For the evaluation of the initial conditions C i ð0Þ we have to refer to c0 ¼ CC ¼ GDG1 C
Eq. (8) and insert the boundary condition given by Eq. (6b) G1 c0 ¼ DG1 C
X
N w0 ¼ Dw
1 ¼ cð0; yÞ ¼ C i ð0ÞWi ðyÞ ð49Þ
i¼1 with w ¼ G1 C. In this form the modes are decoupled so we can fol-
low the same proceedings as in case of a uniform velocity field.
multiplying both sides with Wj and integrating over y yields
Z 1
A.3.2. Effective equation
C j ð0Þ ¼ cð0; yÞWj ðyÞ dy ð50Þ
0
A direct analytical upscaling like in Appendix A.2 is not possible
in case of a parabolic velocity field. Applying the upscaling opera-
because of the ortho-normality of the eigenfunctions Wi ðyÞ. Since R1
tor 0 dy on Eq. (6a) we get
cð0; yÞ ¼ 1 we finally arrive at  
Z 1
Z @ U2
1
sinðkj Þ 1:5 C y2 c dy ¼  eff C: ð53Þ
C j ð0Þ ¼ Wj ðyÞ dy ¼ Aj : ð51Þ @x 0 Pe
0 kj
Unfortunately no explicit solution is known for the remaining inte-
With this equation we get the starting value for every transversal gral in Eq. (53). Therefore we have to pursue an alternative proceed-
mode C j of the solution. ing to arrive at an effective equation. Using the linear system of
ordinary differential Eq. (46) we can get an expression for the lead-
A.2.2. Effective equation ing first mode C 1 ðxÞ. In order to obtain the effective description we
To find the upscaled effective description of Eq. (6) we directly have to rewrite the system of N differential equations of order 1 to
R1
apply the upscaling operator 0 dy to Eq. (6a) and insert the bound- an ordinary differential equation of order N. The general solution of
ary conditions given by Eqs. (6b) and (6c). In case of the uniform this procedure is
velocity field we get
X
N
@n
Z 1 Z 1 2 an C 1 ¼ 0: ð54Þ
@ @ @xn
Pe
c dy ¼ 2
c dy n¼0
0 @x 0 @y
In Eq. (54) the numbers an are the respective coefficients of the
@ @ @
Pe C ¼ cbio  cjy¼0 characteristic polynomial of C in Eq. (46). To link the solution for
@x @y @y
this mode with the upscaled solution C we have to multiply it with
¼ U2 cbio : R
the corresponding y-averaged transversal mode: hC 1 i ¼ C 1 W1 dy.
P
Since C ¼ i hC i i holds, we make an error by neglecting the higher
Here we introduce an effective Thiele modulus U2eff , as modes of C. Nevertheless, these modes decrease very fast so the er-
cbio 2 ror is confined to small values of x and even there it is comparably
U2eff ¼ U : ð52Þ small. An important simplification can be made, regarding the num-
C
ber of modes N, which has to be taken into account, to arrive at a
Since C is only zero at þ1 this equation is valid almost everywhere.
good estimate for C 1 .
It can be shown that U2eff shows only variation for small values of x
A numerical analysis shows that a good approximation is al-
so it can be approximated as a constant.
ready reached by using few modes (see Fig. 20). Only in the case

Fig. 19. First five rows and columns of matrix T in graphical and numerical display, evaluated for U2 ¼ 10 in case of a first-order reaction rate and a parabolic velocity field.
1350 F. Heße et al. / Advances in Water Resources 32 (2009) 1336–1351

1 0.25

1 0.2
0.8
2

square sum error

3
0.6 0.15
4
<C >
1 5
0.4 0.1

0.2 0.05

0 0
0 1 2 3 4 5 1 2 3 4 5
x Number of Modes
(a) The y-averaged first mode C1 calculated using (b) Square sum error for several modes.
different number of modes.

Fig. 20. Error made by using only a limited number of longitudinal modes for the calculation of hC 1 i in case of a first-order reaction rate and a parabolic velocity field.

when one mode is considered, i.e. the first mode itself, we get a sig-
nificant error. This error however decreases dramatically when
using more modes, which justifies the use of only two. By restrict-
ing therefore our analysis to N ¼ 2 we get a differential equation of
second order for C 1 .
so we get again a system of homogeneous linear differential equa-
tions. In contrast to Eq. (46) the entries of the coefficient matrix CðxÞ
are not constants but x-dependent functions.
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