J. Phycol.

49, 608615 (2013)

2013 Phycological Society of America
DOI: 10.1111/jpy.12071

SIMULATING PH EFFECTS IN AN ALGAL-GROWTH HYDRODYNAMICS MODEL1

Scott C. James2
Sandia National Laboratories, Thermal/Fluid Science and Engineering, Livermore, CA 94551-0969, USA
Exponent Inc., 320 Goddard, Suite 200, Irvine, California 92618, USA

Vijayasarathi Janardhanam
Department of Physics & Astronomy, University of New Mexico, MSC03 2020, Albuquerque, New Mexico 87131-0001, USA

and David T. Hanson

Department of Biology, University of New Mexico, Castetter Hall 192, Albuquerque, New Mexico 87131-0001, USA

Fluid Dynamics Code; PEST, Parameter Estimation

code; SNL-EFDC, Sandia National Laboratories
Environmental Fluid Dynamics Code

Models and numerical simulations are relatively

inexpensive tools that can be used to enhance
economic competitiveness through operation and
system optimization to minimize energy and resource
consumption, while maximizing algal oil yield. This
work uses modified versions of the U.S. Environmental
Protection Agencys Environmental Fluid Dynamics
Code (EFDC) in conjunction with the U.S. Army
Corp of Engineers water-quality code (CE-QUAL)
to simulate flow hydrodynamics coupled to algal
growth kinetics. The model allows the flexibility of
manipulating a host of variables associated with
algal growth such as temperature, light intensity, and
nutrient availability. pH of the medium is a newly
added operational parameter governing algal growth
that affects algal photosynthesis, differential
availability of inorganic forms of carbon, enzyme
activity in algae cell walls, and oil production rates. A
single-layer algal-growth/hydrodynamic model without pH
limitation was verified by comparing solution curves of
algal biomass and phosphorus concentrations to an
analytical solution. Media pH, now included in the model
as a growth-limiting factor, can be entered as a measured
value or calculated based on CO2 concentrations.
Upon adding the ability to limit growth due to pH,
physically reasonable results have been obtained
from the model both with and without pH limitation.
When the model was used to simulate algal growth
from a pond experiment in the greenhouse, a leastsquares fitting technique yielded a maximum algal
production (subsequently modulated by limitation
factors) of 1.05 d
1. Overall, the measured and
simulated biomass concentrations in the greenhouse
pond were in close agreement.

Depletion of nonrenewable energy resources and

commensurate environmental impacts of fossil fuels
has focused significant attention on alternative
energy sources. Biofuels are promising renewable
and potentially carbon-neutral alternatives to fossil
fuels. Currently, most biofuels are produced from
plant oils, but the oil-yield-to-harvest-area ratio is
nowhere near that required to displace a significant
fraction of fossil fuels. If high-yield oil palm were to
be grown, 24% of US farming acreage would be
dedicated to meeting only 50% of the nations
transportation fuel needs (Chisti 2007).
Alternatively, biodiesel can be produced from
microalgae. Algae, in part like terrestrial plants, use
photosynthesis to combine water and CO2 to yield
biomass and chemical energy. Photosynthesis in
microalgae is perhaps three times more efficient
than in higher plants due to their single-cell structure. In addition, because algae grow in aqueous
suspensions, they have better access to water and
nutrients. For these reasons, microalgae are capable
of extremely rapid growth and some strains can
double their biomass within 24 h (Dempster and
Sommerfeld 1998). Also, oil contents in many
strains of microalgae range from 20% to 50% by dry
biomass weight and in some strains can reach 80%
(Metting and Pyne 1986, Spolaore et al. 2006).
Beyond their rapid growth, using microalgae as a
source of biomass for biofuel production has a number of other advantages. Producing renewable
energy with low-carbon emissions leads to lower global CO2 emissions, not to mention that 100 kg of
algal biomass fixes ~183 kg of CO2 (Demirbas and
Fatih Demirbas 2011). If no externally produced
energy is used for biomass cultivation, harvesting,
and conversion, then there would be no net emission of CO2 in a full biomass fuel cycle a carbonneutral process (Chisti 2007). Moreover, CO2-rich

Key index words: biofuels; CE-QUAL; CO2; EFDC;

modeling algae growth; pH effects
Abbreviations: CE-QUAL, US Army Corps of Engineers water-quality model; EFDC, Environmental
1

Received 3 August 2012. Accepted 1 February 2013.

Author for correspondence: e-mail sjames@exponent.com.
Editorial Responsibility: T. Mock (Associate Editor)

608

SIMULATING PH EFFECTS ON ALGAL GROWTH

flue gas can be bubbled into open-channel raceway ponds as a source of inorganic carbon, while
helping to mitigate otherwise-emitted CO2. Wastewater discharge may also be used as a source of nutrients for the algae (Sawayama et al. 1995, Yun et al.
1997). Finally, microalgae can be grown on hot,
arid, nonarable land, so they need not displace
existing food crops. In addition to biodiesel, microalgae can also be used to produce methane by
anaerobic digestion of algal biomass (Spolaore et al.
2006) or photobiologically produced biohydrogen
(Ghirardi et al. 2000, Akkerman et al. 2002, Melis
2002, Fedorov et al. 2005, Kapdan and Kargi 2006).
Although microalgae are a promising source of
biofuels, production costs remain excessive. The goal
is to reduce the cost of production from $8
15 to
$0.25  kg
1 of ash-free organic dry biomass (Pedroni et al. 2001). In addition to reducing the production costs, there is still a need to isolate, select,
improve, and maintain algal strains appropriate for
large-scale microalgae cultivation. Issues of species
productivity to neutral-lipid (oil) yield and harvesting are clearly themes central to biomass production.
Algal-species dominance and grazer control (and
other biological invasions) are also troublesome
aspects during scale-up. Moreover, biomass concentration must be monitored and harvest times must
be optimized to prevent excessive build-up of algae
that can yield undue opacity and optically dark
zones. All of these issues and several others can be
effectively studied if numerical models can accurately
describe algal growth in flowing raceways. Models
provide a relatively inexpensive means to simulate
different growth media and represent various environmental conditions with goals of maximizing algal
growth and minimizing operational expense. Such
studies can be completed in the computer laboratory
without risking the physical biomass culture and
without having to build pilot raceways (James and
Boriah 2010). Of course, the same algal-growth algorithms used in this study could be extended to the
internal flows of closed photobioreactors.
MATERIALS AND METHODS

Data requirements. The data requirements for a model of

this complexity are significant and they fall into three basic
categories: physical flow system, meteorological data, and
algae-specific information. First, to set up the model domain
and flow boundary conditions, the physical characteristics of
the algal-growth system (be it pond or open-channel raceway)
must be specified, including geometry, flow rates, water
depth, and any baffling (Sompech et al. 2012). Second, atmospheric data must be collected, such as incident solar radiation, dry and wet bulb temperatures if evaporation is to be
estimated, and precipitation (evaporation and precipitation
were not considered in the greenhouse model because makeup water was added to maintain the depth of the pond).
Finally, perhaps the most challenging and time-consuming
requirements relate to the species of algae being cultivated.
Experience with this model has demonstrated that the most
sensitive parameters have to do with the effects of light on

609

algal growth. In addition to the optimum light intensity, it is

also important to measure each species light extinction coefficient so that the correct amount of light is distributed
through the water column as a function of algal density.
Nearly as important as data related to light is range of temperature tolerance for a species. If the algae are sensitive to
pH or salinity and these parameters are not held constant,
then it will be important to establish how the algae grow as a
function of changes to pH and salinity. Finally, it is important
to measure C:N:P ratios in the algae to specify how CO2,
nitrate, and phosphate nutrients are incorporated into the
algae as they grow. If nutrient deprivation occurs (e.g., to trigger lipid production), then the nutrient half-saturation constants must be measured. Of course, uncertainty is incurred
when extrapolating laboratory data to outdoor systems, so data
collected from the actual system being modeled is besteven
though collecting such outdoor data is expensive and time consuming. As research on outdoor algal culture continues, a
library of these sorts of data would be valuable.
Algae-growth model. The governing equation for biomass
growth in CE-QUAL is (Cerco and Cole 1995, Eq. 3.1):
@B
@
BL
P
BM
PR B ws B
@t
@z
V

where B (g  m
3 or mg  L
1) is the biomass, t (d) is time,

P (d
1) is the production (growth) rate, BM (d
1) is the basal
metabolic rate, PR (d
1) is the predation rate, ws (m  d
1) is
the settling velocity, z (m) is the vertical coordinate, BL
(g  d
1) represent external loading rates from inoculation
and harvesting, and V (m3) is the model cell volume. Biomass
production rates are determined by the availability of nutrients (including CO2), light intensity, local temperature, and
pH. The effect of each is multiplicative and decoupled
(Cerco and Cole 1995, Eq. 3.2),
P PM f mg I h T i pH

Here, PM (d
1) is the maximum production rate under

optimal conditions, f(m) is the effect of nonoptimal nutrients,
which includes CO2 limitation (0  f(v)  1), g(I) is the
effect of nonoptimal illumination (0  g(I)  1), h(T) is
the effect of nonoptimal temperature (0  h(T)  1), and i
(pH) is the effect of nonoptimal pH (0  i(pH)  1). All
of these functions are spatially dependent, and their values
vary from cell to cell in the model according to local nutrient
concentrations (including CO2), incident solar radiation, and
temperature. Another point that must be emphasized is that
there are no generalizable growth-limitation equations applicable to all strains of algae. In fact, even finding relations
that would broadly apply to just green algae, or just diatoms,
or just cyanobacteria would be quite challenging. While this
is not a limitation of the model itself, because any nonoptimal function can be built into the code, it is perhaps a limitation in application because the various growth-limiting
equations should be established for each strain of algae.
Some laboratory or field experimentation is required to
establish each strain-specific growth-limitation equation.
Nutrients. Nutrient availability is based on the Monod
equation (Monod 1949)
m
f m h
;
3
KX m
where m (g  m
3) is the nutrient concentration and KXh is the
half-saturation constant. For example, the nutrient function
for green algae can be limited by dissolved ammonium,
[NH4] (g  m
3), nitrate, [NO3] (g  m
3), phosphate, [PO4]
(g  m
3), or carbon dioxide, [CO2] (g  m
3), concentrations yielding

610

S CO T T C . J A M E S E T A L .

top of the water surface

f v min

NH4 NO3
PO4
CO2
;
;
;
KNh NH4 NO3 KPh PO4 KCh CO2

where, KNh , KPh , and KCh are the corresponding half-saturation

constants.
Figure 1 shows Monod curves of (3) for various phosphate half-saturation constants, KPh where m is the PO4 concentration (x-axis). The half-saturation dashed line at 0.5 is
where the nutrient concentration equals the half-saturation
constant and phosphate limits growth by 50% (assuming
that other constituents do not limit growth). Half-saturation
constants are typically defined for the low concentrations of
nutrients common in environmental systems and are on the
order of 0.01 g  m
3. For algal growth systems (raceways),
nutrients are often added in excess and the nutrient limiting
function is close to unity. When algae are nutrient deprived
(e.g., to trigger lipid production), the value of the half-saturation constant will play a more important role in algae
growth.
Light. Of course, algal production is a strong function of
incident light, which is a function of average daylight, light
extinction due to biomass, light intensity at the water surface,
optimal light intensity, and depth of algae below the water
surface. Algae grow as the light intensity increases to some
saturation (optimum) intensity, Is (W  m
2), beyond which
growth rates decline due to photoinhibition. The function
for nonoptimal illumination is derived from Steeles equation
(DiToro et al. 1971, DiToro et al. 1975):
g I

I z 1
I Iz
e s;
Is

where I(z) (W  m
2) is the instantaneous light intensity at

depth z (m). If the growth medium is not well mixed, then
the rate of change of light intensity I(z) changes with depth
(or model layer) and yields nonuniform growth of algae.
If, on the other hand, the system is well mixed, then the
biomass concentration will be homogeneous (constant light
extinction). For such a system (i.e., the single-layer models
studied in this work), the depth-averaged growth limitation is:
gI

e
e
a1
e
a0 ;
Ke d

a0

I0
;
Is

and the ratio at the bottom (of the layer) is

a1

I0
Ke d
e
:
Is

Note that recursive calculations are necessary for multilayer

models.
Light extinction coefficient, Ke, in a single-layer model or
within a particular layer in a multilayer algal-growth hydrodynamics model is formulated as
Ke kb kB B;

where kb (m
1) is the constant background light extinction

coefficient due to water and other suspended particulates
and kB (g C  m
3  m
1) is the light extinction coefficient
due to suspended biomass in the layer.
An alternative formulation of light extinction coefficient is
given by Rileys empiricism (Riley 1956)
2=3

Ke kb 0:0088BChl 0:054BChl ;

10

where BChl is the biomass chlorophyll concentration and the

background light extinction coefficient is calculated from the
empiricism (Di Toro 1978)
kb kw 0:052N 0:174D;

11

where kw (m
1) is the light extinction due to particle-free

water, N (g  m
3) is concentration of nonvolatile suspended
solids, and D (g  m
3) is the concentration of nonliving
organic suspended solids.
Figure 2 shows an example light limitation function (dotted curve) computed using Rileys empiricism for a singlelayer model described by (6), (10), and (11) with
N = D = 0 g  m
3, kw = 0.1 m
1, and BChl = 0.5 g C  m
3

where d (m) is the water-layer depth, Ke (m
1) is the light

extinction coefficient, a0 (
) is the light intensity ratio at the

FIG. 1. Growth limitation as a function of suboptimal nutrients as described by the Monod equation for phosphate, see (3).

FIG. 2. Growth limitation as a function of suboptimal illumination using Rileys empiricism (N = D = 0 g  m
3, kw = 0.1 m
1,
and B = 0.5 g C  m
3) for light limitation at 10 m depth (dotted
curve) with Steeles equation, (6), provided for reference where
the incident light is measured at the water surface. Note that
photoinhibition can occur for superoptimal illumination.

SIMULATING PH EFFECTS ON ALGAL GROWTH

FIG. 3. Growth limitation as a function of suboptimal temperatures, see (12).

(yielding Ke = 0.138  m
1) at d = 10 m. Steeles equation

(5), is also shown in Figure 2 for comparison (solid curve).
Temperature. Algal growth rate increases with temperature
up to an optimal and decreases with any further increases
(Cossins and Bowler 1987). Temperature effects on each
algae group are defined by an exponential function of water
temperature, the optimal temperatures for growth, and the
temperature-effect coefficients below and above the optimal
temperatures
8
< exp
K1T T1
T 2 
hT 1
:
exp
K2T T
T2 2 

for T < T1
for T1  T  T2 ;
for T > T2

12

where T (C) is the local temperature from the hydrodynamic model, T1 (C) is the lower optimal growth temperature, T2 (C) is the upper optimal growth temperature, K1T
(C
2) is the temperature-effect coefficient below the optimal
growth temperature, and K2T (C
2) is the temperature-effect
coefficient above the optimal growth temperature of the
algae. For example, temperature parameters for green algae
might be T1 = 18C, K1T 0:69 C
2 , T2 = 22C, and
K2T 0:007 C
2 . Figure 3 plots h(T) for green algae between
12C and 45C. Note how T1 and T2 bound the optimal temperature; h(T) = 1 here. Outside T1 and T2, h(T) decreases
as a function of K1T and K2T .
pH limitation. Appendix S1 in the Supporting Information
introduces the importance of pH in algae growth and derives
how pH may be calculated from measured CO2 concentrations. With known pH, the multiplicative function i(pH) ~ i
([H+]) is modeled after the work of Mayo (1997),
H  10
pH
iH 

H 
H 

kOH T H 2 =kH T

13

.
In the preceding equation, the hydration rate constants,
kH and kOH, are modeled as a function of temperature (C),
which are obtained from polynomial fits to data available
from Mayo (1997),


kOH T 10
13 8T 2
500T 8000 ;


kH T 10
7
5T 3 300T 2
5000T 30000 :

14

For example, at T = 20C, kOH = 1.2 9 10
10, kH = 10
3;

the multiplicative function, i(pH), is shown in Figure 4 [note
that [H+] was calculated from pH from (28) and this was
used in (13)]. It is noted that this function is specific to

611

FIG. 4. Growth limitation as a function of suboptimal pH

effects at 20C, see (13).

Chlorella vulgaris and a strain-specific function should be

used if available. While such pH relationship was found for
Nannochloropsis salina, it is known that these algae grow best
in neutral to slightly alkaline waters, so the growth range
shown in Figure 4 is reasonable.
RESULTS AND DISCUSSION

To confirm that the algal-growth model is not

only using the correct equations for the various limiting functions, but also solving them correctly, a
textbook example problem is used for verification
testing. Appendix S2 in the Supporting Information
solves problem 33.2 from Chapra (1997), which
defines the system and presents solution curves for
algae and phosphorus nutrient concentrations. Also,
an extension including the effects of CO2 and pH
limitation is presented.
In addition to verifying the algal-growth model
for the Chapra example described in previous section, the model is also used to simulate algal growth
corresponding to an experimental pond maintained
inside a greenhouse under known temperature and
irradiance conditions. The simulated pond is
1.67 9 1.5 m2 and is 0.211 m deep, containing
approximately 0.53 m3 of growth medium. A schematic of the model would appear similar to that of
the Chapra system shown in Figure S1 in the Supporting Information, except the upstream and
downstream cells have a length of 0.083 m and the
center cell, which represents the fully mixed pond,
has a length of 1.5 m. All cells have a width of
1.5 m. Like the Chapra model, this model has only
a single (fully mixed), 0.211-m-deep layer, assumes
zero benthic flux (no sediment bed), no algal predation, constant background light extinction, and
does not include atmospheric reaeration. Inflow
and outflow are set to zero. CO2 is supplied to the
system through a bubbler that acts as a point
source. While the amount of CO2 added to the
pond was metered, aqueous CO2 concentrations
were not known and some CO2 certainly escaped to
the atmosphere. For the first 7 and last 3 d, air was
bubbled at 2 SCFM, resulting in 40 g of CO2 bubbled per day. For the middle 7 d, 2 SCFM of air was

612

S CO T T C . J A M E S E T A L .

augmented with 0.1 SCFM CO2 (yielding about 5%

CO2). Based on data from Vance and Spalding
(2005), 50% of added CO2 was available to algae
when added at a concentration of 0.04% (atmospheric concentration), while only 1% of it was available when added at 5% concentration (i.e., excess
CO2 was assumed lost to the atmosphere). This
equated to CO2 being added at 20 g  d
1 when
bubbling air and 80 g  d
1 when bubbling 5%
CO2. Whether or not these CO2 source rates are
appropriate for the greenhouse system is questionable because of atmospheric loss; regardless, CO2
was never particularly limiting in this model (minimum i(pH) of 0.96). Details of the greenhouse
experiment are available in the project report by
Timlin et al. (2012).
The model has two contributors to the light
extinction coefficient; one due to the saline water
that forms the growth medium and the other due
to chlorophyll (or algal biomass) as shown in (9).
The background light extinction was specified equal
to the diffuse attenuation coefficient of irradiance
for clear ocean water at 680 nm (the wavelength
that is most attenuated due to chlorophyll), which
is kb = 0.45 m
1 (Smith and Baker 1981). The
absorptivity curve that yields the light extinction
coefficient, kB, was measured for N. salina grown in
the laboratory and used as inoculum for the greenhouse is shown in Figure 5. The measurement consisted of an aqueous suspension of cells that was
serially diluted to produce multiple concentrations.
The dry cell weights of each dilution were measured. Each dilutions dry cell weight was projected
onto the spectrophotometer data (absorbance of
200900 nm light) using classic least-squares fitting
and the pure spectral component representing the
best fit of the concentrations was estimated (Haaland et al. 1985). At 680 nm, the light extinction
value (used in the model) is kB = 0.314
(g  m
3  m
1). Optimal light intensity to grow
N. salina was also estimated in the laboratory. Low
(26 ly  d
1), medium (35 ly  d
1), and high
(88 ly  d
1) light intensities were applied to the
algae and growth rates measured. While the total
biomass at high light intensity was slightly higher

FIG. 5. Light extinction coefficient measured for laboratorygrown Nannochloropsis salina (the 680-nm wavelength is indicated
with the dashed line).

than at medium light intensity, the algae grown

under the high light intensity were notably less
healthy (less green). The optimal light intensity was
specified in the model to be Is = 35 ly  d
1.
Reasonable minimum and maximum temperatures for optimal growth of algae in the pond are
T1 = 18C, and T2 = 22C (NCMA 2013), and
N. salina grows well between 17C and 32C (Boussiba et al. 1987). The minimum and maximum suboptimum temperature-effect coefficients, K1T and
K2T , are 0.693C
2 and 0.007C
2, respectively, so
that at T = 17C and 32C, the suboptimal temperature effects restrict algal growth by 50% (see Fig. 3
for a plot of this specific temperature limitation
function). The greenhouse pond itself was exposed
to the measured solar irradiance, shown in Figure 6;
measured temperatures and pH values are also
shown. Note that the natural light intensity has
been attenuated by about 49 due to the frosted
glass used to build the greenhouse. Also, it is clear
in the pH signature when CO2 was added at 5%
from days 7 to 14; pH measurements were used to
calculate pH limitation according to (13).
Algal elemental composition ratios were measured
three times over the course of the experiment at
the University of New Mexico Biology Annex Analytical Laboratories using Standard Methods (Clesceri
et al. 1998). Nitrogen and phosphorus were measured with standard colorimetric methodologies
(Technion AutoAnalyzer II using Standard Methods
no. 98-70W(3a), 4500-NH3-G(1) and No. 100-70W
(3b), 4500-NO3-F(1) for nitrogen and no. 94-70W

FIG. 6. Insolation, temperature, and pH measurements for the

greenhouse pond.

SIMULATING PH EFFECTS ON ALGAL GROWTH

(3c)-P-F(1) for phosphorus) and carbon with a combustion technique (Shimadzu TOC-5050A using
Standard Method 5310B(1)). Samples were collected on days 7, 11, and 14 of the growth experiment, yielding C:N:P ratios of 358:38:1, 365:36:1,
and 423:39:1, respectively (for reference, the Redfield ratio for marine planktons in open oceans is
106:16:1 (Redfield 1934)). Significant variability of
elemental composition exists across strains and even
within strains due to environmental stressors and
adaptations. Deviations from this ratio can be used
to infer nutrients that limit growth (Hecky et al.
1993, Hillebrand and Sommer 1999, Ricklefs and
Miller 2000). Generally, values of N:P less than 16:1
suggest that nitrogen is the limiting nutrient,
whereas N:P ratios greater than 16:1 indicate limited
phosphorus (Ricklefs and Miller 2000). A C:N:P
ratio of 358:38:1 was applied to N. salina in the simulation. Initial nitrate and phosphate concentrations

FIG. 7. Comparison of measured and simulated algal biomasses. The dashed curves represent the 95% confidence limit for
PM = 1.01 and 1.13 d
1.

613

were 54.7 and 3.1 g  m
3, respectively. Posttest

nitrate was 33.1 g  m
3 and phosphate was below
the detection limit after the required dilution.
Nutrients recycle in the system as algae metabolize
the inorganic forms of nitrate and phosphate into
their dissolved organic forms. These dissolved
organic nitrates and phosphates are mineralized
back into their inorganic forms at rates of 0.015 and
0.1 d
1 (Cerco and Cole 1995, Tables 516). All of
these water-quality variables are tracked in the
model.
Algal growth was measured for 17 d after inoculation at 15.4 g  m
3 of biomass. CO2 was added as
described above (and reflected in Fig. 6). The halfsaturation constant for CO2-limited growth of
N. salina, is KCh 0:028 g  m
3 (Raven and Johnston
1991). Because the actual amount of CO2 used by
the growth medium through bubbling the 0 or 5%
CO2-in-air mixture and atmospheric exchange is not
well known, for hypothesis testing it could have
been selected such that it was never the limiting
nutrient. This would demonstrate the models abil-

FIG. 9. Biomass production rate subject to all limitation factors when PM = 1.05 d
1.

FIG. 8. Light, g(I), and temperature, h(T), limitations (top) and nutrient, f(m), and pH, i(pH) limitations (bottom) in the algae-growth
model. Note that the y axis for i(pH) is inverted and ranges from 1 to 0.9.

614

S CO T T C . J A M E S E T A L .

ity to be used as a tool to optimize CO2 addition.

Additional system-specific parameters for the greenhouse pond model are listed in Table S1 in the
Supporting Information. The basal metabolic rate
was set lower than the Chapra modelto
BM = 0.01 d
1, which is consistent with Cerco and
Cole (1994) and reasonable for a greenhouse experiment. Mineralization rates control how fast dissolved organic nitrogen and phosphorus from algae
metabolism are returned to inorganic forms that
can be consumed by the algae; values were selected
to be consistent with Cerco and Cole (1994).
Maximum growth rate at optimum conditions,
PM, was obtained by performing a least-squares fit of
algal-to-measured biomass using the parameter estimation code, PEST (Doherty 2009, 2010). PEST uses a
nonlinear Gauss-Marquardt-Levenberg method to minimize the objective function (i.e., minimize a weighted
sum-of-squared differences between the model-generated algal biomass and the measured biomass). A
maximum growth rate of PM = 1.05 d
1 was estimated
for the greenhouse model (linearized 95% confidence range is 1.011.13 d
1). This is consistent
with the maximum growth rate of 1.3 d
1 reported by
Van Wagenen et al. (2012). Recall that the maximum
growth rate is mediated by the limitation functions.
Another noteworthy point is that the model simulates a well-mixed system. To the extent that any
deadzones exist and impact the biomass, these
effects will be manifest in a model-estimated PM
different from the experiment.
Figure 7 compares measured and PEST-optimized simulated algal biomasses. Figure 8 (top)
shows the limitations due to light and temperatures calculated according to (6) and (12), respectively, and using data from Figure 6. Note how
light limitation measured at the bottom of the
0.211-m pond increases, which is manifest as lower
values for g(I). This is expected because as biomass increases, there is less light penetration into
the water column due to algae self-shading. Also,
when temperatures are coldest during the first day
or so, biomass production is quite limited. Similarly, Figure 8 (bottom) shows limitations due to
pH and nutrients (including CO2) calculated
according to (13) and (4), respectively. Nutrients,
specifically CO2, and pH were not particularly limiting, especially when the 5% CO2 source was
added between days 7 and 14.
When considering all of the growth limitations
and multiplying by the optimized growth rate of
PM = 1.05 d
1, the total algae biomass production
rate (not including basal metabolism) is shown in
Figure 9. Maximum production was achieved near
day 7 because the product of all limiting factors was
greatest and also because 5% CO2 was added to the
system from days 7 to 14. Measured (and modeled)
pond productivity was about 1.6 g  m
2  d
1.
Estimates from the algal-growth simulation could
be improved with additional experimental data that

help identify and constrain limitations due to nutrients, light, temperature, and pH or if other system
parameters like CO2 concentrations in the medium
were known.
The Laboratory Directed Research and Development program at Sandia National Laboratories (SNL) provided a
majority of the funding for this work within SNL and through
subcontracts to DTH. Additional support was provided by
Exponent Incorporated to SCJ. Special thanks are extended
to Dr. Jerilyn Timlin of SNL for her help funding this effort
and in managing the project as a whole. Sandia National
Laboratories is a multi-program laboratory managed and
operated by Sandia Corporation, a wholly owned subsidiary
of Lockheed Martin Corporation, for the U.S. Department of
Energys National Nuclear Security Administration under contract DEAC0494AL85000.
Akkerman, I., Janssen, M., Rocha, J. & Wijffels, R. H. 2002. Photobiological hydrogen production: photochemical efficiency
and bioreactor design. Int. J. Hydrogen Energ. 27:1195208.
Boussiba, S., Vonshak, A., Cohen, Z., Avissar, Y. & Richmond, A.
1987. Lipid and biomass production by the halotolerant
microalga Nannochloropsis salina. Biomass 12:3747.
Cerco, C. F. & Cole, T. 1994. Three-dimensional Eutrophication Model
of Chesapeake Bay. US Army Corps of Engineers, Washington,
DC, 658 pp.
Cerco, C. F. & Cole, T. 1995. Users Guide to the CE-QUAL-ICM
Three-Dimensional Eutrophication Model, Release Version 1.0. U.S.
Army Corps of Engineers, Washington, DC, 316 pp.
Chapra, S. C. 1997. Surface Water-quality Modeling. McGraw-Hill,
New York, 844 pp.
Chisti, Y. 2007. Biodiesel from microalgae. Biotechnol. Adv.
25:294306.
Clesceri, L. S., Greenberg, A. E. & Eaton, A. D. 1998. Standard Methods for the Examination of Water and Wastewater, 20th ed. APHA
American Public Health Association, Baltimore, MD, pp. 2462.
Cossins, A. R. & Bowler, K. 1987. Temperature Biology of Animals.
Chapman and Hall, New York, NY, 339 pp.
Demirbas, A. & Fatih Demirbas, M. 2011. Importance of algae oil
as a source of biodiesel. Energy Convers. Manage. 52:16370.
Dempster, T. A. & Sommerfeld, M. 1998. Effects of environmental conditions on growth and lipid accumulation in Nitzschia
communis (Bacillariophyceae). J. Phycol. 34:71221.
Di Toro, D. M. 1978. Optics of turbid estuarine waters: approximations and applications. Water Res. 12:105968.
DiToro, D. M., OConnor, D. J., Thomann, R. V. & Mancini, J. L.
1975. Phytoplankton-zooplankton-nutrient interaction model
for Western Lake Erie. In Patten, B. C. [Ed.] Systems Analysis
and Simulation in Ecology. Academic Press, New York, NY, pp.
42374.
DiToro, D. M., OConnor, D. J. & Thomann, R. V. 1971. A
dynamic model of the phytoplankton population in the Sacramento-San Joaquin Delta. In American Chemical Society
[Ed.] Nonequilibrium Systems in Natural Water Chemistry. Washington, DC, pp. 13180.
Doherty, J. E. 2009. Manual for PEST: Model Independent Parameter
Estimation. In Doherty, J. E. [Ed.] Watermark Numerical
Computing, Brisbane, Australia, 336 pp.
Doherty, J. E. 2010. Addendum to the PEST Manual. In Doherty, J.
E. [Ed.] Watermark Numerical Computing, Brisbane, Australia, 131 pp.
Fedorov, A. S., Kosourov, S., Ghirardi, M. L. & Seibert, M. 2005.
Continuous H2 photoproduction by Chlamydomonas reinhardtii
using a novel two-stage, sulfate-limited chemostat system.
Appl. Biochem. Biotechnol. 121124:40312.
Ghirardi, M. L., Zhang, L., Lee, J. W., Flynn, T., Seibert, M.,
Greenbaum, E. & Melis, A. 2000. Microalgae: a green source
of renewable H2. Trends Biotechnol. 18:50611.

SIMULATING PH EFFECTS ON ALGAL GROWTH

Haaland, D. M., Easterling, R. G. & Vopicka, D. A. 1985. Multivariate least-squares methods applied to the quantitative spectral-analysis of multicomponent samples. Appl. Spectrosc.
39:7383.
Hecky, R. E., Campbell, P. & Hendzel, L. L. 1993. The stoichiometry of carbon, nitrogen, and phosphorus in particulate
matter of lakes and oceans. Limnol. Oceanogr. 38:70924.
Hillebrand, H. & Sommer, U. 1999. The nutrient stoichiometry
of benthic microalgal growth: redfield proportions are
optimal. Limnol. Oceanogr. 44:4406.
James, S. C. & Boriah, V. 2010. Modeling algae growth in an
open-channel raceway. J. Comput. Biol. 17:895906.
Kapdan, I. K. & Kargi, F. 2006. Bio-hydrogen production from
waste materials. Enzyme Microb. Tech. 38:56982.
Mayo, A. W. 1997. Effects of temperature and pH on the kinetic
growth of unialga Chlorella vulgaris cultures containing bacteria. Water Environ. Res. 69:6472.
Melis, A. 2002. Green alga hydrogen production: progress, challenges and prospects. Int. J. Hydrogen Energ. 27:121728.
Metting, B. & Pyne, J. W. 1986. Biologically active compounds
from microalgae. Enzyme Microb. Tech. 8:38694.
Monod, J. 1949. The growth of bacterial cultures. Ann. Rev. Microbiol. 3:37194.
NCMA 2013. CCMP1776 Nannochloropsis salina strain information.
National Center for Marine Algae and Microbiota, https://
ncma.bigelow.org/node/1/strain/CCMP1776.
Pedroni, P., Davison, J., Beckert, H., Bergman, P. & Benemann, J.
2001. A proposal to establish an international network on
biofixation of CO2 and greenhouse gas abatement with microalgae. J. Energ. Environ. Res. 1:13650.
Raven, J. A. & Johnston, A. M. 1991. Mechanisms of inorganic-carbon
acquisition in marine phytoplankton and their implications
for the use of other resources. Limnol. Oceanogr. 36:170114.
Redfield, A. C. 1934. On the proportions of organic derivatives in sea
water and their relation to the composition of plankton. In
Daniel, R. J. [Ed.] James Johnstone Memorial Volume. University
Press of Liverpool, London, pp. 17692.
Ricklefs, R. E. & Miller, G. L. 2000. Ecology. Macmillan, New York,
896 pp.
Riley, G. A. 1956. Oceanography of long Island sound, 1952
1954; II. Physical oceanography. Bull. Bingham. Oceanogr. Coll.
15:156.
Sawayama, S., Inoue, S., Dote, Y. & Yokoyama, S.-Y. 1995. CO2 fixation and oil production through microalga. Energy Convers.
Manage. 36:72931.

615

Smith, R. C. & Baker, K. S. 1981. Optical properties of the

clearest natural waters (200800 nm). Appl. Optics 20:177
84.
Sompech, K., Chisti, Y. & Srinophakun, T. 2012. Design of raceway ponds for producing microalgae. Biofuels 3:38797.
Spolaore, P., Joannis-Cassan, C., Duran, E. & Isambert, A. 2006. Commercial applications of microalgae. J. Biosci. Bioeng. 101:8796.
Timlin, J. A., Jones, H. D. T., Reichardt, T. A., Hanson, D. T.,
Powell, A. J., James, S. C., Gharagozloo, P. E. et al. 2012.
From Benchtop to Raceway: Spectroscopic Signatures of Dynamic
Processes in Algal Communities. Sandia National Laboratories,
Albuquerque, NM, 74 pp.
Van Wagenen, J., Miller, T. W., Hobbs, S., Hook, P., Crowe, B. &
Huesemann, M. 2012. Effects of light and temperature on
fatty acid production in Nannochloropsis salina. Energies 5:
73140.
Vance, P. & Spalding, M. H. 2005. Growth, photosynthesis, and
gene expression in Chlamydomonas over a range of CO2 concentrations and CO2/O2 ratios: CO2 regulates multiple acclimation states. Can. J. Bot. 83:796809.
Yun, Y.-S., Lee, S. B., Park, J. M., Lee, C.-I. & Yang, J.-W. 1997.
Carbon dioxide fixation by algal cultivation using wastewater
nutrients. Chem. Technol. Biotechnol. 69:4515.

Supporting Information
Additional Supporting Information may be
found in the online version of this article at the
publishers web site:
Appendix S1. pH and algal growth.
Appendix S2. Verification model.
Figure S1. Schematic of the lake used to verify
the model.
Table S1. Parameters for verification against
Chapra (1997) (Example 33.2).

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