Lan Smith, PhD
(replace "_at_" with "@" in the above address)
Marine Ecosystem Modeling Group
Ecosystem Change Research Program
Frontier Research Center for Global Change
study biogeochemical cycles and lower-trophic ecosystems
using modeling and data analysis. I particularly enjoy studying and
developing models of the coupled
cycles of multiple elements. Recently
I have been applying data assimilation to fit models to data
This allows a quantitative comparison of the ability of different
simulate the measurements.
modeling applied to multi-nutrient uptake kinetics
by the success of the
model of Pahlow (Mar. Ecol. Prog. Ser., 287, p. 33-43, 2005) in describing various processes of
phytoplankton growth with fewer parameters than previous models, I
began thinking about whether such an approach might yield simpler,
better models for uptake of multiple nutrients.
Michaelis-Menten equation often provides a reasonable description of
However, when ratios of ambient nutrient concentrations differ greatly
from the optimal ratio for phytoplankton, straightforward application
of separate Michaelis-Menten equations (one for each nutrient) greatly
overestimates uptake of any nutrient other than the growth-limiting
nutrient. Such extreme nutrient ratios occur because of human
activities (e.g., nitrogen discharge into rivers and coastal waters)
and because of natural processes like nitrogen fixation. Pahlow
(2005) presented a new optimality-based
equation to describe uptake of a single nutrient, and I began by
thinking of how it could be extended to multiple nutrients.
thought and many trials (and errors!) I hit upon a strategy that seems
to work quite well (based on fits to data from chemostat experiments).
I call the new model the SPONGE
(Simple Phytoplankton Optimal Nutrient
Gathering Equations). For a more detailed description, please
see my SPONGE Page.
describing and validating this
model has recently been
accepted for publication in
Limnology and Oceanography. You can download a .pdf of
it here, or from the journal's
website (for free), at: http://aslo.org/lo/toc/vol_52/issue_4/1545.pdf.
There is also an important typesetting
error in an equation that is central to the model. Please see the correct equation, here.
New: I have prepared a brief Users' Guide to applying Optimal
Uptake kinetics in planktonic ecosystem models with fixed-composition
(e.g., fixed C:N:P ratios) for phytoplankton.
(data assimilation) to fit models to data can produce unexpected
results. In a study
(recently accepted for
publication in Ecological Modeling),
I compared two
published models of
photoacclimation for phytoplankton. You can download the file
These models describe
phytoplankton's acclimation to nutrient and light environment. The
author of a recently published model claimed that it had an inherent
over previously publshed models, namely in its ability to simulate the
initial lag phase (before rapid growth begins). Authors of a previously
published model had found that their model could not reproduce this lag
phase. By fitting both models to the same data set, I showed that the
older model could indeed simulate the whole data set, including the
initial lag phase, at least as well as the newer model. The reason this
was possible provided insight into the processes responsible for
the initial lag phase. Still, the newer
optimality-based model has advantages (e.g., fewer parameters and
better agreement with the measured Chl:N ratios).
assimilation can also constrain material flows (e.g. of
or carbon) for which we rarely (if ever) have direct observations.
quantitative chemical and biological observations are of
concentrations.) One of my recent papers describes the application of
assimilation to constrain flows of nitrogen in an ecosystem model that
the flexible composition of phytoplankton. You can download the file
Mohan P. Niraula,
Casareto, S. Lan
Examining the effects of
nutrients on the composition and size of
phytoplankton with a new approach: using incubations of unaltered
mesopelagic seawater. J. Expt. Mar.
Biol. Ecol., In Press, February, 2007
Lan Smith and Yasuhiro Yamanaka.
Optimization-based model of
multi-nutrient uptake kinetics. Limnology
and Oceanography. 52: 1545-1558, 2007.
Lan Smith and
Quantitative comparison of
photoacclimation models for marine
phytoplankton. Ecological Modeling,
S. Lan Smith, B. E. Casareto, M. P. Niraula, Y. Suzuki, J. C.
Hargreaves, J. D. Annan, and Y. Yamanaka.
Examining the regeneration of nitrogen by assimilating data from
incubations into a multi-element ecosystem model. J. Marine Systems, vol. 64, p.
Kishi, M. J., D. L.
Eslinger, M. Kashiwai, B. A. Megrey, D. M. Ware, F.
Werner, M. Aita-Noguchi, T. Azumaya, M. Fujii, S. Hashimoto, H. Iizumi,
Ishida, S. Kang. G. A. Kantakov, H. Kim, K. Komatsu, V. V. Navrotsky,
Smith, K. Tadokoro, A. Tsuda, O. Yamamura, Y. Yamanaka, K. Yokouchi, N.
J. Zhang, Y. I. Zuenko, V. I. Zvalinsky. NEMURO: Introduction to a
lower trophic level model for the North
marine ecosystem. Ecological
Megrey, B. A., K. A. Rose, R.
Klumb, D. Hay, F. E. Werner, D. L.
Eslinger, and S. L.
A biogenic population dynamics
model of Pacific Herring (Clupea,
coupled to NEMURO: Dynamics, description, validation and sensitivity
Modeling, DOI: 10.1016/j.ecolmodel.2006.08.020, 2007
Mohan P. Niraula, Beatriz E.
Casareto, Takayuki Hanai, S. Lan Smith and
assemblages using incubations of unaltered
water; investigating nutrient-size relationships, Journal of
vol.17, no.2, p.
S. Lan Smith, Yasuhiro
Yamanaka and Michio J. Kishi.
simulations of Stn. ALOHA with a multi-element
model, Journal of Oceanography,
vol. 61, no. 1,
P. R. Jaffe, S. Wang,
P. L. Kallin and S. L. Smith.
The Dynamics of Arsenic in
Saturated Porous Media: Fate and Transport
for Deep-Water Sediments, Wetland Sediments and Groundwater
Rock Interactions, Ore deposits, and Environmental Geochemistry: A
David Crerar. R. Hellman and S.A. Wood., Eds. The Geochemical Society,
Publication No 7., 2001
S. Lan Smith and Peter
Modeling the Transport and
Reaction of Trace Metals in Water Saturated
and Sediments, Water Resources Research, vol. 34,
no. 11, p. 3135-3147, 1998
S. Lan Smith, Yasuhiro
Yamanaka and Michio J. Kishi
Simulating the Cycling of
Carbon with a Nitrogen-based Oceanic
PICES (North Pacific Marine Science Organization) Scientific Report No.
20, pp. 6-7, 2002
S. Lan Smith
Modeling the Transport of
Trace Metals in Water Saturated Soils and
as Affected by the Biodegradation of Organic Substrates via Various
Electron Acceptors, Ph.D. Thesis, Princeton University, Dept. of Civil and
Engineering, Environmental Engineering and Water Resources Program,
Engineering and Water
Dept. of Civil Engineering
Princeton University, Princeton, NJ
(attended Sept., 1992 to May, 1998)
Bachelor of Science, Chemical
California Institute of
Technology, Pasadena, CA (attended Sept., 1988
to May, 1992)
note: Under Construction!
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