S. Lan Smith, PhD
Research Scientist
  e-mail:  lanimal_at_jamstec.go.jp
    (replace "_at_" with "@" in the above address)


Marine Ecosystem Modeling Group
Ecosystem Change Research Program
Frontier Research Center for Global Change
Yokohama, Japan

Research Interests

I study biogeochemical cycles and lower-trophic ecosystems (plankton) 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 models to simulate the measurements.

Optimality-based modeling applied to multi-nutrient uptake kinetics

Inspired by the success of the optimality-based 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.

The classic Michaelis-Menten equation often provides a reasonable description of uptake. 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.

After much 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.

A manuscript 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.

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.

Comparing Photoacclimation Models

Sometimes applying a mathematical algorithm (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 (.pdf) here. These models describe the phytoplankton's acclimation to nutrient and light environment. The author of a recently published model claimed that it had an inherent advantage 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).

Constraining Flows

Data assimilation can also constrain material flows (e.g. of nitrogen or carbon) for which we rarely (if ever) have direct observations. (Most quantitative chemical and biological observations are of concentrations.) One of my recent papers describes the application of data assimilation to constrain flows of nitrogen in an ecosystem model that includes the flexible composition of phytoplankton. You can download the file (.pdf) here.

Publications (with peer review)

Mohan P. Niraula, Beatriz E. Casareto, S. Lan Smith, Takayuki Hanai, and Yoshimi Suzuki.
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

S. Lan Smith and Yasuhiro Yamanaka.
Optimization-based model of multi-nutrient uptake kinetics. Limnology and Oceanography. 52: 1545-1558, 2007.

S. Lan Smith and Yasuhiro Yamanaka.
Quantitative comparison of photoacclimation models for marine phytoplankton. Ecological Modeling, DOI: 10.1016/j.ecolmodel.2006.09.016, 2007

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. 135-152, 2007

Kishi, M. J., D. L. Eslinger, M. Kashiwai, B. A. Megrey, D. M. Ware, F. E. Werner, M. Aita-Noguchi, T. Azumaya, M. Fujii, S. Hashimoto, H. Iizumi, Y. Ishida, S. Kang. G. A. Kantakov, H. Kim, K. Komatsu, V. V. Navrotsky, S. L. Smith, K. Tadokoro, A. Tsuda, O. Yamamura, Y. Yamanaka, K. Yokouchi, N. Yoshie, J. Zhang, Y. I. Zuenko, V. I. Zvalinsky. NEMURO: Introduction to a lower trophic level model for the North Pacific marine ecosystem. Ecological Modeling, DOI: 10.1016/j.ecolmodel.2006.08.021, 2007

Megrey, B. A., K. A. Rose, R. Klumb, D. Hay, F. E. Werner, D. L. Eslinger, and S. L. Smith.
A biogenic population dynamics model of Pacific Herring (Clupea, pallasii) coupled to NEMURO: Dynamics, description, validation and sensitivity analysis. Ecological Modeling, DOI: 10.1016/j.ecolmodel.2006.08.020, 2007

Mohan P. Niraula, Beatriz E. Casareto, Takayuki Hanai, S. Lan Smith and Yoshimi Suzuki.
Developing phytoplankton assemblages using incubations of unaltered mesopelagic water; investigating nutrient-size relationships, Journal of Eco-Engineering, vol.17, no.2, p. 121-131, 2005

S. Lan Smith, Yasuhiro Yamanaka and Michio J. Kishi.
Attempting consistent simulations of Stn. ALOHA with a multi-element ecosystem model, Journal of Oceanography, vol. 61, no. 1, p. 1-23, 2005

P. R. Jaffe, S. Wang, P. L. Kallin and S. L. Smith.
The Dynamics of Arsenic in Saturated Porous Media: Fate and Transport Modeling for Deep-Water Sediments, Wetland Sediments and Groundwater Environments, Water Rock Interactions, Ore deposits, and Environmental Geochemistry: A Tribute to David Crerar. R. Hellman and S.A. Wood., Eds. The Geochemical Society, Special Publication No 7., 2001

S. Lan Smith and Peter R. Jaffe.
Modeling the Transport and Reaction of Trace Metals in Water Saturated Soils and Sediments, Water Resources Research, vol. 34, no. 11, p. 3135-3147, 1998

Publications without peer review

S. Lan Smith, Yasuhiro Yamanaka and Michio J. Kishi
Simulating the Cycling of Carbon with a Nitrogen-based Oceanic Ecosystem Model, PICES (North Pacific Marine Science Organization) Scientific Report No. 20, pp. 6-7, 2002

PhD Thesis

S. Lan Smith
Modeling the Transport of Trace Metals in Water Saturated Soils and Sediments as Affected by the Biodegradation of Organic Substrates via Various Terminal Electron Acceptors, Ph.D. Thesis, Princeton University, Dept. of Civil and Environmental Engineering, Environmental Engineering and Water Resources Program, June, 1998


Ph.D., Environmental Engineering and Water Resources Program                                             June, 1998
Dept. of Civil Engineering Princeton University, Princeton, NJ (attended Sept., 1992 to May, 1998)

Bachelor of Science, Chemical Engineering                                                                                  June, 1992
California Institute of Technology, Pasadena, CA (attended Sept., 1988 to May, 1992)

note: Under Construction! ... This page is only the beginning.