Spreadsheet Method for Evaluation of Biochemical Reaction Rate

Coefficients and Their Uncertainties by Weighted Nonlinear

Least-Squares Analysis of the Integrated Monod Equation
1. Laurence H. Smith1,*,
2. Perry L. McCarty2, and
3. Peter K. Kitanidis2
+Author Affiliations
1
1. Institute of Technology and Engineering, Massey University, Palmerston North, New Zealand, and
2. Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305-
2
4020

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ABSTRACT

A convenient method for evaluation of biochemical reaction rate coefficients and their uncertainties is described. The
motivation for developing this method was the complexity of existing statistical methods for analysis of biochemical rate
equations, as well as the shortcomings of linear approaches, such as Lineweaver-Burk plots. The nonlinear least-squares
method provides accurate estimates of the rate coefficients and their uncertainties from experimental data. Linearized
methods that involve inversion of data are unreliable since several important assumptions of linear regression are violated.
Furthermore, when linearized methods are used, there is no basis for calculation of the uncertainties in the rate
coefficients. Uncertainty estimates are crucial to studies involving comparisons of rates for different organisms or
environmental conditions. The spreadsheet method uses weighted least-squares analysis to determine the best-fit values of
the rate coefficients for the integrated Monod equation. Although the integrated Monod equation is an implicit expression
of substrate concentration, weighted least-squares analysis can be employed to calculate approximate differences in
substrate concentration between model predictions and data. An iterative search routine in a spreadsheet program is
utilized to search for the best-fit values of the coefficients by minimizing the sum of squared weighted errors. The
uncertainties in the best-fit values of the rate coefficients are calculated by an approximate method that can also be
implemented in a spreadsheet. The uncertainty method can be used to calculate single-parameter (coefficient) confidence
intervals, degrees of correlation between parameters, and joint confidence regions for two or more parameters. Example
sets of calculations are presented for acetate utilization by a methanogenic mixed culture and trichloroethylene
cometabolism by a methane-oxidizing mixed culture. An additional advantage of application of this method to the
integrated Monod equation compared with application of linearized methods is the economy of obtaining rate coefficients
from a single batch experiment or a few batch experiments rather than having to obtain large numbers of initial rate
measurements. However, when initial rate measurements are used, this method can still be used with greater reliability
than linearized approaches.

Approximate Primal Solutions and Rate Analysis for Dual

Subgradient Methods
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 Article Data
History

Submitted: 13 November 2007

Accepted: 09 October 2008

Published online: 11 February 2009

Keywords

subgradient methods, averaging, approximate primal solutions, convergence rate estimates

AMS Subject Headings

90C25, 90C30

Publication Data
ISSN (print): 1052-6234

ISSN (online): 1095-7189

Publisher: Society for Industrial and Applied Mathematics

Angelia Nedi and Asuman Ozdaglar

https://doi.org/10.1137/070708111

In this paper, we study methods for generating approximate primal solutions as a byproduct of subgradient methods
applied to the Lagrangian dual of a primal convex (possibly nondifferentiable) constrained optimization problem. Our
work is motivated by constrained primal problems with a favorable dual problem structure that leads to efficient
implementation of dual subgradient methods, such as the recent resource allocation problems in large-scale
networks. For such problems, we propose and analyze dual subgradient methods that use averaging schemes to
generate approximate primal optimal solutions. These algorithms use a constant stepsize in view of its simplicity and
practical significance. We provide estimates on the primal infeasibility and primal suboptimality of the generated
approximate primal solutions. These estimates are given per iteration, thus providing a basis for analyzing the trade-
offs between the desired level of error and the selection of the stepsize value. Our analysis relies on the Slater
condition and the inherited boundedness properties of the dual problem under this condition. It also relies on the
boundedness of subgradients, which is ensured by assuming the compactness of the constraint set.

Read More: http://epubs.siam.org/doi/abs/10.1137/070708111