Introduction of a new platform for parameter estimation of kinetically complex environmental systems

A modeling framework (ReKinSim - Reaction Kinetics Simulator) is introduced, within which biogeochemical reactions in environmental systems can be described and inversely fitted to experimental data. Three key features of this simulation environment are: (1) a generic mathematical tool for solving sets of unlimited, arbitrary, non-linear ordinary differential equations; (2) no limitation to the number or type of reactions or other influential dynamics (e.g., isotope fractionation or small-scale mass-transfer limitations); (3) an easy to use and flexible module for nonlinear data-fitting. It allows users to easily define any kinetic model by a set of biogeochemical reactions relevant to the experimental application and to obtain the values of the kinetic parameters by fitting of the model to data. By allowing users to include the environmentally related processes and solving them along with the chemical kinetics, ReKinSim helps the user to elucidate the extent that these processes are controlled by factors other than kinetics. The novelty of the presented program primary lays in its unique combination of flexibility, computational efficiency and user-friendliness. ReKinSim's usability is showcased by four case studies of varying complexity, and compared against a set of currently available modeling tools.

[1]  Gaston H. Gonnet,et al.  On the LambertW function , 1996, Adv. Comput. Math..

[2]  Florian Centler,et al.  Modelling functional resilience of microbial ecosystems: Analysis of governing processes , 2017, Environ. Model. Softw..

[3]  Han-Qing Yu,et al.  Estimating the kinetic parameters of activated sludge storage using weighted non-linear least-squares and accelerating genetic algorithm. , 2009, Water research.

[4]  Douglas M. Bates,et al.  Nonlinear Regression Analysis and Its Applications , 1988 .

[5]  Peter Reichert,et al.  Design techniques of a computer program for the identification of processes and the simulation of water quality in aquatic systems , 1995 .

[6]  Thomas F. Coleman,et al.  An Interior Trust Region Approach for Nonlinear Minimization Subject to Bounds , 1993, SIAM J. Optim..

[7]  P. Kuzmič,et al.  Program DYNAFIT for the analysis of enzyme kinetic data: application to HIV proteinase. , 1996, Analytical biochemistry.

[8]  Pierre Régnier,et al.  A reactive transport modeling approach to simulate biogeochemical processes in pore structures with pore-scale heterogeneities , 2012, Environ. Model. Softw..

[9]  Lawrence F. Shampine,et al.  The MATLAB ODE Suite , 1997, SIAM J. Sci. Comput..

[10]  Stefano Marsili-Libelli,et al.  A modified Activated Sludge Model No. 3 ASM3) with two-step nitrification-denitrification , 2007, Environ. Model. Softw..

[11]  A. Hill,et al.  The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves , 1910 .

[12]  Mehdi Gharasoo,et al.  How the chemotactic characteristics of bacteria can determine their population patterns , 2014 .

[13]  John A. Nelder,et al.  A Simplex Method for Function Minimization , 1965, Comput. J..

[14]  Kenneth Levenberg.  A METHOD FOR THE SOLUTION OF CERTAIN NON – LINEAR PROBLEMS IN LEAST SQUARES , 1944 .

[15]  Robert E. Fuguitt,et al.  The Liquid Phase Thermal Isomerization of α-Pinene1a,1b , 1945 .

[16]  Carl I. Steefel,et al.  Modeling complex multi-component reactive-transport systems: towards a simulation environment based on the concept of a Knowledge Base , 2002 .

[17]  Arlen W. Harbaugh,et al.  MODFLOW-2000, The U.S. Geological Survey Modular Ground-Water Model - User Guide to Modularization Concepts and the Ground-Water Flow Process , 2000 .

[18]  Shmulik P. Friedman,et al.  Physical constraints affecting bacterial habitats and activity in unsaturated porous media – a review , 2007 .

[19]  C. Cho,et al.  CONVECTIVE TRANSPORT OF AMMONIUM WITH NITRIFICATION IN SOIL , 1971 .

[20]  Mudita Singhal,et al.  COPASI - a COmplex PAthway SImulator , 2006, Bioinform..

[21]  R. Rosenzweig,et al.  Modeling biofilm dynamics and hydraulic properties in variably saturated soils using a channel network model , 2014 .

[22]  O. Atteia,et al.  Rayleigh equation for evolution of stable isotope ratios in contaminant decay chains , 2014 .

[23]  Kenneth A. Johnson,et al.  Global kinetic explorer: a new computer program for dynamic simulation and fitting of kinetic data. , 2009, Analytical biochemistry.

[24]  O. Cirpka,et al.  Model complexity needed for quantitative analysis of high resolution isotope and concentration data from a toluene-pulse experiment. , 2013, Environmental science & technology.

[25]  Hauke Harms,et al.  Impact of bioavailability restrictions on microbially induced stable isotope fractionation. 1. Theoretical calculation. , 2008, Environmental science & technology.

[26]  D. Hunkeler,et al.  Modeling chlorine isotope trends during sequential transformation of chlorinated ethenes. , 2009, Environmental science & technology.

[27]  Olaf Kolditz,et al.  GeoSysBRNS - A flexible multidimensional reactive transport model for simulating biogeochemical subsurface processes , 2010, Comput. Geosci..

[28]  D. Marquardt.  An Algorithm for Least-Squares Estimation of Nonlinear Parameters , 1963 .

[29]  I. Langmuir.  THE ADSORPTION OF GASES ON PLANE SURFACES OF GLASS, MICA AND PLATINUM. , 1918 .

[30]  K. Cantrell,et al.  Adsorption–Desorption Processes in Subsurface Reactive Transport Modeling , 2007 .

[31]  F. Centler,et al.  Quantification of organic pollutant degradation in contaminated aquifers using compound specific stable isotope analysis – Review of recent developments , 2012 .

[32]  R. Jennrich,et al.  Dud, A Derivative-Free Algorithm for Nonlinear Least Squares , 1978 .

[33]  Matthew R. Hipsey,et al.  Stable isotopes reduce parameter uncertainty of an estuarine carbon cycling model , 2016, Environ. Model. Softw..

[34]  F. Centler,et al.  Kinetics of Substrate Biodegradation under the Cumulative Effects of Bioavailability and Self-Inhibition. , 2015, Environmental science & technology.

[35]  Albert J. Valocchi,et al.  Two-dimensional concentration distribution for mixing-controlled bioreactive transport in steady state , 2007 .

[36]  J B BEST,et al.  The inference of intracellular enzymatic properties from kinetic data obtained on living cells. I. Some kinetic considerations regarding an enzyme enclosed by a diffusion barrier. , 1955, Journal of cellular and comparative physiology.

[37]  Thomas Petzoldt,et al.  An R-package to boost fitness and life expectancy of environmental models , 2017, Environ. Model. Softw..

[38]  A. G. McKendrick,et al.  XLV.—The Rate of Multiplication of Micro-organisms: A Mathematical Study , 1912 .

[39]  Pierre Regnier,et al.  Modeling the impact of microbial activity on redox dynamics in porous media , 2005 .

[40]  Kevin J Farley,et al.  Tableau input coupled kinetic equilibrium transport (TICKET) model. , 2008, Environmental science & technology.

[41]  John F. MacGregor,et al.  ASQC Chemical Division Technical Conference 1971 Prize Winning Paper Some Problems Associated with the Analysis of Multiresponse Data , 1973 .

[42]  Giuseppe Guglielmi,et al.  Modelling respirometric tests for the assessment of kinetic and stoichiometric parameters on MBBR biofilm for municipal wastewater treatment , 2010, Environ. Model. Softw..

[43]  M. V. van Loosdrecht,et al.  Influence of interfaces on microbial activity. , 1990, Microbiological reviews.

[44]  Albert J. Valocchi,et al.  Accuracy of operator splitting for advection‐dispersion‐reaction problems , 1992 .

[45]  Pierre Regnier,et al.  Modeling Microbially Induced Carbon Degradation in Redox-Stratified Subsurface Environments: Concepts and Open Questions , 2007 .

[46]  B. Sleep,et al.  Evaluation of isotopic enrichment factors for the biodegradation of chlorinated ethenes using a parameter estimation model: toward an improved quantification of biodegradation. , 2006, Environmental science & technology.

[47]  P. Reichert.  AQUASIM-a tool for simulation and data analysis of aquatic systems , 1994 .

[48]  J. Middelburg,et al.  Isotope data improve the predictive capabilities of a marine biogeochemical model , 2012 .

[49]  Sanyi Tang,et al.  One-compartment model with Michaelis-Menten elimination kinetics and therapeutic window: an analytical approach , 2007, Journal of Pharmacokinetics and Pharmacodynamics.

[50]  P. Maloszewski,et al.  Direct experimental evidence of non-first order degradation kinetics and sorption-induced isotopic fractionation in a mesoscale aquifer: 13C/12C analysis of a transient toluene pulse. , 2013, Environmental science & technology.

[51]  M. Elsner.  Stable isotope fractionation to investigate natural transformation mechanisms of organic contaminants: principles, prospects and limitations. , 2010, Journal of environmental monitoring : JEM.

[52]  H. Harms,et al.  Influence of substrate diffusion on degradation of dibenzofuran and 3-chlorodibenzofuran by attached and suspended bacteria , 1994, Applied and environmental microbiology.