Introduction of a New Platform for Parameter Estimation of Kinetically Complex Environmental Systems

Overview

Journal Environ Model Softw

Date 2017 Dec 5

PMID 29200932

Citations 3

Authors

Mehdi Gharasoo

Martin Thullner

Martin Elsner

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Deep Learning Neural Network Approach for Predicting the Sorption of Ionizable and Polar Organic Pollutants to a Wide Range of Carbonaceous Materials.

Sigmund G, Gharasoo M, Huffer T, Hofmann T Environ Sci Technol. 2020; 54(7):4583-4591.

PMID: 32124609 PMC: 7205386. DOI: 10.1021/acs.est.9b06287.

Modeling of Contaminant Biodegradation and Compound-Specific Isotope Fractionation in Chemostats at Low Dilution Rates.

Gharasoo M, Ehrl B, Cirpka O, Elsner M Environ Sci Technol. 2018; 53(3):1186-1196.

PMID: 30339002 PMC: 6986770. DOI: 10.1021/acs.est.8b02498.

Isotope Fractionation Pinpoints Membrane Permeability as a Barrier to Atrazine Biodegradation in Gram-negative Polaromonas sp. Nea-C.

Ehrl B, Gharasoo M, Elsner M Environ Sci Technol. 2018; 52(7):4137-4144.

PMID: 29495658 PMC: 6331012. DOI: 10.1021/acs.est.7b06599.

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