—This paper introduces an improved Differential Evolution algorithm (IDE) which aims at improving its performance in estimating the relevant parameters for metabolic pathway data to simulate glycolysis pathway for yeast. Metabolic pathway data are expected to be of significant help in the development of efficient tools in kinetic modeling and parameter estimation platforms. Many computation alg...

Here we address the problem of parameter estimation (inverse problem) of nonlinear dynamic biochemical pathways. This problem is stated as a nonlinear programming (NLP) problem subject to nonlinear differential-algebraic constraints. These problems are known to be frequently ill-conditioned and multimodal. Thus, traditional (gradient-based) local optimization methods fail to arrive at satisfact...

The Farquhar—von Caemmerer—Berry (FvCB) biochemical model of photosynthesis, commonly used to estimate CO2 assimilation at various spatial scales from leaf to global, has been used to assess the impacts of climate change on crop and ecosystem productivities. However, it is widely known that the parameters in the FvCB model are difficult to accurately estimate. The objective of this study was to...

Nowadays, several techniques such as; Fuzzy Inference System (FIS) and Neural Network (NN) are employed for developing of the predictive models to estimate parameters of water quality. The main objective of this study is to compare between the predictive ability of the Adaptive Neuro-Fuzzy Inference System (ANFIS) model and Artificial Neural Network (ANN) model to estimate the Biochemical Oxyge...

SABIO-RK (http://sabio.villa-bosch.de/SABIORK), a database system we have developed to provide experimental data, offers information about biochemical reactions and their corresponding kinetics [1]. The database is populated by merging information about reactions and pathways mainly derived from public databases with the corresponding kinetic data manually extracted from literature. The integra...

MOTIVATION High-throughput technologies now allow the acquisition of biological data, such as comprehensive biochemical time-courses at unprecedented rates. These temporal profiles carry topological and kinetic information regarding the biochemical network from which they were drawn. Retrieving this information will require systematic application of both experimental and computational methods. ...

A fundamental problem of modelling in Systems Biology is to precisely characterise quantitative parameters, which are hard to measure experimentally. For this reason, it is common practise to estimate these parameter values, using evolutionary and other techniques, by fitting the model behaviour to given data. In this contribution, we extensively investigate the influence of exponentially scale...

Mathematical models in biochemical engineering field are usually composed by nonlinear kinetic equations, where the number of parameters that must be estimated from a set of experimental measurements is usually very high. In these cases, the estimation of the model parameters comprises numerical iterative methods for minimization of the objective function. Classical methods for minimization of ...

Advanced NMR and mass spectroscopy permit simultaneous measurements of time-course in-vivo metabolite concentrations within an organism. These metabolic profiles are loaded with structural and kinetic information regarding the biochemical networks from which they were drawn. Extracting these information will require systematic application of both experimental and computational techniques. S-sys...

We performed numerical analysis and design parameter optimization of a silicon-based grating waveguide refractive index (RI) sensor. The performance of the grating waveguide RI sensor was determined by the full-width at half-maximum (FWHM) and the shift in the resonance wavelength in the transmission spectrum. The transmission extinction, a major figure-of-merit of an RI sensor that reflects bo...