Estimation of kinetic parameters is a key step in modelling biochemical reaction networks as, often, their direct estimation is expensive, time-consuming or even infeasible. This article proposes a parameter estimation procedure, which explicitly takes into account the model structure of the biological systems. The convergence is guaranteed using a dissipativity argument and a coordinate transf...

Reaction networks are commonly used to model the dynamics of populations subject to transformations that follow an imposed stoichiometry. This paper focuses on the efficient characterisation of dynamical properties of Discrete Reaction Networks (DRNs). DRNs can be seen as modeling the underlying discrete nondeterministic transitions of stochastic models of reaction networks. In that sense, a pr...

Currently, kinetic data is either collected under steady-state conditions in flow or by generating time-series data in batch. Batch experiments are generally considered to be more suitable for the generation of kinetic data because of the ability to collect data from many time points in a single experiment. Now, a method that rapidly generates time-series reaction data from flow reactors by con...

Understanding the fundamentals of arsenic adsorption and oxidation reactions is critical for predicting its transport dynamics in groundwater systems. We completed batch experiments to study the interactions of arsenic with a common MnO2(s) mineral, pyrolusite. The reaction kinetics and adsorption isotherm developed from the batch experiments were integrated into a scalable reactive transport m...

Applying molecular-beam methods to a nanolithographically prepared planar PdSiO2 model catalyst, we have performed a detailed study of the kinetics of CO oxidation. The model catalyst was prepared by electron-beam lithography, allowing individual control of particle size and position. The sample was structurally characterized by atomic force microscopy and scanning electron microscopy before an...

mathematical modeling and simulation of microbial polyhydroxybutyrate (phb) production process is beneficial for optimization, design, and control purposes. in this study a batch model developed by mulchandani et al., [1] was used to simulate the process in matlab environment. it was revealed that the kinetic model parameters were estimated off the optimal or at a local optimal point. therefore...

Kinetic fluorescence detection (KFD) was employed to determine the concentrations of two overlapped components after a thin-layer chromatographic ("IC) separation. Two amino acids, glycine and glutamine, were used as model analytes. These species exhibited very similar retardation factors (Rf) under our experimental conditions. A reaction that produced a fluorescent product was performed subseq...

Metabolic networks can be turned into kinetic models in a predefined steady state by sampling the reaction elasticities in this state. Elasticities for many reversible rate laws can be computed from the reaction Gibbs free energies, which are determined by the state, and from physically unconstrained saturation values. Starting from a network structure with allosteric regulation and consistent ...