Tag Archives: Petri nets

Application of petri nets methodology to determine biophysicochemical parameters of mitochondria functioning

H. V. Danylovych*, A. Yu. Chunikhin, Yu. V. Danylovych, S. O. Kosterin

Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, Kyiv;
*e-mail: danylovych@biochem.kiev.ua

Received: 01 Nobember 2020; Accepted: 17 May 2021

With the use of Petri net methodology a mathematical simulation model able to predict simultaneous changes in biophysicochemical parameters of mitochondria functioning was developed. The model allowed to interconnect in time the changes in mitochondria hydrodynamic diameter, electronic transport chain functioning, endogenous fluorescence of adenine nucleotides, DCF fluorescence signal of ROS production and NaN3 effects. It was shown that the calculated values of the studied biophysicalchemical parameters correspond to those obtained experimentally. The model permit to link mitochondrial functional changes and their  structural representation and to optimize significantly experimental procedures.

The use of the Petri net method in the simulation modeling of mitochondrial swelling

Yu. V. Danylovych, A. Y. Chunikhin,  G. V. Danylovych, O. V. Kolomiets

Palladin Institute of Biochemistry, National Academy
of Sciences of Ukraine, Kyiv;
e-mail: danylovych@biochem.kiev.ua

Using photon correlation spectroscopy, which allows investigating changes in the hydrodynamic dia­meter of the particles in suspension, it was shown that ultrahigh concentrations of Ca2+ (over 10 mM) induce swelling of isolated mitochondria. An increase in hydrodynamic diameter was caused by an increase of non-specific mitochondrial membrane permeability to Ca ions, matrix Ca2+ overload, activation of ATP- and Ca2+-sensitive K+-channels, as well as activation of cyclosporin-sensitive permeability transition pore. To formalize the experimental data and to assess conformity of experimental results with theoretical predictions we developed a simulation model using the hybrid functional Petri net method.