Stochastic optimization-based study of dimerization kinetics

We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end, we study dimerization kinetics of protein as a model system. We follow the dimerization kinetics using a stochastic simulation algorithm and combine it with three different optimization techniques (genetic algorithm, simulated annealing and parallel tempering) to obtain the rate constants involved in each reaction step. We find good convergence of the numerical scheme to the rate constants of the process. We also perform a sensitivity test on the reaction kinetic parameters to see the relative effects of the parameters for the associated profile of the monomer/dimer distribution.

Metadaten
Author details:	Srijeeta Talukder, Shrabani Sen, Ralf Metzler ORCiD GND, Suman K. Banik, Pinaki Chaudhury
ISSN:	0974-3626
ISSN:	0973-7103
Title of parent work (English):	JOURNAL OF CHEMICAL SCIENCES
Publisher:	INDIAN ACAD SCIENCES
Place of publishing:	BANGALORE
Publication type:	Article
Language:	English
Year of first publication:	2013
Publication year:	2013
Release date:	2017/03/26
Tag:	Stochastic optimization; dimerization kinetics; probability distribution function; sensitivity analysis; stochastic simulation algorithm
Volume:	125
Issue:	6
Number of pages:	9
First page:	1619
Last Page:	1627
Funding institution:	University Grants Commission (UGC), New Delhi; Academy of Finland; UGC, New Delhi; Centre for Research on Nano Science and Nano Technology, University of Calcutta [Conv/002/Nano RAC (2008)]; Bose Institute through Institutional Programme VI - Development of Systems Biology