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https://www.ias.ac.in/article/fulltext/jcsc/125/06/1619-1627

Stochastic optimization; dimerization kinetics; sensitivity analysis; stochastic simulation algorithm; probability distribution function.

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.

Srijeeta Talukder¹ Shrabani Sen¹ Ralf Metzler^{2 3} Suman K Banik⁴ Pinaki Chaudhury¹

1. Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India
2. Institute for Physics and Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany
3. Physics Department, Tampere University of Technology, FI-33101 Tampere, Finland
4. Department of Chemistry, Bose Institute, 93/1 A P C Road, Kolkata 700 009, India

Published

November 2013

Manuscript received

8 March 2013

Manuscript revised

2 July 2013

Accepted

12 August 2013