Stochastic optimization-based study of dimerization kinetics

Journal of Chemical Sciences

Shrabani Sen²  Suman K Banik4³  Ralf Metzler2 3¹  Srijeeta Talukder²  Pinaki Chaudhury1² 

[1] Institute for Physics and Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany$$;Department of Chemistry, University of Calcutta, 92 A P C Road, Kolkata 700 009, India$$;Department of Chemistry, Bose Institute, 93/1 A P C Road, Kolkata 700 009, India$$

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

DOI  :  

来源: Indian Academy of Sciences

【 摘 要 】

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.

【 授权许可】

Unknown