Articles written in Journal of Chemical Sciences
Volume 121 Issue 5 September 2009 pp 905-911
We have explored the weak noise limit of stochastic processes in nonlinear dissipative systems which admit of stable dynamical attractors in absence of noise. An interesting `detailed balance’ like condition in the steady state which is manifested in the time reversal symmetry between growth and decay of fluctuation far from equilibrium, similar to what is observed in thermally equilibrated systems, is demonstrated.
Volume 125 Issue 6 November 2013 pp 1619-1627 Regular Articles
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.