@article{MaityBandyopadhyayChattopadhyayetal.2013,
  author    = {Maity, Alok Kumar and Bandyopadhyay, Arnab and Chattopadhyay, Sudip and Chaudhuri, Jyotipratim Ray and Metzler, Ralf and Chaudhury, Pinaki and Banik, Suman K.},
  title     = {Quantification of noise in bifunctionality-induced post-translational modification},
  series = {Physical review : E, Statistical, nonlinear and soft matter physics},
  volume    = {88},
  journal   = {Physical review : E, Statistical, nonlinear and soft matter physics},
  number    = {3},
  publisher = {American Physical Society},
  address   = {College Park},
  issn      = {1539-3755},
  doi       = {10.1103/PhysRevE.88.032716},
  pages     = {7},
  year      = {2013},
  abstract  = {We present a generic analytical scheme for the quantification of fluctuations due to bifunctionality-induced signal transduction within the members of a bacterial two-component system. The proposed model takes into account post-translational modifications in terms of elementary phosphotransfer kinetics. Sources of fluctuations due to autophosphorylation, kinase, and phosphatase activity of the sensor kinase have been considered in the model via Langevin equations, which are then solved within the framework of linear noise approximation. The resultant analytical expression of phosphorylated response regulators are then used to quantify the noise profile of biologically motivated single and branched pathways. Enhancement and reduction of noise in terms of extra phosphate outflux and influx, respectively, have been analyzed for the branched system. Furthermore, the role of fluctuations of the network output in the regulation of a promoter with random activation-deactivation dynamics has been analyzed.},
  language  = {en}
}
@article{TalukderSenMetzleretal.2013,
  author    = {Talukder, Srijeeta and Sen, Shrabani and Metzler, Ralf and Banik, Suman K. and Chaudhury, Pinaki},
  title     = {Stochastic optimization-based study of dimerization kinetics},
  series = {JOURNAL OF CHEMICAL SCIENCES},
  volume    = {125},
  journal   = {JOURNAL OF CHEMICAL SCIENCES},
  number    = {6},
  publisher = {INDIAN ACAD SCIENCES},
  address   = {BANGALORE},
  issn      = {0974-3626},
  pages     = {1619 -- 1627},
  year      = {2013},
  abstract  = {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.},
  language  = {en}
}