@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{TalukderSenChakrabortietal.2014,
  author    = {Talukder, Srijeeta and Sen, Shrabani and Chakraborti, Prantik and Metzler, Ralf and Banik, Suman K. and Chaudhury, Pinaki},
  title     = {Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA},
  series = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr},
  volume    = {140},
  journal   = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr},
  number    = {12},
  publisher = {American Institute of Physics},
  address   = {Melville},
  issn      = {0021-9606},
  doi       = {10.1063/1.4869112},
  pages     = {10},
  year      = {2014},
  abstract  = {We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction epsilon(hb)(AT) for an AT base pair and the ring factor. turn out to be the most sensitive parameters. In addition, the stacking interaction epsilon(st)(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased way of optimization. (c) 2014 AIP Publishing LLC.},
  language  = {en}
}
@misc{TalukderSenChakrabortietal.2014,
  author    = {Talukder, Srijeeta and Sen, Shrabani and Chakraborti, Prantik and Metzler, Ralf and Banik, Suman K. and Chaudhury, Pinaki},
  title     = {Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA},
  series = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr},
  volume    = {140},
  journal   = {The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr},
  number    = {14},
  publisher = {American Institute of Physics},
  address   = {Melville},
  issn      = {0021-9606},
  doi       = {10.1063/1.4871297},
  pages     = {1},
  year      = {2014},
  abstract  = {We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters is estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence dependent nature of the breathing dynamics of hetero-polymeric DNA. Out of the 14 model parameters for DNA stability in the statistical Poland-Scheraga approach, the hydrogen bond interaction epsilon(hb)(AT) for an AT base pair and the ring factor. turn out to be the most sensitive parameters. In addition, the stacking interaction epsilon(st)(TA-TA) for an TA-TA nearest neighbor pair of base-pairs is found to be the most sensitive one among all stacking interactions. Moreover, we also establish that the nature of stacking interaction has a deciding effect on the DNA breathing dynamics, not the number of times a particular stacking interaction appears in a sequence. We show that the sensitivity analysis can be used as an effective measure to guide a stochastic optimization technique to find the kinetic rate constants related to the dynamics as opposed to the case where the rate constants are measured using the conventional unbiased way of optimization.},
  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}
}