Dokument-ID Dokumenttyp Verfasser/Autoren Herausgeber Haupttitel Abstract Auflage Verlagsort Verlag Erscheinungsjahr Seitenzahl Schriftenreihe Titel Schriftenreihe Bandzahl ISBN Quelle der Hochschulschrift Konferenzname Quelle:Titel Quelle:Jahrgang Quelle:Heftnummer Quelle:Erste Seite Quelle:Letzte Seite URN DOI Abteilungen
OPUS4-37932 misc Talukder, Srijeeta; Sen, Shrabani; Chakraborti, Prantik; Metzler, Ralf; Banik, Suman K.; Chaudhury, Pinaki Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA 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. Melville American Institute of Physics 2014 1 The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr 140 14 10.1063/1.4871297 Institut für Physik und Astronomie
OPUS4-37985 Wissenschaftlicher Artikel Talukder, Srijeeta; Sen, Shrabani; Chakraborti, Prantik; Metzler, Ralf; Banik, Suman K.; Chaudhury, Pinaki Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA 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. Melville American Institute of Physics 2014 10 The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr 140 12 10.1063/1.4869112 Institut für Physik und Astronomie
OPUS4-34612 Wissenschaftlicher Artikel Talukder, Srijeeta; Sen, Shrabani; Metzler, Ralf; Banik, Suman K.; Chaudhury, Pinaki Stochastic optimization-based study of dimerization kinetics 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. BANGALORE INDIAN ACAD SCIENCES 2013 9 JOURNAL OF CHEMICAL SCIENCES 125 6 1619 1627