TY  - JOUR
A1  - Talukder, Srijeeta
A1  - Sen, Shrabani
A1  - Chakraborti, Prantik
A1  - Metzler, Ralf
A1  - Banik, Suman K.
A1  - Chaudhury, Pinaki
T1  - Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA
JF  - The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr
N2  - 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.
Y1  - 2014
U6  - https://doi.org/10.1063/1.4869112
SN  - 0021-9606
SN  - 1089-7690
VL  - 140
IS  - 12
PB  - American Institute of Physics
CY  - Melville
ER  - 
TY  - GEN
A1  - Talukder, Srijeeta
A1  - Sen, Shrabani
A1  - Chakraborti, Prantik
A1  - Metzler, Ralf
A1  - Banik, Suman K.
A1  - Chaudhury, Pinaki
T1  - Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA
T2  - The journal of chemical physics : bridges a gap between journals of physics and journals of chemistr
N2  - 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.
Y1  - 2014
U6  - https://doi.org/10.1063/1.4871297
SN  - 0021-9606
SN  - 1089-7690
VL  - 140
IS  - 14
PB  - American Institute of Physics
CY  - Melville
ER  - 
TY  - JOUR
A1  - Maity, Alok Kumar
A1  - Bandyopadhyay, Arnab
A1  - Chattopadhyay, Sudip
A1  - Chaudhuri, Jyotipratim Ray
A1  - Metzler, Ralf
A1  - Chaudhury, Pinaki
A1  - Banik, Suman K.
T1  - Quantification of noise in bifunctionality-induced post-translational modification
JF  - Physical review : E, Statistical, nonlinear and soft matter physics
N2  - 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.
Y1  - 2013
U6  - https://doi.org/10.1103/PhysRevE.88.032716
SN  - 1539-3755
VL  - 88
IS  - 3
PB  - American Physical Society
CY  - College Park
ER  -