35 citations · 117 across the 12 of their papers we have counts for
13 papers
Interplay of degeneracy and non-degeneracy in fluctuations propagation in coherent feed-forward loop motif
Tuhin Subhra Roy, Mintu Nandi, Pinaki Chaudhury +2
We present a stochastic framework to decipher fluctuations propagation in classes of coherent feed-forward loops. The systematic contribution of the direct (one-step) and indirect…
Escape kinetics of self-propelled particles from a circular cavity
Tanwi Debnath, Pinaki Chaudhury, Taritra Mukherjee +2
We numerically investigate the mean exit time of an inertial active Brownian particle from a circular cavity with single or multiple exit windows. Our simulation results witness di…
Information transmission in a two-step cascade: Interplay of activation and repression
Tuhin Subhra Roy, Mintu Nandi, Ayan Biswas +2
We present an information-theoretic formalism to study signal transduction in four architectural variants of a model two-step cascade with increasing input population. Our results…
Information processing in a simple one-step cascade
Mintu Nandi, Ayan Biswas, Suman K Banik +1
Using the formalism of information theory, we analyze the mechanism of information transduction in a simple one-step signaling cascade SX representing the gene regulat…
Information theoretical study of cross-talk mediated signal transduction in MAPK pathways
Alok Kumar Maity, Pinaki Chaudhury, Suman K. Banik
Biochemical networks related to similar functional pathways are often correlated due to cross-talk among the homologous proteins in the different networks. Using a stochastic frame…
Role of relaxation time scale in noisy signal transduction
Alok Kumar Maity, Pinaki Chaudhury, Suman K. Banik
Intracellular fluctuations, mainly triggered by gene expression, are an inevitable phenomenon observed in living cells. It influences generation of phenotypic diversity in genetica…
Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA
Srijeeta Talukder, Shrabani Sen, Prantik Chakraborti +3
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 parame…
Role of functionality in two-component signal transduction: A stochastic study
Alok Kumar Maity, Arnab Bandyopadhyay, Pinaki Chaudhury +1
We present a stochastic formalism for signal transduction processes in bacterial two-component system. Using elementary mass action kinetics, the proposed model takes care of signa…
Stochastic Optimization Based Study of Dimerization Kinetics
Srijeeta Talukder, Shrabani Sen, Ralf Metzler +2
We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end we study a dimerization kinetics of p…
Quantification of noise in the bifunctionality-induced post-translational modification
Alok Kumar Maity, Arnab Bandyopadhyay, Sudip Chattopadhyay +4
We present a generic analytical scheme for the quantification of fluctuations due to bifunctionality-induced signal transduction within the members of bacterial two-component syste…
Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization
Srijeeta Talukder, Pinaki Chaudhury, Ralf Metzler +1
We suggest that the thermodynamic stability parameters (nearest neighbor stacking and hydrogen bonding free energies) of double-stranded DNA molecules can be inferred reliably from…
Finding the optimum activation energy in DNA breathing dynamics: A Simulated Annealing approach
Pinaki Chaudhury, Ralf Metzler, Suman K Banik
We demonstrate how the stochastic global optimization scheme of Simulated Annealing can be used to evaluate optimum parameters in the problem of DNA breathing dynamics. The breathi…
Transport and bistable kinetics of a Brownian particle in a nonequilibrium environment
Jyotipratim Ray Chaudhuri, Suman Kumar Banik, Sudip Chattopadhyay +1
A system reservoir model, where the associated reservoir is modulated by an external colored random force, is proposed to study the transport of an overdamped Brownian particle in…