http://192.168.1.40:8080/xmlui/handle/123456789/1106 2026-05-31T12:08:30Z http://192.168.1.40:8080/xmlui/handle/123456789/1513 Finding the optimum activation energy in DNA breathing dynamics: a simulated annealing approach Chaudhury, Pinaki; Metzler, Ralf; Banik, Suman Kumar 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 breathing dynamics is followed in accordance with the stochastic Gillespie scheme, the denaturation bubbles in double-stranded DNA being studied as a single molecule time series. Simulated annealing is used to find the optimum value of the activation energy for which the equilibrium bubble size distribution matches with a given value. It is demonstrated that the method overcomes even large noise in the input surrogate data. DOI: 10.1088/1751-8113/42/33/335101 2009-08-21T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/1511 A model for signal transduction during quorum sensing in Vibrio harveyi Banik, Suman Kumar; Fenley, Andrew T.; Kulkarni, Rahul V. We present a framework for analyzing luminescence regulation during quorum sensing in the bioluminescent bacterium Vibrio harveyi. Using a simplified model for signal transduction in the quorum sensing pathway, we identify key dimensionless parameters that control the system's response. These parameters are estimated using experimental data on luminescence phenotypes for different mutant strains. The corresponding model predictions are consistent with results from other experiments which did not serve as input for determining model parameters. Furthermore, the proposed framework leads to novel testable predictions for luminescence phenotypes and for responses of the network to different perturbations. DOI: 10.1088/1478-3975/6/4/046008 2009-12-01T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/1371 Computational modeling of differences in the quorum sensing induced luminescence phenotypes of Vibrio harveyi and Vibrio cholerae Fenley, Andrew T.; Banik, Suman Kumar; Kulkarni, Rahul V. Vibrio harveyi and Vibrio cholerae have quorum sensing pathways with similar design and highly homologous components including multiple small RNAs (sRNAs). However, the associated luminescence phenotypes of strains with sRNA deletions differ dramatically: in V. harveyi, the sRNAs act additively; however, in V. cholerae, the sRNAs act redundantly. Furthermore, there are striking differences in the luminescence phenotypes for different pathway mutants in V. harveyi and V. cholerae. However, these differences have not been connected with the observed differences for the sRNA deletion strains in these bacteria. In this work, we present a model for quorum sensing induced luminescence phenotypes focusing on the interactions of multiple sRNAs with target mRNA. Within our model, we find that one key parameter - the fold-change in protein concentration necessary for luminescence activation - can control whether the sRNAs appear to act additively or redundantly. For specific parameter choices, we find that differences in this key parameter can also explain hitherto unconnected luminescence phenotypes differences for various pathway mutants in V. harveyi and V. cholerae. The model can thus provide a unifying explanation for observed differences in luminescence phenotypes and can also be used to make testable predictions for future experiments DOI : 10.1016/j.jtbi.2011.01.008 2011-04-07T00:00:00Z http://192.168.1.40:8080/xmlui/handle/123456789/1348 Microscopic realization of cross-correlated noise processes Shit, Anindita; Chattopadhyay, Sudip; Banik, Suman Kumar; Ray Chaudhuri, Jyotipratim We present a microscopic theory of cross-correlated noise processes, starting from a Hamiltonian system-reservoir description. In the proposed model, the system is nonlinearly coupled to a reservoir composed of harmonic oscillators, which in turn is driven by an external fluctuating force. We show that the resultant Langevin equation derived from the composite system (system+reservoir +external modulation) contains the essential features of cross-correlated noise processes. (C) 2010 American Institute of Physics. [doi:10.1063/1.3454590] DOI: 10.1063/1.3454590 2010-01-01T00:00:00Z