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Browsing by Author "Banik, S. K."

Now showing 1 - 3 of 3
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    Breathing dynamics in heteropolymer DNA
    Ambjornsson, T.; Banik, S. K.; Krichevsky, O.; Metzler, R. (CELL PRESS, 2007-04)
    While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule spectroscopy. The dynamical opening of DNA bubbles (DNA breathing) is supposedly crucial for biological functioning during, for instance, transcription initiation and DNA's interaction with selectively single-stranded DNA binding proteins. Motivated by this, we consider the bubble breathing dynamics in a heteropolymer DNA based on a (2+1)-variable master equation and complementary stochastic Gillespie simulations, providing the bubble size and the position of the bubble along the sequence as a function of time. We utilize new experimental data that independently obtain stacking and hydrogen bonding contributions to DNA stability. We calculate the spectrum of relaxation times and the experimentally measurable autocorrelation function of a fluorophore-quencher tagged basepair, and demonstrate good agreement with fluorescence correlation experiments. A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a promoter sequence of the T7 phage. The strong dependence on sequence, temperature and salt concentration for the breathing dynamics of DNA found here points at a good potential for nanosensing applications by utilizing short fluorophore-quencher dressed DNA constructs.
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    Time dependent current in a nonstationary environment: a microscopic approach
    Bhattacharya, S.; Banik, S. K.; Chattopadhyay, S.; Chaudhuri, J. R. (AIP Publishing, 2008-06)
    Based on a microscopic system reservoir model, where the associated bath is not in thermal equilibrium, we simulate the nonstationary Langevin dynamics and obtain the generalized nonstationary fluctuation dissipation relation (FDR) which asymptotically reduces to the traditional form. Our Langevin dynamics incorporates non-Markovian process also, the origin of which lies in the decaying term of the nonstationary FDR. We then follow the stochastic dynamics of the Langevin particle based on the Fokker-Planck-Smoluchowski description in ratchet potential to obtain the steady and time dependent current in an analytic form. We also examine the influence of initial excitation and subsequent relaxation of bath modes on the transport of the Langevin particle to show that the nonequilibrium nature of the bath leads to both strong nonexponential dynamics as well as nonstationary current. (c) 2008 American Institute of Physics.
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    Transport and bistable kinetics of a brownian particle in a nonequilibrium environment
    Chaudhuri, J. R.; Banik, S. K.; Chattopadhyay, S.; Chaudhury, P. (AIP Publishing, 2008-11)
    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 a periodic potential. We then derive the analytical expression for the average velocity, mobility, and diffusion rate. The bistable kinetics and escape rate from a metastable state in the overdamped region are studied consequently. By numerical simulation we then demonstrate that our analytical escape rate is in good agreement with that of the numerical result.