Stochastic resonance in a model of a periodically driven DNA : Multiple transitions, scaling and sequence dependence

Abstract

We numerically study stochastic resonance in the unzipping of a model double-stranded DNA by a periodic force. We observe multiple peaks in stochastic resonance in the output signal as the driving force frequency is varied for different force amplitudes, temperature, chain length, and chain heterogeneity. Multiple peaks point to the existence of multiple stable and metastable states, which correspond to dynamical states of partially zipped and unzipped conformations and transitions between them. We quantify such transitions by looking at the time evolution of the fraction of bound base pairs. We obtain phase diagrams in the force amplitude-temperature plane both in the resonance frequency of the primary peak and the output signal at the peak value. We further obtain an excellent scaling behavior of the output signal for changing lengths of the DNA. Resonance behavior is also affected by chain heterogeneity as it depends strongly on which base pair the periodic forcing is applied.

arXiv comment6 pages, 5 figures; Published version

References in corpus (17)

• Practical implementation of nonlinear time series methods: The TISEAN package
• Dynamical scaling of the DNA unzipping transition
• Measurement of the Phase Diagram of DNA Unzipping in the Temperature- Force Plane
• Phase diagram of force-induced DNA unzipping in exactly solvable models
• Dissipation induced coherence and stochastic resonance of an open two-mode Bose-Einstein condensate
• Complete Phase Diagram of DNA Unzipping: Eye, Y-fork and triple point
• Statistical properties of metastable intermediates in DNA unzipping
• Some stochastic phenomena in a driven double-well system
• Statistical Mechanics of DNA unzipping under periodic force: Scaling behavior of hysteresis loop
• Measurement of work in single-molecule experiments
• Single-molecule stochastic resonance
• Hysteresis and nonequilibrium work theorem for DNA unzipping
• Unzipping DNA by a periodic force: Hysteresis loop area and its scaling
• Stochastic Resonance in the Fermi-Pasta-Ulam Chain
• Unzipping DNA by a periodic force: Hysteresis loops, Dynamical order parameter, Correlations and Equilibrium curves
• Unzipping of a double-stranded block copolymer DNA by a periodic force
• Hysteresis loop area scaling exponents in DNA unzipping by a periodic force: A Langevin dynamics simulation study

Cited by in corpus (1)

• DNA Unzipping Transition