Finding the optimum activation energy in DNA breathing dynamics: a simulated annealing approach

2009/07/07 by Pinaki Chaudhury, Ralf Metzler, Suman K Banik +1
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Advanced Chemical Physics Studies #DNA and Nucleic Acid Chemistry #Spectroscopy and Quantum Chemical Studies #cond-mat.soft #cond-mat.stat-mech #q-bio.BM

paper · pdf · doi:10.1088/1751-8113/42/33/335101

published as J. Phys. A: Math. Theor. 42 (2009) 335101 · 9 pages, 4 figures, iop article package included

arxiv created 2009/07/07 · openalex publication_date 2009/07/28 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/04

Abstract

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.

Citations

• Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials
• A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
• Equation of State Calculations by Fast Computing Machines