2013/12/15 by Sandra Nostheide, Nostheide, Sandra, Viktor Holubec +5
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Biological Physics (physics.bio-ph) #Biomolecules (q-bio.BM) #FOS: Biological sciences #FOS: Physical sciences #Statistical Mechanics (cond-mat.stat-mech) #cond-mat.stat-mech #physics.bio-ph #q-bio.BM
paper · pdf · doi:10.48550/arxiv.1312.4146
16 pages, 9 figures
arxiv created 2013/12/15 · arxiv updated 2013/12/17
DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as function of the number of open base pairs and applied mechanical force. Using a commonly employed model, we first analyse for which types of sequences a particularly simple landscape structure is predicted, where forward and backward energy barriers between partly unfolded states are decreasing linearly with force. Stochastic unfolding trajectories for such molecules with simple FEL are subsequently generated by kinetic Monte Carlo simulations. Introducing probabilities that can be sampled from these trajectories, it is shown how the parameters characterising the FEL can be estimated. Already 300 trajectories, as typically generated in experiments, provide faithful results for the FEL parameters.