Considering a one dimensional mesoscopic model for DNA, we focus on the upper bound for the base pair fluctuations, a relevant parameter in computer simulations for which contrasting estimates have been reported. Noticing that the free energy of the model can be obtained analytically in the thermodynamic limit, we derive a relation for the fluctuations upper bound in terms of temperature and elastic force constant of the stacking potential. At room temperature, the fluctuation cutoff is constrained to values $\sim 2 \AA$ in fair agreement with the threshold above which hydrogen bonds break and base pairs dissociate.
Fluctuations cutoff in a 1D Hamiltonian model for DNA
Zoli, M
2024-01-01
Abstract
Considering a one dimensional mesoscopic model for DNA, we focus on the upper bound for the base pair fluctuations, a relevant parameter in computer simulations for which contrasting estimates have been reported. Noticing that the free energy of the model can be obtained analytically in the thermodynamic limit, we derive a relation for the fluctuations upper bound in terms of temperature and elastic force constant of the stacking potential. At room temperature, the fluctuation cutoff is constrained to values $\sim 2 \AA$ in fair agreement with the threshold above which hydrogen bonds break and base pairs dissociate.File in questo prodotto:
Non ci sono file associati a questo prodotto.
I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
