The mesoscopic Peyrard-Bishop DNA Hamiltonian describes the main molecular interactions with simple potentials , resulting in an efficient calculation of the melting of the duplex helix. It is based on a 2D model which can be simplified to calculate the classical partition function with the transfer-integral technique. At the heart of this approach are simplifications that leave only a single variable to integrate, but also make it impossible to apply the model to situations where a more detailed structural description is needed . Here, we start from a more realistic 3D description and work out several approximations to arrive at a form that can be handled by the transfer-integral technique. We show that this new approach naturally results very sharpopening transition .
The Peyrard-Bishop DNA model describes the molecular interactions with simple potentials which allow efficient calculations of melting temperatures. However, it is based on a Hamiltonian that does not consider the helical twist or any other relevant molecular dimensions . Here, we start from a more realistic 3D model and work out several approximations to arrive at a new non-linear 1D Hamiltonian with a twist angle dependence. Our approximations were numerically compared to full 3D calculations, and established its validity in the regime of small angles. For long DNA sequences we obtain sharp, first-order-like melting, transitions .
D
mesoscopic
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Hamiltonian describes the main
model describes the
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, resulting in an efficient calculation of the melting of the duplex helix. It
which allow efficient calculations of melting temperatures. However, it
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2D model which can be simplified to calculate the classical partition function with the transfer-integral technique. At the heart of this approach are simplifications that leave only a single variable to integrate, but also make it impossible to apply the model to situations where a more detailed structural description is needed
Hamiltonian that does not consider the helical twist or any other relevant molecular dimensions
R
description
model
R
form that can be handled by the transfer-integral technique. We show that this new approach naturally results very sharpopening transition
new non-linear 1D Hamiltonian with a twist angle dependence. Our approximations were numerically compared to full 3D calculations, and established its validity in the regime of small angles. For long DNA sequences we obtain sharp, first-order-like melting, transitions