jax_dna.energy.dna2.interactions
DNA2 interactions.
These functions are based on the oxDNA2 model paper found here: https://arxiv.org/abs/1504.00821
Functions
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Debye-huckel potential. |
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Coaxial stacking energy. |
Module Contents
- jax_dna.energy.dna2.interactions.debye(r: jax_dna.utils.types.ARR_OR_SCALAR, kappa: jax_dna.utils.types.Scalar, prefactor: jax_dna.utils.types.Scalar, smoothing_coeff: jax_dna.utils.types.Scalar, r_cut: jax_dna.utils.types.Scalar, r_high: jax_dna.utils.types.Scalar) jax_dna.utils.types.ARR_OR_SCALAR[source]
Debye-huckel potential.
- jax_dna.energy.dna2.interactions.coaxial_stacking(dr_stack: jax_dna.utils.types.ARR_OR_SCALAR, theta4: jax_dna.utils.types.ARR_OR_SCALAR, theta1: jax_dna.utils.types.ARR_OR_SCALAR, theta5: jax_dna.utils.types.ARR_OR_SCALAR, theta6: jax_dna.utils.types.ARR_OR_SCALAR, dr_low_coax: jax_dna.utils.types.Scalar, dr_high_coax: jax_dna.utils.types.Scalar, dr_c_low_coax: jax_dna.utils.types.Scalar, dr_c_high_coax: jax_dna.utils.types.Scalar, k_coax: jax_dna.utils.types.Scalar, dr0_coax: jax_dna.utils.types.Scalar, dr_c_coax: jax_dna.utils.types.Scalar, b_low_coax: jax_dna.utils.types.Scalar, b_high_coax: jax_dna.utils.types.Scalar, theta0_coax_4: jax_dna.utils.types.Scalar, delta_theta_star_coax_4: jax_dna.utils.types.Scalar, delta_theta_coax_4_c: jax_dna.utils.types.Scalar, a_coax_4: jax_dna.utils.types.Scalar, b_coax_4: jax_dna.utils.types.Scalar, theta0_coax_1: jax_dna.utils.types.Scalar, delta_theta_star_coax_1: jax_dna.utils.types.Scalar, delta_theta_coax_1_c: jax_dna.utils.types.Scalar, a_coax_1: jax_dna.utils.types.Scalar, b_coax_1: jax_dna.utils.types.Scalar, a_coax_1_f6: jax_dna.utils.types.Scalar, b_coax_1_f6: jax_dna.utils.types.Scalar, theta0_coax_5: jax_dna.utils.types.Scalar, delta_theta_star_coax_5: jax_dna.utils.types.Scalar, delta_theta_coax_5_c: jax_dna.utils.types.Scalar, a_coax_5: jax_dna.utils.types.Scalar, b_coax_5: jax_dna.utils.types.Scalar, theta0_coax_6: jax_dna.utils.types.Scalar, delta_theta_star_coax_6: jax_dna.utils.types.Scalar, delta_theta_coax_6_c: jax_dna.utils.types.Scalar, a_coax_6: jax_dna.utils.types.Scalar, b_coax_6: jax_dna.utils.types.Scalar) jax_dna.utils.types.Scalar[source]
Coaxial stacking energy.