jax_dna.energy.dna1.base_functions

Base energy functions for DNA1 model.

These functions are based on the oxDNA1 model paper found here: https://ora.ox.ac.uk/objects/uuid:b2415bb2-7975-4f59-b5e2-8c022b4a3719/files/mdcac62bc9133143fc05070ed20048c50

Functions

`f1`(→ jax_dna.utils.types.ARR_OR_SCALAR)	The radial part of the stacking and hydrogen-bonding potentials.
`f2`(→ jax_dna.utils.types.ARR_OR_SCALAR)	The radial part of the cross-stacking and coaxial stacking potentials.
`f3`(→ jax_dna.utils.types.ARR_OR_SCALAR)	The radial part of the excluded volume potential.
`f4`(→ jax_dna.utils.types.ARR_OR_SCALAR)	The angular modulation factor used in stacking, hydrogen-bonding, cross-stacking and coaxial stacking.
`f5`(→ jax_dna.utils.types.ARR_OR_SCALAR)	Another modulating term which is used to impose right-handedness (effectively a one-sided modulation).

Module Contents

jax_dna.energy.dna1.base_functions.f1(r: jax_dna.utils.types.ARR_OR_SCALAR, r_low: jax_dna.utils.types.Scalar, r_high: jax_dna.utils.types.Scalar, r_c_low: jax_dna.utils.types.Scalar, r_c_high: jax_dna.utils.types.Scalar, eps: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar, r0: jax_dna.utils.types.Scalar, r_c: jax_dna.utils.types.Scalar, b_low: jax_dna.utils.types.Scalar, b_high: jax_dna.utils.types.Scalar) → jax_dna.utils.types.ARR_OR_SCALAR[source]

The radial part of the stacking and hydrogen-bonding potentials.

This is based on equation 2.7 from the oxDNA paper.

jax_dna.energy.dna1.base_functions.f2(r: jax_dna.utils.types.ARR_OR_SCALAR, r_low: jax_dna.utils.types.Scalar, r_high: jax_dna.utils.types.Scalar, r_c_low: jax_dna.utils.types.Scalar, r_c_high: jax_dna.utils.types.Scalar, k: jax_dna.utils.types.Scalar, r0: jax_dna.utils.types.Scalar, r_c: jax_dna.utils.types.Scalar, b_low: jax_dna.utils.types.Scalar, b_high: jax_dna.utils.types.Scalar) → jax_dna.utils.types.ARR_OR_SCALAR[source]

The radial part of the cross-stacking and coaxial stacking potentials.

This is based on equation 2.8 from the oxDNA paper.

jax_dna.energy.dna1.base_functions.f3(r: jax_dna.utils.types.ARR_OR_SCALAR, r_star: jax_dna.utils.types.Scalar, r_c: jax_dna.utils.types.Scalar, eps: jax_dna.utils.types.Scalar, sigma: jax_dna.utils.types.Scalar, b: jax_dna.utils.types.Scalar) → jax_dna.utils.types.ARR_OR_SCALAR[source]

The radial part of the excluded volume potential.

This is based on equation 2.9 from the oxDNA paper.

jax_dna.energy.dna1.base_functions.f4(theta: jax_dna.utils.types.ARR_OR_SCALAR, theta0: jax_dna.utils.types.Scalar, delta_theta_star: jax_dna.utils.types.Scalar, delta_theta_c: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar, b: jax_dna.utils.types.Scalar) → jax_dna.utils.types.ARR_OR_SCALAR[source]

The angular modulation factor used in stacking, hydrogen-bonding, cross-stacking and coaxial stacking.

This is based on equation 2.10 from the oxDNA paper.

jax_dna.energy.dna1.base_functions.f5(x: jax_dna.utils.types.ARR_OR_SCALAR, x_star: jax_dna.utils.types.Scalar, x_c: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar, b: jax_dna.utils.types.Scalar) → jax_dna.utils.types.ARR_OR_SCALAR[source]

Another modulating term which is used to impose right-handedness (effectively a one-sided modulation).

This is based on equation 2.11 from the oxDNA paper.