jax_dna.energy.potentials

This module contains the potential energy functions used in the oxDNA DNA1 model.

Functions

`v_fene`(→ jax_dna.utils.types.ARR_OR_SCALAR)	FENE spring (used to connect backbones).
`v_morse`(→ jax_dna.utils.types.ARR_OR_SCALAR)	Morse potential (used for stacking and H-bonding).
`v_harmonic`(→ jax_dna.utils.types.ARR_OR_SCALAR)	Harmonic potential (used for cross-stacking and coaxial stacking).
`v_lj`(→ jax_dna.utils.types.ARR_OR_SCALAR)	Lennard - Jones potential (used for soft repulsion).
`v_mod`(→ jax_dna.utils.types.ARR_OR_SCALAR)	Quadratic terms (used for modulation).
`v_smooth`(→ jax_dna.utils.types.ARR_OR_SCALAR)	Quadratic smoothing terms for truncation.

Module Contents

jax_dna.energy.potentials.v_fene(r: jax_dna.utils.types.ARR_OR_SCALAR, eps: jax_dna.utils.types.Scalar, r0: jax_dna.utils.types.Scalar, delt: jax_dna.utils.types.Scalar) → jax_dna.utils.types.ARR_OR_SCALAR[source]

FENE spring (used to connect backbones).

This is based on equation 2.1 from the oxDNA paper.

jax_dna.energy.potentials.v_morse(r: jax_dna.utils.types.ARR_OR_SCALAR, eps: jax_dna.utils.types.Scalar, r0: jax_dna.utils.types.Scalar, a: jax_dna.utils.types.Scalar) → jax_dna.utils.types.ARR_OR_SCALAR[source]

Morse potential (used for stacking and H-bonding).

This is based on equation 2.2 from the oxDNA paper.

jax_dna.energy.potentials.v_harmonic(r: jax_dna.utils.types.ARR_OR_SCALAR, k: jax_dna.utils.types.Scalar, r0: jax_dna.utils.types.Scalar) → jax_dna.utils.types.ARR_OR_SCALAR[source]

Harmonic potential (used for cross-stacking and coaxial stacking).

This is based on equation 2.3 from the oxDNA paper.

jax_dna.energy.potentials.v_lj(r: jax_dna.utils.types.ARR_OR_SCALAR, eps: jax_dna.utils.types.Scalar, sigma: jax_dna.utils.types.Scalar) → jax_dna.utils.types.ARR_OR_SCALAR[source]

Lennard - Jones potential (used for soft repulsion).

This is based on equation 2.4 from the oxDNA paper.

jax_dna.energy.potentials.v_mod(theta: jax_dna.utils.types.ARR_OR_SCALAR, a: jax_dna.utils.types.Scalar, theta0: jax_dna.utils.types.Scalar) → jax_dna.utils.types.ARR_OR_SCALAR[source]

Quadratic terms (used for modulation).

This is based on equation 2.5 from the oxDNA paper.

jax_dna.energy.potentials.v_smooth(x: jax_dna.utils.types.ARR_OR_SCALAR, b: jax_dna.utils.types.Scalar, x_c: jax_dna.utils.types.Scalar) → jax_dna.utils.types.ARR_OR_SCALAR[source]

Quadratic smoothing terms for truncation.

This is based on equation 2.6 from the oxDNA paper.