Bonded Interactions

Fig. 2 Tissue Forge models of thymine (left) and adenine (right) molecules using bonded interactions.

A bonded interaction is an interaction due to a bond between a group of particles. A bond describes an interaction exclusively between the group of particles using a potential. Tissue Forge currently supports bond and bond-like angle and dihedral. To optimize simulation performance, bonds are visualized with simple lines by default. However, three-dimensional visualization of bonded interactions can be enabled using the rendering interface.

Bonds

A bond describes an interaction between two particles in terms of the distance between the two particles. A bond can be created using the method create on the class Bond, which returns a handle to the newly created bond. A bond can be manually destroyed using the BondHandle method destroy.

import tissue_forge as tf
# Create a bond between particles "p0" and "p1" using the potential "pot_bond"
bond_handle = tf.Bond.create(pot_bond, p0, p1)

Bond instances have an optional dissociation energy that, when set, describes an energy threshold above which the bond is automatically destroyed. Likewise, each Bond instance has an optional half life that, when set, describes the probability of destroying the bond at each simulation step, which Tissue Forge automatically implements,

bond_handle.dissociation_energy = 1E-3
bond_handle.half_life = 10.0

All bonds in the universe are accessible using the Universe property bonds,

all_bonds = tf.Universe.bonds  # Get updated list of all bonds

A bond is rendered as a line joining the two particles of the bond.

Angles

An angle describes an interaction between two particles in terms of the angle made by their relative position vectors with respect to a third particle. An angle can be created using the method create on the class Angle, which returns a handle to the newly created angle. An angle can be manually destroyed using the AngleHandle method destroy. Angle instances have analogous properties and methods to most of those defined for Bond instances, including accessing each constituent particle by indexing, and optional dissociation energy and half life. All angles in the universe are accessible using the Universe property angles,

# Create a bond between particles "p0" and "p2" w.r.t.
#   particle "p1" using the potential "pot_ang"
angle_handle = tf.Angle.create(pot_ang, p0, p1, p2)
all_angles = tf.Universe.angles  # Get updated list of all angles

An angle is rendered as a line joining the center particle and each end particle, and a line joining the midpoint of those two lines.

Dihedrals

A dihedral describes an interaction between four particles in terms of the angle between the planes made by their relative position vectors. A dihedral can be created using the method create on the class Dihedral, which returns a handle to the newly created dihedral. A dihedral can be manually destroyed using the DihedralHandle method destroy. Dihedral instances have analogous properties and methods to most of those defined for Bond instances, including accessing each constituent particle by indexing, and optional dissociation energy and half life. All dihedrals in the universe are accessible using the Universe property dihedrals,

# Create a bond between the plane made by particles "p0", "p1" and "p2"
#   and the plane made by particles "p1", "p2" and "p3"
#   using the potential "pot_dih"
dihedral_handle = tf.Dihedral.create(pot_dih, p0, p1, p2, p3)
all_dihedrals = tf.Universe.dihedrals  # Get updated list of all dihedrals

A dihedral is rendered as a line joining the first and second particles, a line joining the third and fourth particles, and a line joining the midpoint of those two lines.