flins.support package

Subpackages

• flins.support.hexmath package
  • Submodules
  • flins.support.hexmath.axial module
  • flins.support.hexmath.cube module
  • flins.support.hexmath.offset module
  • Module contents

Submodules

flins.support.binding_site module

What is bound to what.

Let different proteins link to and unlink from each other.

class flins.support.binding_site.BindingSite(parent)

Bases: object

A link between this (thing) and that (thing)

Create the binding site

Parameters

parent (protein) – Protein on which this binding site is located

bind(other)

Bind to other object

property bound

Are you currently bound?

property linked

Return the parent object of the linked site (None if unbound)

unbind()

Unbind from other object

flins.support.diffuse module

Stagger around.

Allow random diffusion of various shapes in various directions.

class flins.support.diffuse.Drag

Bases: object

Drag coefficients drawn from Howard_2001, Pg 107 and Berg_1983. We assume that our coefficient of viscosity, \(\eta\), defaults to that of water (0.0114 poise at 288K), referenced from units

class Cylinder

Bases: object

Drag coefficients for cylinders. The cylinder has a length \(L\), a radius \(r\), and is in a fluid of viscosity \(\eta\). This assumes \(L>>r\) and an unbounded space.

long_axis_rotation(r, eta=1.14e-09)

Drag coefficient for cylinder rotating about the long axis

long_axis_translation(r, eta=1.14e-09)

Drag coefficient for cylinder moving along long axis

short_axis_rotation(r, eta=1.14e-09)

Drag coefficient for cylinder rotating about the radial axis

short_axis_translation(r, eta=1.14e-09)

Drag coefficient for cylinder moving along the radial axis

class Ellipsoid

Bases: object

Drag coefficients for an ellipsoid. The ellipsoid has a minor axis radius of \(a\), a major axis radius of \(b\), and immersion in a fluid of viscosity \(\eta\). This assumes \(b>>a\) and an unbounded space.

long_axis_rotation(a, eta=1.14e-09)

Drag coefficient for an ellipsoid rotating about the long axis

long_axis_translation(a, eta=1.14e-09)

Drag coefficient for an ellipsoid moving along long axis

short_axis_rotation(a, eta=1.14e-09)

Drag coefficient for an ellipsoid rotating about the minor axis

short_axis_translation(a, eta=1.14e-09)

Drag coefficient for an ellipsoid moving along the minor axis

class Sphere

Bases: object

Drag coefficients for a sphere. The sphere has a radius of \(r\) and is embedded in a fluid of viscosity \(\eta\).

rotation(eta=1.14e-09)

Drag coefficient for a sphere rotating in a fluid

translation(eta=1.14e-09)

Drag coefficient for a sphere moving through a fluid

flins.support.diffuse.Dx(f_drag)

How far do we move because of diffusion subject to drag? From the Einstein-Smoluchowski relation via Berg_1983 we know that the diffusion coefficient for a particle subject to a viscous drag, \(f\) (in \(g/s\)) is \(D=kT/f\). Further, from the same source and Howard_2001 we know the drag on cylinders, ellipsoids, and spheres and calculate them above for reference.

We add a correction factor of 1/3.2 to account for the difference in diffusion between water and eukaryotic cytoplasm (Swaminathan_1997).

An alternate treatment would be to use the Stoke’s radius for all molecules, approximating them as spheres. There is an argument that anything beyond the spherical approximation is false precision.

flins.support.diffuse.coerce_to_bounds(mol_start, mol_end, boundaries)

When a molecule has diffused out of bounds, coerce it back into bounds

A choice is made here to reflect the molecule back into bounds rather than stopping it dead at the boundary. This is to prevent the boundaries of the system from acting as absorbing ends that will tend to build up diffusing proteins over time.

Parameters

• mol_start (float) – X location of the right side of the protein

• mol_end (float) – X location of left side of the protein

• boundaries (tuple) – Upper and lower bounds of the 1D space the molecule is diffusing within

flins.support.kinetics module

Transitions are always hard.

Help us decide when we change from one state to another.

flins.support.kinetics.rate_to_prob(rate, obs_duration)

Convert a rate to a probability, based on an observation duration length and the assumption that the rate is for a Poisson process. We are asking, what is the probability that at least one Poisson distributed value would occur during the timestep.

Parameters

• rate (float) – a per ms rate to convert to probability

• obs_duration (float) – how many seconds we are watching over

Returns

probability – probability the event occurs during the ms we watched

Return type

float

flins.support.kinetics.reverse_rate(rate_12, free_energy_1, free_energy_2)

What is the balanced reverse rate from state 2 to state 1?

Parameters

• rate_12 (float) – transition rate from state 1 to state 2

• free_energy_1 (float) – free energy in state 1, state we are querying reversing into

• free_energy_2 (float) – free energy in state 2, state we are currently in

Returns

rate – per ms rate of transitioning from state 1 back to state 2

Return type

float

flins.support.names module

Ged thinks such things are important.

Proving a shorter unique name with which to reference objects in the world.

flins.support.names.name_to_uuid(name)

If, for some reason, you want the name back to UUID format

flins.support.names.unique_name(name_uuid=None)

Create a unique name, from uuid if given

flins.support.spring module

Spring forward, an elastic helper

Provide a linear spring that can be subject to thermal forcing.

class flins.support.spring.Spring(k, rest)

Bases: object

A generic one-state spring

Give me a spring

The spring can be extensional or torsional, the module works in both cases.

Parameters

• k (float) – Spring constant in pN per nm

• rest (float) – Rest angle or length of spring in radians or nm

bop_dx()

Bop for a displacement from rest length Assume an exponential energy distribution.

bop_length()

Bop for a new spring length that differs from rest value by dx Assume an exponential energy distribution.

energy(length)

Given a current length/angle, return stored energy

Parameters

length (float) – a spring length or angle in radians or nm

Returns

the energy required to achieve the given value

Return type

energy

force(length)

Given a current length/angle, return the force/torque.

This is given signs as though the spring is attached at origin and we are looking at the force needed to hold the spring in place.

Parameters

length (float) – a spring length or angle in radians or nm

Returns

force exerted by the spring at current length/angle

Return type

force

property k

flins.support.units module

To protect constants and serve unit conversions

Gather all the parameters that define the units in our universe, and the particular section of it we are interested in, into one spot.

class flins.support.units.constants

Bases: object

Universal constants we don’t expect to change across runs

avogadro = 6.0219999999999996e+23

boltzmann = 0.013799999999999998

eta = 1.14e-09

kT = 3.9743999999999993

temperature = 288

flins.support.units.joules(input_in_joules)

Convert energy, in joules, to pN*nm

flins.support.units.kcal(input_in_kcal)

Convert energy, in kcal, to pN*nm

flins.support.units.milliseconds(input_in_ms)

Convert time, in ms, to seconds

flins.support.units.poise(input_in_poise)

Convert the input viscosity, in poise, to g/nm*s

class flins.support.units.world

Bases: object

Things that are constant for our (simulated) world

• timestep is the number of ms we advance each tick

• D_cyto_corr comes from the difference in diffusion between water and eukaryotic cytoplasm (Swaminathan_1997).

D_cyto_corr = 3.2

timestep = 0.001

Module contents