Molecular motor hand-over-hand

Inspired by classes of Biological Physics given by F.Falo at Universidad de Zaragoza (UNIZAR) during 2022.

Simple implementation of a flashing ratchet model in two dimensions on two headead molecule (red and blue heads). Each head experiences a flashing ratchet potential in which the minimum are not aligned.

This model shows how a intermittent potential with brownian motion can cause net fordward motion.

How to use

Potential visualization

In the Jupyther notebook there is an explanation of the two dimentional ratchet potential implementation. In two dimensions and as a three dimensional surface.

Simulation

In the simulation you can see the 2 heads of the molecule, blue and red, connected with a highly stiff spring (in black).

The plot is divided in two backgrounds, bluish and reddish, each one represents the potential affectig the same coloured head. When the backgroud is semi-transparent the potential is not active and the movement of the head is only limited by the spring.

Configuration

All configurable variables are in main.py file:

• period: potentials flashing period.

• length_potential: length of ratchet potential in x axis.

• low_point_potential: position of lowest potential value, must be lower than length_potential.

• potential_offset: offset between red and blue head ratchet potential lowest position in x axis.

• max_value_potential: difference between lowest and highest values of ratchet potential.

• confinement_potential_coefficient: spring constant.

• steps_per_frame: integrations steps per frame.

• frames_per_second: frames per second.

Reference

J.Munárriz, J.J. Mazo and F.Falo. "Model for hand-over-hand motion of molecular motors". Physical Review E 77, 031915. 17 March 2008.