Thermal Writhing


An in silico representation of a biological filament should have the expected thermal motions. The mechanical properties of biological filaments can be characterized by a single measurement: filament persistence length Lp. Persistence length is formally defined as the path length through which the time-averaged angular correlation (i.e. the dot product of the path tangentials) is 1/e.


In SimFil, each filament segment is subjected to a single random force and torque that are crude stand-ins for the millions of water molecules that would bombard that section of filament during the course of a time-step. We can "tune" the strength of this Brownian force and torque such that the angular correlation between segments of a single filament are as expected from the experimentally determined persistence lengths.


The relevant tuning coefficients are the "Brownian Translational" and "Brownian Rotational" coefficients (B_t and B_theta, respectively, in SimFil ). These coefficients multiply a Brownian force and torque calculated for a free rigid segment.