Single molecule measurements and biological motors

Simulation of Optical Tweezers

In a recent paper (Knight et al., 2001) we described a simple method for simulating optical tweezers recordings, as a means of testing different algortihms for detecting actomyosin interaction events. The Java applet shown below is a simplified implementation of this simulation. The applet illustrates what the effect of parameters like trap stiffness and myosin power stroke will be on experimental records.

The Simulation

Briefly the simulation works as follows. There are two states, attached and detached. Each state has an associated stiffness value and a time constant. The other parameters of the system are the myosin power stroke and the temperature. The user can also control the duration, sampling frequency and scaling of the display.

The system starts in the detached state. The time which is spent in each state is determined by an exponentially distributed random number, using the state's time constant parameter. For each interval in a particular state, a sequence of normally distributed random numbers (i.e. white noise) is generated, using the event duration and sampling frequency. For detached intervals, the mean position is zero; for an attached interval, the mean position is the last detached position plus the myosin power stroke. The variance of the noise in each state is determined by the state's stiffness parameter.

This simple model generates realistic looking plots, although it is limited in several important ways:

the thermal noise generated by this simulation does not have the correct frequency spectrum - it is "white noise" rather than "pink noise". However this does not markedly change the visual appearance of the record.
the simulation assumes that only one myosin molecule is present; in reality more than one may be present and events may overlap.
other sources of experimental noise and drift are not modelled.

Using the simulation

Clicking on the plot below will perform a new simulation. The red bars indicate actomyosin attachment events. Change the parameters used in the simulation in the form below the plot. Clicking on the “Reset Form” button restore the default parameter values.

Here are some things to try:

change the myosin power stroke value. At the default value, some of the events will have negative or close to zero displacements, a few will have large positive displacements. Increasing the value will mean that more and more events emerge from the thermal noise background.
reduce the stiffness of the attached state. Notice how much less psominent the events become, especially when they are near zero displacement.
increasing the time constant of the attached state will prolong the events.

You may find it helpful to increase the duration of records to see more events, or to rescale the y axis.

You are using an old browser which does not understand the <APPLET> tag.

Parameter	Value
Sampling Frequency, Fs	Hz
Length of Record	samples
Y axis range	nm
Myosin Power Stroke	nm
Temperature	K
State:	DET	ATT
Stiffness (pN/nm)
Time Constant (s)

Contents