Model | Special | Sedimentation Time Offset

In some cases, it can be useful to introduce an offset time of simulated
sedimentation. This will set the start of the sedimentation to a specified time *t*
(in sec).

One possible use of this function is an alternative, ad hoc way of treating
the time necessary for the acceleration of the rotor (alternative to the
preferred functions scan
times for w^{2}t
or ramp
rotor speed).

Most likely, however, this function will be useful for cases where temperature-driven convection causes mixing in the initial part of the experiment, and an empirical modeling of the profiles is still desired. The results of such an empirical velocity analysis should be interpreted with greatest care. (If you have convection, the only rigorous analysis methods possible are the Lamm equation initialized with an experimental scan [single macromolecular component only], or the differential second moment method [gives sw only].)

Occasionally, the sedimentation parameters may not be those of greatest interest, e.g. when attempting to calculate the time-invariant noise from an approach to equilibrium run (ref 1).

After clicking on the menu, a entry box appears

in which an offset means that the experimental scans will be treated as if they have a time entry that is by the specified time (in this example 500 sec) too large. As a consequence, the modeled curves will move to earlier times compared to the data.

Note that 'Cancel' does not switch this function off. The way to switch this function off is to press the menu function again (-- this is a toggle). In order to change this value, click on this menu function twice. If a nonzero offset time is a floating fitting parameter, a checkmark appears at this menu item.

This function can be useful in conjunction with fit
t_{0} of sedimentation (see below).

If a nonzero offset time is being used, a checkmark appears at this menu item.

__Please Note__: This feature only works with
the non-interacting Lamm equation modeling and should be switched off when using
other models.

Model | Special | fit t0 of sedimentation

This function is an extension of the sedimentation time offset introduced above, in that it allows to treat the time offset as a floating parameter to be optimized during the Fit command.

A situation where this option can be useful is the calculation of systematic
noise through approach to equilibrium scans, with the intent to subtract the
systematic noise from the equilibrium data. Floating the offset time may
not make direct sense for the interpretation of the approach to equilibrium in
terms of s-values of the components, but it can be helpful to find Lamm equation
solutions that "fit and smooth" the data appropriately with **any**
Lamm equation solution to extract the systematic noise. (The offset time, for example,
may be able to adapt to the effects of convection caused by temperature
gradients, which would effectively delay the sedimentation process.) (Note:
If you have convection, the only rigorous analysis methods possible are the Lamm
equation initialized with an experimental scan [single macromolecular
component only], or the differential
second moment method [gives sw only].)

While the function sedimentation time offset sets a specific time as starting time, this function determines this time as a floating parameter to be optimized.

If t_{0} is an active fitting parameter, this menu function will have
a checkmark. When executing the Fit
command next time, text output in the Sedfit
window will display the current
value of t_{0} during the optimization of the fit.

This function can be switched off by toggling off the sedimentation time offset function (see above). When it is switched off, the checkmark disappears.

__Please Note__: This feature only works with
the non-interacting Lamm equation modeling and should be switched off when using
other models.

**References**

(1) P. Schuck (1999) Sedimentation equilibrium analysis of interference optical
data by systematic noise decomposition. * Analytical Biochemistry*
272:199-208