[RASMB] "wavy" interference optics residuals

[Arthur Rowe]

Greetings Debra

I have noticed a very similar effect. I have a little routine which I use to
check up on stochastic noise in final scans, in which I estimate the
magnitude of the latter by subtracting 2 final equilibrium scans from each
other. That (obviously) eliminates TI noise. Yet resulting residuals have a
waveform pattern superimposed on top of the high frequency 'shot noise'
stuff. The amplitude (SD around mean) of the latter is of the order of 0.006
fringes, with the mysterious longer frequency waveform being just a little
larger than that. And, just like your case, Debra, I find 7 or so
wavelengths in this pattern.

I'm not sure that I have any very good ideas as to what the cause is of this
phenomenon. I do not think that this bit of waveform noise will have all
that much effect of fits - maybe if I can find a moment to do it I ought to
simulate addition of a bit of waveform noise, and see what effect this has
on SE fits.

Kind regards to you and to all

Arthur

-- 
*************************
Arthur Rowe
Lab at Sutton Bonington
tel: +44 115 951 6156
fax: +44 115 951 6157
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> 
> Hi All,
> 
> We have been experiencing a problem with our interference data in which
> after data fitting, the residuals frequently have a systematic "wavy" look
> to them where they rise above and below zero multiple times >7 across the
> fitted data.  Subtracting a water blank does not fix the problem, and it has
> occurred an several different samples.  In real time, the fringes also
> "jump" during centrifugation.  Is this an indication of an equipment
> problem, perhaps that there is something unstable in the centrifuge and/or
> optical system that is leading to the movement of the fringe pattern
> detected by the camera?  If so, is there a likely culprit?  If not, what is
> likely to cause this?
> 
> Thanks for the help,
> 
> Debra M. Eckert, Ph.D.
> 
> Research Assistant Professor of Biochemistry
> 
> University of Utah
> 
> deckert at biochem.utah.edu
> 

Debra,

have you tried to fit the data with time invariant noise subtraction?
It sounds like you have a time invariant noise contribution to your data
that
can easily be removed. In UltraScan, you would do that during your initial
fit of the data with the 2-dimensional spectrum analysis. These TI noise
contributions are common in interference data, especially if you have
low protein concentration, or if use quartz instead of sapphire windows.

For equilibrium data, you have two options: either collect approach-to-
equilibrium data and subtract the ti noise calculated from the early
scans, or collect a baseline scan to get the ti noise contributions.
The latter process could be a bit tricky if the protein doesn't pellet
during a high speed run. But for velocity data this works great.

Regards, -Borries
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