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--></style><title>Re: [RASMB] time to reach
equilibrium</title></head><body>
<div>Dear Arthur et alias,</div>
<div><br></div>
<div><x-tab> </x-tab>Such a
application does indeed exist. Although it doesn't run continuously,
it can be run at anytime to check for equilibrium. It is called
WinMatch (a Windows version of an even earlier program called Match).
WinMatch is available from the National Analytical Ultracentrifugation
Facility (NAUF) at the University if Connecticut at<font
color="#000000">
http://vm.uconn.edu/~wwwbiotc/AUFFTP.HTML</font></div>
<div><br></div>
<div>WinMatch essentially performs least squares fits of a series of
scans (usually taken every hour) against the last scan taken (the
reference scan) and fits for horizontal (precession and vibrations)
and vertical (vibrations and other variations in baseline) offsets.
The result is a plot of the RMS deviation vs. time. This curve looks a
lot like an exponential decay which tends toward zero slope as
equilibrium is reached. It is quite useful for identifying
systems that fail to reach equilibrium.</div>
<div><br></div>
<div>Although calculations are handy for planning an experiment, it is
the empirical determination of attainment of equilibrium that should
be the deciding factor. WinMatch works very well and has been
available from the NAUF for many years now.</div>
<div><br></div>
<div>Walter</div>
<div><br></div>
<div><br></div>
<div>At 5:31 PM +0100 9/29/04, Arthur Rowe wrote:</div>
<blockquote type="cite" cite>Perhaps someone could write a nice little
app which would continuously monitor at (say) hourly intervals the
shift in fringe position at a radial position near to the base of the
column, and report back to the screen when this shift either<br>
<br>
(1) went down to below noise level, or<br>
(2) failed to do so (i.e. system in some sort of steady state, rather
than attaining equilibrium) ?<br>
<br>
Just to make it nice and easy for folks . . .<br>
<br>
Arthur<br>
--<br>
*************************<br>
Arthur Rowe<br>
Lab at Sutton Bonington<br>
tel: +44 115 951 6156<br>
fax: +44 115 951 6157<br>
*************************<br>
<blockquote><br>
<b>From:</b> "John Correia"
<jcorreia@biochem.umsmed.edu><br>
<b>Date:</b> Wed, 29 Sep 2004 10:31:11 -0500<br>
<b>To:</b> <strauss@fmp-berlin.de>,
<rasmb@server1.bbri.org><br>
<b>Subject:</b> Re: [RASMB] time to reach equilibrium<br>
</blockquote>
</blockquote>
<blockquote type="cite" cite><br>
<blockquote>Cheers<br>
<br>
We published a paper in 1977 that predicted the equilibrium
distribution from earlier scans:<font size="-2"> J.J. CORREIA, G.H.
Weiss and D.A. Yphantis (1977). "An Extrapolation Method for
Reducing Equilibrium Times in Sedimentation Equilibrium Systems,"
Biophysical J. 20, 153-168. The point being, as Holger
just mentioned, many samples aggregate with time, or display
insolubility, instability. Many of us have observed this with
proteins like tubulin which like to associate in polymorphic forms,
and with many His tagged proteins. In many of these cases there
is a slow loss of material from a "stable" exponential
distribution. Information can still be extracted, with caution.
Solutions to this problem have included change the pH, ionic
strength, etc (obvious), drop the temperature, add reducing agent
(TCEP has worked best in limiting cases), remove the His tag, go to a
short column format (which speeds up the time dramatically (16-fold
for a 4-fold reduction in column height). <br>
</font><br>
<font size="-2">I not only agree with Bo, I insist that you do Sed
velocity before you waste time doing sed equilibrium - I suspect most
people do this - furthermore for many systems the quantitative
analysis<b> must</b> also come from Sed velocity - Sedanal, Sedphat,
etc make this very inviting. In our lab sed velocity rules, ie
we have no alternative!<br>
</font><br>
<font
size="-2"
>-------------------------------------------------------------------<br
>
Dr. John J. "Jack" Correia<br>
Department of Biochemistry<br>
University of Mississippi Medical Center<br>
2500 North State Street<br>
Jackson, MS 39216<br>
(601) 984-1522
<span
></span
> <span
></span> <br
>
fax (601) 984-1501
<span
></span
> <span
></span> <br>
email address: jcorreia@biochem.umsmed.edu
<br>
homepage location: http://biochemistry.umc.edu/correia.html<br>
dept homepage location:
http://biochemistry.umc.edu/<br>
-------------------------------------------------------------------<br
>
<br>
</font></blockquote>
</blockquote>
<blockquote type="cite" cite><br>
<br>
</blockquote>
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<div><br></div>
<x-sigsep><pre>--
</pre></x-sigsep>
<div><font face="Times"
color="#0000FF"
>----------------------------------------------------------</font></div
>
<div><font face="Times" color="#0000FF">Walter Stafford</font></div>
<div><font face="Times"
color="#0000FF">mailto:stafford@bbri.org</font></div>
<div><font face="Times" color="#0000FF">direct dial:
617-658-7808</font></div>
<div><font face="Times" color="#0000FF">receptionist:
617-658-7700</font></div>
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