[RASMB] time to reach equilibrium

[Walter Stafford]

Dear Arthur et alias,

	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 http://vm.uconn.edu/~wwwbiotc/AUFFTP.HTML

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.

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.

Walter


At 5:31 PM +0100 9/29/04, Arthur Rowe wrote:
>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
>
>(1) went down to below noise level, or
>(2) failed to do so (i.e. system in some sort of steady state, 
>rather than attaining equilibrium) ?
>
>Just to make it nice and easy for folks . . .
>
>Arthur
>--
>*************************
>Arthur Rowe
>Lab at Sutton Bonington
>tel: +44 115 951 6156
>fax: +44 115 951 6157
>*************************
>
>
>From: "John Correia" <jcorreia at biochem.umsmed.edu>
>Date: Wed, 29 Sep 2004 10:31:11 -0500
>To: <strauss at fmp-berlin.de>, <rasmb at server1.bbri.org>
>Subject: Re: [RASMB] time to reach equilibrium
>
>
>Cheers
>
>We published a paper in 1977 that predicted the equilibrium 
>distribution from earlier scans: 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).  
>
>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 must also 
>come from Sed velocity - Sedanal, Sedphat, etc make this very 
>inviting.  In our lab sed velocity rules, ie we have no alternative!
>
>-------------------------------------------------------------------
>Dr. John J. "Jack" Correia
>Department of Biochemistry
>University of Mississippi Medical Center
>2500 North State Street
>Jackson, MS  39216
>(601) 984-1522                                 
>fax (601) 984-1501                             
>email address: jcorreia at biochem.umsmed.edu     
>homepage location: http://biochemistry.umc.edu/correia.html
>dept homepage location:    http://biochemistry.umc.edu/
>-------------------------------------------------------------------
>
>
>
>
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-- 
----------------------------------------------------------
Walter Stafford
mailto:stafford at bbri.org
direct dial:    617-658-7808
receptionist: 617-658-7700
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