[RASMB] more on systematic differences

[John Philo]

Jack, you asked whether one can damage a centerpiece at 40K if one sector is
empty and the other is full. The official rating for the standard charcoal
epon centerpieces is 42K, which means Beckman guarantees they won't actually
break if you get a leak and a channel empties at 42K. However, I think 'not
broken' and 'not damaged' are different issues. There are circumstances
where the center rib bends but does not break. Afterward that centerpiece
may be leak-tight, but whether the rib is really straight rather than bowed
at that point is questionable, and if it is bowed you are very likely to get
convection. So the bottom line is that in my lab, if I have a full leak at
40K, that centerpiece goes into the trash (after a good round of therapeutic
expletives, of course).
 
John

-----Original Message-----
From: rasmb-bounces at rasmb.bbri.org [mailto:rasmb-bounces at rasmb.bbri.org] On
Behalf Of Jack Kornblatt
Sent: Wednesday, September 06, 2006 8:52 AM
To: rasmb at server1.bbri.org
Subject: [RASMB] more on systematic differences


A follow up on "systematic differences"
There were two questions:
1.  If there are three cells in the AUC during a sedimentation velocity run,
one cell yields an s value that I arbitrarily set at 100, cell 2 yields a
value of 99.4 and cell 3 a value of 99.7. What are possible causes of the
differences?
2.  The meniscus of cell one if always found at shorter radius than the
meniscus of cell 2.  Cell 3 is intermediate between the other two.  What are
possible causes?

Thanks to John, Andrew and Tom for their most recent comments.
One of John's struck me as being especially insightful: 

If you (me, in this case) have found that the three cells do not yield the
same s values in a velocity run, and if you apply correction factors to two
of them so as to get them to agree with the third, how do you know which is
the correct one to use as a the reference value?  
The answer: You do not know which is the correct value.  If I understand
correctly, to have knowledge of the s value to a precision of  0.1%, you
would have to have experimentally determined diffusion coefficients (to
better than 0.1% precision) as well as rho and vbar values to much better
than 0.1%; mass spectroscopy now gives us molecular masses to high
precision. Correction factors of less than 1% are useful in that they allow
me to judge the sedimentation in one cell relative to the others.
Correction factors permit one to level the playing field but one doesn't
know whether the game being played is football in San Francisco or cricket
in Nairobi.
Like biologists all over, I had hoped for absolute knowledge when I started
working with the AUC but ........

There seems to be general agreement that the differences between cells are
probably the result of differences in the center pieces:  
I can easily check for leaks.  

NB. If I run one chamber empty, one full at 40 KRPM, am I likely to deform
the center piece?

As for the other ideas as why the cells might differ as much as they do,
they are all useful.  If the differences between cells were larger than it
is, it would be worthwhile delving more deeply. The major unanswered
question is why the s values differ.  Here you three all seem to agree that
it might result from convection or from a leak.  I'll check the archives for
how to detect convection problems and will get back to you about leaks when
I have the data.  (Hopefully < 1 year)
thanks again
jack 

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