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<DIV dir=ltr align=left><SPAN class=951120119-02102008><FONT face=Arial
color=#0000ff size=2>James,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=951120119-02102008><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=951120119-02102008><FONT face=Arial
color=#0000ff size=2>I am wondering if you are possibly
getting intermittent leakage between the channels as the rotor accelerates.
This can sometimes make it seem like sedimentation has started somewhere
far away from the true meniscus position, as seems to be the case in the
second 'bad' run. In that data your reference meniscus seems to be at ~5.96
cm, i.e. not right on top of the sample meniscus as it will be if there is
extensive cross-channel leaking, but possibly the reference started out
significantly further to the left and moved as the rotor
accelerated.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=951120119-02102008><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=951120119-02102008><FONT face=Arial
color=#0000ff size=2>You also want to be very careful about aligning the cell in
the rotor or you will get convection (and very screwy data).</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=951120119-02102008><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=951120119-02102008><FONT face=Arial
color=#0000ff size=2>Another possibility is that your leaked gold particles
are getting into the slit assembly and causing problems with the radial
scanning. </FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=951120119-02102008><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=951120119-02102008><FONT face=Arial
color=#0000ff size=2>I'm not clear what rotor speed you are using but when you
leak out half a sample and the speed is high enough the center rib of the
centerpiece can get permanently bent, after which you will always get
strange data with that centerpiece.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=951120119-02102008><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=951120119-02102008><FONT face=Arial
color=#0000ff size=2>I am not clear why you keep doing radial calibration and in
general I would not recommend this, but I doubt that is the fundamental problem
here. The calibration should not change during normal operation---it will only
change if someone works on the optical components. Also you should not turn off
the delay calibration. Definitely <U>never</U> ask for radial calibration at
speeds above 3000 rpm.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=951120119-02102008><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=951120119-02102008><FONT face=Arial
color=#0000ff size=2>Having said that I do wonder whether your radial
calibration is correct. It looks to me like you are getting good data (flat
plateaus) well beyond 7.14 cm, which is typically not true for the standard
epon centerpieces and window holders, which suggests the radial calibration may
be faulty. The true base of the channel should be very close to 7.2 cm (and
seems not to be positioned correctly in your fits). If the radial cal
is bad it might be the counterbalance itself. The masks that slip into the sides
of the counterbalance to create the precision reference points can fall out and
hence can be put back in upside down.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=951120119-02102008><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=951120119-02102008><FONT face=Arial
color=#0000ff size=2>John</FONT></SPAN></DIV><BR>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left>
<HR tabIndex=-1>
<FONT face=Tahoma size=2><B>From:</B> rasmb-bounces@rasmb.bbri.org
[mailto:rasmb-bounces@rasmb.bbri.org] <B>On Behalf Of </B>James<BR><B>Sent:</B>
Thursday, October 02, 2008 10:38 AM<BR><B>To:</B>
rasmb@server1.bbri.org<BR><B>Subject:</B> [RASMB] Bad scans from
XLA<BR></FONT><BR></DIV>
<DIV></DIV>
<DIV class=Section1>
<P class=MsoNormal><FONT face="Times New Roman" size=2><SPAN
style="FONT-SIZE: 11pt">Dear RASMB members,<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face="Times New Roman" size=2><SPAN
style="FONT-SIZE: 11pt"><o:p> </o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face="Times New Roman" size=2><SPAN
style="FONT-SIZE: 11pt">I have recently been struggling with a recurring problem
when I centrifuge 10 and 20nm gold particles that causes my XLA to generate
poorly formed OD data scans that cannot be fit by Sedfit. I had initially been
getting well formed scans that were easily fit by Sedfit using the continuous
c(s) model however after half of the sample side in one cell (in a 4 cell rotor)
leaked out during a run I was no longer able to get the nice sigmoidal scans
that I originally had even though I tightened and refilled the leaking cell. I
asked the Beckman service rep to investigate and he cleaned the optics and told
me to have the XLA perform a radial calibration and the scans were back to a
sigmoidal shape using the same sample of gold nanoparticles and Sedfit could fit
the data well again. However after another cell leaked in the centrifuge, the
scans could not be fit with Sedfit even though the cell was tightened and
refilled and no longer leaked. I have been performing a radial calibration
before each run and have not turned off the delay calibration hoping the
instrument will recalibrate and improve the scans however, this has not
happened. I have attached screen shots showing the quality of the data before
and after the cell leak. It looks like it could be the optics but I am not
convinced this is the whole story since it seems extreme that one cell leak can
alter the XLA performance this much until the optics are
cleaned.<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face="Times New Roman" size=2><SPAN
style="FONT-SIZE: 11pt"><o:p> </o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face="Times New Roman" size=2><SPAN
style="FONT-SIZE: 11pt"><o:p> </o:p></SPAN></FONT></P>
<P class=MsoAutoSig><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt">James B. Falabella<o:p></o:p></SPAN></FONT></P>
<P class=MsoAutoSig><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt">Process Sensing Group<o:p></o:p></SPAN></FONT></P>
<P class=MsoAutoSig><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt">National <st1:PlaceType
w:st="on">Institute</st1:PlaceType> of <st1:PlaceName
w:st="on">Standards</st1:PlaceName> and Technology <st1:place
w:st="on"><st1:City w:st="on">Gaithersburg</st1:City>, <st1:State
w:st="on">MD</st1:State></st1:place><o:p></o:p></SPAN></FONT></P>
<P class=MsoAutoSig><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt">Tel: 301-975-5041<o:p></o:p></SPAN></FONT></P>
<P class=MsoAutoSig><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt">Fax: 301-975-2643<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt"><o:p> </o:p></SPAN></FONT></P></DIV></BODY></HTML>