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<DIV dir=ltr align=left><SPAN class=700582920-02102008><FONT face=Arial
color=#0000ff size=2>James, after seeing the 2nd, correct PDF I notice one other
symptom: in that last experiment the data all the way at the left in the air-air
space are actually changing with time, which obviously should never happen, and
seem to be extraordinarily noisy too. So that does suggest there may be a
problem with the optics or slit assembly movement.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=700582920-02102008><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=700582920-02102008><FONT face=Arial
color=#0000ff size=2>Sorry, if I'd paid attention to the sedimentation
coefficient scale it should have been obvious you are running at low speeds so I
strongly doubt the leaks caused bending of the centerpiece
rib.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=700582920-02102008><FONT face=Arial
color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=700582920-02102008><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> James [mailto:james.falabella@nist.gov]
<BR><B>Sent:</B> Thursday, October 02, 2008 12:58 PM<BR><B>To:</B>
jphilo@mailway.com; rasmb@server1.bbri.org<BR><B>Subject:</B> RE: [RASMB] Bad
scans from XLA<BR></FONT><BR></DIV>
<DIV></DIV>
<DIV class=Section1>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 11pt; COLOR: navy; FONT-FAMILY: Arial">John,<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 11pt; COLOR: navy; FONT-FAMILY: Arial"><o:p> </o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 11pt; COLOR: navy; FONT-FAMILY: Arial">Thank you for your
insight into the problem, I will make certain that the reference meniscus does
not move throughout the run. I am using 15,000 rpm for the 10 nm gold particles
and 5,000 rpm for the 20 nm particles I will apply the other corrections and
hopefully the data will not show a bent center rib. I will run another radial
calibration at 3000 rpm to ensure that this is not the issue. I will also check
the masks in the centerpiece to ensure that they are not inserted upside down. I
think also my fit of the data may be a problem too with the right boundary too
far over and I will correct this in the future data analysis.
<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 11pt; COLOR: navy; FONT-FAMILY: Arial"><o:p> </o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 11pt; COLOR: navy; FONT-FAMILY: Arial">If all of this does not
work, I will call Beckman to clean the slit assembly since I am a rather new
user with about a year of experience using the XLA.<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 11pt; COLOR: navy; FONT-FAMILY: Arial"><o:p> </o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 11pt; COLOR: navy; FONT-FAMILY: Arial">Thank you so much for
your advice on rectifying this problem that I am experiencing. I will follow up
with results when I try these things.<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 11pt; COLOR: navy; FONT-FAMILY: Arial"><o:p> </o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 11pt; COLOR: navy; FONT-FAMILY: Arial">James<o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=navy size=2><SPAN
style="FONT-SIZE: 11pt; COLOR: navy; FONT-FAMILY: Arial"><o:p> </o:p></SPAN></FONT></P>
<DIV>
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</SPAN></FONT></DIV>
<P class=MsoNormal><B><FONT face=Tahoma size=2><SPAN
style="FONT-WEIGHT: bold; FONT-SIZE: 10pt; FONT-FAMILY: Tahoma">From:</SPAN></FONT></B><FONT
face=Tahoma size=2><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Tahoma"> John
Philo [mailto:jphilo@mailway.com] <BR><B><SPAN
style="FONT-WEIGHT: bold">Sent:</SPAN></B> Thursday, October 02, 2008 3:27
PM<BR><B><SPAN style="FONT-WEIGHT: bold">To:</SPAN></B> 'James';
rasmb@server1.bbri.org<BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B>
RE: [RASMB] Bad scans from XLA</SPAN></FONT><o:p></o:p></P></DIV>
<P class=MsoNormal><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt"><o:p> </o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=blue size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: blue; FONT-FAMILY: Arial">James,</SPAN></FONT><o:p></o:p></P>
<P class=MsoNormal><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt"> <o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=blue size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: blue; FONT-FAMILY: Arial">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.</SPAN></FONT><o:p></o:p></P>
<P class=MsoNormal><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt"> <o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=blue size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: blue; FONT-FAMILY: Arial">You also want to be
very careful about aligning the cell in the rotor or you will get convection
(and very screwy data).</SPAN></FONT><o:p></o:p></P>
<P class=MsoNormal><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt"> <o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=blue size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: blue; FONT-FAMILY: Arial">Another possibility
is that your leaked gold particles are getting into the slit assembly and
causing problems with the radial scanning. </SPAN></FONT><o:p></o:p></P>
<P class=MsoNormal><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt"> <o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=blue size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: blue; FONT-FAMILY: Arial">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.</SPAN></FONT><o:p></o:p></P>
<P class=MsoNormal><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt"> <o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=blue size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: blue; FONT-FAMILY: Arial">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.</SPAN></FONT><o:p></o:p></P>
<P class=MsoNormal><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt"> <o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=blue size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: blue; FONT-FAMILY: Arial">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.</SPAN></FONT><o:p></o:p></P>
<P class=MsoNormal><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt"> <o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal><FONT face=Arial color=blue size=2><SPAN
style="FONT-SIZE: 10pt; COLOR: blue; FONT-FAMILY: Arial">John</SPAN></FONT><o:p></o:p></P>
<P class=MsoNormal><FONT face="Times New Roman" size=3><SPAN
style="FONT-SIZE: 12pt"><o:p> </o:p></SPAN></FONT></P>
<DIV class=MsoNormal style="TEXT-ALIGN: center" align=center><FONT
face="Times New Roman" size=3><SPAN style="FONT-SIZE: 12pt">
<HR tabIndex=-1 align=center width="100%" SIZE=2>
</SPAN></FONT></DIV>
<P class=MsoNormal style="MARGIN-BOTTOM: 12pt"><B><FONT face=Tahoma size=2><SPAN
style="FONT-WEIGHT: bold; FONT-SIZE: 10pt; FONT-FAMILY: Tahoma">From:</SPAN></FONT></B><FONT
face=Tahoma size=2><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Tahoma">
rasmb-bounces@rasmb.bbri.org [mailto:rasmb-bounces@rasmb.bbri.org] <B><SPAN
style="FONT-WEIGHT: bold">On Behalf Of </SPAN></B>James<BR><B><SPAN
style="FONT-WEIGHT: bold">Sent:</SPAN></B> Thursday, October 02, 2008 10:38
AM<BR><B><SPAN style="FONT-WEIGHT: bold">To:</SPAN></B>
rasmb@server1.bbri.org<BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B>
[RASMB] Bad scans from XLA</SPAN></FONT><o:p></o:p></P>
<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>
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style="FONT-SIZE: 12pt"><o:p> </o:p></SPAN></FONT></P></DIV></BODY></HTML>