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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>John,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>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 size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>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 size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>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 size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'>James<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
11.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;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 size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>James,</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>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 size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>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 size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>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 size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>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 size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>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 size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>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 size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>John</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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<p class=MsoNormal style='margin-bottom:12.0pt'><b><font size=2 face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span style='font-size:10.0pt;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 size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Dear RASMB members,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>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 size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>James B. Falabella<o:p></o:p></span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Process Sensing Group<o:p></o:p></span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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 size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Tel: 301-975-5041<o:p></o:p></span></font></p>
<p class=MsoAutoSig><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Fax: 301-975-2643<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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