<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; "><span>Hi Ute,</span></div><div style="font-family: arial, helvetica, sans-serif; font-size: 16px; color: rgb(0, 0, 0); background-color: transparent; font-style: normal; "><span><br></span></div><div style="font-family: arial, helvetica, sans-serif; font-size: 16px; color: rgb(0, 0, 0); background-color: transparent; font-style: normal; ">For clarification, it is tradition in AUC circles to call "jitter" the small variations in y axis offset which is in interference data. The huge offsets you see are "jumps". There is no valid interference data in the meniscus position, so the fourier transform that is following the position of the fringes can "jump" one or more whole fringes when the algorithm crosses the meniscus. </div><div style="font-family:
arial, helvetica, sans-serif; font-size: 16px; color: rgb(0, 0, 0); background-color: transparent; font-style: normal; "><br></div><div style="background-color: transparent; ">As you note, SEDFIT can fit the data and fit the noise and then subtract the noise out of the data set. The jitter and jump are just the RI, or radially independent noise. The time independent noise is the possible slant and the rough baseline of the optical system and the cell windows which is most evident when you have a spec of dust on your cells (this data set has observably very clean cells and a basically flat interference baseline) Of course, this works best when the data is able to be well fit by SEDFIT. </div><div style="font-family: arial, helvetica, sans-serif; font-size: 16px; color: rgb(0, 0, 0); background-color: transparent; font-style: normal; "><br></div><div style="font-family: arial, helvetica, sans-serif; font-size: 16px;
color: rgb(0, 0, 0); background-color: transparent; font-style: normal; ">The program SEDANAL by Walter Stafford uses two simple algorithms to subtract out jitter and jump before fitting the data. Since it does this to the raw data in two steps, it is easy to distinguish the two causes of noise. In SEDANAL the time independent noise is subtracted out by using the dcdt method where two scans are subtracted from each other and then the dcdt transformed data is fit.</div><div style="font-family: arial, helvetica, sans-serif; font-size: 16px; color: rgb(0, 0, 0); background-color: transparent; font-style: normal; "><br></div><div style="background-color: transparent; ">As a scientist interpreting AUC data, you can not ever get rid of noise. The jitter can be reduced by mechanical improvements to the optical system: such as the planned improvements for next generation of AUC devices. The fringe jumps are trivial because they
really are exact integers and by fitting or just by an inspection algorithm they can be corrected. You can't get rid of the meniscus with interferometry data. Likewise, no lens or cell window is going to be perfectly flat, so the interferometer will measure that noise. The time independent noise can be reduced mostly by better radial reproducibility in the raw data so that fitting or dcdt subtraction will work better.</div><div style="background-color: transparent; "><br></div><div style="background-color: transparent; color: rgb(0, 0, 0); font-size: 16px; font-family: arial, helvetica, sans-serif; font-style: normal; ">There are more subtle sources of noise that affect boundary shape and are unavoidable, like the bending of the incident light because of the concentration gradient, buffer mismatch, and the precession of the rotor so even when the major sources of noise are minimized, then other sources of noise will start to
be noticed.</div><div style="background-color: transparent; color: rgb(0, 0, 0); font-size: 16px; font-family: arial, helvetica, sans-serif; font-style: normal; "><br></div><div style="background-color: transparent; color: rgb(0, 0, 0); font-size: 16px; font-family: arial, helvetica, sans-serif; font-style: normal; ">My advise is that this data sets look good: I see no obvious problems worthwhile to try fixing. You may have a bit of a wobbly baseline due to buffer mismatch, which might be minimized by using meniscus matching cells and more extensive dialysis -- but even with these improvements, your curve fit probably wouldn't be noticeably better.</div><div style="background-color: transparent; color: rgb(0, 0, 0); font-size: 16px; font-family: arial, helvetica, sans-serif; font-style: normal; "><br></div><div style="background-color: transparent; color: rgb(0, 0, 0); font-size: 16px; font-family: arial, helvetica, sans-serif; font-style:
normal; ">David Hayes</div><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; "><br></div> <div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; "> <div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Ute Curth <curth.ute@mh-hannover.de><br> <b><span style="font-weight: bold;">To:</span></b> rasmb@list.rasmb.org <br> <b><span style="font-weight: bold;">Sent:</span></b> Tuesday, January 15, 2013 12:41 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> [RASMB] interference optics<br> </font> </div> <br>
<div id="yiv1151028359">
<div>
<font size="-1">Dear all,<br>
<br>
<font size="-1">I hope you had a good start in 2013 and some of
you can possibly gi<font size="-1">ve me </font>advice on <font size="-1">a <font size="-1">pro<font size="-1">blem with ou</font></font>r
Xl-I machine.<font size="-1"> The raw data of our
interference op<font size="-1">tics</font> show (and always
showed) such an enormous vertical jitter that it is hard to
j<font size="-1">udge whether the <font size="-1">sample
sediments at all and where the meniscus is located </font></font></font><font size="-1"><font size="-1"><font size="-1"><font size="-1">(see
attached file)</font></font></font><font size="-1"><font size="-1"><font size="-1"><font size="-1"><font size="-1"><font size="-1"><font size="-1">. Whereas<font size="-1">, a</font>fter
subtraction of T<font size="-1">I and RI noise the
data look quite nice, I a<font size="-1">m wondering
<font size="-1">what <font size="-1">the reason
of this jitter is. Has anyone an idea a<font size="-1">bout its possible source and how <font size="-1">I can get rid of it?</font> <br>
<br>
<font size="-1">Thank you in advance<br>
<br>
<font size="-1">Ute</font><br>
</font></font>
<pre class="yiv1151028359moz-signature">--
PD Dr. rer. nat. Ute Curth
> Medizinische Hochschule Hannover
> Strukturanalyse
> OE 8830
> Carl-Neuberg-Str. 1
> 30625 Hannover
> Germany
>
> Tel.: +49-511-5329372
> Fax : +49-511-5325966</pre>
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