<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>Hi all,</span></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: arial, helvetica, sans-serif; background-color: transparent; font-style: normal;"><span><br></span></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: arial, helvetica, sans-serif; background-color: transparent; font-style: normal;"><span>John Sumida has managed to confuse me a bit here, which is not too hard to do: but I thought to ask clarification questions on the loop.</span></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: arial, helvetica, sans-serif; background-color: transparent; font-style: normal;"><span><br></span></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: arial, helvetica, sans-serif; background-color: transparent; font-style: normal;"><span><span style="font-family:
'times new roman', 'new york', times, serif; font-size: 19px;">"If I use equation 19 in cited in the SEDNTERP documentation, from the s20w value=17.3, I calculate s* = 16.4s."</span><br></span></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: arial, helvetica, sans-serif; background-color: transparent; font-style: normal;"><span><span style="font-family: 'times new roman', 'new york', times, serif; font-size: 19px;"><br></span></span></div><div style="color: rgb(0, 0, 0); font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal;"><span><span style="font-family: 'times new roman', 'new york', times, serif; font-size: 19px;">I don't use SEDANAL in the mode of s20w, so I am not sure why you back calculate the s*; s* is the apparent sedimentation coefficient from the experiment, so you should not calculate it but just turn off the s20w correction and see what s*
is.</span></span></div><div style="color: rgb(0, 0, 0); font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal;"><span><span style="font-family: 'times new roman', 'new york', times, serif; font-size: 19px;"><br></span></span></div><div style="color: rgb(0, 0, 0); font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal;"><span><span style="font-family: 'times new roman', 'new york', times, serif; font-size: 19px;">Since you said "experiment page" can you confirm what version of SEDNTERP you are using? Iassume it is the Beta SEDNTERP java version (either web or desktop). I have noticed something strange going on in that version and filed a bug report, but do not have time to follow up on it. One strange thing that I noticed was that changing the temperature of the sed. equilibrium box changed the
s20w result, which should not happen since s20w is about only the sed velocity experiment and I type in the molecular weight anyway.</span></span></div><div style="color: rgb(0, 0, 0); font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal;"><span><span style="font-family: 'times new roman', 'new york', times, serif; font-size: 19px;"><br></span></span></div><div style="color: rgb(0, 0, 0); font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal;"><span><span style="font-family: 'times new roman', 'new york', times, serif; font-size: 19px;">"</span></span>to get SEDNTERP to return a value of 17.3s, I have to decrease S* to be 2.91s." Given that your buffer is not much different than water, s20w should be very close to s*. If the SEDNTERP software you are using is working at all, then I would suggest that
you slipped a decimal point somewhere. But as I said, I am not convinced the s20w calculation works at all in the web SEDNTERP.</div><div style="color: rgb(0, 0, 0); font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal;">David Hayes</div><div style="color: rgb(0, 0, 0); font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal;"><br></div><div style="color: rgb(0, 0, 0); font-size: 19px; font-family: 'times new roman', 'new york', times, serif; background-color: transparent; font-style: normal;"><span><span style="font-family: 'times new roman', 'new york', times, serif; font-size: 19px;"><br></span></span></div><div style="color: rgb(0, 0, 0);
font-size: 16px; font-family: arial, helvetica, sans-serif; background-color: transparent; font-style: normal;"><span><br></span></div><div style="color: rgb(0, 0, 0); font-size: 16px; font-family: arial, helvetica, sans-serif; background-color: transparent; font-style: normal;"><span> </span></div><div><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"> <hr size="1"> <font size="2" face="Arial"> <b><span style="font-weight:bold;">From:</span></b> John Sumida <jpsumida@u.washington.edu><br> <b><span style="font-weight: bold;">To:</span></b> rasmb@rasmb.org <br> <b><span style="font-weight: bold;">Sent:</span></b> Thursday, August 8, 2013 8:38 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> [RASMB] s20w calculation<br> </font> </div> <div class="y_msg_container"><br><div
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--></style><div><div class="yiv6772383961WordSection1"><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;">Dear RASMB</span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;"> </span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;">Wondering about the s020w calculation in SEDNTERP </span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;"> </span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;">For one of our polymer micelles with which we’ve been working, a SEDANAL analysis returns an s20w value (not corrected for concentration) of 17.3.</span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;"> </span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;">If I use equation 19 in cited in the SEDNTERP documentation, from the s20w value=17.3, I calculate s* = 16.4s. </span></div><div
class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;">Phsyical parameters used: </span></div><div class="yiv6772383961MsoListParagraph" style=""><span style="font-size:14.0pt;"><span style="">1.<span style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman';"> </span></span></span><span style="font-size:14.0pt;">experiment temp=20oC, </span></div><div class="yiv6772383961MsoListParagraph" style=""><span style="font-size:14.0pt;"><span style="">2.<span style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman';"> </span></span></span><span style="font-size:14.0pt;">vbar=0.8312 (measured by densitometry at 20oC)</span></div><div class="yiv6772383961MsoListParagraph" style=""><span style="font-size:14.0pt;"><span style="">3.<span
style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman';"> </span></span></span><span style="font-size:14.0pt;">density of solution 1.00506 gms/cm3 (measured)</span></div><div class="yiv6772383961MsoListParagraph" style=""><span style="font-size:14.0pt;"><span style="">4.<span style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman';"> </span></span></span><span style="font-size:14.0pt;">viscosity 0.010281 (measured)</span></div><div class="yiv6772383961MsoListParagraph" style=""><span style="font-size:14.0pt;"><span style="">5.<span style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman';"> </span></span></span><span
style="font-size:14.0pt;">Assuming viscosity of water to be 0.01002, and the density to be 0.998234</span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;"> </span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;">However if I use the Experiment page in the SEDNTERP and enter value of s* calculated above, then s20w returned is 27.8 which is much higher than the value returned from SEDANAL. In fact in order to get SEDNTERP to return a value of 17.3s, I have to decrease S* to be 2.91s.</span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;"> </span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;">In SEDFIT, if I input 16.4s, calculated from Equation 19 in the SEDNTERP documentation, and input the same physical parameter listed above, I get 17.4s in agreement with the SEDANAL result.</span></div><div class="yiv6772383961MsoNormal"><span
style="font-size:14.0pt;"> </span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;">I think in both SEDNTERP and SEDFIT, the same equation is used to correct s* to s20w, so I’m not clear what I’m missing.</span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;"> </span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;">Any suggestions and comments are welcome and thank you, in advance, for taking the time to consider my question.</span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;"> </span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;">Best regards,</span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;"> </span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;">John Sumida</span></div><div class="yiv6772383961MsoNormal"><span style="font-size:14.0pt;"><a
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