[RASMB] s20w calculation

[David Hayes]

Hi all,

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.

"If I use equation 19 in cited in the SEDNTERP documentation, from the s20w value=17.3, I calculate s* = 16.4s."


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.

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.

"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.

David Hayes



 


________________________________
 From: John Sumida <jpsumida at u.washington.edu>
To: rasmb at rasmb.org 
Sent: Thursday, August 8, 2013 8:38 PM
Subject: [RASMB] s20w calculation
 


Dear RASMB
 
Wondering about the s020w calculation in SEDNTERP 
 
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.
 
If I use equation 19 in cited in the SEDNTERP documentation, from the s20w value=17.3, I calculate s* = 16.4s. 
Phsyical parameters used: 
1.     experiment temp=20oC, 
2.     vbar=0.8312 (measured by densitometry at 20oC)
3.     density of solution 1.00506 gms/cm3 (measured)
4.     viscosity 0.010281 (measured)
5.     Assuming viscosity of water to be 0.01002, and the density to be 0.998234
 
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.
 
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.
 
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.
 
Any suggestions and comments are welcome and thank you, in advance, for taking the time to consider my question.
 
Best regards,
 
John Sumida
Analytical Biopharmacy Core Facility
University of Washington
Molecular Engineering & Sciences Institute, G22
3946 West Stevens Way NE
Seattle WA 98195-1653
 
_______________________________________________
RASMB mailing list
RASMB at list.rasmb.org
http://list.rasmb.org/listinfo.cgi/rasmb-rasmb.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://list.rasmb.org/pipermail/rasmb-rasmb.org/attachments/20130809/67fd04af/attachment.htm>