[RASMB] s20w calculation ... more

Sat Aug 10 20:35:30 PDT 2013

On 08/10/13 06:41, Walter Stafford wrote:
>
> SEDANAL does the conversion to s(20,w)  only in DCDT and the only if 
> the v-vbar and density_and viscosity ratio _have been entered into the 
> database though the Preprocessor. All other values of s* are the raw 
> value. I.e. s(t,b). The equation used is the standard equation used by 
> Svedberg in "The Ultracentrifuge" and hasn't changed since then.
>
> In the Fitter the correct value of density increment must be entered 
> to get the correct molar mass. So in the fitter only the buoyancy 
> correction is made since the correction from s*(t,b) to s(20,w) and 
> from D(t,b) to D(20,w) is the same and cancels out. The values used by 
> the fitter are the raw values, i.e. the actual values that pertain to 
> solution conditions being fitted.
>
> Sent from my iPad Mini
>
> On Aug 9, 2013, at 5:25 PM, "Laue, Thomas" <Tom.Laue at unh.edu 
> <mailto:Tom.Laue at unh.edu>> wrote:
>
>> Hi-
>> Sorry to be late replying... I am out of town... and sorry there is a 
>> problem with Sednterp.
>> I've forwarded this thread to the gang to see what the problem might be.
>> One thing they might try is to see if the desktop and web version 
>> give the same error. The calculations are identical, but the 
>> rendering engines are different.
>> Again, sorry for any trouble.
>> Tom
>> ------------------------------------------------------------------------
>> *From:* rasmb-bounces at list.rasmb.org 
>> <mailto:rasmb-bounces at list.rasmb.org> [rasmb-bounces at list.rasmb.org 
>> <mailto:rasmb-bounces at list.rasmb.org>] on behalf of David Hayes 
>> [drdavidbhayes at yahoo.com <mailto:drdavidbhayes at yahoo.com>]
>> *Sent:* Friday, August 09, 2013 5:04 PM
>> *To:* rasmb at rasmb.org <mailto:rasmb at rasmb.org>
>> *Subject:* Re: [RASMB] s20w calculation
>>
>> Hi John,
>>
>> I sent some off list response with extra information and opinion I am 
>> not sure about and don't want to be on list.
>> I am also waiting for Walter or Peter Sherwood to answer about 
>> SEDANAL questions, but I suspect that you are thinking SEDANAL is 
>> doing s20w corrections that it really is not, but I don't know if 
>> that is the problem.
>>
>> Everyone should know that the Web SEDNTERP and the desktop beta share 
>> the exact same calculation source code, so if they are the same 
>> version, they better agree on everything, feature for feature, bug 
>> for bug.
>>
>> But also, basically trust the by hand calculations as was posted 
>> previously, ask the programmers which numbers are s20w and which are 
>> not, and thank you for posting the problems so the developers of 
>> SEDNTERP can work out the bugs.  Due to John Philo's incredible and 
>> meticulous work, SEDNTERP 1.2 was incredibly reliable and calculated 
>> things to 5 decimal places reliably and exactly the same as the 
>> published equations.  the new version of SEDNTERP will take a lot of 
>> sweat to get to that level of excellence.
>>
>> David Hayes
>>
>> ------------------------------------------------------------------------
>> *From:* John Sumida <jpsumida at u.washington.edu 
>> <mailto:jpsumida at u.washington.edu>>
>> *To:* drdavidbhayes at yahoo.com <mailto:drdavidbhayes at yahoo.com>
>> *Cc:* rasmb at rasmb.org <mailto:rasmb at rasmb.org>
>> *Sent:* Friday, August 9, 2013 1:44 PM
>> *Subject:* Re: [RASMB] s20w calculation
>>
>> Hi David,
>> Thanks for taking the time to respond. I'm attempting to respond to 
>> your post. Apologies if I'm committing some type of etiquette 
>> violation in responding to the group, but as you requested some 
>> clarification as to my process I thought to respond publicly.
>> To answer your questions.
>> I've been trying to understand why this particular polymer material 
>> produces a large s20w value when another material with different 
>> surface charge properties produces an s20w of 7.9s and sediments very 
>> differently.
>> So the back calculation, going from s20w to s*, was me playing with 
>> the data to see if I could go from the 17.3 s20w back to s* which I 
>> would have hoped -- as you point out -- would not have been much 
>> different from 17.3s.
>> My initial calculation using the s20w correction equation  (equation 
>> 19) was comforting in that the calculated s* was 16.4s. I used SEDFIT 
>> to perform the same calculation just to check that all was in order 
>> -- and as I stated SEDFIT returned the 16.4s value as had the 
>> calculation and the analysis in SEDANAL.  Note that vbar and solvent 
>> parameters had been entered in into the experiment file and gOfs 
>> files had been generated by running DCDT.  So I believe the s values 
>> returned in SEDNAL are s20w values.
>> The problem arose when I used the Experiment page in SEDNTERP 
>> (version 20120828 BETA). Using the calculated value of s*, SEDNTERP 
>> did not return the same value for s20w that SEDANAL output.
>> I also attempted the same operation using the web version of SEDNTERP 
>> which resulted in the same result, namely calculating an s20w of 
>> 27.8s when the experimentally observed s20w was17.3s.
>> I had not thought to turn off the s20w calculation (in order to do so 
>> do I just remove vbar from the experiment info?) and attempt to fit 
>> for s*. Will try that next.
>> Best regards,
>> John Sumida, Ph.D.
>> Analytical Biopharmacy Core Facility 
>> <http://depts.washington.edu/cidb4bio/index.shtml>
>> University of Washington
>> Molecular Engineering & Sciences Institute, G22 
>> <http://www.moles.washington.edu/>
>> 3946 West Stevens Way NE
>> Seattle WA 98195-1653
>>
>>
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>
>
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Can I be so cruel as to suggest to the questioner that a firm 
understanding of what s and s20,w is before one blindly uses a computer 
program on dc/dr/dt data.  Given that s is a function of rho, vbar, t 
and frictional coefficient, it might just be necessary to have known 
rho, vbar, viscosity and temperature to translate a measured s at that 
condition to s at 20C in water.   The computer program can't know what 
solvent, temperature and vbar to use unless you supply it, I suspect.

2 cents from a retired former Model E user!

-- 
Kirk C Aune, Ph.D.
16289 Cambridge Court
Granger, IN 46530
(574)277-8589
Linux User #1720

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