[RASMB] Chaos Summary & Quest.

[Walter Stafford]

Hi Olin,

	A slowly re-equilibrating system would not be expected to 
lead to convection.

	One possibility is that you have an association-dissociation 
equilibrium with a significant positive volume change on association. 
The higher pressures at the bottom of the cell would shift the 
equilibrium to the dissociated form leading to negative concentration 
gradients which will result in convection in the absence of a 
stabilizing gradient. For small volume changes, redistribution of 
buffer components (i.e. higher NaCl concentration) may be enough to 
stabilize the solution against convection.

You could try running at a lower speed to reduce the pressure to see 
if that made any difference.

Walter Stafford



>---
>
>Dear Friends,
>
>    I have a summary and a related questions concerning the chaotic 
>behavior I described in the message of 11/16/01.
>
>    I received only two suggestions as I recall.  They suggested that 
>it was probably convection considering its pattern and behavior.  I 
>agree.  I don't see how it can be anything else, but find it strange 
>that it should occur only with this sample and not the thyroglobulin 
>control with a similar molec. wt.   Perhaps it is due to the slow 
>association equilibria in this protein we are studying.  If the 
>centrifugal distribution is faster than the chemical equilibration, 
>could this lead to an unstable density gradient that keeps recurring 
>in time?  This is more than I can rationalize now.  If my colleague 
>whose protein exhibits this chaotic behavior desires, we will run 
>the next sample with a density stabilizer.
>
>    What do you recommend for this density stabilization for 
>absorption optics?  We don't want to use high concentrations of 
>stabilizers, e.g., sucrose, which will alter the activity 
>coefficient of water and thus possibly affect the extent of 
>self-association of the protein.  Metrizamide has far too much 
>absorbance at 280 nm to use.  Allen Minton has used 0.25-0.75% 
>polyethyleneglycol 20,000 and 4,000, 0.25-0.5% T-70 dextran, and 
>0.5% sucrose with his preparative centrifuge method.  However, it 
>isn't clear from the results if any density stabilization was 
>necessary.  I don't know which of these provides better density 
>stabilization in principle - does one of you? I suspect that the 
>higher MW substances provide the density stabilization quicker in 
>time, which might be important in this case. Of course we will test 
>a series of concentrations of this stabilizer.
>
>    One of my most pleasant blessings is the marvelous communication 
>and help this RASMB provides.  This makes research fun.  Thank you 
>all and best wishes to you for a merry season and new year,
>
>Olin
>
>--
>H. Olin Spivey                       Phone: (405) 744-6192
>Dept. Biochem. & Molec. Biology      Fax:   (405) 744-7799
>246 NRC                              Email: OSpivey at Biochem.Okstate.Edu
>Oklahoma State University
>Stillwater, OK 74078-3035
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-- 
Walter Stafford
mailto:stafford at bbri.org