From: Borries Demeler <demeler@bioc02.uthscsa.edu>
  To  : rasmb@bbri.eri.harvard.edu
  Date: Fri, 23 Jun 1995 18:40:36 -0500 (CDT)

Re: w^2*t

Michael,

> 1. When is time zero taken in a sedimentation velocity run in the XLA?

I assume the XLA data acquisition program queries the computer clock 
(or data acquisition board clock) as soon as the rotor begins 
accelerating and then queries the clock again each time a data scan
is written to a file, writing the difference in time to the data file.
This would mean that the time at the beginning of acceleration is zero.

> 
> 2. Does the magnitude of omega and/or time as used by the XLA represent that 
> obtained during acceleration and that obtained at constant velocity or just 
> that subsequent to a constant velocity being reached?
> 
> 3. How is the integral omega^2*t derived?

I didn't write the data acquisition program, but I assume it is a hardware
encoded function on the data acquisition board that calculates a (discrete) 
sum of omega^2*delta-t values, the current value gets written to the datafile.
I am not sure how long delta-t is, anybody knows more detail on this, Tom 
maybe? If I am not mistaken on this, and the value of delta-t is not too
long, then it wouldn't matter if you accelerate or decelerate during the 
run or run at 2 different speeds, etc., the omega^2*t integral and the t
value should always allow you to calculate the theoretical start of the 
experiment (run).
> 
> 4. Does this derivation take into account events of different speeds used 
> within the one sedimentation velocity experiment (viz. leakage tests at a 
> lower speed)?

yes, for an explanation, see above.

> 
> 5. What of other analysis packages currently available-do these also rely on 
> the integral obtained by the XLA?

I am pretty sure Walt Stafford's DC/DT program does. My package 
UltraScan automatically corrects for this for all velocity
methods coded (second moment, van Holde - Weischet, finite element
fitting).

> 6. Does the "time" format stipulated by the user (viz. HOLD, TIME, w2t) bear 
> any affect upon what value of the integral of w2t "comes up" above each scan?

Please see John Philo's answer.

Hope that helps.

Best regards, -Borries
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* Borries Demeler                                                             *
* The University of Texas Health Science Center at San Antonio                *
* Dept. of Biochemistry                                                       *
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