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biochemistry, textile applications?

  • To: mathgroup at
  • Subject: biochemistry, textile applications?
  • From: stevec at
  • Date: Thu, 2 Jun 94 00:31:58 EDT

MathGroup et al:

I have a question about the extent of the use of Mathematica in 
two areas.  The first is in biochemistry research - in particular
in applications in the break up of protein molecules into peptide
fragments.  As part of a project I have been doing for some biochemists
here at UNC, I have written a Mathematica package that does the 

They have proteins that are constructed from 14 possible peptide
fragments.  It is possible to "cut" the molecules in many ways to
produce smaller fragments.  Their experimental apparatus is set up
to measure the mass/charge ratios of whatever appears in their treated
samples.  In the process of breaking up and reconnecting, hydrogen and
water masses are added or subtracted, disulfide links can occur and
carbon dioxide molecules can hook to the fragments changing their masses.
They get graphs showing peaks where significant concentractions of
fragments occur.  Mass/charge ratios for the major peaks are given also.
It is very difficult to identify what fragments are being produced.

I have written a package/notebook that computes all possible mass/charge
values for all possible fragment structures and then gives them a way
to enter one of their mass/charge experimental values and have the computer
tell them (within some range) which fragments might have that mass/charge, what
the other possible mass/charge values that fragment might also have, and
how much carboxylation has occured.   It seems to work very well and
quite quickly even on a PC.  It is being used successfully.

The program is flexible enough to be generalized to molecules with
more fragments, different masses, etc.  They have urged me to find
a way to generalize the program so that other researchers outside
their group might find a use for the package.

I am not a biochemist so I am not sure which directions such a generalization
might take.  So, I am asking any of you who have connections or knowledge
in this area to make some suggestions.

My second project is in a completely different area. I am working with
some textile researchers who want to use fluid flow methods to study
the production of thread and yarn from fibers.  I would like to hear
from Mathematica users who are working in textiles or fluid flow.  I
have only just begun this work so do not have much more detail than


Steve Christensen
stevec at

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