Hansmann: A Better Way for Finding the Best Way
If you wanted to drive from
Hancock to Houghton, you'd probably just cross the Portage Lift Bridge.
Theoretically, you could take any number of other routes, some of which
might involve transoceanic travel, but the most direct route is evident
from any local map.
Other "best" routes
from Point A to Point B aren't so simple. Ask anyone who has ever meandered
helplessly through a myriad of small Wisconsin towns on a shortcut to
Chicago.
How, then, does one find the
shortest, cheapest, quickest way to do anything, from travel cross country
to assemble a widgit? Especially if there are many pretty-good solutions?
Often, the answer lies in statistical
physics. Since the 1980s, scientists have used a mathematical technique
called "simulated annealing."
"The process mimics a
slow, cooling process in which the search is gently coaxed toward the
best solution," Associate Professor Ulrich Hansmann (Physics) said.
"The method has been used very successfully over the years, but it
can be notoriously slow and sometimes needs operator intervention."
Recent work by Hansmann and
his colleague Luc Wille, of Florida Atlantic University, which appeared
Jan. 29 in Physical Review Letters (see http://ojps.aip.org/journal_cgi/dbt?KEY=PRLTAO&Volume=88&Issue=6#MINOR9)
, promises to overcome these drawbacks. Hansmann and Wille have designed
an "Energy Landscape Paving" method which circumvents the problems
of the annealing algorithm.
Their new method is fast and
automatic, so much so that they use it to address the notorious protein
folding problem, which has baffled scientists for decades. Without understanding proteins'
3D nature, we can't understand what they do or how they do it, so we can't
truly understand how organisms, from yeast to human beings, function in
this world.
Hansmann and Wille have brought
us one step closer, however.
Their new method has found
the folded configuration of two test molecules. They stress that their
technique is no panacea; for large proteins, the computing time may still
be prohibitive. But for smaller biomolecules, it promises better results,
faster.
"If you know the structure,
you can predict the function," Hansmann said. "This could be
important for the development of new chemicals and materials, including
pharmaceuticals."
Proteins are the stuff that we are made of. They are long strings of amino
acids, and determining the amino-acid sequence of proteins isn't too difficult.
But as proteins are formed, they almost immediately begin folding into
incredibly complex structures that interact with other proteins, often
in lock-and-key type arrangements. So far, scientists have not been able
to determine or predict what form most proteins actually take.
