Rob Phillips, Markus Dittrich, and Klaus Schulten.
Quasicontinuum representations of atomic-scale mechanics: From
proteins to dislocations.
Annual Review of Materials Research, 32:219-233, 2002.
PHIL2002
Computation is one of the centerpieces of both the physical and
biological sciences. One key thrust in computational science is the
explicit mechanistic simulation of the spatiotemporal evolution of
materials ranging from macromolecules to inter metallic alloys.
On the other hand, our ability to simulate such systems is in the
end always
limited in both the spatial extent of the systems that are considered
as well as the duration of the time that can be simulated. As a
result, a variety of efforts have
been put forth which aim to finesse these challenges in both space
and time through new techniques in which constraint is exploited
to reduce the overall computational burden. The aim of this article
is to describe in general terms some of the key ideas that have
been set forth in both the materials and biological setting and to
speculate on future developments along these lines. To that end,
we begin by
developing general ideas on the exploitation of constraint as a
systematic tool for degree of freedom thinning. These ideas are
then applied to case studies ranging from the plastic deformation
of solids to the interactions of proteins
and DNA.
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