Biology Reference
In-Depth Information
and processes with great detail. Simply stated, modeling and simula-
tion refer to computations that are based on approximations of the
energies of systems of one or more molecules as a function of their
conformations and relative orientations. (The term “simulation” usually
also includes the idea that we are interested in modeling not only the
energies, but also the temporal behavior of the system.)
The techniques available for computing the energies as a function
of molecular conformation within a modeling or simulation study
range from approaches based on quantum mechanics all the way to
rather coarse-grained classical ones. Those based on quantum mechan-
ics are capable of a higher degree of accuracy but are computationally
much more expensive. Consequently, they are practical only for rela-
tively small molecular systems. The classical approaches approximate
the inherently quantum mechanical molecular interactions with a
parameterized function that is very easy to evaluate, and so they may
be used to study larger molecular systems like proteins or cell mem-
branes, and processes that involve long time scales such as protein
folding or drug-protein binding phenomena. However, the accuracy
of these approximations is always an important issue; although they
have been shown to work for a range of problems, they must be reval-
idated for each new type of use. There are also hybrid methods where
some regions of the system are treated quantum mechanically and the
rest is treated classically.
The right level of approximation needed for modeling a molecular
system depends critically on the types of processes and phenomena
one is interested in studying. For example, the behavior of electroni-
cally excited molecules, and chemical bond breaking and formation,
involve the rearrangement of electrons in the molecular system and
one must use quantum mechanics to evaluate the energies associated
with these kinds of processes. Therefore, if one is interested in how
enzymes catalyze the making and breaking of bonds during, say,
metabolism, one would need to include the role of electronic structure
and a quantum mechanical approach would be required.
If one is not interested in these kinds of phenomena, classical
approaches may be adequate. These have their greatest applicability
for biological phenomena that do not involve large changes in the
electronic state of the molecules of interest. This includes a very wide
range of important problems including the structure, function, ener-
getics, and dynamics of biologically functional molecules and systems.
For example, to study protein folding, classical models of the process
have been shown to be adequate for a variety of proteins.
The mathematical expression that approximates the conforma-
tional energies and interaction energies between molecules in a
classical molecular simulation is commonly called a potential energy
function, or force field. It is a scalar function of all the coordinates of
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