Biology Reference
In-Depth Information
Fig. 1.
(a) Shaded view of a 3D computer reconstruction of the geometry of an
endoplasmic reticulum (ER) of a live cell.
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(b) Close-up of a reconstructed ER, illus-
trating the geometric complexity of this intracellular structure.
by the fact that common computational methods, such as normal mode
analysis, Fourier transforms, or the superposition principle, break down
in nonlinear systems because a nonlinear system is not equal to the sum
of its parts.
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2.5. Coupling Across Scales
Coupling across scales means that events on the microscopic scale such
as changes in molecular conformation can have significant effects on the
global, macroscopic behavior of the system. This is certainly the case for
many biological systems — bioluminescence due to bacterial quorum
sensing
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for example, or the effect on the behavior of a whole organism
when hormones bind to their receptors. Such multi-scale systems share
the property that the individual scales cannot be separated and treated
independently. There is a continuous spectrum of scales with coupled
interactions that impose stringent limits on the use of computer simu-
lations. Direct numerical simulation of the complete system would
require resolving it in all detail everywhere. Applied to the simulation of
a living cell, this would mean resolving the dynamics of all atoms in the
cell. A cell consists of about 10
15
atoms, and biologically relevant
processes such as protein folding and enzymatic reactions occur on
the time scale of milliseconds. The largest molecular dynamics (MD)
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