Chemistry - Molecular Theory of the Living Cell - page 73

Table 3.1 Three classes of dissipative structures: (1) dissipative structures with fixed boundaries,
(2) dissipative structures with moving boundaries, and (3) dissipative structures with informed
boundaries

Dissipative structures with
Fixed boundaries

Moving boundaries “Informed” moving boundaries

Boundaries Walls of reaction
vessels

Surface of the
object moving
in fluid

Catalytic residues of enzymes
at their active sites whose
spatiotemporal arrangements
are determined by genetic
information (see Sects. 11.3.2
and 11.3.3 )

Examples Belousov-Zhabotinsky

reaction

Turbulent fluid
flow patterns
around moving
objects

Enzymes utilizing binding energy
to regulate the rates of chemical
reactions (also called the Circe
effect [Jencks 1975])

Theoretical
models

Brusselator (Prigogine
and Lefever 1968)

Navier-Stokes
equation (Moin
and Kim 1997)

Conformon model of enzymic
catalysis (Ji 1974a, b, 2004a)

If the classification scheme in Table 3.1 is valid, we can identify all molecular
machines and motors in action driven by chemical reactions as “dissipative
structures with informed moving boundaries.” Because of the informed nature of
the molecular structures of enzymes, enzymes can search out their target molecules
to bind or target reactions to catalyze and execute motions in the direction of
achieving informed/instructed functions. When a right set of such informed molec-
ular machines are put in a confined space such as the interior of the cell, the
molecular machines (Alberts 1998) can find their correct targets to interact with,
forming a molecular machine network, which executes collective nonrandom
molecular motions that we recognize as life. Therefore, we are entitled to view
the living cell as a “super-dissipative structure with informed boundaries” or
“SDSIMB.” I suggest that SDSIMBs are capable of any computation, communica-
tion , and construction on the molecular level, which may be regarded as the
microscopic realization of the Turing machine and the von Neumann's Universal
Constructor (von Neumann 1966) combined.

3.1.5 The Triadic Relation Between Dissipative Structures
(Dissipatons) and Equilibrium Structures (Equilibrons)

The living cell can be viewed as a prototypical example of dissipative structures
or a dissipaton. We can recognize two kinds of structures in the cell - those that
disappear within time upon the cessation of free energy input and those that

remain unaltered for times longer than

t

following the removal of the free energy
from the cell. We will identify the former as processes (since all processes will stop
without free energy dissipation) and the latter as equilibrium structures or

t