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pathway bifurcation with considerably different final conditions, this could lead
to probabilistic outcomes considerably different from simple Boolean logic
rules described above.
Solutions to the stochastic formulation of coupled reactions can be com-
puted using the Monte Carlo procedure described by Gillespie [43]. This al-
gorithm calculates a stochastic description of the temporal behavior of the
coupled reactions by calculating the probabilistic outcome of each discrete
chemical event and the resulting changes in the number of each molecular
species. By accumulating the results for all reactions over time, the statistics
of the inherent fluctuations in the reaction products can be estimated [69].
Deterministic information-processing circuits engineered into these cells must
deal with the stochastic nature of these nanoscale chemical systems through
reduction of noise by feedback [8] or through the development of information-
processing algorithms that make use of probabilistic rather than deterministic
outcomes.
INTERCONNECTIVITY AND INPUT/OUTPUT
Engineering information transport within individual cells only partially answers
the challenges associated with deploying cells as components in engineered
devices. To construct systems of even moderate complexity requires the inter-
connection of these information pathways within cells and cellular communities
and between cells and the synthetic portions of these systems. Figure 5.7 illus-
trates the information transport pathways through the type of hybrid systems
considered here. Three communication pathways and interfaces must be con-
sidered (we will use the generic term chip to refer to all of the possible synthetic
components that may be interfaced to the cells): (1) cell to chip; (2) cell to cell;
and (3) chip to cell.
Figure 5.7 Communication pathways in a hybrid whole-cell/synthetic device system.
Three separate communication pathways are seen: (1) cell to chip, (2) cell to cell, and
(3) chip to cell.
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