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The intracellular level of the inducer,
υ A , is also affected by the surrounding
extracellular concentration of the inducer.
The next section describes biocircuit design and analysis with BioSPICE.
BIOCIRCUIT DESIGN AND ANALYSIS
Biocircuit design poses several important challanges, some that are in com-
mon with electrical circuit design, and some that are unique. As with electrical
circuits, the behavior of biocircuits depends on the characteristics of the com-
ponent gates. It is therefore important to first characterize the behavior of the
gates by measuring their device physics before attempting to design circuits of
significant complexity. Based on the characteristics of individual gates, one can
predict the behavior of complex circuits built from these components. Here, we
use BioSPICE to develop and simulate a model of biochemical inversion and
then demonstrate how to predict the behavior of biocircuits based on this model.
We also show that the correct behavior of these circuits is highly dependent on
using gates with matching characteristics.
Initial attempts at constructing gates often yield devices with unacceptable
behavior. For example, a particular device may have insufficient signal restora-
tion capabilities or inadequate noise margins. In designing electrical circuits,
one uses process engineering to modify the characteristics of the devices (e.g.,
gain or trigger levels) until they obtain the desired behavior. In this section, we
introduce genetic process engineering, the analogous mechanism for biocircuit
design. We demonstrate how BioSPICE facilitates genetic process engineering
by predicting the new behavior of devices that results from genetic modification
to specific stages in biochemical inversion. The analysis and insights gained
from these BioSPICE predictions guide the engineer in genetically modifying
existing components to achieve the appropriate behavior for building reliable
circuits of significant complexity.
In contrast to electrical circuit design where identical components are sepa-
rated spatially, each component in a biocircuit shares the same physical space but
relies on different biochemical reactions. The complexity of biocircuit design
is exacerbated by the fact that the components typically have widely vary-
ing kinetic characteristics. These gates are built from DNA-binding proteins,
ribosome-binding sites, and protein-binding sites with inherently different ki-
netic characteristics. Therefore, a critical element in biocircuit design is analyz-
ing and optimizing the behavior of each new gate included in the cellular gate
library. In this section, we describe the conditions necessary for matching gates
to achieve correct digital behavior. This analysis motivates specific genetic
modifications to achieve gate-device physics that match with other gates for
correct design and construction of complex circuitry.
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