Biomolecular Computing - Bionanoelectronics: Bioinquiring and Bioinspired Devices - page 191

input data provides at the same time the energy necessary for a biomolecular
automaton performing 6:6 10 10 transitions/s l and dissipates 5 10 9 W l 1
as heat ( Benenson et al. 2003 ). This energy stored in the bonds of the biomolecule
is released as the input data are destroyed during computation. Such a process
has no correspondent in electronic computation. The key for understanding the
low energy consumption of reversible biomolecular computers is the fact that, at
each computation step, a state of equilibrium is reached between reactants and
products, which assures thermodynamic (and logical) reversibility. In electronic,
digital computation, the minimum energy required to transfer or delete one bit of
information is E D k B T ln 2 ( Szaciłowski 2008 ); in standard silicon switching
devices operating in hard drives, the energy cost per computational step could be
orders of magnitude higher than this minimum value. The energy cost is related
to the irreversibility of logical gates. In reversible logic operations, which can
take place in biomolecular computers when operated at or near thermodynamic
equilibrium, the energy cost per computational step can decrease up to 0:01k B T
(in perfect equilibrium this energy cost should vanish).
However, no biologic circuit reaches yet the reliability and complexity of
silicon-based electronics. In addition, unlike electronic computers, biomolecular
computation is certainly not fast. The results of chemical processes catalyzed by
enzymes reveal themselves in several minutes or hours. Therefore, biomolecular
computing will probably not replace electronic computing; it is much more suitable
for analyzing biological/stochastic information rather than deterministic informa-
tion ( Ezziane 2006 ). The applications of biomolecular computation tend to focus
not so much on in vitro (inside a recipient) but on in vivo (inside the cell) operations,
with the ultimate goal of smart diagnosis and drug delivery.
One of the still-standing issues of biomolecular computing is the efficient
cascading of several logic gates. Unlike in electronic systems, where both the
input and output signals are of the same (electronic) nature, in biomolecular logic
input/output incompatibilities can arise. In many cases, the logic gates are “single-
use” devices. Ideally, the output of a gate should act as input for the next logic gate.
Important for implementing logical gates but also to concatenate such gates are the
sticky ends. Matching sticky ends from DNA molecules cut by the same restriction
enzyme can be joined by ligase.
The different mechanisms at work in electronic processors and biological
computers justify the search for specific algorithms for the latter, which would
enable the implementation of logical circuits in only one molecule. An example
of such a moleculator, i.e., a molecular computer on a truly molecular scale, is the
fluorescent molecule known as fluorescein in which advanced arithmetic operations
such as full-adder and full-subtractor can be implemented. Fluorescein exists in
four ionization forms with different spectral properties: F. 1/; F.0/; F. C 1/,and
F. C 2/. In solution, logic operations can be implemented by switching between these
states through a controlled change of the pH ( Margulies et al. 2006 ). Input signals
are acids and/or bases, which change the predominant F(0) form of a neutral solution
in cations F. C 1/ and/or anions F. 1/ and F. 2/, both types of inputs annihilating
each other. The output is read by monitoring the transmittance or absorbance at