7 research outputs found
Optimization of Enzymatic Logic Gates and Networks for Noise Reduction and Stability
Biochemical computing attempts to process information with biomolecules and
biological objects. In this work we review our results on analysis and
optimization of single biochemical logic gates based on enzymatic reactions,
and a network of three gates, for reduction of the "analog" noise buildup. For
a single gate, optimization is achieved by analyzing the enzymatic reactions
within a framework of kinetic equations. We demonstrate that using
co-substrates with much smaller affinities than the primary substrate, a
negligible increase in the noise output from the logic gate is obtained as
compared to the input noise. A network of enzymatic gates is analyzed by
varying selective inputs and fitting standardized few-parameters response
functions assumed for each gate. This allows probing of the individual gate
quality but primarily yields information on the relative contribution of the
gates to noise amplification. The derived information is then used to modify
experimental single gate and network systems to operate them in a regime of
reduced analog noise amplification.Comment: 7 pages in PD
Enzymatic AND Logic Gates Operated Under Conditions Characteristic of Biomedical Applications
Experimental and theoretical analyses of the lactate dehydrogenase and
glutathione reductase based enzymatic AND logic gates in which the enzymes and
their substrates serve as logic inputs are performed. These two systems are
examples of the novel, previously unexplored, class of biochemical logic gates
that illustrate potential biomedical applications of biochemical logic. They
are characterized by input concentrations at logic 0 and 1 states corresponding
to normal and abnormal physiological conditions. Our analysis shows that the
logic gates under investigation have similar noise characteristics. Both
significantly amplify random noise present in inputs, however we establish that
for realistic widths of the input noise distributions, it is still possible to
differentiate between the logic 0 and 1 states of the output. This indicates
that reliable detection of abnormal biomedical conditions is indeed possible
with such enzyme-logic systems.Comment: PDF, 29 page
Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Enzyme Inhibition by a Substrate
We consider a realization of the XOR logic gate in a process biocatalyzed by
an enzyme (here horseradish peroxidase: HRP), the function of which can be
inhibited by a substrate (hydrogen peroxide for HRP), when the latter is
inputted at large enough concentrations. A model is developed for describing
such systems in an approach suitable for evaluation of the analog noise
amplification properties of the gate. The obtained data are fitted for gate
quality evaluation within the developed model, and we discuss aspects of
devising XOR gates for functioning in "biocomputing" systems utilizing
biomolecules for information processing
Artificial Muscle Reversibly Controlled by Enzyme Reactions
Chemically induced actuation of a polypyrrole (Ppy) artificial muscle was controlled by biocatalytic reactions, resulting in changes in the redox state of the polymer film mediated by soluble redox species. The biocatalytic process triggered by diaphorase in the presence of NADH resulting in the reduction of the Ppy film was reflected by the potential shift in the negative direction generated in the film. Conversely, the biocatalytic process driven by laccase in the presence of O<sub>2</sub> resulted in the oxidation of the Ppy film, thus yielding the positive potential shift. Both reactions produced opposite bending of the Ppy flexible strip, allowing reversible actuation controlled by the biocatalytic processes. The biocatalytic reactions governing the chemical actuator can be extended to multistep cascades processing various patterns of biochemical signals and mimicking logic networks. The present chemical actuator exemplifies the first mechanochemical device controlled by biochemical means with the possibility to scale up the complexity of the biochemical signal-processing system